elife02755.xml

<?xml version="1.0" encoding="UTF-8"?><!DOCTYPE article PUBLIC "-//NLM//DTD JATS (Z39.96) Journal Archiving and Interchange DTD v1.1d1 20130915//EN"  "JATS-archivearticle1.dtd"><article article-type="research-article" dtd-version="1.1d1" xmlns:xlink="http://www.w3.org/1999/xlink"><front><journal-meta><journal-id journal-id-type="nlm-ta">elife</journal-id><journal-id journal-id-type="hwp">eLife</journal-id><journal-id journal-id-type="publisher-id">eLife</journal-id><journal-title-group><journal-title>eLife</journal-title></journal-title-group><issn publication-format="electronic">2050-084X</issn><publisher><publisher-name>eLife Sciences Publications, Ltd</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="publisher-id">02755</article-id><article-id pub-id-type="doi">10.7554/eLife.02755</article-id><article-categories><subj-group subj-group-type="display-channel"><subject>Research article</subject></subj-group><subj-group subj-group-type="heading"><subject>Neuroscience</subject></subj-group></article-categories><title-group><article-title>MicroRNA-9 controls dendritic development by targeting REST</article-title></title-group><contrib-group><contrib contrib-type="author" id="author-12220"><name><surname>Giusti</surname><given-names>Sebastian A</given-names></name><xref ref-type="aff" rid="aff1"/><xref ref-type="fn" rid="con1"/><xref ref-type="fn" rid="conf1"/></contrib><contrib contrib-type="author" id="author-12212"><name><surname>Vogl</surname><given-names>Annette M</given-names></name><xref ref-type="aff" rid="aff1"/><xref ref-type="fn" rid="con2"/><xref ref-type="fn" rid="conf1"/></contrib><contrib contrib-type="author" id="author-12213"><name><surname>Brockmann</surname><given-names>Marisa M</given-names></name><xref ref-type="aff" rid="aff1"/><xref ref-type="aff" rid="aff2"/><xref ref-type="fn" rid="con4"/><xref ref-type="fn" rid="conf1"/></contrib><contrib contrib-type="author" id="author-12214"><name><surname>Vercelli</surname><given-names>Claudia A</given-names></name><xref ref-type="aff" rid="aff3"/><xref ref-type="fn" rid="con3"/><xref ref-type="fn" rid="conf1"/></contrib><contrib contrib-type="author" id="author-12215"><name><surname>Rein</surname><given-names>Martin L</given-names></name><xref ref-type="aff" rid="aff4"/><xref ref-type="fn" rid="con5"/><xref ref-type="fn" rid="conf1"/></contrib><contrib contrib-type="author" id="author-12217"><name><surname>Trümbach</surname><given-names>Dietrich</given-names></name><xref ref-type="aff" rid="aff5"/><xref ref-type="fn" rid="con6"/><xref ref-type="fn" rid="conf1"/></contrib><contrib contrib-type="author" id="author-12211"><name><surname>Wurst</surname><given-names>Wolfgang</given-names></name><xref ref-type="aff" rid="aff5"/><xref ref-type="aff" rid="aff6"/><xref ref-type="aff" rid="aff7"/><xref ref-type="aff" rid="aff8"/><xref ref-type="other" rid="par-1"/><xref ref-type="other" rid="par-2"/><xref ref-type="other" rid="par-3"/><xref ref-type="fn" rid="con7"/><xref ref-type="fn" rid="conf1"/></contrib><contrib contrib-type="author" id="author-12218"><name><surname>Cazalla</surname><given-names>Demian</given-names></name><xref ref-type="aff" rid="aff9"/><xref ref-type="fn" rid="con8"/><xref ref-type="fn" rid="conf1"/></contrib><contrib contrib-type="author" id="author-12219"><name><surname>Stein</surname><given-names>Valentin</given-names></name><xref ref-type="aff" rid="aff2"/><xref ref-type="fn" rid="con10"/><xref ref-type="fn" rid="conf1"/></contrib><contrib contrib-type="author" id="author-12216"><name><surname>Deussing</surname><given-names>Jan M</given-names></name><xref ref-type="aff" rid="aff4"/><xref ref-type="other" rid="par-4"/><xref ref-type="other" rid="par-5"/><xref ref-type="other" rid="par-6"/><xref ref-type="fn" rid="con9"/><xref ref-type="fn" rid="conf1"/></contrib><contrib contrib-type="author" corresp="yes" id="author-12105"><name><surname>Refojo</surname><given-names>Damian</given-names></name><xref ref-type="aff" rid="aff1"/><xref ref-type="corresp" rid="cor1">*</xref><xref ref-type="other" rid="par-6"/><xref ref-type="fn" rid="con11"/><xref ref-type="fn" rid="conf1"/></contrib><aff id="aff1"><institution content-type="dept">Department of Molecular Neurobiology</institution>, <institution>Max Planck Institute of Psychiatry</institution>, <addr-line><named-content content-type="city">Munich</named-content></addr-line>, <country>Germany</country></aff><aff id="aff2"><institution content-type="dept">Institute of Physiology</institution>, <institution>University of Bonn</institution>, <addr-line><named-content content-type="city">Bonn</named-content></addr-line>, <country>Germany</country></aff><aff id="aff3"><institution content-type="dept">Department of Molecular Neurobiology</institution>, <institution>Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA)-CONICET-Partner Institute of the Max Planck Society</institution>, <addr-line><named-content content-type="city">Buenos Aires</named-content></addr-line>, <country>Argentina</country></aff><aff id="aff4"><institution content-type="dept">Department of Neurobiology of Stress and Neurogenetics</institution>, <institution>Max Planck Institute of Psychiatry</institution>, <addr-line><named-content content-type="city">Munich</named-content></addr-line>, <country>Germany</country></aff><aff id="aff5"><institution content-type="dept">Institute of Developmental Genetics</institution>, <institution>Helmholtz Zentrum München</institution>, <addr-line><named-content content-type="city">Neuherberg</named-content></addr-line>, <country>Germany</country></aff><aff id="aff6"><institution>Technische Universität</institution>, <addr-line><named-content content-type="city">Munich</named-content></addr-line>, <country>Germany</country></aff><aff id="aff7"><institution>Deutsches Zentrum für Neurodegenerative Erkrankungen</institution>, <addr-line><named-content content-type="city">Munich</named-content></addr-line>, <country>Germany</country></aff><aff id="aff8"><institution>Munich Cluster for System Neurology</institution>, <addr-line><named-content content-type="city">Munich</named-content></addr-line>, <country>Germany</country></aff><aff id="aff9"><institution content-type="dept">Department of Biochemistry</institution>, <institution>University of Utah School of Medicine</institution>, <addr-line><named-content content-type="city">Salt Lake City</named-content></addr-line>, <country>United States</country></aff></contrib-group><contrib-group content-type="section"><contrib contrib-type="editor"><name><surname>Nelson</surname><given-names>Sacha B</given-names></name><role>Reviewing editor</role><aff><institution>Brandeis University</institution>, <country>United States</country></aff></contrib></contrib-group><author-notes><corresp id="cor1"><label>*</label>For correspondence: <email>refojo@mpipsykl.mpg.de</email></corresp></author-notes><pub-date date-type="pub" publication-format="electronic"><day>18</day><month>11</month><year>2014</year></pub-date><pub-date pub-type="collection"><year>2014</year></pub-date><volume>3</volume><elocation-id>e02755</elocation-id><history><date date-type="received"><day>11</day><month>03</month><year>2014</year></date><date date-type="accepted"><day>15</day><month>10</month><year>2014</year></date></history><permissions><copyright-statement>© 2014, Giusti et al</copyright-statement><copyright-year>2014</copyright-year><copyright-holder>Giusti et al</copyright-holder><license xlink:href="http://creativecommons.org/licenses/by/4.0/"><license-p>This article is distributed under the terms of the <ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution License</ext-link>, which permits unrestricted use and redistribution provided that the original author and source are credited.</license-p></license></permissions><self-uri content-type="pdf" xlink:href="elife02755.pdf"/><abstract><object-id pub-id-type="doi">10.7554/eLife.02755.001</object-id><p>MicroRNAs (miRNAs) are conserved noncoding RNAs that function as posttranscriptional regulators of gene expression. miR-9 is one of the most abundant miRNAs in the brain. Although the function of miR-9 has been well characterized in neural progenitors, its role in dendritic and synaptic development remains largely unknown. In order to target miR-9 in vivo, we developed a transgenic miRNA sponge mouse line allowing conditional inactivation of the miR-9 family in a spatio-temporal-controlled manner. Using this novel approach, we found that miR-9 controls dendritic growth and synaptic transmission in vivo. Furthermore, we demonstrate that miR-9-mediated downregulation of the transcriptional repressor REST is essential for proper dendritic growth.</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.02755.001">http://dx.doi.org/10.7554/eLife.02755.001</ext-link></p></abstract><abstract abstract-type="executive-summary"><object-id pub-id-type="doi">10.7554/eLife.02755.002</object-id><title>eLife digest</title><p>Messages are sent back and forth in our brains by cells called neurons that connect to each other in complex networks. Neurons develop from stem cells in a complicated process that involves a number of different stages. In one of the final stages, tree-like structures called dendrites emerge from the neurons and connect with neighboring neurons via special junctions called synapses.</p><p>A group of small RNA molecules called microRNAs have roles in controlling the development of neurons. One microRNA, called miR-9, is abundant in the brain and is known to be involved in the early stages of neuron development. However, its role in the formation of dendrites and synapses remains unclear.</p><p>Giusti et al. studied this microRNA in mice. A length of DNA, coding for an RNA molecule that binds to miR-9 molecules and stops them performing their normal function, was inserted into the mice. These experiments showed that miR-9 is involved in controlling dendrite growth and synaptic function.</p><p>To enable a neuron to produce dendrites, miR-9 binds to and interferes with the RNA molecules that are needed to make a protein called REST. This protein is a transcription factor that switches off the expression of other genes so, in effect, miR-9 allows a set of genes that are needed for dendrite growth to be switched on.</p><p>The methodology developed by Giusti et al. could be used to study the functions of other microRNAs.</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.02755.002">http://dx.doi.org/10.7554/eLife.02755.002</ext-link></p></abstract><kwd-group kwd-group-type="author-keywords"><title>Author keywords</title><kwd>miR-9</kwd><kwd>miR-9 sponge</kwd><kwd>miR-9 reporter</kwd><kwd>dendrite development</kwd><kwd>REST</kwd></kwd-group><kwd-group kwd-group-type="research-organism"><title>Research organism</title><kwd>mouse</kwd></kwd-group><funding-group><award-group id="par-1"><funding-source><institution-wrap><institution>European Union</institution></institution-wrap></funding-source><award-id>SyBoSS FP7-Health-F4-2010-242129</award-id><principal-award-recipient><name><surname>Wurst</surname><given-names>Wolfgang</given-names></name></principal-award-recipient></award-group><award-group id="par-2"><funding-source><institution-wrap><institution>Bavarian State Ministry of Education, Science and Arts</institution></institution-wrap></funding-source><award-id>Bavarian Research Network - ForIPs</award-id><principal-award-recipient><name><surname>Wurst</surname><given-names>Wolfgang</given-names></name></principal-award-recipient></award-group><award-group id="par-3"><funding-source><institution-wrap><institution-id institution-id-type="FundRef">http://dx.doi.org/10.13039/501100002347</institution-id><institution>Bundesministerium für Bildung und Forschung</institution></institution-wrap></funding-source><award-id>FKZ 01GN1009C</award-id><principal-award-recipient><name><surname>Wurst</surname><given-names>Wolfgang</given-names></name></principal-award-recipient></award-group><award-group id="par-4"><funding-source><institution-wrap><institution-id institution-id-type="FundRef">http://dx.doi.org/10.13039/501100002347</institution-id><institution>Bundesministerium für Bildung und Forschung</institution></institution-wrap></funding-source><award-id>FKZ 01GS08151</award-id><principal-award-recipient><name><surname>Deussing</surname><given-names>Jan M</given-names></name></principal-award-recipient></award-group><award-group id="par-5"><funding-source><institution-wrap><institution-id institution-id-type="FundRef">http://dx.doi.org/10.13039/501100002347</institution-id><institution>Bundesministerium für Bildung und Forschung</institution></institution-wrap></funding-source><award-id>FKZ 01GS08155</award-id><principal-award-recipient><name><surname>Deussing</surname><given-names>Jan M</given-names></name></principal-award-recipient></award-group><award-group id="par-6"><funding-source><institution-wrap><institution-id institution-id-type="FundRef">http://dx.doi.org/10.13039/501100004189</institution-id><institution>Max-Planck-Gesellschaft</institution></institution-wrap></funding-source><award-id>Institute of Psychiatry</award-id><principal-award-recipient><name><surname>Refojo</surname><given-names>Damian</given-names></name><name><surname>Deussing</surname><given-names>Jan M</given-names></name></principal-award-recipient></award-group><funding-statement>The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.</funding-statement></funding-group><custom-meta-group><custom-meta><meta-name>elife-xml-version</meta-name><meta-value>2</meta-value></custom-meta><custom-meta specific-use="meta-only"><meta-name>Author impact statement</meta-name><meta-value>Conditional transgenic miR-9 sponge mice exhibit developmental defects in dendrite growth due to up-regulation of the transcriptional repressor REST.</meta-value></custom-meta></custom-meta-group></article-meta></front><body><sec id="s1" sec-type="intro"><title>Introduction</title><p>Early neuronal development consists of a stereotypic progression of events involving neurite extension, axonal polarization and growth, dendritic arborization, and synaptic formation (<xref ref-type="bibr" rid="bib88">Urbanska et al., 2008</xref>; <xref ref-type="bibr" rid="bib9">Barnes and Polleux, 2009</xref>; <xref ref-type="bibr" rid="bib14">Caceres et al., 2012</xref>). Dendrites are the main site of information input into neurons. The architecture of the dendritic tree and the targeting of dendrites into appropriate territories critically shape the input properties of neurons and are therefore of profound importance for the establishment of neuronal networks (<xref ref-type="bibr" rid="bib56">London and Hausser, 2005</xref>; <xref ref-type="bibr" rid="bib62">Mumm et al., 2006</xref>; <xref ref-type="bibr" rid="bib68">Parrish et al., 2007</xref>; <xref ref-type="bibr" rid="bib84">Spruston, 2008</xref>). The most relevant synaptic specialization of dendrites is dendritic spines. These actin-rich, structurally plastic protrusions represent the major sites of excitatory synaptic contact (<xref ref-type="bibr" rid="bib12">Bonhoeffer and Yuste, 2002</xref>; <xref ref-type="bibr" rid="bib35">Hering and Sheng, 2001</xref>). The development of both, dendrites and spines, represents a multistep process influenced by external signals and intrinsic genetic programs (<xref ref-type="bibr" rid="bib38">Jan and Jan, 2003</xref>; <xref ref-type="bibr" rid="bib92">Wong and Ghosh, 2002</xref>). Emerging data suggest that specific miRNAs exert critical regulatory functions during neuronal differentiation by controlling developmental gene expression programs driving dendritic and spine maturation (<xref ref-type="bibr" rid="bib79">Schratt et al., 2006</xref>; <xref ref-type="bibr" rid="bib27">Fiore et al., 2009</xref>; <xref ref-type="bibr" rid="bib69">Parrish et al., 2009</xref>; <xref ref-type="bibr" rid="bib61">Magill et al., 2010</xref>).</p><p>MicroRNAs (miRNAs) have arisen as a powerful class of conserved noncoding RNAs regulating gene expression. They are particularly enriched in the nervous system where they have been shown to influence neuronal development and function (<xref ref-type="bibr" rid="bib30">Giraldez et al., 2005</xref>; <xref ref-type="bibr" rid="bib79">Schratt et al., 2006</xref>; <xref ref-type="bibr" rid="bib32">Han et al., 2013</xref>). Importantly, miR-9 is one of the most abundant miRNAs in the developing and adult brain (<xref ref-type="bibr" rid="bib51">Lagos-Quintana et al., 2002</xref>; <xref ref-type="bibr" rid="bib46">Krichevsky et al., 2003</xref>). In mammals, miR-9 precursors are encoded by three genes, <italic>miR-9-1</italic>, <italic>miR-9-2,</italic> and <italic>miR-9-3</italic>, located in different chromosomes. After processing, these paralogous transcripts give rise to a unique mature miR-9. Although the function of miR-9 is well established in neural precursors (<xref ref-type="bibr" rid="bib52">Leucht et al., 2008</xref>; <xref ref-type="bibr" rid="bib96">Zhao et al., 2009</xref>; <xref ref-type="bibr" rid="bib21">Delaloy et al., 2010</xref>; <xref ref-type="bibr" rid="bib11">Bonev et al., 2011</xref>; <xref ref-type="bibr" rid="bib19">Coolen et al., 2012</xref>), its role in differentiated neurons is largely unknown. This is surprising since miR-9 levels are higher in mature neurons than in neural precursors (<xref ref-type="bibr" rid="bib53">Liu et al., 2012</xref>), suggesting that important biological processes beyond proliferation or specification are regulated by miR-9. Recently, a role for miR-9 in axonal extension and branching has been described (<xref ref-type="bibr" rid="bib20">Dajas-Bailador et al., 2012</xref>), indicating the importance of miR-9 in the establishment of neuronal networks. However, the involvement of this microRNA in the later stages of neuronal development remains unexplored.</p><p>In this study, we aimed to characterize a potential role for miR-9 in dendritic and spine development in vivo. In order to efficiently knock-down miR-9 in a living animal, we employed miRNA sponges as a long-lasting miRNA inhibition strategy. miRNA sponges are transcripts that carry several in tandem copies of a sequence complementary to the miRNA of interest in their 3′UTRs (<xref ref-type="bibr" rid="bib24">Ebert et al., 2007</xref>). When expressed at high levels, miRNA sponges act as specific competitive inhibitors by binding and sequestering the miRNA of interest. In addition, miRNA sponges can be used to monitor miRNA activity when expressed together in the same transcript with a fluorescent protein gene, which is downregulated upon the binding of the miRNA (<xref ref-type="bibr" rid="bib24">Ebert et al., 2007</xref>).</p><p>Analysis of the genomic organization or miRNA genes, revealed that approximately 50% of all mammalian miRNAs reside within either protein coding genes or long noncoding RNAs (lncRNAs) genes (<xref ref-type="bibr" rid="bib50">Lagos-Quintana et al., 2001</xref>; <xref ref-type="bibr" rid="bib75">Rodriguez et al., 2004</xref>). In addition, a large proportion of microRNA genes from different families are clustered and expressed as polycistronic transcripts (<xref ref-type="bibr" rid="bib64">Olena and Patton, 2010</xref>). Therefore, it is a major challenge to develop KO models for miRNA genes, since the targeted deletion of a miRNA might affect overlapping protein-coding or lncRNA genes, or alter the expression of neighbor miRNAs, clustered in the same genomic region. Furthermore, many miRNAs have seed family members encoded at multiple distant loci, which requires that multiple genes have to be simultaneously knocked-out to obtain full ablation and avoid gene compensations based on functional redundancy. These obstacles severely limit the use of conditional targeting strategies, usually based on the Cre-<italic>loxP</italic> system, for the study of miRNA function.</p><p>Strategies based on the use of miRNA sponges as dominant negative genetic tools, can overcome the limitations presented by miRNA-gene-KO approaches. Sponges act in <italic>trans</italic> without interfering with the expression of other genes that could localize with the gene that expresses the miRNA of interest. Moreover, a single sponge transgene allows the simultaneous silencing of ‘seed’ sequence redundant microRNAs encoded at distant loci.</p><p>Here, we describe for the first time a conditional transgenic sponge mouse model. We derived two different strains for in vivo analysis: (i) a reporter mouse line to monitor miR-9 activity with single-cell resolution and (ii) a line for miR-9 loss-of-function studies. Using the latter, we revealed a novel developmental role of miR-9 in the postmitotic differentiation of neurons, as a key regulator of dendritic growth and synaptic transmission in vivo. Furthermore, we show that regulation of the transcriptional repressor REST by miR-9 is essential for normal dendritic maturation.</p></sec><sec id="s2" sec-type="results"><title>Results</title><sec id="s2-1"><title>Fully complementary and bulged miR-9 sponges are equally effective</title><p>Depending on the configuration of the binding sites, two sponge designs have been described: fully complementary (FC) sponges, which function by both sequestering miRNA and promoting miRNA degradation (<xref ref-type="bibr" rid="bib3">Ameres et al., 2010</xref>); and bulged (Bg) sponge variants, which carry mismatches that prevent base-pairing with the miRNA at positions 9–12, thereby avoiding AGO2-mediated decay of the sponge (<xref ref-type="bibr" rid="bib24">Ebert et al., 2007</xref>) (<xref ref-type="fig" rid="fig1s1">Figure 1—figure supplement 1</xref>).</p><p>Before studying the role of miR-9 on dendritic and spine development in vivo, we tested the efficiency of GFP-FC and GFP-Bg miR-9 sponge variants as decoy targets and miR-9 reporters in cell culture systems. Both the sponge variants displayed similar efficacies to inhibit miR-9 activity (<xref ref-type="fig" rid="fig1s2">Figure 1—figure supplement 2</xref>). We selected FC sponges for further studies since they displayed a higher predicted binding affinity for miR-9 (FC sponge: −42.9 kcal/mol vs Bg sponge: −32 kcal/mol) and a higher sensitivity as reporters (<xref ref-type="fig" rid="fig1s2">Figure 1—figure supplement 2</xref>). This last feature might be crucial for precise analysis of miR-9 expression and activity in vivo.</p></sec><sec id="s2-2"><title>MiR-9 regulates dendritic development in primary neuronal cultures</title><p>To define a potential role of miR-9 in the maturation of dendritic arbors and spines, we used transiently transfected sponge constructs in developing mouse primary hippocampal neurons. Neurons transfected with GFP-FC-miR-9 sponge showed significantly reduced total dendritic length and complexity after 10 days in vitro (DIV) compared to neurons transfected with GFP (spongeless) or a GFP-scrambled control sponge (<xref ref-type="fig" rid="fig1">Figure 1A–C</xref>). The specificity of the miR-9 sponge was further confirmed, as miR-9 overexpression rescued the phenotype induced by the GFP-FC-miR-9 sponge (<xref ref-type="fig" rid="fig1">Figure 1A–C</xref>). miR-9*, encoded by the same miRNA precursor as miR-9, has been postulated to contribute to activity-dependent dendritic growth, although no direct evidence was shown (<xref ref-type="bibr" rid="bib95">Yoo et al., 2009</xref>). Interestingly, expression of FC sponges directed to miR-9* showed no effects on dendritic growth (<xref ref-type="fig" rid="fig1">Figure 1A–C</xref>). In addition, we found that miR-9 overexpression in hippocampal neurons did not affect total dendritic length and had only a mild impact on dendritic complexity (data not shown). Together, these results indicate that miR-9, but not miR-9*, participates in the developmental programs controlling dendritic growth and that endogenous mir-9 levels have a saturating effect of on dendritic maturation.<fig-group><fig id="fig1" position="float"><object-id pub-id-type="doi">10.7554/eLife.02755.003</object-id><label>Figure 1.</label><caption><title>miR-9 regulates dendritic development.</title><p>(<bold>A</bold>) Representative images of primary hippocampal neurons transiently transfected at DIV4 with the indicated constructs and fixed at DIV10. mRFP was cotransfected for visualization. Scale bar 50 μm. (<bold>B</bold>) Quantification of the total dendritic length (mean + SEM, one-way ANOVA, and Bonferroni post-test) and (<bold>C</bold>) quantification of dendritic complexity by Sholl analysis of neurons transfected as described in (<bold>A</bold>) (mean + SEM, repeated measures two-way ANOVA and Bonferroni post-test showing GFP-scrambled vs GFP-miR-9 sponge). **p &lt; 0.01, n ≥ 30 neurons per condition.</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.02755.003">http://dx.doi.org/10.7554/eLife.02755.003</ext-link></p></caption><graphic xlink:href="elife02755f001"/></fig><fig id="fig1s1" position="float" specific-use="child-fig"><object-id pub-id-type="doi">10.7554/eLife.02755.004</object-id><label>Figure 1—figure supplement 1.</label><caption><title>FC and Bg miR-9 sponges.</title><p>Schematic representation of the GFP-miR-9 sponge construct and the interaction between miR-9 and the FC (left) or Bg (right) binding sites.</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.02755.004">http://dx.doi.org/10.7554/eLife.02755.004</ext-link></p></caption><graphic xlink:href="elife02755fs001"/></fig><fig id="fig1s2" position="float" specific-use="child-fig"><object-id pub-id-type="doi">10.7554/eLife.02755.005</object-id><label>Figure 1—figure supplement 2.</label><caption><title>Comparison of the efficacy of FC and Bg miR-9 sponges.</title><p>(<bold>A</bold>) The efficacy of miR-9 sponges to inhibit miR-9 activity was assessed by cotransfection of Neuro-2a cells with a luciferase-based miR-9 sensor, a CMV-lacZ construct to normalize transfection efficiency, and the indicated sponge constructs. Overexpression of miR-9 induced a strong downregulation in the luciferase activity (GFP + empty vs GFP + miR-9). GFP-FC- and GFP-Bg-miR-9 sponges were equally effective to rescue the expression of the miR-9 sensor in a dose-dependent manner. To control the specificity of the effect of the miR-9 sponges, a scrambled version of the miR-9 sponge and sponges designed to bind other microRNAs (miR-9*, miR-124) were used. To check the specificity of the sensor, a mutated version of miR-9 was expressed. (<bold>B</bold>) Primary neurons were transfected with the sponge plasmids described in (<bold>A</bold>). Both miR-9 sponges were also equally effective to rescue the expression of the miR-9 sensor. Values represent mean + SEM, one-way ANOVA, and Bonferroni post-test, **p &lt; 0.01.</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.02755.005">http://dx.doi.org/10.7554/eLife.02755.005</ext-link></p></caption><graphic xlink:href="elife02755fs002"/></fig><fig id="fig1s3" position="float" specific-use="child-fig"><object-id pub-id-type="doi">10.7554/eLife.02755.006</object-id><label>Figure 1—figure supplement 3.</label><caption><title>FC and BG sponges as reporters of miR-9 activity.</title><p>Neuro-2a cells were cotransfected with a plasmid expressing either a GFP-sponge-construct (FC-miR-9, Bg-miR-9, miR-124) or GFP, and an empty vector (control), a plasmid expressing miR-9, or a plasmid expressing the mutated form of miR-9. (<bold>A</bold>) Microscopic images of Neuro-2a cells showing native GFP fluorescence. Note that GFP encoded by both FC and Bg miR-9 sponges is downregulated in miR-9-cotransfected cells. Scale bar: 25 μm. (<bold>B</bold>) To quantify miR-9-induced GFP downregulation, GFP-derived fluorescence was quantified in protein lysates from transfected Neuro-2a. Quantification of GFP downregulation is expressed as the percentage of remaining GFP fluorescence (normalized) after miR-9 cotransfection. For each condition, 100% represents GFP fluorescence when an empty control vector was cotransfected. FC sponges are more sensitive reporters of miR-9 activity. (<bold>C</bold>) The stability of the sponge transcripts was estimated by qPCR in transfected Neuro-2a cells. Quantification of the sponge transcript levels by qPCR (GFP) after miR-9 cotransfection. For each condition, 100% represents the amount of GFP transcript when an empty control vector was cotransfected. The lower stability of the FC sponge likely reflects AGO2-mediated degradation and is probably the basis of the higher sensitivity of this sponge variant as reporter. Values represent mean + SEM, one-way ANOVA, and Bonferroni post-test, **p &lt; 0.01.</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.02755.006">http://dx.doi.org/10.7554/eLife.02755.006</ext-link></p></caption><graphic xlink:href="elife02755fs003"/></fig></fig-group></p><p>Further, we evaluated the density and morphology of spines in transfected neurons at DIV21. No effects of miR-9 inhibition on spine development were observed (GFP-scrambled sponge: 6.48 ± 0.64 vs GFP-FC-miR-9-sponge: 5.85 ± 0.48 spines per 10 μm of dendritic segment, n.s., Student's <italic>t</italic> test).</p><p>Dendrite differentiation during brain development involves not only the growth and maturation of the dendritic arbors, but also the establishment of a refined specific connectivity pattern with thousands of inputs arriving from presynaptic neurons. In vivo, these processes are under the strong influence of extrinsic factors such as adhesion molecules, proteins of the extracellular matrix, growth factors, glial contacts, and guidance cues (<xref ref-type="bibr" rid="bib38">Jan and Jan, 2003</xref>; <xref ref-type="bibr" rid="bib85">Sudhof, 2008</xref>). These factors are mostly absent in cell culture systems and consequently not modeled in primary neurons. Therefore, to study the effects of miR-9 in vivo, we generated conditional transgenic GFP-FC-miR-9 sponge mice by homologous recombination in the <italic>Rosa26</italic> (<italic>R26</italic>) locus (miR-9-Sp<sup>fl-Stop</sup>) (<xref ref-type="fig" rid="fig2s1">Figure 2—figure supplement 1</xref>).</p></sec><sec id="s2-3"><title>Characterization of miR-9 activity in the adult mouse brain</title><p>The miR-9 sponge transgene allowed us to characterize miR-9 activity in the adult mouse brain. The reporter function relies on the miR-9-induced GFP downregulation of the sponge transcript. However, an often underestimated problem of sponge-based reporters is the impossibility to distinguish between a truly downregulated signal reporting miR-9 activity and a non-specific lack of sponge expression due to promoter a inactivity or locus silencing. We therefore developed a reporter mouse line encoding a fluorescent tdTomato control protein in the other allele of the <italic>R26</italic> locus (see details in <xref ref-type="fig" rid="fig2s2">Figure 2—figure supplement 2</xref>). The tdTomato transgene acts as a control allele since it is located in the same locus and is also driven by a CAG promoter. The absence of GFP signal would therefore imply miR-9 activity only if the tdTomato signal is present, excluding lack of expression of the sponge transgene. Histological evaluation of the miR-9-Sp/tdTomato reporter mouse line revealed a strong signal for both proteins in most organs, indicating the absence of miR-9 activity (<xref ref-type="fig" rid="fig2">Figure 2A</xref>). Lack of expression of both transgenes was observed in seminiferous tubules and in follicular cells of the ovary due to either silencing of the <italic>R26</italic> locus or inactivity of the CAG promoter. Interestingly, we observed a scattered population of GFP-negative/tdTomato-positive hepatocytes, suggesting that a subpopulation of liver cells express miR-9.<fig-group><fig id="fig2" position="float"><object-id pub-id-type="doi">10.7554/eLife.02755.007</object-id><label>Figure 2.</label><caption><title>Histological analysis of miR-9-Sp/tdTomato reporter mouse line.</title><p>(<bold>A</bold>) Confocal images of different organs of the reporter mice showing native GFP and tdTomato fluorescence. Scale bar: 50 μm. (<bold>B</bold>) Low power images of sections from brain and kidney showing native GFP and tdTomato fluorescence. Scale bar: 1 mm. (<bold>C</bold>) At microscopic level within the brain, strong native GFP signal could be only detected in blood vessels (top) and in the choroid plexus. Note the downregulation of GFP in the <italic>stratum pyramidale</italic> (dashed lines) of hippocampal CA1 (bottom). Scale bar: 50 μm. (<bold>D</bold>) Brain sections showing native GFP and tdTomato fluorescence with immunohistochemistry for different cell-specific markers: NeuN (neurons), GFAP (astrocytes), and Iba1 (microglia). Arrows show examples of individual cells. Note the faint native GFP signal in microglial cells. Scale bar: 20 μm.</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.02755.007">http://dx.doi.org/10.7554/eLife.02755.007</ext-link></p></caption><graphic xlink:href="elife02755f002"/></fig><fig id="fig2s1" position="float" specific-use="child-fig"><object-id pub-id-type="doi">10.7554/eLife.02755.008</object-id><label>Figure 2—figure supplement 1.</label><caption><title>Generation of conditional GFP-FC-miR-9 sponge mice.</title><p>Strategy for conditional, Cre-mediated expression of FC-miR-9 sponge from the <italic>Rosa26</italic> (<italic>R26</italic>) locus. Schematic representation of wild-type <italic>R26</italic> locus, targeting vector, recombined miR-9-Sp<sup>fl-Stop</sup> allele and activated miR-9-Sp allele resulting from Cre-mediated excision of the ‘Stop’ cassette. To maximize the level of transcription of the transgene, we used a CAG promoter, significantly stronger than the endogenous <italic>R26</italic> promoter.</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.02755.008">http://dx.doi.org/10.7554/eLife.02755.008</ext-link></p></caption><graphic xlink:href="elife02755fs004"/></fig><fig id="fig2s2" position="float" specific-use="child-fig"><object-id pub-id-type="doi">10.7554/eLife.02755.009</object-id><label>Figure 2—figure supplement 2.</label><caption><title>miR-9 reporter mouse line.</title><p>(<bold>A</bold>) Breeding strategy to generate the miR-9-Sp/tdTomato reporter mouse line from conditional miR-9-Sp<sup>fl-Stop</sup> and tdTomato<sup>fl−Stop</sup> mouse lines. The genotypes described below each mouse cartoon indicate the alleles in the <italic>Rosa26</italic> (<italic>R26</italic>) locus. In the F0, homozygous mice for miR-9-Sp<sup>fl-Stop</sup> and the tdTomato<sup>fl-Stop</sup> alleles were independently bred with a Deleter-Cre mouse line, carrying a ubiquitously expressed Cre transgene in the <italic>R26</italic> locus. This leads to a removal of the ‘Stop’ cassette from the miR-9-Sp<sup>fl-Stop</sup> and the tdTomato<sup>fl-Stop</sup> alleles in all tissues of F1 mice, including the germ line. As a result, the miR-9-Sp and tdTomato alleles are ubiquitously expressed. An additional breeding step was needed to generate in the F2 the heterozygous reporter mice, carrying one miR-9-Sp allele and one tdTomato allele, both in the <italic>R26</italic> locus. Note that both transgenes are active and that the Deleter-Cre transgene is not present in the reporter mice. (<bold>B</bold>) The reporter function of the mouse line relies on the miR-9-induced GFP down-regulation of the sponge transcript. The tdTomato transgene acts as a control allele since it is located in the same locus and is also driven by a CAG promoter. The absence of GFP signal would therefore imply miR-9 activity only if tdTomato signal is present, excluding lack of expression of the sponge transgene.</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.02755.009">http://dx.doi.org/10.7554/eLife.02755.009</ext-link></p></caption><graphic xlink:href="elife02755fs005"/></fig></fig-group></p><p>A robust downregulation of GFP expression was observed throughout the entire brain, indicating elevated miR-9 activity (<xref ref-type="fig" rid="fig2">Figure 2B,C</xref>). In particular, GFP expression was strongly downregulated in neurons and astrocytes while we observed a faint GFP signal in microglia (<xref ref-type="fig" rid="fig2">Figure 2D</xref>). These results suggest that miR-9 expression levels are higher in neurons and astrocytes than in microglia.</p></sec><sec id="s2-4"><title>miR-9 sponge transgenic mice exhibit dendritic growth defects and impaired synaptic transmission</title><p>To address the impact of miR-9 loss of function on dendritic growth in vivo, we generated a miR-9-Sp<sup>Nestin-Cre</sup> mouse line by breeding miR-9-Sp<sup>fl-Stop</sup> mice with the Nestin-Cre mouse line. This newly generated mouse line conditionally expresses the GFP-FC-miR-9-sponge in the CNS. Unlike the reporter line, miR-9-Sp<sup>Nestin-Cre</sup> mice are homozygous for the sponge transgene and lack a tdTomato allele. miR-9-Sp<sup>Nestin-Cre</sup> mice are viable and fertile and do not show any obvious abnormalities. The expression of the sponge in miR-9-Sp<sup>Nestin-Cre</sup> mice was confirmed by in situ hybridization, quantitative PCR, and immunodetection of GFP (<xref ref-type="fig" rid="fig3">Figure 3A–E</xref>), indicating that the expression level of the sponge transgene is sufficiently high to overcome a full repression by endogenous miR-9 activity.<fig id="fig3" position="float"><object-id pub-id-type="doi">10.7554/eLife.02755.010</object-id><label>Figure 3.</label><caption><title>Characterization of miR-9-Sp<sup>Nestin-Cre</sup> mouse line.</title><p>miR-9-Sp<sup>fl-Stop</sup> littermates were used as controls. The expression of the sponge construct was evaluated by (<bold>A</bold>) in situ hybridization using anti-GFP riboprobe and (<bold>B</bold>) qPCR. As an additional readout of the expression of the sponge, GFP protein content was determined by (<bold>C</bold>) Western blotting and (<bold>D</bold> and <bold>E</bold>) immunohistochemistry with anti-GFP antibodies. (<bold>D</bold>) Note that only a faint native GFP fluorescence is observed in miR-9-Sp<sup>Nestin-Cre</sup> brain sections, whereas a strong GFP signal can be detected after immunofluorescence, indicating that GFP protein levels are low but not completely down-regulated by miR-9. Scale bar: 100 μm. (<bold>E</bold>) Co-immunohistochemistry of GFP and NeuN, showing GFP expression in CA1 neurons. Scale bar: 50 μm. (<bold>F</bold>) Quantification of miR-9 levels in hippocampal and cortical samples by qPCR using Taqman probes. (<bold>G</bold>) Quantification of miR-9 precursors (miR-9-1, miR-9-2, and miR-9-3) in hippocampal and cortical samples by qPCR. Values represent mean + SEM, one-way ANOVA, and Bonferroni post-test, *p &lt; 0.05, **p &lt; 0.01, n = 4.</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.02755.010">http://dx.doi.org/10.7554/eLife.02755.010</ext-link></p></caption><graphic xlink:href="elife02755f003"/></fig></p><p>Despite the fact that sponges reduce miRNA activity by sequestration, we observed that miR-9 abundance was also reduced in miR-9-Sp<sup>Nestin-Cre</sup> mice (<xref ref-type="fig" rid="fig3">Figure 3F</xref>), probably due to increased degradation of miR-9 in the presence of a FC target (<xref ref-type="bibr" rid="bib3">Ameres et al., 2010</xref>). No compensatory increase in miR-9 precursors levels was observed (<xref ref-type="fig" rid="fig3">Figure 3G</xref>).</p><p>To analyze dendrite arborization in vivo, miR-9-Sp<sup>Nestin-Cre</sup> mice were crossed with Thy1<sup><italic>EGFP</italic></sup> mice (<xref ref-type="bibr" rid="bib26">Feng et al., 2000</xref>). We prepared hippocampal slices from 3-month-old animals, and traced individual CA1 neurons using Neurolucida software. Pyramidal CA1 neurons from miR-9-Sp<sup>Nestin-Cre</sup> mice exhibited a reduction in total dendritic length and arborization complexity compared to control littermates (miR-9-Sp<sup>fl-Stop</sup>) (<xref ref-type="fig" rid="fig4">Figure 4A–C</xref>). Similar results were obtained when neurons were visualized by Golgi staining (<xref ref-type="fig" rid="fig4s1">Figure 4—figure supplement 1</xref>). Importantly, this phenotype was not restricted to hippocampal neurons and it was also observed in layer V cortical neurons (<xref ref-type="fig" rid="fig4s2">Figure 4—figure supplement 2</xref>), suggesting that the reduction in dendritic arborization might be a generalized effect of miR-9 loss of function.<fig-group><fig id="fig4" position="float"><object-id pub-id-type="doi">10.7554/eLife.02755.011</object-id><label>Figure 4.</label><caption><title>miR-9 sponge transgenic mice exhibit dendritic growth defects and impaired synaptic transmission.</title><p>(<bold>A</bold>) Confocal stack images (left) and representative tracings (right) of CA1 neurons of Thy1<sup><italic>EGFP</italic></sup>-miR-9-Sp<sup>fl-Stop</sup> (control) and Thy1<sup><italic>EGFP</italic></sup>-miR-9-Sp<sup>Nestin-Cre</sup> mice. Scale bar: 50 μm. (<bold>B</bold>) Quantification of the total dendritic length of neuronal tracings (mean + SEM, Student's <italic>t</italic> test), (<bold>C</bold>) Sholl analysis of neuronal tracings (mean + SEM, two-way ANOVA and Bonferroni post-test). (<bold>B</bold> and <bold>C</bold>) **p &lt; 0.01, n ≥ 30 neurons per condition recruited from five mice per genotype. (<bold>D</bold>–<bold>F</bold>) GFP-miR-9 sponge or GFP (control) plus mRFP plasmids (for visualization) were in utero electroporated at E14.5. At P30, pyramidal hippocampal neurons in CA1 were traced with the Neurolucida software. (<bold>D</bold>) Images of transfected brain sections (left). Note the downregulation of GFP encoded in the miR-9 sponge plasmid. Scale bar: 100 μm. Representative tracings (right). Scale bar: 50 μm. (<bold>E</bold>) miR-9 sponge-transfected neurons show a reduced total dendritic length (mean + SEM, Student’s <italic>t</italic> test) (<bold>F</bold>) and reduced dendritic complexity (mean + SEM, two-way ANOVA and Bonferroni post-test). (<bold>E</bold> and <bold>F</bold>) **p &lt; 0.01, n ≥ 18–20 neurons per condition. (<bold>G</bold>) Dendritic spines on secondary apical dendrites of CA1 neurons of Thy1<sup><italic>EGFP</italic></sup>-miR-9-Sp<sup>fl-Stop</sup> (control) and Thy1<sup><italic>EGFP</italic></sup>-miR-9-Sp<sup>Nestin-Cre</sup> mice and quantification of spine density (n.s, Student's <italic>t</italic> test, n ≥ 30 neurons per condition recruited from five mice per genotype). Scale bar: 1 μm. (<bold>H</bold>–<bold>J</bold>) fEPSP recordings in acute hippocampal brain slices demonstrate an impairment of synaptic transmission. (<bold>H</bold>) Sample traces. (<bold>I</bold>) Input–output curve showing reduced synaptic transmission and (<bold>J</bold>) reduced excitability in miR-9-Sp<sup>Nestin-Cre</sup> slices (mean ± SEM, two-way ANOVA and Bonferroni post-test, *p &lt; 0.05, **p &lt; 0.01, n ≥ 9 recordings per condition recruited from 4 mice per genotype). (<bold>K</bold>–<bold>N</bold>) Current-clamp recordings. (<bold>K</bold>) Sample traces of current-clamp recordings. Inset shows the current step protocol, and the same colors indicate same injected currents: dark blue, −100 pA; green, −50 pA; red, 0 pA; light blue, 25 pA; magenta, 50 pA; yellow, 75 pA. Calibration (for inset): 250 ms, 50 pA. (<bold>L</bold>) Action potential (AP) threshold is shifted to more positive membrane potentials in CA1 neurons form miR-9-Sp<sup>Nestin-Cre</sup> mice (mean + SEM, Student's <italic>t</italic> test) and (<bold>M</bold>) fewer APs were elicited with the same current injected (mean ± SEM, two-way ANOVA and Bonferroni post-test, *p &lt; 0.05, **p &lt; 0.01, n ≥ 9 recordings per condition recruited from four mice per genotype). (<bold>N</bold>) Input resistance was not changed (mean + SEM, Student's <italic>t</italic> test, n.s).</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.02755.011">http://dx.doi.org/10.7554/eLife.02755.011</ext-link></p></caption><graphic xlink:href="elife02755f004"/></fig><fig id="fig4s1" position="float" specific-use="child-fig"><object-id pub-id-type="doi">10.7554/eLife.02755.012</object-id><label>Figure 4—figure supplement 1.</label><caption><title>miR-9 loss of function induces dendritic growth defects.</title><p>Golgi-stained sections from miR-9-Sp<sup>Nestin-Cre</sup> and miR-9-Sp<sup>fl-Stop</sup> (control) mice were used to trace CA1 neurons with the Neurolucida software. (<bold>A</bold>) Neurons from miR-9-Sp<sup>Nestin-Cre</sup> mice display a reduced total dendritic length (mean + SEM, Student's <italic>t</italic> test) and (<bold>B</bold>) reduced dendritic complexity maeasured by Sholl analysis (mean + SEM, two-way ANOVA and Bonferroni post-test). **p &lt; 0.01, n ≥ 30 neurons per condition recruited from five mice per genotype.</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.02755.012">http://dx.doi.org/10.7554/eLife.02755.012</ext-link></p></caption><graphic xlink:href="elife02755fs006"/></fig><fig id="fig4s2" position="float" specific-use="child-fig"><object-id pub-id-type="doi">10.7554/eLife.02755.013</object-id><label>Figure 4—figure supplement 2.</label><caption><title>Dendritic defects in cortical neurons of miR-9 sponge transgenic mice.</title><p>(<bold>A</bold>) Confocal stack images (left) and representative tracings (right) of layer V cortical neurons in the primary somatosensory region of Thy1<sup><italic>EGFP</italic></sup>-miR-9-Sp<sup>fl-Stop</sup> (control) and Thy1<sup><italic>EGFP</italic></sup>-miR-9-Sp<sup>Nestin-Cre</sup> mice. Scale bar: 100 μm. (<bold>B</bold>) Quantification of the total dendritic length of neuronal tracings (mean + SEM, Student's <italic>t</italic> test) (<bold>C</bold>) Sholl analysis of neuronal tracings (mean + SEM, two-way ANOVA and Bonferroni post-test). (<bold>B</bold> and <bold>C</bold>) **p &lt; 0.01, n ≥ 30 neurons per condition recruited from five mice per genotype.</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.02755.013">http://dx.doi.org/10.7554/eLife.02755.013</ext-link></p></caption><graphic xlink:href="elife02755fs007"/></fig><fig id="fig4s3" position="float" specific-use="child-fig"><object-id pub-id-type="doi">10.7554/eLife.02755.014</object-id><label>Figure 4—figure supplement 3.</label><caption><title>sEPSC and mEPSC are affected by miR-9 loss of function.</title><p>(<bold>A</bold>) sEPSC sample traces. (<bold>B</bold>) sEPSC amplitude is reduced in miR-9-Sp<sup>Nestin-Cre</sup> neurons. (<bold>C</bold>) sEPSC frequency is strongly reduced in miR-9-Sp<sup>Nestin-Cre</sup> neurons. (<bold>D</bold>) mEPSC sample traces. (<bold>E</bold>) mEPSC amplitude and (<bold>F</bold>) frequency are reduced in miR-9-Sp<sup>Nestin-Cre</sup> neurons. (<bold>G</bold>) No changes were found in paired-pulse facilitation. *p &lt; 0.05, **p &lt; 0.01. Distributions were analyzed by <italic>KS</italic> test; average values were analyzed by Student's <italic>t</italic> test. n ≥ 9 recordings per condition recruited from four mice per genotype.</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.02755.014">http://dx.doi.org/10.7554/eLife.02755.014</ext-link></p></caption><graphic xlink:href="elife02755fs008"/></fig></fig-group></p><p>The reduction in the dendritic complexity observed in miR-9-Sp<sup>Nestin-Cre</sup> mice might be influenced by changes in cell-extrinsic factors of the extracellular milieu, glial cells, or decreased activity of neuronal inputs affecting dendritic differentiation (<xref ref-type="bibr" rid="bib71">Polleux et al., 2000</xref>; <xref ref-type="bibr" rid="bib37">Horch and Katz, 2002</xref>; <xref ref-type="bibr" rid="bib90">Whitford et al., 2002</xref>; <xref ref-type="bibr" rid="bib92">Wong and Ghosh, 2002</xref>; <xref ref-type="bibr" rid="bib93">Yamamoto et al., 2006</xref>). To address this question, we expressed the GFP-FC-miR-9 sponge in a subset of sparse CA1 neurons by in utero electroporation. Hippocampal neural precursors of E14.5 wild-type embryos were transfected with a plasmid expressing mRFP (volume marker) together with either a GFP-FC-miR-9 expressing construct or a GFP spongless control plasmid. Total dendritic length and dendrite complexity were analyzed 1 month after birth. In utero gene transfer of GFP-FC-miR-9-sponge plasmids resulted in changes comparable to those observed in miR-9-Sp<sup>Nestin-Cre</sup> mice. These results demonstrate that the dendritic changes observed with stable ablation of miR-9 are essentially cell autonomous and not caused by changes of cell extrinsic factors (<xref ref-type="fig" rid="fig4">Figure 4D–F</xref>).</p><p>Alterations in dendrite complexity occurring during development might induce structural or functional compensatory mechanisms at the synaptic level in order to preserve the functionality and computational power of the postsynaptic neuron (<xref ref-type="bibr" rid="bib45">Kolb et al., 1997</xref>; <xref ref-type="bibr" rid="bib22">Dieni and Rees, 2003</xref>). We first investigated dendritic spine density of CA1 hippocampal neurons in miR-9 Sp<sup>Nestin-Cre</sup> Thy1<sup><italic>EGFP</italic></sup> mice. No effects were observed in spine density or morphology compared to littermate controls (miR-9-Sp<sup>fl-Stop</sup>) (<xref ref-type="fig" rid="fig4">Figure 4G</xref>). To assess the strength of synaptic transmission in pyramidal hippocampal neurons, we performed field recordings in acute hippocampal slices and analyzed the neural transmission at Schaffer collaterals-CA1 synapses. The size of the presynaptic fiber volley (FV) was compared with the slope of the EPSP in the <italic>stratum radiatum</italic>. We found that synaptic transmission was significantly reduced in miR-9-Sp<sup>Nestin-Cre</sup> mice compared to miR-9-Sp<sup>fl-Stop</sup> littermate controls (<xref ref-type="fig" rid="fig4">Figure 4H,I</xref>). Interestingly, during the course of our experiments, we noted that higher stimulus intensities were required in miR-9-Sp<sup>Nestin-Cre</sup> mice to elicit the same FV amplitude (<xref ref-type="fig" rid="fig4">Figure 4J</xref>). This prompted us to directly test the excitability of CA1 pyramidal cells. In current-clamp recordings we observed a shift of the action potential (AP) threshold to more positive membrane potentials in miR-9-Sp<sup>Nestin-Cre</sup> neurons (<xref ref-type="fig" rid="fig4">Figure 4K,L</xref>). In turn, the same current injected elicited fewer APs (<xref ref-type="fig" rid="fig4">Figure 4M</xref>). The input resistance was not changed (<xref ref-type="fig" rid="fig4">Figure 4N</xref>). If pyramidal neurons are less excitable and therefore generate fewer APs, we should observe a reduced frequency of spontaneous EPSCs (sEPSC). Indeed, the mean sEPSC frequency was largely reduced in CA1 neurons of sponge-expressing animals (<xref ref-type="fig" rid="fig4s3">Figure 4—figure supplement 3A,C</xref>). The reduced sEPSC amplitude (<xref ref-type="fig" rid="fig4s3">Figure 4—figure supplement 3B</xref>) could be caused by the reduced number of AP driven events; however, to test whether the quantal size is reduced in miR-9-Sp<sup>Nestin-Cre</sup> mice, we recorded miniature EPSCs (mEPSC). Here, mEPSC amplitude and frequency were significantly reduced (<xref ref-type="fig" rid="fig4s3">Figure 4—figure supplement 3D–F</xref>). The reduced frequency reflects the reduced number of synapses, while the reduced mEPSC amplitude indicates a change in quantal size. To exclude presynaptic effects, we tested paired-pulse facilitation, a sensitive measure of changes in the probability of transmitter release, which was unchanged (<xref ref-type="fig" rid="fig4s3">Figure 4—figure supplement 3G</xref>). Taken together, these results suggest that the impaired synaptic transmission is caused by a reduction in the absolute number of synapses per neuron (with preserved synapse density), resulting from the shortened dendrites in miR-9-Sp<sup>Nestin-Cre</sup> mice. Additionally, inhibiting miR-9 affects neuronal excitability by changing the AP threshold.</p></sec><sec id="s2-5"><title>Dendritic growth defects after miR-9 loss are mediated by REST</title><p>The cell-intrinsic nature of the effects of the GFP-FC-miR-9 sponge indicates that miR-9 regulates neuronal targets primarily involved in the process of dendritogenesis. To gain further insight into the mechanisms by which miR-9 affects dendritic growth, we used quantitative PCR to determine the expression levels of several predicted miR-9 neuronal targets (<xref ref-type="supplementary-material" rid="SD1-data">Supplementary file 1</xref>). To avoid contaminations by other cell types, we analyzed DIV3 primary hippocampal neurons derived from miR-9-Sp<sup>Nestin-Cre</sup> and littermate control embryos.</p><p>We found that 13 out of 26 miR-9 predicted targets were upregulated in miR-9-Sp<sup>Nestin-Cre</sup> neurons (<xref ref-type="fig" rid="fig5">Figure 5A</xref>). Interestingly, one of the upregulated mRNAs encodes the global transcriptional repressor element 1 (RE-1) silencing transcription factor (REST/NRSF). We speculated that REST is an interesting candidate, which could explain the effects triggered by GFP-FC-miR-9 sponge considering that REST (i) is actively repressing a large array of neuron-specific genes (<xref ref-type="bibr" rid="bib8">Ballas and Mandel, 2005</xref>), (ii) is strongly downregulated during neuronal development (<xref ref-type="bibr" rid="bib78">Schoenherr and Anderson, 1995</xref>; <xref ref-type="bibr" rid="bib7">Ballas et al., 2005</xref>), and (iii) has been experimentally validated as a bona fide target of miR-9 (<xref ref-type="bibr" rid="bib67">Packer et al., 2008</xref>). Importantly, we also found elevated REST protein levels in sponge expressing neurons (<xref ref-type="fig" rid="fig5">Figure 5B</xref>). As expected, increased REST activity resulted in the downregulation of several REST-target genes (<xref ref-type="fig" rid="fig5">Figure 5C</xref>). Moreover, miR-9 sponges reversed the miR-9-induced downregulation of REST in HEK-293 cells (<xref ref-type="fig" rid="fig5">Figure 5D</xref>) further demonstrating the regulatory effect of miR-9 on REST levels.<fig-group><fig id="fig5" position="float"><object-id pub-id-type="doi">10.7554/eLife.02755.015</object-id><label>Figure 5.</label><caption><title>Dendritic growth defects after miR-9 loss are mediated by REST.</title><p>(<bold>A</bold>) Quantitative PCR analysis of predicted miR-9 target mRNAs in hippocampal primary neurons (DIV3) prepared from miR-9-Sp<sup>Nestin-Cre</sup> and miR-9 Sp<sup>fl−Stop</sup> (control) E17.5 embryos (mean + SEM, paired Student's <italic>t</italic> test, n = 4, *p&lt;0.05; <xref ref-type="supplementary-material" rid="SD1-data">Supplementary file 1</xref>). (<bold>B</bold>) Representative immunoblot and quantification of the normalized OD (mean + SEM, Student's <italic>t</italic> test, n = 3, *p &lt; 0.05). (<bold>C</bold>) Quantitative PCR analysis of the expression of REST targets in the same neurons as in (<bold>A</bold>) (mean + SEM, paired Student's <italic>t</italic> test, n = 4, *p &lt; 0.05; **p &lt; 0.01). (<bold>D</bold>) Representative immunoblot (left) and quantification (right) showing that FC-miR-9 sponges reversed miR-9-induced silencing of endogenous REST in transfected HEK-293 cells. Note that REST levels are not upregulated in the condition ‘<italic>empty vector + GFP-miR-9 sponge’</italic>, because miR-9 is not expressed in HEK-293 cells (mean + SEM, one-way ANOVA, and Bonferroni post-test, *p &lt; 0.05, n = 3.). (<bold>E</bold>) REST knock-down has no effect on dendritic length and complexity. Primary hippocampal neurons were transfected at DIV4 with shRNAs against REST (shREST) or shControl. (<bold>F</bold>) Efficacy of shREST vectors. Representative immunoblot showing the downregulation of endogenous REST induced by shRNAs against REST in transfected HEK cells. (<bold>G</bold>) REST overexpression reduces dendritic length and complexity in primary neurons. Primary hippocampal neurons were transfected at DIV4 with REST or empty vector (control). (<bold>H</bold>) Primary hippocampal neurons were transfected via ex vivo electroporation. (<bold>E</bold>, <bold>G</bold>, <bold>H</bold>) Scale bar 50 μm. RFP was cotransfected for visualization. Values represent mean + SEM, Student's <italic>t</italic> test (dendritic length) or two-way ANOVA and Bonferroni post-test (Sholl analysis), *p &lt; 0.05, **p &lt; 0.01. (<bold>E</bold> and <bold>G</bold>) n ≥ 20 neurons per condition. (<bold>H</bold>) n ≥ 30 neurons per condition.</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.02755.015">http://dx.doi.org/10.7554/eLife.02755.015</ext-link></p></caption><graphic xlink:href="elife02755f005"/></fig><fig id="fig5s1" position="float" specific-use="child-fig"><object-id pub-id-type="doi">10.7554/eLife.02755.016</object-id><label>Figure 5—figure supplement 1.</label><caption><title>Increased levels of Foxp4, Creb, or Map1b have no impact on dendritic length and complexity.</title><p>(<bold>A</bold>) Representative images of primary hippocampal neurons transiently transfected with the indicated constructs and fixed at DIV10. mRFP was cotransfected for visualization. Scale bar 50 μm. (<bold>B</bold>) Quantification of the total dendritic length (mean + SEM, one-way ANOVA, n.s) and (<bold>C</bold>) quantification of dendritic complexity by Sholl analysis (mean + SEM, repeated measures two-way ANOVA, n.s). n ≥ 30 neurons per condition.</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.02755.016">http://dx.doi.org/10.7554/eLife.02755.016</ext-link></p></caption><graphic xlink:href="elife02755fs009"/></fig></fig-group></p><p>To fulfill the criteria as a potential mediator of miR-9-dependent effects on dendritic arborization in miR-9-Sp<sup>Nestin-Cre</sup> mice, REST should negatively regulate dendritic growth. However, this is not evident from REST loss-of-function models. Conditional deletion of <italic>Rest</italic> in early neural progenitors in <italic>Rest</italic><sup>Sox1−Cre</sup> mice, did not affect brain histology and had no impact on the expression of REST-target genes (<xref ref-type="bibr" rid="bib5">Aoki et al., 2012</xref>). In agreement, we found no difference in dendritic development between shREST- and shControl-transfected neurons (<xref ref-type="fig" rid="fig5">Figure 5E</xref>). The efficiency of shREST constructs to downregulate REST was assessed in HEK-293 cells (<xref ref-type="fig" rid="fig5">Figure 5F</xref>). Together with the lack of phenotype observed in <italic>Rest</italic><sup>Sox1−Cre</sup> mice, these results suggest that the transcriptional repressive activity of endogenous REST is minimal in neurons. Since REST is strongly downregulated during neuronal development, we next hypothesized that maintenance of high levels of this transcriptional repressor might be detrimental for neuronal development and that, consequently, a key function of miR-9 would be to keep low REST levels across neuronal maturation. In agreement with this hypothesis, we found that overexpression of REST in primary hippocampal neurons significantly reduces dendritic length and arborization (<xref ref-type="fig" rid="fig5">Figure 5G</xref>). In contrast, overexpression of other miR-9 targets that were found to be upregulated in sponge expressing neurons, such as Foxp4, Creb1, and Map1b, had no effect on dendritic length and complexity (<xref ref-type="fig" rid="fig5s1">Figure 5—figure supplement 1</xref>), indicating that they are not contributing to the dendritic phenotype of miR-9-Sp<sup>Nestin-Cre</sup> neurons.</p><p>To test whether REST upregulation mediates the impaired dendritic growth in sponge mice, we transfected neural precursors with shRNAs against REST by ex vivo electroporation. In this approach, miR-9-Sp<sup>Nestin-Cre</sup> and littermate control embryos were decapitated at E17.5, DNA was injected into lateral ventricles followed by electroporation targeting hippocampal neural precursors directly before dissociated primary hippocampal neurons were prepared. We observed that shREST transfection strongly rescued the dendritic growth defects in miR-9-Sp<sup>Nestin-Cre</sup> neurons (<xref ref-type="fig" rid="fig5">Figure 5H</xref>), indicating that increased REST level is indeed the major mediator of miR-9 effects on dendritic growth.</p></sec></sec><sec id="s3" sec-type="discussion"><title>Discussion</title><p>The results of this study define a key role for miR-9 during postmitotic differentiation of neurons.</p><p>We present a new double reporter mouse line that helped to characterize the activity pattern of miR-9 in different cell types in the brain. The analysis of the miR-9-Sp<sup>Nestin-Cre</sup> mouse line showed that inhibition of miR-9 results in aberrant dendritic growth in vivo, accompanied by a concomitant impairment in synaptic transmission. Experiments using primary neurons and in utero gene transfer approaches indicate that the observed dendritic changes are cell-autonomous. Importantly, we described an essential function of miR-9 in dendritic growth as a regulator of the expression of the transcriptional repressor REST.</p><p>The widespread involvement of miRNAs in both the regulation of developmental and physiological processes and disease is well established (<xref ref-type="bibr" rid="bib13">Bushati and Cohen, 2007</xref>; <xref ref-type="bibr" rid="bib10">Bartel, 2009</xref>; <xref ref-type="bibr" rid="bib32">Han et al., 2013</xref>). However, uncovering the function of specific microRNA families has been limited by the lack of technologies for in vivo analysis. Much of our current knowledge regarding the role of microRNAs in neuronal biology stems from overexpression-based studies. However, overexpression approaches may lead to silencing of genes that normally escape regulation resulting in artificial, neomorphic phenotypes. Therefore, loss-of-function strategies are required to validate physiological miRNA functions. The generation of KO mice has several limitations in this context: (i) requires the ablation of the multiple gene copies of miRNAs belonging to the same family, often placed at distant genomic loci and (ii) miRNAs genes are frequently encoded in clusters together with other miRNAs from different families or directly overlapping other protein-coding or lncRNA genes. Therefore, the ablation of the miRNA sequence by gene targeting KO strategies also affects the expression of the ‘host’ genes coding for proteins or lncRNAs, or miRNA genes from other families encoded in tandem; and (iii) the complementary miRNA* strand is entirely removed by the gene deletion.</p><p>In the case of miR-9, recently generated <italic>miR-9-2</italic>/<italic>miR-9-3</italic> double KO mice showed profound phenotypic brain defects, growth retardation, and reduced life-span (<xref ref-type="bibr" rid="bib81">Shibata et al., 2011</xref>). In this model, both miR-9 and miR-9* levels are reduced. Unlike other mRNA* species, miR-9* accumulates to substantial levels in vivo (<xref ref-type="bibr" rid="bib6">Bak et al., 2008</xref>; <xref ref-type="bibr" rid="bib94">Yao et al., 2012</xref>), and since miR-9* has a different seed sequence compared to miR-9, it is predicted to regulate a different set of targets. Importantly, miR-9* regulation of BAF53a has been shown to contribute to activity-dependent dendritic growth (<xref ref-type="bibr" rid="bib95">Yoo et al., 2009</xref>). In addition, two transcripts (C130071C03Rik-001 and C130071C03Rik-201) that overlap with the murine <italic>miR-9-2</italic> gene and encode for lncRNAs, are deleted in this mouse model. Although the function of these transcripts is still unknown, recent evidence demonstrates that ablation of lncRNA genes can produce severe phenotypes at brain level (<xref ref-type="bibr" rid="bib77">Sauvageau et al., 2013</xref>), indicating that they would play more critical roles in vivo than previously considered. In view of these facts, other functional products in addition to miR-9 might contribute to the phenotype of <italic>miR-9-2</italic>/<italic>miR-9-3</italic> KO mice and further investigations will be required to clarify this issue. In contrast, the use of miR-9 sponges as dominant negative genetic tools, allowed us to dissect the specific role of miR-9 on dendritic and spine development. Previously, miRNA sponges have been proven as useful genetic loss-of-function tools in <italic>Drosophila</italic> (<xref ref-type="bibr" rid="bib57">Loya et al., 2009</xref>), and non-conditional expression of sponges has been reported in mice (<xref ref-type="bibr" rid="bib59">Ma et al., 2011</xref>). Here, we provide a new layer of complexity to the existing battery of in vivo tools for genetic manipulation of microRNAs by describing the first conditional transgenic miRNA sponge mouse line.</p><p>We initially tested the efficiency of FC vs bulged miR-9 sponges and found that both designs were equally effective to inhibit miR-9 activity. Although several studies describe efficient inhibitory activity of FC sponges (<xref ref-type="bibr" rid="bib15">Care et al., 2007</xref>; <xref ref-type="bibr" rid="bib24">Ebert et al., 2007</xref>; <xref ref-type="bibr" rid="bib29">Gentner et al., 2009</xref>), a recent study by Kluiver et al. (<xref ref-type="bibr" rid="bib43">Kluiver et al., 2012</xref>), reported that bulged sponges are more effective. The discrepancy with our results could arise from differences in promoter strengths. We employed a CAG promoter for the sponge constructs instead of the PGK promoter used in the referred study. The CAG promoter is stronger than the PGK in most mammalian cell systems (<xref ref-type="bibr" rid="bib72">Qin et al., 2010</xref>; <xref ref-type="bibr" rid="bib16">Chen et al., 2011</xref>) and in the Neuro-2a cells used in this study (data not shown). Thus, high levels of expression of the sponge achieved in our experiments could compensate the degradation of FC sponge transcript due to endonucleolytic cleavage activity of AGO2, resulting in high steady-state levels of the decoy target.</p><p>Histological approaches to study miRNA expression have often relied on in situ hybridization (ISH) techniques (<xref ref-type="bibr" rid="bib1">Akerblom et al., 2012</xref>). However, with these techniques, it is not possible to discriminate between precursor and mature miRNAs. Moreover, the design of the probes is very limited due to the very short sequence of miRNAs, preventing the optimization steps usually necessary to obtain adequately specific and sensitive riboprobes for ISH (<xref ref-type="bibr" rid="bib74">Refojo et al., 2011</xref>). In this study, we used the reporter function of miRNA sponges that have the advantage of reporting miRNA activity instead of expression. The miR-9-Sp/tdTomato mouse line was used to analyze the activity pattern of miR-9 in the adult mouse brain. We observed high miR-9 activity in neurons and astrocytes and a lower activity in microglial cells. While miR-9 has been detected in microglia (<xref ref-type="bibr" rid="bib54">Liu et al., 2013a</xref>) and other cells of myeloid origin (<xref ref-type="bibr" rid="bib80">Senyuk et al., 2013</xref>), findings obtained with a recently developed miR-9 reporter mouse line, miR-9.T, suggest that miR-9 activity is absent in microglia (<xref ref-type="bibr" rid="bib2">Akerblom et al., 2013</xref>). Lower levels of the PGK-driven GFP-miR-9 sensor transgene may account for the lower sensitivity shown by that mouse model. Although the expression of the sensor is not shown outside the brain, an indication of the low expression of the sensor of miR-9.T mice is that GFP expression could only be analyzed after the enhancement of the signal via immunofluorescence (<xref ref-type="bibr" rid="bib2">Akerblom et al., 2013</xref>), in contrast to our characterization that fully relies on the detection of the native fluorescence of GFP.</p><p>The function of miR-9 has been mainly studied in the context of neurogenesis, where it plays a role as a regulator of the balance between progenitor proliferation and neuronal differentiation (<xref ref-type="bibr" rid="bib52">Leucht et al., 2008</xref>; <xref ref-type="bibr" rid="bib96">Zhao et al., 2009</xref>; <xref ref-type="bibr" rid="bib21">Delaloy et al., 2010</xref>; <xref ref-type="bibr" rid="bib11">Bonev et al., 2011</xref>; <xref ref-type="bibr" rid="bib19">Coolen et al., 2012</xref>). These studies showed that miR-9 does not act as a differentiation switch, but rather facilitates the transition from the proliferative to the neurogenic mode (<xref ref-type="bibr" rid="bib19">Coolen et al., 2012</xref>, <xref ref-type="bibr" rid="bib18">2013</xref>). In contrast, only few studies have unraveled additional functions of miR-9 at later steps of neural development. A role of miR-9 on the specification of spinal cord motoneurons has been described (<xref ref-type="bibr" rid="bib66">Otaegi et al., 2011</xref>; <xref ref-type="bibr" rid="bib58">Luxenhofer et al., 2014</xref>). MiR-9 dysregulation has also been linked to spinal motor neuron disease (<xref ref-type="bibr" rid="bib34">Haramati et al., 2010</xref>). Recently, <xref ref-type="bibr" rid="bib20">Dajas-Bailador et al. (2012)</xref> showed that inhibition of miR-9 in mouse cultured cortical neurons increase axonal length and reduce axonal branching. In this study, we focused in the postmitotic stages of neuronal differentiation and demonstrated a critical role for miR-9 in the control of dendritic development in vivo. Other miRNAs have also been shown to influence dendritic growth (<xref ref-type="bibr" rid="bib89">Wayman et al., 2008</xref>; <xref ref-type="bibr" rid="bib27">Fiore et al., 2009</xref>; <xref ref-type="bibr" rid="bib69">Parrish et al., 2009</xref>; <xref ref-type="bibr" rid="bib61">Magill et al., 2010</xref>; <xref ref-type="bibr" rid="bib70">Pathania et al., 2012</xref>; <xref ref-type="bibr" rid="bib55">Liu et al., 2013b</xref>) suggesting that the expression of genes orchestrating this process is under a complex post-transcriptional regulation.</p><p>Our studies in cultured primary neurons associated to the morphological analysis performed in miR-9-Sp<sup>Nestin-Cre</sup> mice suggests that neuronal miR-9 mainly acts in a cell-intrinsic manner controlling dendritic differentiation genetic programs. However, dendritic growth and branching in vivo are influenced by synaptic activity (<xref ref-type="bibr" rid="bib73">Rajan and Cline, 1998</xref>; <xref ref-type="bibr" rid="bib92">Wong and Ghosh, 2002</xref>) or by a multiplicity of extrinsic factors either present in or secreted by neighbor neurons or glial cells, such as neurotrophins, semaphorins, or Slits (<xref ref-type="bibr" rid="bib71">Polleux et al., 2000</xref>; <xref ref-type="bibr" rid="bib37">Horch and Katz, 2002</xref>; <xref ref-type="bibr" rid="bib90">Whitford et al., 2002</xref>; <xref ref-type="bibr" rid="bib93">Yamamoto et al., 2006</xref>).</p><p>The results obtained in our in utero gene transfer studies targeting CA1 hippocampal neurons, which develop later among a vast majority of non-transfected wild-type neurons and glial cells, are comparable to the dendritic phenotype observed in miR-9-Sp<sup>Nestin-Cre</sup> mice. This indicates that effects found in miR-9-Sp<sup>Nestin-Cre</sup> mice are essentially cell-intrinsic and that miR-9 exerts its proactive function in modeling dendritic arbors as a key player of neuronal genetic programs controlling dendrite development. Furthermore, we found that basal synaptic transmission was impaired in miR-9 sponge expressing mice. Since the morphology and density of dendritic spines were not affected, the reduced postsynaptic responses are most likely due to a reduction in the total number of synapses as expected from less-arborized dendrites (<xref ref-type="bibr" rid="bib41">Kawabe et al., 2010</xref>), as those found in miR-9-Sp<sup>Nestin-Cre</sup> mice. Additionally, we showed that inhibiting miR-9 affects neuronal excitability by shifting the AP threshold to more positive potentials. Since Map1b has already been described to be a miR-9 target critical for terminal axonal arborization (<xref ref-type="bibr" rid="bib20">Dajas-Bailador et al., 2012</xref>), a potential contribution of the tandem miR-9/Map1b to the electrophysiological phenotype cannot be discarded.</p><p>Intrinsic proteins controlling the establishment of neuronal dendritic fields include several transcription factors, Rho and Ras family GTPases, kinases, and adaptors involved in Ca<sup>2+</sup>-mediated signal transduction cascades (<xref ref-type="bibr" rid="bib33">Hand et al., 2005</xref>; <xref ref-type="bibr" rid="bib86">Takemoto-Kimura et al., 2007</xref>; <xref ref-type="bibr" rid="bib82">Simo and Cooper, 2012</xref>). MiR-9 downregulation would lead to the increase in transcriptional rates of direct miR-9 targets. This suggests that the factor/s mediating the effects of miR-9 inhibition in miR-9-Sp<sup>Nestin-Cre</sup> mice would fit best with targets negatively influencing cellular processes potentially involved in dendritic maturation. We found that the zinc-finger transcriptional repressor REST (also known as NRSF), an experimentally validated target of miR-9 (<xref ref-type="bibr" rid="bib67">Packer et al., 2008</xref>), is upregulated in miR-9 sponge expressing neurons. Along this line, the fact that REST is a transcriptional repressor made this factor a specially attractive candidate to explain the effects observed in miR-9-Sp<sup>Nestin-Cre</sup> mice.</p><p>REST is essential for repressing neuronal genes in neural progenitors (<xref ref-type="bibr" rid="bib65">Ooi and Wood, 2007</xref>). A prevailing view is that downregulation of REST during neuronal differentiation favors the acquisition and maintenance of the neuronal phenotype (<xref ref-type="bibr" rid="bib7">Ballas et al., 2005</xref>). REST binds the RE1 consensus element of target genes and recruits corepressors including mSin3, CoREST, and methyl CpG binding protein 2 (MeCP2), inducing silencing by epigenetic remodeling (<xref ref-type="bibr" rid="bib4">Andres et al., 1999</xref>).</p><p>The influence of REST on the dendritic development of pyramidal neurons remains unexplored. Although a mild effect on neurite outgrowth was reported in cultured retinal ganglion cells upon titration of REST with sequestering plasmids (<xref ref-type="bibr" rid="bib44">Koch et al., 2011</xref>), we were unable to observe any effect of REST downregulation on the dendritic length or complexity of hippocampal pyramidal neurons during development. In agreement with our results, the conditional deletion of <italic>Rest</italic> in early neural progenitors had no impact on the expression of REST-target genes in postnatal day 0 brains, when dendrite differentiation is taking place (<xref ref-type="bibr" rid="bib5">Aoki et al., 2012</xref>). Together, these results suggest that the repressive activity of endogenous REST is minimal during postmitotic differentiation of neurons.</p><p>Considering that REST is strongly downregulated during neuronal development, we hypothesized that maintenance of high levels of this transcriptional repressor might be detrimental for neuronal development. Therefore, a key function of miR-9 would be to keep low REST levels across neuronal maturation. Consistent with this hypothesis, we show that REST overexpression in primary neurons has a negative impact on dendritic length and complexity. Importantly, by performing ex vivo gene transfer of REST shRNAs into neural precursors, we determined that the increased REST activity in miR-9 sponge neurons is underlying the impairment in dendritic growth. However, the fact that the rescue of the dendritic defects was extensive but not complete, suggests that other miR-9-regulated proteins may also contribute to the dendritic phenotype of miR-9 sponge expressing neurons. Together, these experiments delineate a central mechanism in which miR-9 restricts REST expression and thereby promotes neuronal postmitotic differentiation. Interestingly, it has been observed that REST levels are restored in some neuronal populations following a biphasic expression (<xref ref-type="bibr" rid="bib28">Gao et al., 2011</xref>). Consequently, REST expression have been shown to be increased in some adult hippocampal and cortical neurons (<xref ref-type="bibr" rid="bib48">Kuwabara et al., 2004</xref>), suggesting that miR-9/REST regulation might play other non-developmental roles in some mature neuronal populations.</p><p>In summary, we describe the first transgenic sponge mouse line that allows for conditional inactivation of an miRNA family in a spatio-temporal-controlled manner. Analysis of this miR-9-Sp<sup>Nestin-Cre</sup> mouse line reveals a prominent role for miR-9 on postmitotic neuronal differentiation as a regulator of dendritic development through repression of REST expression.</p></sec><sec id="s4" sec-type="materials|methods"><title>Materials and methods</title><sec id="s4-1"><title>Animals</title><p>In all experiments, mice were housed under standard laboratory conditions (22 ± 1°C, 55 ± 5% humidity) with food and water ad libitum. For staging of embryos, noon on the day of the appearance of a vaginal plug was treated as embryonic day 0.5 (E0.5), and the day of birth was considered postnatal day 0 (P0). Animals were handled according to the Guide for the Care and Use of Laboratory Animals of Government of Bavaria, Germany.</p></sec><sec id="s4-2"><title>DNA constructs</title><p>The CAG-GFP-sponge-bGH-polyA plasmids were self-constructed using a modified pCRII vector as backbone (Life Technologies, Darmstadt, Germany). Sponges consisting of 18 repetitive sequences separated by a variable four-nucleotide linker were chemically synthesized (GenScript Corp., Piscataway, NJ, USA) and introduced in the 3′UTR of GFP cDNA. Individual sequences for each sponge are as follows: FC miR-9 sponge 5′-TCAT-ACAGCTAGATAACCAAAGA-3′; Bg miR-9 sponge 5′-TCATACAGCTATATACCAAAGA-3′; scrambled miR-9 sponge 5′-ATG-ATAACAACGAACGATTACAC-3′; FC miR-9* sponge 5′-ACTTTCGGTTATCTAGCTTTAT-3′; Bg miR-124 sponge 5′-GGCATTCACAAGTGCCTTA-3′. The control spongeless plasmid pCAG-GFP was subsequently generated by removing the sponge sequence and religated after adding a short linker. Overexpression of miR-9 was performed with the vector pFhSynW-mCherry-pri-miR-9 generously provided by D Edbauer (<xref ref-type="bibr" rid="bib25">Edbauer et al., 2010</xref>). Based on that construct, we generated an overexpression construct for mutated miR-9 (5′-U<underline>AACGACG</underline>UAUCUAGCUGUAUGA-3′) using the QuikChange Site-Directed Mutagenesis Kit (Stratagene, La Jolla, CA). To generate the luciferase miR-9 sensor, the firefly luciferase cDNA was cloned into the pCRII vector containing the CAG promoter described before. A short sequence containing a single fully complementary binding site to miR-9 was added as 3′UTR. In luciferase assays, a CMV-lacZ plasmid was cotransfected to normalize transfection efficiency. The plasmid pHR'-NRSF-CITE-GFP (Addgene plasmid 21310) (<xref ref-type="bibr" rid="bib63">Nadeau and Lester, 2002</xref>) was used to overexpress REST (insensitive to miR-9 regulation since lacks 3′UTR). To downregulate REST, we used a mixture of two shRNA constructs generously shared by A Fisher (<xref ref-type="bibr" rid="bib40">Jorgensen et al., 2009</xref>) who also provided the shControl construct. A strong downregulation of REST levels was observed following transfection of shREST constructs in HEK cells (<xref ref-type="fig" rid="fig5">Figure 5F</xref>). The plasmid CAG-Map1b, used to overexpress Map1b, was generously provided by T Kawauchi (<xref ref-type="bibr" rid="bib42">Kawauchi et al., 2005</xref>). To overexpress Foxp4, Foxp4 mouse cDNA was cloned into a pcDNA3 expression vector. The targeting vector to generate miR-9 sponge transgenic mice was based on pROSA26-1 bearing 5.5-kb homology to the murine <italic>ROSA26</italic> locus (<italic>R26</italic>) (<xref ref-type="bibr" rid="bib83">Soriano, 1999</xref>). It was cloned by introducing the following components: <italic>frt</italic> site, CAG prmoter, <italic>frt</italic> site, <italic>loxP</italic> site, STOP cassette, <italic>loxP</italic> site, EGFP, FC miR-9 sponge, bGH polyadenylation sequence (pA) (from 5′ to 3′) (<xref ref-type="fig" rid="fig2s1">Figure 2—figure supplement 1</xref>).</p></sec><sec id="s4-3"><title>Generation of conditional GFP-FC-miR-9 sponge mice and derived mouse lines</title><p>The linearized targeting vector was electroporated into mouse F1 embryonic stem (ES) cells (IDG 3.2) (<xref ref-type="bibr" rid="bib36">Hitz et al., 2007</xref>). Mutant ES cell clones were identified by Southern blot analysis of genomic ES cell DNA. Mutant ES cells were used to generate chimeric mice by blastocyst injection. Germ-line transmission of the modified <italic>R26</italic> (miR-9-Sp<sup>fl-Stop</sup>) allele was confirmed in offsprings from male chimeras bred to wild-type C57BL/6J mice. Conditional, CNS-restricted expression of the GFP-FC-miR-9 sponge transcript was achieved by breeding miR-9-Sp<sup>fl-Stop</sup> mice with transgenic Nestin-Cre mice (<xref ref-type="bibr" rid="bib87">Tronche et al., 1999</xref>).</p><p>To generate the miR-9 reporter mouse line, miR-9-Sp<sup>fl-Stop</sup> and tdTomato<sup>fl−Stop</sup> (Ai9 line <xref ref-type="bibr" rid="bib60">Madisen et al., 2010</xref>) homozygous mice were bred with a Deleter-Cre mouse line (TaconicArtemis GmbH, Köln, Germany) carrying an ubiquitously expressed Cre transgene in the <italic>R26</italic> locus. This leads to a removal of the ‘Stop’ cassette from the miR-9-Sp<sup>fl-Stop</sup> and the tdTomato<sup>fl−Stop</sup> alleles (both also in the <italic>R26</italic> locus) in all tissues of F1 mice, including the germ line. Resulting heterozygous miR-9-Sp/Deleter-Cre and tdTomato/Deleter-Cre F1 animals were intercrossed to obtain in the F2 generation miR-9-Sp/tdTomato reporter mice (<xref ref-type="fig" rid="fig2s2">Figure 2—figure supplement 2</xref>).</p></sec><sec id="s4-4"><title>Culture of cell lines and transient transfections</title><p>Neuro-2a and HEK293 cells were grown in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% heat-inactivated FCS, Penicillin (100 units/ml), Streptomycin (100 μg/ml), and 2 mM L-Glutamine (Gibco, Kalsruhe, Germany) at 37°C and 5% CO<sub>2</sub>. For transient transfection experiments, cells were seeded at a desired density on poly-D-Lysine (0.05 mg/ml, 30.000–70.000 MW, Sigma Aldrich)-coated cell culture plates. 24 hr later cells were transfected with the respective expression vectors using Lipofectamine 2000 (Invitrogen, Kalsruhe, Germany).</p></sec><sec id="s4-5"><title>Primary cell cultures and transfection</title><p>Primary hippocampal neurons were prepared from CD1 or miR-9-Sp<sup>fl-Stop</sup>/miR-9-Sp<sup>Nestin</sup> mouse embryos (E17.5–18.5) and maintained in Neurobasal-A medium with 2% B27 and 0.5 mM GlutaMAX-I (Gibco) at 37°C and 5% CO<sub>2</sub> (<xref ref-type="bibr" rid="bib23">Dotti et al., 1988</xref>; <xref ref-type="bibr" rid="bib31">Goslin et al., 1998</xref>). Neurons were transfected via a calcium phosphate protocol (<xref ref-type="bibr" rid="bib39">Jiang and Chen, 2006</xref>) unless otherwise stated. To analyze dendrite length and arborization, neurons were transfected at the DIV 4 and fixed at DIV 10. To study spine density and morphology, neurons were transfected at DIV12-14 and fixed at DIV 21.</p></sec><sec id="s4-6"><title>Luciferase and fluorometry assays</title><p>For luciferase assays, Neuro-2a cells and primary neurons were transfected as described above, and luciferase expression was analyzed in cell lysates 24 hr after transfection (Promega, Mannheim, Germany). Fluorometric quantitation of GFP was performed on cell lysates using a microplate fluorometer (Tecan Genios Pro, MTX Lab Systems Inc, Crailsheim, Germany.) with excitation and emission wavelengths of 485 nm and 535 nm respectively. Firefly luciferase activity and GFP fluorescence were normalized to β-galactosidase activity and expressed as a percentage of the control.</p></sec><sec id="s4-7"><title>Analysis of neuronal morphology</title><p>For the analysis of dendrites in culture, primary hippocampal neurons were fixed at DIV 10 and images taken from at least four independent preparations. Dendrites were traced with open access NeuronJ (ImageJ, <ext-link ext-link-type="uri" xlink:href="http://rsbweb.nih.gov/ij/">http://rsbweb.nih.gov/ij/</ext-link>) and further evaluated with the same software to calculate total dendritic length and perform Sholl analysis.</p><p>For the in vivo analysis, neurons were visualized by breeding sponge mice with Thy1-EGFP mice (M) (<xref ref-type="bibr" rid="bib26">Feng et al., 2000</xref>) or by performing Golgi staining with the FD Rapid GolgiStain Kit (FD Neurotechnologies, Columbia, MD). Dendrites form CA1 pyramidal neurons or layer V neurons in the primary somatosensory cortex were traced under a 40× objective lens using the Olympus BX51 microscope installed with Neurolucida 6 (MBF Bioscience, Williston, VT). Analyses of dendritic length and Sholl analysis were evaluated with Neurolucida Explorer (MBF Bioscience). n ≥ 30 neurons per condition were analyzed, recruited from five mice per genotype.</p></sec><sec id="s4-8"><title>Electrophysiology</title><p>Acute brain slices for electrophysiological recordings were obtained from P14-P19 miR-9-Spfl-Stop and miR-9-SpNestin littermates which were anesthetized with isoflurane and decapitated. The brain was removed and chilled in ice cold carbonated artificial cerebrospinal fluid (ACSF) containing the following (in mM): 130 NaCl, 2.75 KCl, 1.43 MgSO<sub>4</sub>, 1.1 NaH<sub>2</sub>PO<sub>4</sub>, 28.01 NaHCO<sub>3</sub>, 2.5 CaCl<sub>2</sub>, 11 glucose.</p><p>All electrophysiological recordings were performed at room temperature. Data were acquired using a Multiclamp 700B amplifier (Axon Instruments, Foster City, CA) and digitized with a Digidata 1440A (Axon Instruments).</p><p>For field recordings, Schaffer collaterals were stimulated and postsynaptic potentials recorded in the stratum radiatum of CA1. Recording and stimulation electrodes were filled with ASCF.</p><p>Whole cell recordings were obtained in ACSF supplemented with picrotoxin (100 µM) and an internal solution was used containing the following (in mM): 150 Cs-gluconate, 8 NaCl, 2 MgATP, 10 HEPES, 0.2 EGTA, and 0.5 QX-314. Miniature EPSCs (mEPSCs) were recorded at −70 mV in ACSF supplemented with TTX (0.2 µM), picrotoxin (100 µM), and trichlormethiazide (250 µM) to increase mEPSC frequency. Spontaneous EPSCs (sEPSCs) were recorded at −70 mV in ACSF supplemented with picrotoxin (100 µM) and trichlormethiazide (250 µM). mEPSCs and sEPSCs were detected offline and analyzed with a custom written MATLAB routine. Paired-pulse facilitation (PPF) was determined with a stimulus interval of 40 ms.</p><p>Current-clamp recordings were performed with a pipette solution containing the following (in mM): 150 K-methylsulfhonate, 4 KCl, 4 NaCl, 4 MgATP, 0.4 MgGTP, and 10 HEPES. Action potential thresholds (AP) were determined from the first derivative of single APs.</p></sec><sec id="s4-9"><title>In silico analysis</title><p>The binding affinity of miR-9 to the FC or Bg miR-9 sponges was predicted with RNAhybrid and miRanda software. The RNAhybrid program, Version 2.1, is available online at <ext-link ext-link-type="uri" xlink:href="http://bibiserv.techfak.uni-bielefeld.de/rnahybrid/">http://bibiserv.techfak.uni-bielefeld.de/rnahybrid/</ext-link> (<xref ref-type="bibr" rid="bib47">Kruger and Rehmsmeier, 2006</xref>) whereas miRanda, September 2008 release, can be accessed at <ext-link ext-link-type="uri" xlink:href="http://www.microrna.org/microrna/home.do">http://www.microrna.org/microrna/home.do</ext-link> (<xref ref-type="bibr" rid="bib91">Witkos et al., 2011</xref>). Values obtained with RNAhybrid are provided in the main text. Similar values were obtained with miRanda (FC sponge: 39.61 vs Bg sponge: 28.31 kcal/mol).</p></sec><sec id="s4-10"><title>In utero and ex vivo electroporation</title><p>In utero electroporation of CD1 mouse embryos was performed at E14.4 as previously described (<xref ref-type="bibr" rid="bib76">Saito, 2006</xref>) with small modifications. In other experiments, hippocampal progenitors from miR-9-Sp<sup>fl-Stop</sup> and miR-9-Sp<sup>Nestin</sup> littermates were electroporated ex vivo at E17.5 as described previously (<xref ref-type="bibr" rid="bib33">Hand et al., 2005</xref>). Briefly, E17.5 embryos were decapitated and heads were kept in complete HBSS buffer before use. Plasmid DNA was injected into lateral ventricles followed by electroporation with an Electro Square Porator ECM830 and tweezertrodes (BTX Genetronics, San Diego, CA). Five pulses with 40V, 50-ms duration and with 950-ms intervals, were delivered to each embryo. Directly after electroporation, primary hippocampal neuronal culture was prepared.</p></sec><sec id="s4-11"><title>In situ hybridization (<italic>IS</italic>H)</title><p>In situ hybridization (ISH) was performed as previously described (<xref ref-type="bibr" rid="bib74">Refojo et al., 2011</xref>). Brains were carefully removed and immediately shock-frozen on dry ice. Frozen brains were cut on a cryostat in 20-μm thick sections and mounted on SuperFrost Plus slides. Specific riboprobes for GFP were generated by PCR applying T7 and T3 or SP6 primers using plasmids containing the above-mentioned cDNA as template. Radiolabeled sense and antisense cRNA probes were generated from the respective PCR products by in vitro transcription with <sup>35</sup>S-UTP using T7 and T3 or SP6 RNA polymerase.</p><p>Hybridization was performed overnight with a probe concentration of 7 × 10<sup>6</sup> CPM/ml at 57°C and slides were washed at 64°C in 0.1× saline sodium citrate (SSC) and 0.1 M dithiothreitol. Hybridized slides were dipped in autoradiographic emulsion (type NTB2), developed after 2 weeks and counterstained with cresyl violet.</p><p>Dark-field photomicrographs were captured with digital cameras adapted to an imaging microscope and a stereomicroscope. Images were digitalized using Axio Vision 4.5, and afterwards photomicrographs were integrated into plates using image-editing software. Only sharpness, brightness, and contrast were adjusted. For an adequate comparative analysis in corresponding miR-9-Sp<sup>fl-Stop</sup> (control) and miR-9-Sp<sup>Nestin-Cre</sup> sections the same adjustments were undertaken. Brain slices were digitally cut out and set onto an artificial black background.</p></sec><sec id="s4-12"><title>Immunoblotting experiments</title><p>Cells and tissue were lysed in RIPA buffer containing protease inhibitors (Roche, Mannheim, Germany). Protein samples were separated by 8–10% SDS-PAGE (<xref ref-type="bibr" rid="bib49">Laemmli, 1970</xref>) and transferred to 0.45-μm PVDF membranes (Millipore, Darmstadt, Germany). Chemiluminescence signal was acquired in a ChemiDoc station (BioRad, Munich, Germany) and analyzed using Image Lab (Bio-Rad). REST mAb (12C11-1) was kindly provided by D J Anderson (<xref ref-type="bibr" rid="bib17">Chen et al., 1998</xref>).</p></sec><sec id="s4-13"><title>Image acquisition</title><p>Low power imaging of tissue sections was performed in an Olympus SZX10 fluorescence stereomicroscope. For microscopic imaging, 1024 × 1024 pixel pictures were taken with an Olympus IX81 inverted laser scanning confocal microscope equipped with Fluoview 1000 software.</p></sec><sec id="s4-14"><title>Immunocytochemistry</title><p>Immunocytochemistry was performed as previously described (<xref ref-type="bibr" rid="bib74">Refojo et al., 2011</xref>). The following antibodies were used: chicken anti-GFP 1:3000 (Abcam, Cambridge, MA) (only when specified. In most cases, native GFP is imaged), rabbit anti-GFAP 1:2000 (DAKO, Carpinteria, CA), mouse anti-NeuN 1:1000 (Millipore), rabbit anti-Iba1 1:1000 (WAKO, Osaka, Japan).</p></sec><sec id="s4-15"><title>RNA isolation and qRT-PCRs</title><p>Total RNA was prepared from cells using mirVana miRNA Isolation Kit (Life Tecnologies). cDNA was generated using Reverse Trancriptase Superscript II and oligo-dT primers (Invitrogen). Quantitative real-time PCR was performed with a Light Cycler (Roche) using QuantiFast SYBR Green PCR Kit (Qiagen, Hilden, Germany). Primer sequences are listed in <xref ref-type="supplementary-material" rid="SD2-data">Supplementary file 2</xref>. To quantify miR-9 levels, TaqMan probes and Universal Master Mix II were used (Life Technologies).</p></sec><sec id="s4-16"><title>Statistical analysis</title><p>Each set of numerical data shown was obtained at least in three independent experiments. Statistical analysis was carried out using GraphPad Prism 5 software (Graph Pad Software, San Diego, CA). All values are given as mean ± standard error of the mean (SEM). Statistical significance was assessed as indicated by Student's t-test, one-way ANOVA or two-way ANOVA with repeated measures followed by Bonferroni's post hoc comparisons when appropriate. Differences were considered statistically significant at *p &lt; 0.05 and **p &lt; 0.01.</p></sec></sec></body><back><ack id="ack"><title>Acknowledgements</title><p>We thank A Moebus, S Bauer, S Weidemann, A Tasdemir, and A Krause for their technical assistance, R Kuhn for help with blastocyst injection, N Prakash for critical reading of this manuscript, and A Chen for general advice on the project. We are grateful to DJ Anderson for sharing anti-REST antibody, DC Lie for providing CAG-mRFP, T Kawauchi for CAG-Map1b, and A Fisher for shRNA-REST plasmids.</p></ack><sec sec-type="additional-information"><title>Additional information</title><fn-group content-type="competing-interest"><title>Competing interests</title><fn fn-type="conflict" id="conf1"><p>The authors declare that no competing interests exist.</p></fn></fn-group><fn-group content-type="author-contribution"><title>Author contributions</title><fn fn-type="con" id="con1"><p>SAG, Designed, executed and analyzed most of the experiments, Wrote the manuscript</p></fn><fn fn-type="con" id="con2"><p>AMV, Contributed with molecular biology and histological studies</p></fn><fn fn-type="con" id="con3"><p>CAV, Contributed with molecular biology and histological studies</p></fn><fn fn-type="con" id="con4"><p>MMB, Conducted and analyzed the data of electrophysiology experiments</p></fn><fn fn-type="con" id="con5"><p>MLR, Assisted with the ES cell culture</p></fn><fn fn-type="con" id="con6"><p>DT, Performed the in silico analysis</p></fn><fn fn-type="con" id="con7"><p>WW, Contributed in the experimental design, Commented on the manuscript</p></fn><fn fn-type="con" id="con8"><p>DC, Contributed in the experimental design, Commented on the manuscript</p></fn><fn fn-type="con" id="con9"><p>JMD, Contributed in the experimental design, Commented on the manuscript</p></fn><fn fn-type="con" id="con10"><p>VS, Conceived and analyzed electrophysiology data, Revised the manuscript</p></fn><fn fn-type="con" id="con11"><p>DR, Conceived and supervised the study, Wrote the manuscript</p></fn></fn-group><fn-group content-type="ethics-information"><title>Ethics</title><fn fn-type="other"><p>Animal experimentation: Animal experiments were conducted under the regulations and protocols for animal experimentation by the local government authorities (the ‘Regierung von Oberbayern’ Munich, Germany, Permit No. 55.2-1-54-2532-168-10). Every attempt was made to ensure minimum discomfort to the animals at all times.</p></fn></fn-group></sec><sec sec-type="supplementary-material"><title>Additional files</title><supplementary-material id="SD1-data"><object-id pub-id-type="doi">10.7554/eLife.02755.017</object-id><label>Supplementary file 1.</label><caption><p>Predicted miR-9 targets screened in miR-9-Sp<sup>Nestin-Cre</sup> mice.</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.02755.017">http://dx.doi.org/10.7554/eLife.02755.017</ext-link></p></caption><media mime-subtype="docx" mimetype="application" xlink:href="elife02755s001.docx"/></supplementary-material><supplementary-material id="SD2-data"><object-id pub-id-type="doi">10.7554/eLife.02755.018</object-id><label>Supplementary file 2.</label><caption><p>List of primers used in qPCR experiments.</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.02755.018">http://dx.doi.org/10.7554/eLife.02755.018</ext-link></p></caption><media mime-subtype="xlsx" mimetype="application" xlink:href="elife02755s002.xlsx"/></supplementary-material></sec><ref-list><title>References</title><ref id="bib1"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Akerblom</surname><given-names>M</given-names></name><name><surname>Sachdeva</surname><given-names>R</given-names></name><name><surname>Jakobsson</surname><given-names>J</given-names></name></person-group><year>2012</year><article-title>Functional studies of microRNAs in neural stem cells: problems and perspectives</article-title><source>Frontiers in Neuroscience</source><volume>6</volume><fpage>14</fpage><pub-id pub-id-type="doi">10.3389/fnins.2012.00014</pub-id></element-citation></ref><ref id="bib2"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Akerblom</surname><given-names>M</given-names></name><name><surname>Sachdeva</surname><given-names>R</given-names></name><name><surname>Quintino</surname><given-names>L</given-names></name><name><surname>Wettergren</surname><given-names>EE</given-names></name><name><surname>Chapman</surname><given-names>KZ</given-names></name><name><surname>Manfre</surname><given-names>G</given-names></name><name><surname>Lindvall</surname><given-names>O</given-names></name><name><surname>Lundberg</surname><given-names>C</given-names></name><name><surname>Jakobsson</surname><given-names>J</given-names></name></person-group><year>2013</year><article-title>Visualization and genetic modification of resident brain microglia using lentiviral vectors regulated by microRNA-9</article-title><source>Nature Communications</source><volume>4</volume><fpage>1770</fpage><pub-id pub-id-type="doi">10.1038/ncomms2801</pub-id></element-citation></ref><ref id="bib3"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Ameres</surname><given-names>SL</given-names></name><name><surname>Horwich</surname><given-names>MD</given-names></name><name><surname>Hung</surname><given-names>JH</given-names></name><name><surname>Xu</surname><given-names>J</given-names></name><name><surname>Ghildiyal</surname><given-names>M</given-names></name><name><surname>Weng</surname><given-names>Z</given-names></name><name><surname>Zamore</surname><given-names>PD</given-names></name></person-group><year>2010</year><article-title>Target RNA-directed trimming and tailing of small silencing RNAs</article-title><source>Science</source><volume>328</volume><fpage>1534</fpage><lpage>1539</lpage><pub-id pub-id-type="doi">10.1126/science.1187058</pub-id></element-citation></ref><ref id="bib4"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Andres</surname><given-names>ME</given-names></name><name><surname>Burger</surname><given-names>C</given-names></name><name><surname>Peral-Rubio</surname><given-names>MJ</given-names></name><name><surname>Battaglioli</surname><given-names>E</given-names></name><name><surname>Anderson</surname><given-names>ME</given-names></name><name><surname>Grimes</surname><given-names>J</given-names></name><name><surname>Dallman</surname><given-names>J</given-names></name><name><surname>Ballas</surname><given-names>N</given-names></name><name><surname>Mandel</surname><given-names>G</given-names></name></person-group><year>1999</year><article-title>CoREST: a functional corepressor required for regulation of neural-specific gene expression</article-title><source>Proceedings of the National Academy of Sciences of USA</source><volume>96</volume><fpage>9873</fpage><lpage>9878</lpage><pub-id pub-id-type="doi">10.1073/pnas.96.17.9873</pub-id></element-citation></ref><ref id="bib5"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Aoki</surname><given-names>H</given-names></name><name><surname>Hara</surname><given-names>A</given-names></name><name><surname>Era</surname><given-names>T</given-names></name><name><surname>Kunisada</surname><given-names>T</given-names></name><name><surname>Yamada</surname><given-names>Y</given-names></name></person-group><year>2012</year><article-title>Genetic ablation of Rest leads to in vitro-specific derepression of neuronal genes during neurogenesis</article-title><source>Development</source><volume>139</volume><fpage>667</fpage><lpage>677</lpage><pub-id pub-id-type="doi">10.1242/dev.072272</pub-id></element-citation></ref><ref id="bib6"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Bak</surname><given-names>M</given-names></name><name><surname>Silahtaroglu</surname><given-names>A</given-names></name><name><surname>Moller</surname><given-names>M</given-names></name><name><surname>Christensen</surname><given-names>M</given-names></name><name><surname>Rath</surname><given-names>MF</given-names></name><name><surname>Skryabin</surname><given-names>B</given-names></name><name><surname>Tommerup</surname><given-names>N</given-names></name><name><surname>Kauppinen</surname><given-names>S</given-names></name></person-group><year>2008</year><article-title>MicroRNA expression in the adult mouse central nervous system</article-title><source>RNA</source><volume>14</volume><fpage>432</fpage><lpage>444</lpage><pub-id pub-id-type="doi">10.1261/rna.783108</pub-id></element-citation></ref><ref id="bib7"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Ballas</surname><given-names>N</given-names></name><name><surname>Grunseich</surname><given-names>C</given-names></name><name><surname>Lu</surname><given-names>DD</given-names></name><name><surname>Speh</surname><given-names>JC</given-names></name><name><surname>Mandel</surname><given-names>G</given-names></name></person-group><year>2005</year><article-title>REST and its corepressors mediate plasticity of neuronal gene chromatin throughout neurogenesis</article-title><source>Cell</source><volume>121</volume><fpage>645</fpage><lpage>657</lpage><pub-id pub-id-type="doi">10.1016/j.cell.2005.03.013</pub-id></element-citation></ref><ref id="bib8"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Ballas</surname><given-names>N</given-names></name><name><surname>Mandel</surname><given-names>G</given-names></name></person-group><year>2005</year><article-title>The many faces of REST oversee epigenetic programming of neuronal genes</article-title><source>Current Opinion in Neurobiology</source><volume>15</volume><fpage>500</fpage><lpage>506</lpage><pub-id pub-id-type="doi">10.1016/j.conb.2005.08.015</pub-id></element-citation></ref><ref id="bib9"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Barnes</surname><given-names>AP</given-names></name><name><surname>Polleux</surname><given-names>F</given-names></name></person-group><year>2009</year><article-title>Establishment of axon-dendrite polarity in developing neurons</article-title><source>Annual Review of Neuroscience</source><volume>32</volume><fpage>347</fpage><lpage>381</lpage><pub-id pub-id-type="doi">10.1146/annurev.neuro.31.060407.125536</pub-id></element-citation></ref><ref id="bib10"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Bartel</surname><given-names>DP</given-names></name></person-group><year>2009</year><article-title>MicroRNAs: target recognition and regulatory functions</article-title><source>Cell</source><volume>136</volume><fpage>215</fpage><lpage>233</lpage><pub-id pub-id-type="doi">10.1016/j.cell.2009.01.002</pub-id></element-citation></ref><ref id="bib11"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Bonev</surname><given-names>B</given-names></name><name><surname>Pisco</surname><given-names>A</given-names></name><name><surname>Papalopulu</surname><given-names>N</given-names></name></person-group><year>2011</year><article-title>MicroRNA-9 reveals regional diversity of neural progenitors along the anterior-posterior axis</article-title><source>Developmental Cell</source><volume>20</volume><fpage>19</fpage><lpage>32</lpage><pub-id pub-id-type="doi">10.1016/j.devcel.2010.11.018</pub-id></element-citation></ref><ref id="bib12"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Bonhoeffer</surname><given-names>T</given-names></name><name><surname>Yuste</surname><given-names>R</given-names></name></person-group><year>2002</year><article-title>Spine motility. Phenomenology, mechanisms, and function</article-title><source>Neuron</source><volume>35</volume><fpage>1019</fpage><lpage>1027</lpage><pub-id pub-id-type="doi">10.1016/S0896-6273(02)00906-6</pub-id></element-citation></ref><ref id="bib13"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Bushati</surname><given-names>N</given-names></name><name><surname>Cohen</surname><given-names>SM</given-names></name></person-group><year>2007</year><article-title>microRNA functions</article-title><source>Annual Review of Cell and Developmental Biology</source><volume>23</volume><fpage>175</fpage><lpage>205</lpage><pub-id pub-id-type="doi">10.1146/annurev.cellbio.23.090506.123406</pub-id></element-citation></ref><ref id="bib14"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Caceres</surname><given-names>A</given-names></name><name><surname>Ye</surname><given-names>B</given-names></name><name><surname>Dotti</surname><given-names>CG</given-names></name></person-group><year>2012</year><article-title>Neuronal polarity: demarcation, growth and commitment</article-title><source>Current Opinion in Cell Biology</source><volume>24</volume><fpage>547</fpage><lpage>553</lpage><pub-id pub-id-type="doi">10.1016/j.ceb.2012.05.011</pub-id></element-citation></ref><ref id="bib15"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Care</surname><given-names>A</given-names></name><name><surname>Catalucci</surname><given-names>D</given-names></name><name><surname>Felicetti</surname><given-names>F</given-names></name><name><surname>Bonci</surname><given-names>D</given-names></name><name><surname>Addario</surname><given-names>A</given-names></name><name><surname>Gallo</surname><given-names>P</given-names></name><name><surname>Bang</surname><given-names>ML</given-names></name><name><surname>Segnalini</surname><given-names>P</given-names></name><name><surname>Gu</surname><given-names>Y</given-names></name><name><surname>Dalton</surname><given-names>ND</given-names></name><name><surname>Elia</surname><given-names>L</given-names></name><name><surname>Latronico</surname><given-names>MV</given-names></name><name><surname>Høydal</surname><given-names>M</given-names></name><name><surname>Autore</surname><given-names>C</given-names></name><name><surname>Russo</surname><given-names>MA</given-names></name><name><surname>Dorn</surname><given-names>GW</given-names><suffix>II</suffix></name><name><surname>Ellingsen</surname><given-names>O</given-names></name><name><surname>Ruiz-Lozano</surname><given-names>P</given-names></name><name><surname>Peterson</surname><given-names>KL</given-names></name><name><surname>Croce</surname><given-names>CM</given-names></name><name><surname>Peschle</surname><given-names>C</given-names></name><name><surname>Condorelli</surname><given-names>G</given-names></name></person-group><year>2007</year><article-title>MicroRNA-133 controls cardiac hypertrophy</article-title><source>Nature Medicine</source><volume>13</volume><fpage>613</fpage><lpage>618</lpage><pub-id pub-id-type="doi">10.1038/nm1582</pub-id></element-citation></ref><ref id="bib16"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Chen</surname><given-names>CM</given-names></name><name><surname>Krohn</surname><given-names>J</given-names></name><name><surname>Bhattacharya</surname><given-names>S</given-names></name><name><surname>Davies</surname><given-names>B</given-names></name></person-group><year>2011</year><article-title>A comparison of exogenous promoter activity at the ROSA26 locus using a PhiiC31 integrase mediated cassette exchange approach in mouse ES cells</article-title><source>PLOS ONE</source><volume>6</volume><fpage>e23376</fpage><pub-id pub-id-type="doi">10.1371/journal.pone.0023376</pub-id></element-citation></ref><ref id="bib17"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Chen</surname><given-names>ZF</given-names></name><name><surname>Paquette</surname><given-names>AJ</given-names></name><name><surname>Anderson</surname><given-names>DJ</given-names></name></person-group><year>1998</year><article-title>NRSF/REST is required in vivo for repression of multiple neuronal target genes during embryogenesis</article-title><source>Nature Genetics</source><volume>20</volume><fpage>136</fpage><lpage>142</lpage><pub-id pub-id-type="doi">10.1038/2431</pub-id></element-citation></ref><ref id="bib18"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Coolen</surname><given-names>M</given-names></name><name><surname>Katz</surname><given-names>S</given-names></name><name><surname>Bally-Cuif</surname><given-names>L</given-names></name></person-group><year>2013</year><article-title>miR-9: a versatile regulator of neurogenesis</article-title><source>Frontiers in Neuroscience</source><volume>7</volume><fpage>220</fpage><pub-id pub-id-type="doi">10.3389/fncel.2013.00220</pub-id></element-citation></ref><ref id="bib19"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Coolen</surname><given-names>M</given-names></name><name><surname>Thieffry</surname><given-names>D</given-names></name><name><surname>Drivenes</surname><given-names>O</given-names></name><name><surname>Becker</surname><given-names>TS</given-names></name><name><surname>Bally-Cuif</surname><given-names>L</given-names></name></person-group><year>2012</year><article-title>miR-9 controls the timing of neurogenesis through the direct inhibition of antagonistic factors</article-title><source>Developmental Cell</source><volume>22</volume><fpage>1052</fpage><lpage>1064</lpage><pub-id pub-id-type="doi">10.1016/j.devcel.2012.03.003</pub-id></element-citation></ref><ref id="bib20"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Dajas-Bailador</surname><given-names>F</given-names></name><name><surname>Bonev</surname><given-names>B</given-names></name><name><surname>Garcez</surname><given-names>P</given-names></name><name><surname>Stanley</surname><given-names>P</given-names></name><name><surname>Guillemot</surname><given-names>F</given-names></name><name><surname>Papalopulu</surname><given-names>N</given-names></name></person-group><year>2012</year><article-title>microRNA-9 regulates axon extension and branching by targeting Map1b in mouse cortical neurons</article-title><source>Nature Neuroscience</source><volume>15</volume><fpage>697</fpage><lpage>699</lpage><pub-id pub-id-type="doi">10.1038/nn.3082</pub-id></element-citation></ref><ref id="bib21"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Delaloy</surname><given-names>C</given-names></name><name><surname>Liu</surname><given-names>L</given-names></name><name><surname>Lee</surname><given-names>JA</given-names></name><name><surname>Su</surname><given-names>H</given-names></name><name><surname>Shen</surname><given-names>F</given-names></name><name><surname>Yang</surname><given-names>GY</given-names></name><name><surname>Young</surname><given-names>WL</given-names></name><name><surname>Ivey</surname><given-names>KN</given-names></name><name><surname>Gao</surname><given-names>FB</given-names></name></person-group><year>2010</year><article-title>MicroRNA-9 coordinates proliferation and migration of human embryonic stem cell-derived neural progenitors</article-title><source>Cell Stem Cell</source><volume>6</volume><fpage>323</fpage><lpage>335</lpage><pub-id pub-id-type="doi">10.1016/j.stem.2010.02.015</pub-id></element-citation></ref><ref id="bib22"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Dieni</surname><given-names>S</given-names></name><name><surname>Rees</surname><given-names>S</given-names></name></person-group><year>2003</year><article-title>Dendritic morphology is altered in hippocampal neurons following prenatal compromise</article-title><source>Journal of Neurobiology</source><volume>55</volume><fpage>41</fpage><lpage>52</lpage><pub-id pub-id-type="doi">10.1002/neu.10194</pub-id></element-citation></ref><ref id="bib23"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Dotti</surname><given-names>CG</given-names></name><name><surname>Sullivan</surname><given-names>CA</given-names></name><name><surname>Banker</surname><given-names>GA</given-names></name></person-group><year>1988</year><article-title>The establishment of polarity by hippocampal-neurons in culture</article-title><source>Journal of Neuroscience</source><volume>8</volume><fpage>1454</fpage><lpage>1468</lpage></element-citation></ref><ref id="bib24"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Ebert</surname><given-names>MS</given-names></name><name><surname>Neilson</surname><given-names>JR</given-names></name><name><surname>Sharp</surname><given-names>PA</given-names></name></person-group><year>2007</year><article-title>MicroRNA sponges: competitive inhibitors of small RNAs in mammalian cells</article-title><source>Nature Methods</source><volume>4</volume><fpage>721</fpage><lpage>726</lpage><pub-id pub-id-type="doi">10.1038/nmeth1079</pub-id></element-citation></ref><ref id="bib25"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Edbauer</surname><given-names>D</given-names></name><name><surname>Neilson</surname><given-names>JR</given-names></name><name><surname>Foster</surname><given-names>KA</given-names></name><name><surname>Wang</surname><given-names>CF</given-names></name><name><surname>Seeburg</surname><given-names>DP</given-names></name><name><surname>Batterton</surname><given-names>MN</given-names></name><name><surname>Tada</surname><given-names>T</given-names></name><name><surname>Dolan</surname><given-names>BM</given-names></name><name><surname>Sharp</surname><given-names>PA</given-names></name><name><surname>Sheng</surname><given-names>M</given-names></name></person-group><year>2010</year><article-title>Regulation of synaptic structure and function by FMRP-associated microRNAs miR-125b and miR-132</article-title><source>Neuron</source><volume>65</volume><fpage>373</fpage><lpage>384</lpage><pub-id pub-id-type="doi">10.1016/j.neuron.2010.01.005</pub-id></element-citation></ref><ref id="bib26"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Feng</surname><given-names>G</given-names></name><name><surname>Mellor</surname><given-names>RH</given-names></name><name><surname>Bernstein</surname><given-names>M</given-names></name><name><surname>Keller-Peck</surname><given-names>C</given-names></name><name><surname>Nguyen</surname><given-names>QT</given-names></name><name><surname>Wallace</surname><given-names>M</given-names></name><name><surname>Nerbonne</surname><given-names>JM</given-names></name><name><surname>Lichtman</surname><given-names>JW</given-names></name><name><surname>Sanes</surname><given-names>JR</given-names></name></person-group><year>2000</year><article-title>Imaging neuronal subsets in transgenic mice expressing multiple spectral variants of GFP</article-title><source>Neuron</source><volume>28</volume><fpage>41</fpage><lpage>51</lpage><pub-id pub-id-type="doi">10.1016/S0896-6273(00)00084-2</pub-id></element-citation></ref><ref id="bib27"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Fiore</surname><given-names>R</given-names></name><name><surname>Khudayberdiev</surname><given-names>S</given-names></name><name><surname>Christensen</surname><given-names>M</given-names></name><name><surname>Siegel</surname><given-names>G</given-names></name><name><surname>Flavell</surname><given-names>SW</given-names></name><name><surname>Kim</surname><given-names>TK</given-names></name><name><surname>Greenberg</surname><given-names>ME</given-names></name><name><surname>Schratt</surname><given-names>G</given-names></name></person-group><year>2009</year><article-title>Mef2-mediated transcription of the miR379-410 cluster regulates activity-dependent dendritogenesis by fine-tuning Pumilio2 protein levels</article-title><source>The EMBO Journal</source><volume>28</volume><fpage>697</fpage><lpage>710</lpage><pub-id pub-id-type="doi">10.1038/emboj.2009.10</pub-id></element-citation></ref><ref id="bib28"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Gao</surname><given-names>Z</given-names></name><name><surname>Ure</surname><given-names>K</given-names></name><name><surname>Ding</surname><given-names>P</given-names></name><name><surname>Nashaat</surname><given-names>M</given-names></name><name><surname>Yuan</surname><given-names>L</given-names></name><name><surname>Ma</surname><given-names>J</given-names></name><name><surname>Hammer</surname><given-names>RE</given-names></name><name><surname>Hsieh</surname><given-names>J</given-names></name></person-group><year>2011</year><article-title>The master negative regulator REST/NRSF controls adult neurogenesis by restraining the neurogenic program in quiescent stem cells</article-title><source>The Journal of Neuroscience</source><volume>31</volume><fpage>9772</fpage><lpage>9786</lpage><pub-id pub-id-type="doi">10.1523/JNEUROSCI.1604-11.2011</pub-id></element-citation></ref><ref id="bib29"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Gentner</surname><given-names>B</given-names></name><name><surname>Schira</surname><given-names>G</given-names></name><name><surname>Giustacchini</surname><given-names>A</given-names></name><name><surname>Amendola</surname><given-names>M</given-names></name><name><surname>Brown</surname><given-names>BD</given-names></name><name><surname>Ponzoni</surname><given-names>M</given-names></name><name><surname>Naldini</surname><given-names>L</given-names></name></person-group><year>2009</year><article-title>Stable knockdown of microRNA in vivo by lentiviral vectors</article-title><source>Nature Methods</source><volume>6</volume><fpage>63</fpage><lpage>66</lpage><pub-id pub-id-type="doi">10.1038/nmeth.1277</pub-id></element-citation></ref><ref id="bib30"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Giraldez</surname><given-names>AJ</given-names></name><name><surname>Cinalli</surname><given-names>RM</given-names></name><name><surname>Glasner</surname><given-names>ME</given-names></name><name><surname>Enright</surname><given-names>AJ</given-names></name><name><surname>Thomson</surname><given-names>JM</given-names></name><name><surname>Baskerville</surname><given-names>S</given-names></name><name><surname>Hammond</surname><given-names>SM</given-names></name><name><surname>Bartel</surname><given-names>DP</given-names></name><name><surname>Schier</surname><given-names>AF</given-names></name></person-group><year>2005</year><article-title>MicroRNAs regulate brain morphogenesis in zebrafish</article-title><source>Science</source><volume>308</volume><fpage>833</fpage><lpage>838</lpage><pub-id pub-id-type="doi">10.1126/science.1109020</pub-id></element-citation></ref><ref id="bib31"><element-citation publication-type="book"><person-group person-group-type="author"><name><surname>Goslin</surname><given-names>K</given-names></name><name><surname>Asmussen</surname><given-names>H</given-names></name><name><surname>Banker</surname><given-names>G</given-names></name></person-group><year>1998</year><article-title>Rat hippocampal neurons in low-density culture</article-title><source>Culturing Nerve Cells, Rat hippocampal neurons in low-density culture</source><person-group person-group-type="editor"><name><surname>Banker</surname><given-names>G</given-names></name><name><surname>Goslin</surname><given-names>K</given-names></name></person-group><publisher-loc>Camebridge, Massachusetts</publisher-loc><publisher-name>MIT Press</publisher-name><fpage>339</fpage><lpage>370</lpage></element-citation></ref><ref id="bib32"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Han</surname><given-names>K</given-names></name><name><surname>Gennarino</surname><given-names>VA</given-names></name><name><surname>Lee</surname><given-names>Y</given-names></name><name><surname>Pang</surname><given-names>K</given-names></name><name><surname>Hashimoto-Torii</surname><given-names>K</given-names></name><name><surname>Choufani</surname><given-names>S</given-names></name><name><surname>Raju</surname><given-names>CS</given-names></name><name><surname>Oldham</surname><given-names>MC</given-names></name><name><surname>Weksberg</surname><given-names>R</given-names></name><name><surname>Rakic</surname><given-names>P</given-names></name><name><surname>Liu</surname><given-names>Z</given-names></name><name><surname>Zoghbi</surname><given-names>HY</given-names></name></person-group><year>2013</year><article-title>Human-specific regulation of MeCP2 levels in fetal brains by microRNA miR-483-5p</article-title><source>Genes &amp; Development</source><volume>27</volume><fpage>485</fpage><lpage>490</lpage><pub-id pub-id-type="doi">10.1101/gad.207456.112</pub-id></element-citation></ref><ref id="bib33"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Hand</surname><given-names>R</given-names></name><name><surname>Bortone</surname><given-names>D</given-names></name><name><surname>Mattar</surname><given-names>P</given-names></name><name><surname>Nguyen</surname><given-names>L</given-names></name><name><surname>Heng</surname><given-names>JI</given-names></name><name><surname>Guerrier</surname><given-names>S</given-names></name><name><surname>Boutt</surname><given-names>E</given-names></name><name><surname>Peters</surname><given-names>E</given-names></name><name><surname>Barnes</surname><given-names>AP</given-names></name><name><surname>Parras</surname><given-names>C</given-names></name><name><surname>Schuurmans</surname><given-names>C</given-names></name><name><surname>Guillemot</surname><given-names>F</given-names></name><name><surname>Polleux</surname><given-names>F</given-names></name></person-group><year>2005</year><article-title>Phosphorylation of Neurogenin2 specifies the migration properties and the dendritic morphology of pyramidal neurons in the neocortex</article-title><source>Neuron</source><volume>48</volume><fpage>45</fpage><lpage>62</lpage><pub-id pub-id-type="doi">10.1016/j.neuron.2005.08.032</pub-id></element-citation></ref><ref id="bib34"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Haramati</surname><given-names>S</given-names></name><name><surname>Chapnik</surname><given-names>E</given-names></name><name><surname>Sztainberg</surname><given-names>Y</given-names></name><name><surname>Eilam</surname><given-names>R</given-names></name><name><surname>Zwang</surname><given-names>R</given-names></name><name><surname>Gershoni</surname><given-names>N</given-names></name><name><surname>McGlinn</surname><given-names>E</given-names></name><name><surname>Heiser</surname><given-names>PW</given-names></name><name><surname>Wills</surname><given-names>AM</given-names></name><name><surname>Wirguin</surname><given-names>I</given-names></name><name><surname>Rubin</surname><given-names>LL</given-names></name><name><surname>Misawa</surname><given-names>H</given-names></name><name><surname>Tabin</surname><given-names>CJ</given-names></name><name><surname>Brown</surname><given-names>R</given-names><suffix>Jnr</suffix></name><name><surname>Chen</surname><given-names>A</given-names></name><name><surname>Hornstein</surname><given-names>E</given-names></name></person-group><year>2010</year><article-title>miRNA malfunction causes spinal motor neuron disease</article-title><source>Proceedings of the National Academy of Sciences of USA</source><volume>107</volume><fpage>13111</fpage><lpage>13116</lpage><pub-id pub-id-type="doi">10.1073/pnas.1006151107</pub-id></element-citation></ref><ref id="bib35"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Hering</surname><given-names>H</given-names></name><name><surname>Sheng</surname><given-names>M</given-names></name></person-group><year>2001</year><article-title>Dendritic spines: structure, dynamics and regulation</article-title><source>Nature Reviews Neuroscience</source><volume>2</volume><fpage>880</fpage><lpage>888</lpage><pub-id pub-id-type="doi">10.1038/35104061</pub-id></element-citation></ref><ref id="bib36"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Hitz</surname><given-names>C</given-names></name><name><surname>Wurst</surname><given-names>W</given-names></name><name><surname>Kuhn</surname><given-names>R</given-names></name></person-group><year>2007</year><article-title>Conditional brain-specific knockdown of MAPK using Cre/loxP regulated RNA interference</article-title><source>Nucleic Acids Research</source><volume>35</volume><fpage>e90</fpage><pub-id pub-id-type="doi">10.1038/35104061</pub-id></element-citation></ref><ref id="bib37"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Horch</surname><given-names>HW</given-names></name><name><surname>Katz</surname><given-names>LC</given-names></name></person-group><year>2002</year><article-title>BDNF release from single cells elicits local dendritic growth in nearby neurons</article-title><source>Nature Neuroscience</source><volume>5</volume><fpage>1177</fpage><lpage>1184</lpage><pub-id pub-id-type="doi">10.1038/nn927</pub-id></element-citation></ref><ref id="bib38"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Jan</surname><given-names>YN</given-names></name><name><surname>Jan</surname><given-names>LY</given-names></name></person-group><year>2003</year><article-title>The control of dendrite development</article-title><source>Neuron</source><volume>40</volume><fpage>229</fpage><lpage>242</lpage><pub-id pub-id-type="doi">10.1016/S0896-6273(03)00631-7</pub-id></element-citation></ref><ref id="bib39"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Jiang</surname><given-names>M</given-names></name><name><surname>Chen</surname><given-names>G</given-names></name></person-group><year>2006</year><article-title>High Ca(2+)-phosphate transfection efficiency in low-density neuronal cultures</article-title><source>Nature Protocols</source><volume>1</volume><fpage>695</fpage><lpage>700</lpage><pub-id pub-id-type="doi">10.1038/nprot.2006.86</pub-id></element-citation></ref><ref id="bib40"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Jorgensen</surname><given-names>HF</given-names></name><name><surname>Terry</surname><given-names>A</given-names></name><name><surname>Beretta</surname><given-names>C</given-names></name><name><surname>Pereira</surname><given-names>CF</given-names></name><name><surname>Leleu</surname><given-names>M</given-names></name><name><surname>Chen</surname><given-names>ZF</given-names></name><name><surname>Kelly</surname><given-names>C</given-names></name><name><surname>Merkenschlager</surname><given-names>M</given-names></name><name><surname>Fisher</surname><given-names>AG</given-names></name></person-group><year>2009</year><article-title>REST selectively represses a subset of RE1-containing neuronal genes in mouse embryonic stem cells</article-title><source>Development</source><volume>136</volume><fpage>715</fpage><lpage>721</lpage><pub-id pub-id-type="doi">10.1242/dev.028548</pub-id></element-citation></ref><ref id="bib41"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Kawabe</surname><given-names>H</given-names></name><name><surname>Neeb</surname><given-names>A</given-names></name><name><surname>Dimova</surname><given-names>K</given-names></name><name><surname>Young</surname><given-names>SM</given-names><suffix>Jnr</suffix></name><name><surname>Takeda</surname><given-names>M</given-names></name><name><surname>Katsurabayashi</surname><given-names>S</given-names></name><name><surname>Mitkovski</surname><given-names>M</given-names></name><name><surname>Malakhova</surname><given-names>OA</given-names></name><name><surname>Zhang</surname><given-names>DE</given-names></name><name><surname>Umikawa</surname><given-names>M</given-names></name><name><surname>Kariya</surname><given-names>K</given-names></name><name><surname>Goebbels</surname><given-names>S</given-names></name><name><surname>Nave</surname><given-names>KA</given-names></name><name><surname>Rosenmund</surname><given-names>C</given-names></name><name><surname>Jahn</surname><given-names>O</given-names></name><name><surname>Rhee</surname><given-names>J</given-names></name><name><surname>Brose</surname><given-names>N</given-names></name></person-group><year>2010</year><article-title>Regulation of Rap2A by the ubiquitin ligase Nedd4-1 controls neurite development</article-title><source>Neuron</source><volume>65</volume><fpage>358</fpage><lpage>372</lpage><pub-id pub-id-type="doi">10.1016/j.neuron.2010.01.007</pub-id></element-citation></ref><ref id="bib42"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Kawauchi</surname><given-names>T</given-names></name><name><surname>Chihama</surname><given-names>K</given-names></name><name><surname>Nishimura</surname><given-names>YV</given-names></name><name><surname>Nabeshima</surname><given-names>Y</given-names></name><name><surname>Hoshino</surname><given-names>M</given-names></name></person-group><year>2005</year><article-title>MAP1B phosphorylation is differentially regulated by Cdk5/p35, Cdk5/p25, and JNK</article-title><source>Biochemical and Biophysical Research Communications</source><volume>331</volume><fpage>50</fpage><lpage>55</lpage><pub-id pub-id-type="doi">10.1016/j.bbrc.2005.03.132</pub-id></element-citation></ref><ref id="bib43"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Kluiver</surname><given-names>J</given-names></name><name><surname>Gibcus</surname><given-names>JH</given-names></name><name><surname>Hettinga</surname><given-names>C</given-names></name><name><surname>Adema</surname><given-names>A</given-names></name><name><surname>Richter</surname><given-names>MK</given-names></name><name><surname>Halsema</surname><given-names>N</given-names></name><name><surname>Slezak-Prochazka</surname><given-names>I</given-names></name><name><surname>Ding</surname><given-names>Y</given-names></name><name><surname>Kroesen</surname><given-names>BJ</given-names></name><name><surname>van den Berg</surname><given-names>A</given-names></name></person-group><year>2012</year><article-title>Rapid generation of microRNA sponges for microRNA inhibition</article-title><source>PLOS ONE</source><volume>7</volume><fpage>e29275</fpage><pub-id pub-id-type="doi">10.1371/journal.pone.0029275</pub-id></element-citation></ref><ref id="bib44"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Koch</surname><given-names>JC</given-names></name><name><surname>Barski</surname><given-names>E</given-names></name><name><surname>Lingor</surname><given-names>P</given-names></name><name><surname>Bahr</surname><given-names>M</given-names></name><name><surname>Michel</surname><given-names>U</given-names></name></person-group><year>2011</year><article-title>Plasmids containing NRSE/RE1 sites enhance neurite outgrowth of retinal ganglion cells via sequestration of REST independent of NRSE dsRNA expression</article-title><source>The FEBS Journal</source><volume>278</volume><fpage>3472</fpage><lpage>3483</lpage><pub-id pub-id-type="doi">10.1111/j.1742-4658.2011.08269.x</pub-id></element-citation></ref><ref id="bib45"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Kolb</surname><given-names>B</given-names></name><name><surname>Stewart</surname><given-names>J</given-names></name><name><surname>Sutherland</surname><given-names>RJ</given-names></name></person-group><year>1997</year><article-title>Recovery of function is associated with increased spine density in cortical pyramidal cells after frontal lesions and/or noradrenaline depletion in neonatal rats</article-title><source>Behavioural Brain Research</source><volume>89</volume><fpage>61</fpage><lpage>70</lpage><pub-id pub-id-type="doi">10.1016/S0166-4328(97)00058-2</pub-id></element-citation></ref><ref id="bib46"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Krichevsky</surname><given-names>AM</given-names></name><name><surname>King</surname><given-names>KS</given-names></name><name><surname>Donahue</surname><given-names>CP</given-names></name><name><surname>Khrapko</surname><given-names>K</given-names></name><name><surname>Kosik</surname><given-names>KS</given-names></name></person-group><year>2003</year><article-title>A microRNA array reveals extensive regulation of microRNAs during brain development</article-title><source>RNA</source><volume>9</volume><fpage>1274</fpage><lpage>1281</lpage><pub-id pub-id-type="doi">10.1261/rna.5980303</pub-id></element-citation></ref><ref id="bib47"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Kruger</surname><given-names>J</given-names></name><name><surname>Rehmsmeier</surname><given-names>M</given-names></name></person-group><year>2006</year><article-title>RNAhybrid: microRNA target prediction easy, fast and flexible</article-title><source>Nucleic Acids Research</source><volume>34</volume><fpage>W451</fpage><lpage>W454</lpage><pub-id pub-id-type="doi">10.1093/nar/gkl243</pub-id></element-citation></ref><ref id="bib48"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Kuwabara</surname><given-names>T</given-names></name><name><surname>Hsieh</surname><given-names>J</given-names></name><name><surname>Nakashima</surname><given-names>K</given-names></name><name><surname>Taira</surname><given-names>K</given-names></name><name><surname>Gage</surname><given-names>FH</given-names></name></person-group><year>2004</year><article-title>A small modulatory dsRNA specifies the fate of adult neural stem cells</article-title><source>Cell</source><volume>116</volume><fpage>779</fpage><lpage>793</lpage><pub-id pub-id-type="doi">10.1016/S0092-8674(04)00248-X</pub-id></element-citation></ref><ref id="bib49"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Laemmli</surname><given-names>UK</given-names></name></person-group><year>1970</year><article-title>Cleavage of structural proteins during assembly of head of bacteriophage-T4</article-title><source>Nature</source><volume>227</volume><fpage>680</fpage><lpage>685</lpage><pub-id pub-id-type="doi">10.1016/S0092-8674(04)00248-X</pub-id></element-citation></ref><ref id="bib50"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Lagos-Quintana</surname><given-names>M</given-names></name><name><surname>Rauhut</surname><given-names>R</given-names></name><name><surname>Lendeckel</surname><given-names>W</given-names></name><name><surname>Tuschl</surname><given-names>T</given-names></name></person-group><year>2001</year><article-title>Identification of novel genes coding for small expressed RNAs</article-title><source>Science</source><volume>294</volume><fpage>853</fpage><lpage>858</lpage><pub-id pub-id-type="doi">10.1126/science.1064921</pub-id></element-citation></ref><ref id="bib51"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Lagos-Quintana</surname><given-names>M</given-names></name><name><surname>Rauhut</surname><given-names>R</given-names></name><name><surname>Yalcin</surname><given-names>A</given-names></name><name><surname>Meyer</surname><given-names>J</given-names></name><name><surname>Lendeckel</surname><given-names>W</given-names></name><name><surname>Tuschl</surname><given-names>T</given-names></name></person-group><year>2002</year><article-title>Identification of tissue-specific microRNAs from mouse</article-title><source>Current Biology</source><volume>12</volume><fpage>735</fpage><lpage>739</lpage><pub-id pub-id-type="doi">10.1016/S0960-9822(02)00809-6</pub-id></element-citation></ref><ref id="bib52"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Leucht</surname><given-names>C</given-names></name><name><surname>Stigloher</surname><given-names>C</given-names></name><name><surname>Wizenmann</surname><given-names>A</given-names></name><name><surname>Klafke</surname><given-names>R</given-names></name><name><surname>Folchert</surname><given-names>A</given-names></name><name><surname>Bally-Cuif</surname><given-names>L</given-names></name></person-group><year>2008</year><article-title>MicroRNA-9 directs late organizer activity of the midbrain-hindbrain boundary</article-title><source>Nature Neuroscience</source><volume>11</volume><fpage>641</fpage><lpage>648</lpage><pub-id pub-id-type="doi">10.1038/nn.2115</pub-id></element-citation></ref><ref id="bib53"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Liu</surname><given-names>DZ</given-names></name><name><surname>Ander</surname><given-names>BP</given-names></name><name><surname>Tian</surname><given-names>Y</given-names></name><name><surname>Stamova</surname><given-names>B</given-names></name><name><surname>Jickling</surname><given-names>GC</given-names></name><name><surname>Davis</surname><given-names>RR</given-names></name><name><surname>Sharp</surname><given-names>FR</given-names></name></person-group><year>2012</year><article-title>Integrated analysis of mRNA and microRNA expression in mature neurons, neural progenitor cells and neuroblastoma cells</article-title><source>Gene</source><volume>495</volume><fpage>120</fpage><lpage>127</lpage><pub-id pub-id-type="doi">10.1016/j.gene.2011.12.041</pub-id></element-citation></ref><ref id="bib54"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Liu</surname><given-names>GD</given-names></name><name><surname>Zhang</surname><given-names>H</given-names></name><name><surname>Wang</surname><given-names>L</given-names></name><name><surname>Han</surname><given-names>Q</given-names></name><name><surname>Zhou</surname><given-names>SF</given-names></name><name><surname>Liu</surname><given-names>P</given-names></name></person-group><year>2013a</year><article-title>Molecular hydrogen regulates the expression of miR-9, miR-21 and miR-199 in LPS-activated retinal microglia cells</article-title><source>International Journal of Ophthalmology</source><volume>6</volume><fpage>280</fpage><lpage>285</lpage><pub-id pub-id-type="doi">10.3980/j.issn.2222-3959.2013.03.05</pub-id></element-citation></ref><ref id="bib55"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Liu</surname><given-names>Y</given-names></name><name><surname>Zhao</surname><given-names>Z</given-names></name><name><surname>Yang</surname><given-names>F</given-names></name><name><surname>Gao</surname><given-names>Y</given-names></name><name><surname>Song</surname><given-names>J</given-names></name><name><surname>Wan</surname><given-names>Y</given-names></name></person-group><year>2013b</year><article-title>microRNA-181a is involved in insulin-like growth factor-1-mediated regulation of the transcription factor CREB1</article-title><source>Journal of Neurochemistry</source><volume>126</volume><fpage>771</fpage><lpage>780</lpage><pub-id pub-id-type="doi">10.1111/jnc.12370</pub-id></element-citation></ref><ref id="bib56"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>London</surname><given-names>M</given-names></name><name><surname>Hausser</surname><given-names>M</given-names></name></person-group><year>2005</year><article-title>Dendritic computation</article-title><source>Annual Review of Neuroscience</source><volume>28</volume><fpage>503</fpage><lpage>532</lpage><pub-id pub-id-type="doi">10.1146/annurev.neuro.28.061604.135703</pub-id></element-citation></ref><ref id="bib57"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Loya</surname><given-names>CM</given-names></name><name><surname>Lu</surname><given-names>CS</given-names></name><name><surname>Van</surname><given-names>VD</given-names></name><name><surname>Fulga</surname><given-names>TA</given-names></name></person-group><year>2009</year><article-title>Transgenic microRNA inhibition with spatiotemporal specificity in intact organisms</article-title><source>Nature Methods</source><volume>6</volume><fpage>897</fpage><lpage>903</lpage><pub-id pub-id-type="doi">10.1038/nmeth.1402</pub-id></element-citation></ref><ref id="bib58"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Luxenhofer</surname><given-names>G</given-names></name><name><surname>Helmbrecht</surname><given-names>MS</given-names></name><name><surname>Langhoff</surname><given-names>J</given-names></name><name><surname>Giusti</surname><given-names>SA</given-names></name><name><surname>Refojo</surname><given-names>D</given-names></name><name><surname>Huber</surname><given-names>AB</given-names></name></person-group><year>2014</year><article-title>MicroRNA-9 promotes the switch from early-born to late-born motor neuron populations by regulating Onecut transcription factor expression</article-title><source>Developmental Biology</source><volume>386</volume><fpage>358</fpage><lpage>370</lpage><pub-id pub-id-type="doi">10.1016/j.ydbio.2013.12.023</pub-id></element-citation></ref><ref id="bib59"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Ma</surname><given-names>F</given-names></name><name><surname>Xu</surname><given-names>S</given-names></name><name><surname>Liu</surname><given-names>X</given-names></name><name><surname>Zhang</surname><given-names>Q</given-names></name><name><surname>Xu</surname><given-names>X</given-names></name><name><surname>Liu</surname><given-names>M</given-names></name><name><surname>Hua</surname><given-names>M</given-names></name><name><surname>Li</surname><given-names>N</given-names></name><name><surname>Yao</surname><given-names>H</given-names></name><name><surname>Cao</surname><given-names>X</given-names></name></person-group><year>2011</year><article-title>The microRNA miR-29 controls innate and adaptive immune responses to intracellular bacterial infection by targeting interferon-gamma</article-title><source>Nature Immunology</source><volume>12</volume><fpage>861</fpage><lpage>869</lpage><pub-id pub-id-type="doi">10.1038/ni.2073</pub-id></element-citation></ref><ref id="bib60"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Madisen</surname><given-names>L</given-names></name><name><surname>Zwingman</surname><given-names>TA</given-names></name><name><surname>Sunkin</surname><given-names>SM</given-names></name><name><surname>Oh</surname><given-names>SW</given-names></name><name><surname>Zariwala</surname><given-names>HA</given-names></name><name><surname>Gu</surname><given-names>H</given-names></name><name><surname>Ng</surname><given-names>LL</given-names></name><name><surname>Palmiter</surname><given-names>RD</given-names></name><name><surname>Hawrylycz</surname><given-names>MJ</given-names></name><name><surname>Jones</surname><given-names>AR</given-names></name><name><surname>Lein</surname><given-names>ES</given-names></name><name><surname>Zeng</surname><given-names>H</given-names></name></person-group><year>2010</year><article-title>A robust and high-throughput Cre reporting and characterization system for the whole mouse brain</article-title><source>Nature Neuroscience</source><volume>13</volume><fpage>133</fpage><lpage>140</lpage><pub-id pub-id-type="doi">10.1038/nn.2467</pub-id></element-citation></ref><ref id="bib61"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Magill</surname><given-names>ST</given-names></name><name><surname>Cambronne</surname><given-names>XA</given-names></name><name><surname>Luikart</surname><given-names>BW</given-names></name><name><surname>Lioy</surname><given-names>DT</given-names></name><name><surname>Leighton</surname><given-names>BH</given-names></name><name><surname>Westbrook</surname><given-names>GL</given-names></name><name><surname>Mandel</surname><given-names>G</given-names></name><name><surname>Goodman</surname><given-names>RH</given-names></name></person-group><year>2010</year><article-title>microRNA-132 regulates dendritic growth and arborization of newborn neurons in the adult hippocampus</article-title><source>Proceedings of the National Academy of Sciences of USA</source><volume>107</volume><fpage>20382</fpage><lpage>20387</lpage><pub-id pub-id-type="doi">10.1073/pnas.1015691107</pub-id></element-citation></ref><ref id="bib62"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Mumm</surname><given-names>JS</given-names></name><name><surname>Williams</surname><given-names>PR</given-names></name><name><surname>Godinho</surname><given-names>L</given-names></name><name><surname>Koerber</surname><given-names>A</given-names></name><name><surname>Pittman</surname><given-names>AJ</given-names></name><name><surname>Roeser</surname><given-names>T</given-names></name><name><surname>Chien</surname><given-names>CB</given-names></name><name><surname>Baier</surname><given-names>H</given-names></name><name><surname>Wong</surname><given-names>RO</given-names></name></person-group><year>2006</year><article-title>In vivo imaging reveals dendritic targeting of laminated afferents by zebrafish retinal ganglion cells</article-title><source>Neuron</source><volume>52</volume><fpage>609</fpage><lpage>621</lpage><pub-id pub-id-type="doi">10.1016/j.neuron.2006.10.004</pub-id></element-citation></ref><ref id="bib63"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Nadeau</surname><given-names>H</given-names></name><name><surname>Lester</surname><given-names>HA</given-names></name></person-group><year>2002</year><article-title>NRSF causes cAMP-sensitive suppression of sodium current in cultured hippocampal neurons</article-title><source>Journal of Neurophysiology</source><volume>88</volume><fpage>409</fpage><lpage>421</lpage></element-citation></ref><ref id="bib64"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Olena</surname><given-names>AF</given-names></name><name><surname>Patton</surname><given-names>JG</given-names></name></person-group><year>2010</year><article-title>Genomic organization of microRNAs</article-title><source>Journal of Cellular Physiology</source><volume>222</volume><fpage>540</fpage><lpage>545</lpage><pub-id pub-id-type="doi">10.1002/jcp.21993</pub-id></element-citation></ref><ref id="bib65"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Ooi</surname><given-names>L</given-names></name><name><surname>Wood</surname><given-names>IC</given-names></name></person-group><year>2007</year><article-title>Chromatin crosstalk in development and disease: lessons from REST</article-title><source>Nature Reviews Genetics</source><volume>8</volume><fpage>544</fpage><lpage>554</lpage><pub-id pub-id-type="doi">10.1038/nrg2100</pub-id></element-citation></ref><ref id="bib66"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Otaegi</surname><given-names>G</given-names></name><name><surname>Pollock</surname><given-names>A</given-names></name><name><surname>Hong</surname><given-names>J</given-names></name><name><surname>Sun</surname><given-names>T</given-names></name></person-group><year>2011</year><article-title>MicroRNA miR-9 modifies motor neuron columns by a tuning regulation of FoxP1 levels in developing spinal cords</article-title><source>The Journal of Neuroscience</source><volume>31</volume><fpage>809</fpage><lpage>818</lpage><pub-id pub-id-type="doi">10.1523/JNEUROSCI.4330-10.2011</pub-id></element-citation></ref><ref id="bib67"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Packer</surname><given-names>AN</given-names></name><name><surname>Xing</surname><given-names>Y</given-names></name><name><surname>Harper</surname><given-names>SQ</given-names></name><name><surname>Jones</surname><given-names>L</given-names></name><name><surname>Davidson</surname><given-names>BL</given-names></name></person-group><year>2008</year><article-title>The bifunctional microRNA miR-9/miR-9* regulates REST and CoREST and is downregulated in Huntington's disease</article-title><source>The Journal of Neuroscience</source><volume>28</volume><fpage>14341</fpage><lpage>14346</lpage><pub-id pub-id-type="doi">10.1523/JNEUROSCI.2390-08.2008</pub-id></element-citation></ref><ref id="bib68"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Parrish</surname><given-names>JZ</given-names></name><name><surname>Emoto</surname><given-names>K</given-names></name><name><surname>Kim</surname><given-names>MD</given-names></name><name><surname>Jan</surname><given-names>YN</given-names></name></person-group><year>2007</year><article-title>Mechanisms that regulate establishment, maintenance, and remodeling of dendritic fields</article-title><source>Annual Review of Neuroscience</source><volume>30</volume><fpage>399</fpage><lpage>423</lpage><pub-id pub-id-type="doi">10.1146/annurev.neuro.29.051605.112907</pub-id></element-citation></ref><ref id="bib69"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Parrish</surname><given-names>JZ</given-names></name><name><surname>Xu</surname><given-names>P</given-names></name><name><surname>Kim</surname><given-names>CC</given-names></name><name><surname>Jan</surname><given-names>LY</given-names></name><name><surname>Jan</surname><given-names>YN</given-names></name></person-group><year>2009</year><article-title>The microRNA bantam functions in epithelial cells to regulate scaling growth of dendrite arbors in drosophila sensory neurons</article-title><source>Neuron</source><volume>63</volume><fpage>788</fpage><lpage>802</lpage><pub-id pub-id-type="doi">10.1016/j.neuron.2009.08.006</pub-id></element-citation></ref><ref id="bib70"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Pathania</surname><given-names>M</given-names></name><name><surname>Torres-Reveron</surname><given-names>J</given-names></name><name><surname>Yan</surname><given-names>L</given-names></name><name><surname>Kimura</surname><given-names>T</given-names></name><name><surname>Lin</surname><given-names>TV</given-names></name><name><surname>Gordon</surname><given-names>V</given-names></name><name><surname>Teng</surname><given-names>ZQ</given-names></name><name><surname>Zhao</surname><given-names>X</given-names></name><name><surname>Fulga</surname><given-names>TA</given-names></name><name><surname>Van</surname><given-names>VD</given-names></name><name><surname>Bordey</surname><given-names>A</given-names></name></person-group><year>2012</year><article-title>miR-132 enhances dendritic morphogenesis, spine density, synaptic integration, and survival of newborn olfactory bulb neurons</article-title><source>PLOS ONE</source><volume>7</volume><fpage>e38174</fpage><pub-id pub-id-type="doi">10.1371/journal.pone.0038174</pub-id></element-citation></ref><ref id="bib71"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Polleux</surname><given-names>F</given-names></name><name><surname>Morrow</surname><given-names>T</given-names></name><name><surname>Ghosh</surname><given-names>A</given-names></name></person-group><year>2000</year><article-title>Semaphorin 3A is a chemoattractant for cortical apical dendrites</article-title><source>Nature</source><volume>404</volume><fpage>567</fpage><lpage>573</lpage><pub-id pub-id-type="doi">10.1038/35007001</pub-id></element-citation></ref><ref id="bib72"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Qin</surname><given-names>JY</given-names></name><name><surname>Zhang</surname><given-names>L</given-names></name><name><surname>Clift</surname><given-names>KL</given-names></name><name><surname>Hulur</surname><given-names>I</given-names></name><name><surname>Xiang</surname><given-names>AP</given-names></name><name><surname>Ren</surname><given-names>BZ</given-names></name><name><surname>Lahn</surname><given-names>BT</given-names></name></person-group><year>2010</year><article-title>Systematic comparison of constitutive promoters and the doxycycline-inducible promoter</article-title><source>PLOS ONE</source><volume>5</volume><fpage>e10611</fpage><pub-id pub-id-type="doi">10.1371/journal.pone.0010611</pub-id></element-citation></ref><ref id="bib73"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Rajan</surname><given-names>I</given-names></name><name><surname>Cline</surname><given-names>HT</given-names></name></person-group><year>1998</year><article-title>Glutamate receptor activity is required for normal development of tectal cell dendrites in vivo</article-title><source>The Journal of Neuroscience</source><volume>18</volume><fpage>7836</fpage><lpage>7846</lpage></element-citation></ref><ref id="bib74"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Refojo</surname><given-names>D</given-names></name><name><surname>Schweizer</surname><given-names>M</given-names></name><name><surname>Kuehne</surname><given-names>C</given-names></name><name><surname>Ehrenberg</surname><given-names>S</given-names></name><name><surname>Thoeringer</surname><given-names>C</given-names></name><name><surname>Vogl</surname><given-names>AM</given-names></name><name><surname>Dedic</surname><given-names>N</given-names></name><name><surname>Schumacher</surname><given-names>M</given-names></name><name><surname>von</surname><given-names>WG</given-names></name><name><surname>Avrabos</surname><given-names>C</given-names></name><name><surname>Touma</surname><given-names>C</given-names></name><name><surname>Engblom</surname><given-names>D</given-names></name><name><surname>Schutz</surname><given-names>G</given-names></name><name><surname>Nave</surname><given-names>KA</given-names></name><name><surname>Eder</surname><given-names>M</given-names></name><name><surname>Wotjak</surname><given-names>CT</given-names></name><name><surname>Sillaber</surname><given-names>I</given-names></name><name><surname>Holsboer</surname><given-names>F</given-names></name><name><surname>Wurst</surname><given-names>W</given-names></name><name><surname>Deussing</surname><given-names>JM</given-names></name></person-group><year>2011</year><article-title>Glutamatergic and dopaminergic neurons mediate anxiogenic and anxiolytic effects of CRHR1</article-title><source>Science</source><volume>333</volume><fpage>1903</fpage><lpage>1907</lpage><pub-id pub-id-type="doi">10.1126/science.1202107</pub-id></element-citation></ref><ref id="bib75"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Rodriguez</surname><given-names>A</given-names></name><name><surname>Griffiths-Jones</surname><given-names>S</given-names></name><name><surname>Ashurst</surname><given-names>JL</given-names></name><name><surname>Bradley</surname><given-names>A</given-names></name></person-group><year>2004</year><article-title>Identification of mammalian microRNA host genes and transcription units</article-title><source>Genome Research</source><volume>14</volume><fpage>1902</fpage><lpage>1910</lpage><pub-id pub-id-type="doi">10.1101/gr.2722704</pub-id></element-citation></ref><ref id="bib76"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Saito</surname><given-names>T</given-names></name></person-group><year>2006</year><article-title>In vivo electroporation in the embryonic mouse central nervous system</article-title><source>Nature Protocols</source><volume>1</volume><fpage>1552</fpage><lpage>1558</lpage><pub-id pub-id-type="doi">10.1038/nprot.2006.276</pub-id></element-citation></ref><ref id="bib77"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Sauvageau</surname><given-names>M</given-names></name><name><surname>Goff</surname><given-names>LA</given-names></name><name><surname>Lodato</surname><given-names>S</given-names></name><name><surname>Bonev</surname><given-names>B</given-names></name><name><surname>Groff</surname><given-names>AF</given-names></name><name><surname>Gerhardinger</surname><given-names>C</given-names></name><name><surname>Sanchez-Gomez</surname><given-names>DB</given-names></name><name><surname>Hacisuleyman</surname><given-names>E</given-names></name><name><surname>Li</surname><given-names>E</given-names></name><name><surname>Spence</surname><given-names>M</given-names></name><name><surname>Liapis</surname><given-names>SC</given-names></name><name><surname>Mallard</surname><given-names>W</given-names></name><name><surname>Morse</surname><given-names>M</given-names></name><name><surname>Swerdel</surname><given-names>MR</given-names></name><name><surname>D'Ecclessis</surname><given-names>MF</given-names></name><name><surname>Moore</surname><given-names>JC</given-names></name><name><surname>Lai</surname><given-names>V</given-names></name><name><surname>Gong</surname><given-names>G</given-names></name><name><surname>Yancopoulos</surname><given-names>GD</given-names></name><name><surname>Frendewey</surname><given-names>D</given-names></name><name><surname>Kellis</surname><given-names>M</given-names></name><name><surname>Hart</surname><given-names>RP</given-names></name><name><surname>Valenzuela</surname><given-names>DM</given-names></name><name><surname>Arlotta</surname><given-names>P</given-names></name><name><surname>Rinn</surname><given-names>JL</given-names></name></person-group><year>2013</year><article-title>Multiple knockout mouse models reveal lincRNAs are required for life and brain development</article-title><source>eLife</source><volume>2</volume><fpage>e01749</fpage><pub-id pub-id-type="doi">10.7554/eLife.01749</pub-id></element-citation></ref><ref id="bib78"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Schoenherr</surname><given-names>CJ</given-names></name><name><surname>Anderson</surname><given-names>DJ</given-names></name></person-group><year>1995</year><article-title>The neuron-restrictive silencer factor (NRSF): a coordinate repressor of multiple neuron-specific genes</article-title><source>Science</source><volume>267</volume><fpage>1360</fpage><lpage>1363</lpage><pub-id pub-id-type="doi">10.1126/science.7871435</pub-id></element-citation></ref><ref id="bib79"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Schratt</surname><given-names>GM</given-names></name><name><surname>Tuebing</surname><given-names>F</given-names></name><name><surname>Nigh</surname><given-names>EA</given-names></name><name><surname>Kane</surname><given-names>CG</given-names></name><name><surname>Sabatini</surname><given-names>ME</given-names></name><name><surname>Kiebler</surname><given-names>M</given-names></name><name><surname>Greenberg</surname><given-names>ME</given-names></name></person-group><year>2006</year><article-title>A brain-specific microRNA regulates dendritic spine development</article-title><source>Nature</source><volume>439</volume><fpage>283</fpage><lpage>289</lpage><pub-id pub-id-type="doi">10.1038/nature04367</pub-id></element-citation></ref><ref id="bib80"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Senyuk</surname><given-names>V</given-names></name><name><surname>Zhang</surname><given-names>Y</given-names></name><name><surname>Liu</surname><given-names>Y</given-names></name><name><surname>Ming</surname><given-names>M</given-names></name><name><surname>Premanand</surname><given-names>K</given-names></name><name><surname>Zhou</surname><given-names>L</given-names></name><name><surname>Chen</surname><given-names>P</given-names></name><name><surname>Chen</surname><given-names>J</given-names></name><name><surname>Rowley</surname><given-names>JD</given-names></name><name><surname>Nucifora</surname><given-names>G</given-names></name><name><surname>Qian</surname><given-names>Z</given-names></name></person-group><year>2013</year><article-title>Critical role of miR-9 in myelopoiesis and EVI1-induced leukemogenesis</article-title><source>Proceedings of the National Academy of Sciences of USA</source><volume>110</volume><fpage>5594</fpage><lpage>5599</lpage><pub-id pub-id-type="doi">10.1073/pnas.1302645110</pub-id></element-citation></ref><ref id="bib81"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Shibata</surname><given-names>M</given-names></name><name><surname>Nakao</surname><given-names>H</given-names></name><name><surname>Kiyonari</surname><given-names>H</given-names></name><name><surname>Abe</surname><given-names>T</given-names></name><name><surname>Aizawa</surname><given-names>S</given-names></name></person-group><year>2011</year><article-title>MicroRNA-9 regulates neurogenesis in mouse telencephalon by targeting multiple transcription factors</article-title><source>The Journal of Neuroscience</source><volume>31</volume><fpage>3407</fpage><lpage>3422</lpage><pub-id pub-id-type="doi">10.1523/JNEUROSCI.5085-10.2011</pub-id></element-citation></ref><ref id="bib82"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Simó</surname><given-names>S</given-names></name><name><surname>Cooper</surname><given-names>JA</given-names></name></person-group><year>2012</year><article-title>Regulation of dendritic branching by Cdc42 GAPs</article-title><source>Genes &amp; Development</source><volume>26</volume><fpage>1653</fpage><lpage>1658</lpage><pub-id pub-id-type="doi">10.1101/gad.199034.112</pub-id></element-citation></ref><ref id="bib83"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Soriano</surname><given-names>P</given-names></name></person-group><year>1999</year><article-title>Generalized lacZ expression with the ROSA26 Cre reporter strain</article-title><source>Nature Genetics</source><volume>21</volume><fpage>70</fpage><lpage>71</lpage><pub-id pub-id-type="doi">10.1038/5007</pub-id></element-citation></ref><ref id="bib84"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Spruston</surname><given-names>N</given-names></name></person-group><year>2008</year><article-title>Pyramidal neurons: dendritic structure and synaptic integration</article-title><source>Nature Reviews Neuroscience</source><volume>9</volume><fpage>206</fpage><lpage>221</lpage><pub-id pub-id-type="doi">10.1038/nrn2286</pub-id></element-citation></ref><ref id="bib85"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Sudhof</surname><given-names>TC</given-names></name></person-group><year>2008</year><article-title>Neuroligins and neurexins link synaptic function to cognitive disease</article-title><source>Nature</source><volume>455</volume><fpage>903</fpage><lpage>911</lpage><pub-id pub-id-type="doi">10.1038/nature07456</pub-id></element-citation></ref><ref id="bib86"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Takemoto-Kimura</surname><given-names>S</given-names></name><name><surname>Ageta-Ishihara</surname><given-names>N</given-names></name><name><surname>Nonaka</surname><given-names>M</given-names></name><name><surname>Adachi-Morishima</surname><given-names>A</given-names></name><name><surname>Mano</surname><given-names>T</given-names></name><name><surname>Okamura</surname><given-names>M</given-names></name><name><surname>Fujii</surname><given-names>H</given-names></name><name><surname>Fuse</surname><given-names>T</given-names></name><name><surname>Hoshino</surname><given-names>M</given-names></name><name><surname>Suzuki</surname><given-names>S</given-names></name><name><surname>Kojima</surname><given-names>M</given-names></name><name><surname>Mishina</surname><given-names>M</given-names></name><name><surname>Okuno</surname><given-names>H</given-names></name><name><surname>Bito</surname><given-names>H</given-names></name></person-group><year>2007</year><article-title>Regulation of dendritogenesis via a lipid-raft-associated Ca2+/calmodulin-dependent protein kinase CLICK-III/CaMKIgamma</article-title><source>Neuron</source><volume>54</volume><fpage>755</fpage><lpage>770</lpage><pub-id pub-id-type="doi">10.1016/j.neuron.2007.05.021</pub-id></element-citation></ref><ref id="bib87"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Tronche</surname><given-names>F</given-names></name><name><surname>Kellendonk</surname><given-names>C</given-names></name><name><surname>Kretz</surname><given-names>O</given-names></name><name><surname>Gass</surname><given-names>P</given-names></name><name><surname>Anlag</surname><given-names>K</given-names></name><name><surname>Orban</surname><given-names>PC</given-names></name><name><surname>Bock</surname><given-names>R</given-names></name><name><surname>Klein</surname><given-names>R</given-names></name><name><surname>Schutz</surname><given-names>G</given-names></name></person-group><year>1999</year><article-title>Disruption of the glucocorticoid receptor gene in the nervous system results in reduced anxiety</article-title><source>Nature Genetics</source><volume>23</volume><fpage>99</fpage><lpage>103</lpage><pub-id pub-id-type="doi">10.1038/12703</pub-id></element-citation></ref><ref id="bib88"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Urbanska</surname><given-names>M</given-names></name><name><surname>Blazejczyk</surname><given-names>M</given-names></name><name><surname>Jaworski</surname><given-names>J</given-names></name></person-group><year>2008</year><article-title>Molecular basis of dendritic arborization</article-title><source>Acta Neurobiologiae Experimentalis</source><volume>68</volume><fpage>264</fpage><lpage>288</lpage></element-citation></ref><ref id="bib89"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Wayman</surname><given-names>GA</given-names></name><name><surname>Davare</surname><given-names>M</given-names></name><name><surname>Ando</surname><given-names>H</given-names></name><name><surname>Fortin</surname><given-names>D</given-names></name><name><surname>Varlamova</surname><given-names>O</given-names></name><name><surname>Cheng</surname><given-names>HY</given-names></name><name><surname>Marks</surname><given-names>D</given-names></name><name><surname>Obrietan</surname><given-names>K</given-names></name><name><surname>Soderling</surname><given-names>TR</given-names></name><name><surname>Goodman</surname><given-names>RH</given-names></name><name><surname>Impey</surname><given-names>S</given-names></name></person-group><year>2008</year><article-title>An activity-regulated microRNA controls dendritic plasticity by down-regulating p250GAP</article-title><source>Proceedings of the National Academy of Sciences of USA</source><volume>105</volume><fpage>9093</fpage><lpage>9098</lpage><pub-id pub-id-type="doi">10.1073/pnas.0803072105</pub-id></element-citation></ref><ref id="bib90"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Whitford</surname><given-names>KL</given-names></name><name><surname>Marillat</surname><given-names>V</given-names></name><name><surname>Stein</surname><given-names>E</given-names></name><name><surname>Goodman</surname><given-names>CS</given-names></name><name><surname>Tessier-Lavigne</surname><given-names>M</given-names></name><name><surname>Chedotal</surname><given-names>A</given-names></name><name><surname>Ghosh</surname><given-names>A</given-names></name></person-group><year>2002</year><article-title>Regulation of cortical dendrite development by Slit-Robo interactions</article-title><source>Neuron</source><volume>33</volume><fpage>47</fpage><lpage>61</lpage><pub-id pub-id-type="doi">10.1016/S0896-6273(01)00566-9</pub-id></element-citation></ref><ref id="bib91"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Witkos</surname><given-names>TM</given-names></name><name><surname>Koscianska</surname><given-names>E</given-names></name><name><surname>Krzyzosiak</surname><given-names>WJ</given-names></name></person-group><year>2011</year><article-title>Practical Aspects of microRNA Target Prediction</article-title><source>Current Molecular Medicine</source><volume>11</volume><fpage>93</fpage><lpage>109</lpage><pub-id pub-id-type="doi">10.2174/156652411794859250</pub-id></element-citation></ref><ref id="bib92"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Wong</surname><given-names>RO</given-names></name><name><surname>Ghosh</surname><given-names>A</given-names></name></person-group><year>2002</year><article-title>Activity-dependent regulation of dendritic growth and patterning</article-title><source>Nature Reviews Neuroscience</source><volume>3</volume><fpage>803</fpage><lpage>812</lpage><pub-id pub-id-type="doi">10.1038/nrn941</pub-id></element-citation></ref><ref id="bib93"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Yamamoto</surname><given-names>M</given-names></name><name><surname>Ueda</surname><given-names>R</given-names></name><name><surname>Takahashi</surname><given-names>K</given-names></name><name><surname>Saigo</surname><given-names>K</given-names></name><name><surname>Uemura</surname><given-names>T</given-names></name></person-group><year>2006</year><article-title>Control of axonal sprouting and dendrite branching by the Nrg-Ank complex at the neuron-glia interface</article-title><source>Current Biology</source><volume>16</volume><fpage>1678</fpage><lpage>1683</lpage><pub-id pub-id-type="doi">10.1016/j.cub.2006.06.061</pub-id></element-citation></ref><ref id="bib94"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Yao</surname><given-names>MJ</given-names></name><name><surname>Chen</surname><given-names>G</given-names></name><name><surname>Zhao</surname><given-names>PP</given-names></name><name><surname>Lu</surname><given-names>MH</given-names></name><name><surname>Jian</surname><given-names>J</given-names></name><name><surname>Liu</surname><given-names>MF</given-names></name><name><surname>Yuan</surname><given-names>XB</given-names></name></person-group><year>2012</year><article-title>Transcriptome analysis of microRNAs in developing cerebral cortex of rat</article-title><source>BMC Genomics</source><volume>13</volume><fpage>232</fpage><pub-id pub-id-type="doi">10.1186/1471-2164-13-232</pub-id></element-citation></ref><ref id="bib95"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Yoo</surname><given-names>AS</given-names></name><name><surname>Staahl</surname><given-names>BT</given-names></name><name><surname>Chen</surname><given-names>L</given-names></name><name><surname>Crabtree</surname><given-names>GR</given-names></name></person-group><year>2009</year><article-title>MicroRNA-mediated switching of chromatin-remodelling complexes in neural development</article-title><source>Nature</source><volume>460</volume><fpage>642</fpage><lpage>646</lpage><pub-id pub-id-type="doi">10.1038/nature08139</pub-id></element-citation></ref><ref id="bib96"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Zhao</surname><given-names>C</given-names></name><name><surname>Sun</surname><given-names>G</given-names></name><name><surname>Li</surname><given-names>S</given-names></name><name><surname>Shi</surname><given-names>Y</given-names></name></person-group><year>2009</year><article-title>A feedback regulatory loop involving microRNA-9 and nuclear receptor TLX in neural stem cell fate determination</article-title><source>Nature Structural &amp; Molecular Biology</source><volume>16</volume><fpage>365</fpage><lpage>371</lpage><pub-id pub-id-type="doi">10.1038/nsmb.1576</pub-id></element-citation></ref></ref-list></back><sub-article article-type="article-commentary" id="SA1"><front-stub><article-id pub-id-type="doi">10.7554/eLife.02755.019</article-id><title-group><article-title>Decision letter</article-title></title-group><contrib-group content-type="section"><contrib contrib-type="editor"><name><surname>Nelson</surname><given-names>Sacha B</given-names></name><role>Reviewing editor</role><aff><institution>Brandeis University</institution>, <country>United States</country></aff></contrib></contrib-group></front-stub><body><boxed-text><p>eLife posts the editorial decision letter and author response on a selection of the published articles (subject to the approval of the authors). An edited version of the letter sent to the authors after peer review is shown, indicating the substantive concerns or comments; minor concerns are not usually shown. Reviewers have the opportunity to discuss the decision before the letter is sent (see <ext-link ext-link-type="uri" xlink:href="http://elifesciences.org/review-process">review process</ext-link>). Similarly, the author response typically shows only responses to the major concerns raised by the reviewers.</p></boxed-text><p>Thank you for sending your work entitled “MicroRNA-9 controls dendritic development by targeting REST” for consideration at <italic>eLife.</italic> Your article has been favorably evaluated by a Senior editor and 3 reviewers, one of whom, Sacha Nelson, is a member of our Board of Reviewing Editors, and one of whom, Jenny Hsieh, has agreed to reveal her identity.</p><p>The Reviewing editor and the other reviewers discussed their comments before we reached this decision, and the Reviewing editor has assembled the following comments to help you prepare a revised submission.</p><p>All three reviewers felt that this was a detailed and carefully carried out study that revealed a novel function for a broadly expressed microRNA in the regulation of dendritic arborization via regulation of the repressor REST. Although the reviewers felt that the available evidence mostly supported the conclusions reached there were several issues raised that require revision, and at least two of these will require additional experimental work.</p><p>All three reviewers wondered about how general the effects were throughout the nervous system. One reviewer noted that prior published reports indicate that REST expression persists in some neuronal populations in hippocampus and neocortex and perhaps elsewhere and so suggest that the authors should consider the possibility that the role of miR-9/REST in dendritic growth regulation may differ as a function of development and/or which neuronal populations are assayed. Given the broad expression of miR-9, the other reviewers wondered about phenotypes at the level of the whole animal resulting from widespread changes in dendritic and axonal arborization. Although a more detailed functional analysis would improve the paper, one relatively simple suggestion is to determine more carefully whether or not there is any gross anatomical change in brain size or cortical thickness, or a consistent change in the soma size of affected hippocampal neurons. These differences can be readily seen in some developmental disorders that produce more modest changes in dendritic arborization than those seen here.</p><p>A second issue concerns a missing negative control. The conclusion that REST is the only relevant target for the phenotype would be more convincing if the authors demonstrated that other targets (e.g. CREB or Map1b) are not implicated in miR-9 dependent dendritic branching through a similar series of experiment as was performed for REST. The Map1b target is particularly interesting given its involvement in neurite outgrowth in general, and a recent report demonstrating miR-9 regulation of axonal length via Map1b regulation (Dajas-Bailador). Manipulation of Map1b expression could serve as an important control ideally by recapitulating the previously reported Map1b-dependent axonal phenotype in the sponge mice in the absence of a Map1b-dependent dendritic phenotype. Less ideal, but requiring less additional work, would be to show the lack of a Map1b-dependent dendritic phenotype and acknowledge in the discussion the prior publication and the possibility that other miR-9 targets contribute to axonal phenotypes which were not directly measured.</p><p>Minor comments:</p><p>1) The morphological analyses of dendrites are relatively complete, but the physiological analysis is somewhat superficial. The authors should probably hedge their bets by noting that the reduced field potential amplitude could be influenced by other factors not measured including neuronal excitability and levels of inhibition.</p><p>2) In <xref ref-type="fig" rid="fig4">Figure 4F, E</xref> compared to <xref ref-type="fig" rid="fig4">Figure 4 B</xref> and C-both the dendritic length and Sholl analysis are on vastly different scales. Why?</p></body></sub-article><sub-article article-type="reply" id="SA2"><front-stub><article-id pub-id-type="doi">10.7554/eLife.02755.020</article-id><title-group><article-title>Author response</article-title></title-group></front-stub><body><p><italic>All three reviewers felt that this was a detailed and carefully carried out study that revealed a novel function for a broadly expressed microRNA in the regulation of dendritic arborization via regulation of the repressor REST. Although the reviewers felt that the available evidence mostly supported the conclusions reached there were several issues raised that require revision, and at least two of these will require additional experimental work</italic>.</p><p><italic>All three reviewers wondered about how general the effects were throughout the nervous system. One reviewer noted that prior published reports indicate that REST expression persists in some neuronal populations in hippocampus and neocortex and perhaps elsewhere and so suggest that the authors should consider the possibility that the role of miR-9/REST in dendritic growth regulation may differ as a function of development and/or which neuronal populations are assayed. Given the broad expression of miR-9, the other reviewers wondered about phenotypes at the level of the whole animal resulting from widespread changes in dendritic and axonal arborization. Although a more detailed functional analysis would improve the paper, one relatively simple suggestion is to determine more carefully whether or not there is any gross anatomical change in brain size or cortical thickness, or a consistent change in the soma size of affected hippocampal neurons. These differences can be readily seen in some developmental disorders that produce more modest changes in dendritic arborization than those seen here</italic>.</p><p>We thank the first reviewer for pointing out this very thoughtful comment. We have acknowledged the fact that REST levels are restored in some neuronal populations following a biphasic expression (<xref ref-type="bibr" rid="bib28">Gao et al., 2011</xref>; <xref ref-type="bibr" rid="bib48">Kuwabara et al., 2004</xref>), suggesting that miR-9/REST regulation might play other non-developmental roles in some mature neuronal populations This is included in the Discussion section.</p><p>Regarding the phenotypes at the level of the whole animal resulting from widespread changes in dendritic and axonal arborization, we have observed, among other behavioral tasks designed to assess sensorimotor performance, that the acoustic startle response is strongly impaired in miR-9-Sp<sup>Nestin-Cre</sup> mice. This highlights the functional impact from the morphological and electrophysiological impairments. However these studies are still preliminary and other batteries of behavioral tests to assess cognition, emotional-like states and locomotion are still ongoing. The completion of this comprehensive behavioral characterization will take few additional months and consequently we believe that those results will be more suitable for a further study.</p><p>We have now extended our morphological analysis finding that the dendritic defects in miR-9 sponge expressing neurons are not restricted to hippocampal neurons but are also observed in cortical neurons (layer V), suggesting that this is a generalized effect of miR-9 loss of function. These results are now included in <xref ref-type="fig" rid="fig4s2">Figure 4–figure supplement 2</xref>. Accordingly we describe this new set of experiments in the Results section. Despite this fact, miR-9-Sp<sup>Nestin-Cre</sup> mice did not present any gross anatomical change in brain size and also no significant differences were found in cortical thickness measured both directly on tissue sections or using NMR (e.g. data of brain sections: miR-9-Sp<sup>fl-Stop</sup>: 1061 ± 18.60 μm vs. miR-9-Sp<sup>Nestin-Cre</sup>: 1034 ± 22.20 μm, n.s, Student’s <italic>t</italic> test).</p><p>It is important to note at this point that alterations in dendritic complexity do not always correlate with brain or cortical size changes. Several mouse models showing diminished dendritic arborization do not have reduced brain size (Krey et al., 2013; Hoogenraad et al., 2005; Henkemeyer et al., 2003). Similarly, dendritic overgrowth can occur without changes in brain size (Jiang et al., 2013; Collins et al., 2004). This suggests that other factors, not directly assessed in this study, might compensate variations in dendritic arborization preserving brain size.</p><p><italic>A second issue concerns a missing negative control. The conclusion that REST is the only relevant target for the phenotype would be more convincing if the authors demonstrated that other targets (e.g. CREB or Map1b) are not implicated in miR-9 dependent dendritic branching through a similar series of experiment as was performed for REST. The Map1b target is particularly interesting given its involvement in neurite outgrowth in general, and a recent report demonstrating miR-9 regulation of axonal length via Map1b regulation (Dajas-Bailador). Manipulation of Map1b expression could serve as an important control ideally by recapitulating the previously reported Map1b-dependent axonal phenotype in the sponge mice in the absence of a Map1b-dependent dendritic phenotype. Less ideal, but requiring less additional work, would be to show the lack of a Map1b-dependent dendritic phenotype and acknowledge in the discussion the prior publication and the possibility that other miR-9 targets contribute to axonal phenotypes which were not directly measured</italic>.</p><p>The reviewers address here an important point and we have followed this suggestion.</p><p>First we would like to underline that we have not claimed that REST is the only relevant target of miR-9, but on the contrary we consider that it is unrealistic to envision that all the effects observed in miR-9-Sp<sup>Nestin-Cre</sup> mice might be explained by the regulation of only one single target. Concretely, in the reversion experiments depicted in <xref ref-type="fig" rid="fig5">Figure 5</xref>, we show that the expression of shRNAs against REST rescue the effects triggered by the sponge. However the reversion did not reach the 100%, suggesting that other targets beyond REST might also contribute, though in a minor proportion, to the phenotypes observed in miR-9-Sp<sup>Nestin-Cre</sup> mice. This idea is now expressed in the Discussion.</p><p>Regarding the possibility that other miR-9 targets (e.g. Map1b) contribute to axonal phenotypes, we would like to point out that the excellent description of Dajas-Bailador and colleagues of the role of miR-9/Map1b on axonal growth, prompted us to focus in the less explored dendritic role of this microRNA, leaving the well-described axonal phenotypes out of the scope of this study. Following the suggestion of the reviewers, we added an additional layer of complexity to the interpretation of the electrophysiology results. In the Discussion section, we mention that even though impairments in neurotransmission are in agreement with neurons bearing less-arborized dendritic trees, a potential contribution of the tandem miR-9/Map1b, which has already been described to be critical for terminal axonal arborization (<xref ref-type="bibr" rid="bib20">Dajas-Bailador et al., 2012</xref>) might also contribute to the functional phenotypes observed.</p><p>Beside these considerations, we followed the suggestions of the reviewers and analyzed the effect of shRNAs against Map1b on the dendritic arborization in a similar series of experiments as performed for REST. During the course of the experiments we observed that the shMap1b had a strong effect <italic>per se</italic> on the dendritic development of control neurons. As can be observed in the <xref ref-type="fig" rid="fig6">Author response Figure 1</xref>, downregulation of Map1b results in the absence of normal dendrites that are replaced by long filopodia-like structures. Unfortunately, due to this strong <italic>per se</italic> effect, we could not use this tool to evaluate a potential rescue of the dendritic impairment in sponge expressing neurons. Similar effects were observed with a different shRNAi indicating that the results observed are not due to off-target effects of the silencing sequence.<fig id="fig6" position="float"><label>Author response image 1.</label><caption><p>Representative images of primary hippocampal neurons transiently transfected with the indicated constructs and fixed at DIV10. mRFP was cotransfected for visualization. Scale bar 25 μm.</p></caption><graphic xlink:href="elife02755f006"/></fig></p><p>As an alternative, we evaluated the effect of overexpressing the top-three candidates of our previous screening: Foxp4, Creb1 or Map1b on dendritic length and complexity of <italic>wild-type</italic> neurons. Together with REST, those were the highest upregulated targets found in miR-9-Sp<sup>Nestin-Cre</sup> neurons (<xref ref-type="fig" rid="fig5">Figure 5A</xref>). We reasoned that if any of those miR-9 targets would contribute to the dendritic phenotype observed in sponge expressing neurons, their overexpression should negatively regulate dendritic growth. In contrast to REST overexpression, we found that increased levels of Foxp4, Creb1 or Map1b had no impact on dendritic length and complexity. These results are now included in <xref ref-type="fig" rid="fig5s1">Figure 5–figure supplement 1</xref>. It is worth noting that even though the down-regulation of Creb1 sensibly impairs activity-dependent dendritic arborization (Wayman et al., 2006), the forced expression of Creb1 does not trigger the opposite effects. Similar to our results obtained in hippocampal neurons Redmond and colleagues (2002) have sown that Creb1 overexpression in culture cortical neurons during development does not exert any effects on dendritic differentiation.</p><p><italic>Minor comments</italic>:</p><p><italic>1) The morphological analyses of dendrites are relatively complete, but the physiological analysis is somewhat superficial. The authors should probably hedge their bets by noting that the reduced field potential amplitude could be influenced by other factors not measured including neuronal excitability and levels of inhibition</italic>.</p><p>We extended the electrophysiological characterization of miR-9-Sp<sup>Nestin-Cre</sup> mice by testing the excitability of CA1 pyramidal cells. Our data show that the action potential (AP) threshold is shifted to more positive membrane potentials in sponge-expressing neurons. The lower excitability leads to fewer AP in neurons projecting onto CA1 pyramidal neurons, thereby strongly reducing the spontaneous EPSC (sEPSC) frequency. In addition, we recorded miniature EPSCs (mEPSC). Here, mEPSC amplitude and frequency were significantly reduced. The reduced frequency reflects the reduced number of synapses, while the reduced mEPSC amplitude indicates a change in quantal size. To exclude presynaptic effects we tested paired-pulse facilitation, a sensitive measure of changes in the probability of transmitter release, which was unchanged. These results are now included in <xref ref-type="fig" rid="fig4">Figure 4</xref> and <xref ref-type="fig" rid="fig4s3">Figure 4–figure supplement 3</xref> and in the Results section.</p><p><italic>2) In</italic> <xref ref-type="fig" rid="fig4"><italic>Figure 4F, E</italic></xref> <italic>compared to</italic> <xref ref-type="fig" rid="fig4"><italic>Figure 4 B</italic></xref> <italic>and C-both the dendritic length and Sholl analysis are on vastly different scales</italic>. <italic>Why?</italic></p><p>The reviewers are absolutely right. Two factors might contribute to the differences in dendritic length and complexity between the measurements performed in Thy1-eGFP mice (<xref ref-type="fig" rid="fig4">Figure 4 B, C</xref>) and the in utero electroporation experiments (<xref ref-type="fig" rid="fig4">Figure 4 E,F</xref>). First, differences in the genetic backgrounds; Thy1-eGFP mice are in a C57BL/6J background while CD1 mice were used for in utero electroporation. Second, and in our view more relevant, the relative high density of transfected neurons in in utero electroporated brains makes sometimes difficult to discriminate between terminal branches belonging to the neuron being traced or to other neighboring neuron. Since these terminal branches from non-clear sources are excluded from the analyses, tracings from these experiments tend to underestimate the real complexity of the neurons, yielding lower values for total dendritic length and neuronal complexity. Since the same criteria apply to both control- and sponge-transfected groups, this does not represent an intrinsic confounding factor in the comparison between these experimental groups.</p><p><italic>References</italic></p><p>Collins AL, Levenson JM, Vilaythong AP, Richman R, Armstrong DL, Noebels JL, David SJ, Zoghbi HY (2004) Mild overexpression of MeCP2 causes a progressive neurological disorder in mice. Hum Mol Genet 13:2679-2689.</p><p>Dajas-Bailador F, Bonev B, Garcez P, Stanley P, Guillemot F, Papalopulu N (2012) microRNA-9 regulates axon extension and branching by targeting Map1b in mouse cortical neurons. Nat Neurosci 15:697-699.</p><p>Gao Z, Ure K, Ding P, Nashaat M, Yuan L, Ma J, Hammer RE, Hsieh J (2011) The master negative regulator REST/NRSF controls adult neurogenesis by restraining the neurogenic program in quiescent stem cells. J Neurosci 31:9772-9786.</p><p>Henkemeyer M, Itkis OS, Ngo M, Hickmott PW, Ethell IM (2003) Multiple EphB receptor tyrosine kinases shape dendritic spines in the hippocampus. J Cell Biol 163:1313-1326.</p><p>Hoogenraad CC, Milstein AD, Ethell IM, Henkemeyer M, Sheng M (2005) GRIP1 controls dendrite morphogenesis by regulating EphB receptor trafficking. Nat Neurosci 8:906-915.</p><p>Jiang M, Ash RT, Baker SA, Suter B, Ferguson A, Park J, Rudy J, Torsky SP, Chao HT, Zoghbi HY, Smirnakis SM (2013) Dendritic arborization and spine dynamics are abnormal in the mouse model of MECP2 duplication syndrome. J Neurosci 33:19518-19533.</p><p>Krey JF, Pasca SP, Shcheglovitov A, Yazawa M, Schwemberger R, Rasmusson R, Dolmetsch RE (2013) Timothy syndrome is associated with activity-dependent dendritic retraction in rodent and human neurons. Nat Neurosci 16:201-209.</p><p>Kuwabara T, Hsieh J, Nakashima K, Taira K, Gage FH (2004) A small modulatory dsRNA specifies the fate of adult neural stem cells. Cell 116:779-793.</p><p>Redmond L, Kashani AH, Ghosh A (2002) Calcium regulation of dendritic growth via CaM kinase IV and CREB-mediated transcription. Neuron 34:999-1010.</p><p>Wayman GA, Impey S, Marks D, Saneyoshi T, Grant WF, Derkach V, Soderling TR (2006) Activity-dependent dendritic arborization mediated by CaM-kinase I activation and enhanced CREB-dependent transcription of Wnt-2. Neuron 50:897-909.</p></body></sub-article></article>