<?xml version="1.0" ?>
<!DOCTYPE PubmedArticleSet PUBLIC "-//NLM//DTD PubMedArticle, 1st January 2025//EN" "https://dtd.nlm.nih.gov/ncbi/pubmed/out/pubmed_250101.dtd">
<PubmedArticleSet>
<PubmedArticle><MedlineCitation Status="MEDLINE" Owner="NLM" IndexingMethod="Manual"><PMID Version="1">33766917</PMID><DateCompleted><Year>2021</Year><Month>10</Month><Day>26</Day></DateCompleted><DateRevised><Year>2021</Year><Month>10</Month><Day>26</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Electronic">1091-6490</ISSN><JournalIssue CitedMedium="Internet"><Volume>118</Volume><Issue>13</Issue><PubDate><Year>2021</Year><Month>Mar</Month><Day>30</Day></PubDate></JournalIssue><Title>Proceedings of the National Academy of Sciences of the United States of America</Title><ISOAbbreviation>Proc Natl Acad Sci U S A</ISOAbbreviation></Journal><ArticleTitle><i>Drosophila</i> Fezf functions as a transcriptional repressor to direct layer-specific synaptic connectivity in the fly visual system.</ArticleTitle><ELocationID EIdType="pii" ValidYN="Y">e2025530118</ELocationID><ELocationID EIdType="doi" ValidYN="Y">10.1073/pnas.2025530118</ELocationID><Abstract><AbstractText>The layered compartmentalization of synaptic connections, a common feature of nervous systems, underlies proper connectivity between neurons and enables parallel processing of neural information. However, the stepwise development of layered neuronal connections is not well understood. The medulla neuropil of the <i>Drosophila</i> visual system, which comprises 10 discrete layers (M1 to M10), where neural computations underlying distinct visual features are processed, serves as a model system for understanding layered synaptic connectivity. The first step in establishing layer-specific connectivity in the outer medulla (M1 to M6) is the innervation by lamina (L) neurons of one of two broad, primordial domains that will subsequently expand and transform into discrete layers. We previously found that the transcription factor dFezf cell-autonomously directs L3 lamina neurons to their proper primordial broad domain before they form synapses within the developing M3 layer. Here, we show that dFezf controls L3 broad domain selection through temporally precise transcriptional repression of the transcription factor <i>slp1</i> (sloppy paired 1). In wild-type L3 neurons, <i>slp1</i> is transiently expressed at a low level during broad domain selection. When <i>dFezf</i> is deleted, <i>slp1</i> expression is up-regulated, and ablation of <i>slp1</i> fully rescues the defect of broad domain selection in <i>dFezf</i>-null L3 neurons. Although the early, transient expression of <i>slp1</i> is expendable for broad domain selection, it is surprisingly necessary for the subsequent L3 innervation of the M3 layer. DFezf thus functions as a transcriptional repressor to coordinate the temporal dynamics of a transcriptional cascade that orchestrates sequential steps of layer-specific synapse formation.</AbstractText><CopyrightInformation>Copyright &#xa9; 2021 the Author(s). Published by PNAS.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Santiago</LastName><ForeName>Ivan J</ForeName><Initials>IJ</Initials><AffiliationInfo><Affiliation>Department of Neurobiology, Harvard Medical School, Boston, MA 02115.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhang</LastName><ForeName>Dawei</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>Department of Neurobiology, Harvard Medical School, Boston, MA 02115.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Saras</LastName><ForeName>Arunesh</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Department of Neurobiology, Harvard Medical School, Boston, MA 02115.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Pontillo</LastName><ForeName>Nicholas</ForeName><Initials>N</Initials><AffiliationInfo><Affiliation>Department of Neurobiology, Harvard Medical School, Boston, MA 02115.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Xu</LastName><ForeName>Chundi</ForeName><Initials>C</Initials><Identifier Source="ORCID">0000-0002-1056-8893</Identifier><AffiliationInfo><Affiliation>Department of Neurobiology, Harvard Medical School, Boston, MA 02115.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Chen</LastName><ForeName>Xiaoting</ForeName><Initials>X</Initials><AffiliationInfo><Affiliation>Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Weirauch</LastName><ForeName>Matthew T</ForeName><Initials>MT</Initials><AffiliationInfo><Affiliation>Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45267.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Mistry</LastName><ForeName>Meeta</ForeName><Initials>M</Initials><Identifier Source="ORCID">0000-0002-5830-9479</Identifier><AffiliationInfo><Affiliation>Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ginty</LastName><ForeName>David D</ForeName><Initials>DD</Initials><AffiliationInfo><Affiliation>HHMI, Harvard Medical School, Boston, MA 02115 david_ginty@hms.harvard.edu Jing_Peng@hms.harvard.edu.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Pecot</LastName><ForeName>Matthew Y</ForeName><Initials>MY</Initials><AffiliationInfo><Affiliation>Department of Neurobiology, Harvard Medical School, Boston, MA 02115.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Peng</LastName><ForeName>Jing</ForeName><Initials>J</Initials><Identifier Source="ORCID">0000-0003-2762-7148</Identifier><AffiliationInfo><Affiliation>Department of Neurobiology, Harvard Medical School, Boston, MA 02115; david_ginty@hms.harvard.edu Jing_Peng@hms.harvard.edu.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>R01 NS099068</GrantID><Acronym>NS</Acronym><Agency>NINDS NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>R01 NS103905</GrantID><Acronym>NS</Acronym><Agency>NINDS NIH HHS</Agency><Country>United States</Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D052061">Research Support, N.I.H., Extramural</PublicationType></PublicationTypeList></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Proc Natl Acad Sci U S A</MedlineTA><NlmUniqueID>7505876</NlmUniqueID><ISSNLinking>0027-8424</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D029721">Drosophila Proteins</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D012097">Repressor Proteins</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D014157">Transcription Factors</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="C547809">erm protein, Drosophila</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="C074838">slp1 protein, Drosophila</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D000818" MajorTopicYN="N">Animals</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D029721" MajorTopicYN="N">Drosophila Proteins</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D004331" MajorTopicYN="N">Drosophila melanogaster</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000254" MajorTopicYN="Y">growth &amp; development</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D018507" MajorTopicYN="Y">Gene Expression Regulation, Developmental</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D009474" MajorTopicYN="N">Neurons</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName><QualifierName UI="Q000502" MajorTopicYN="Y">physiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D017354" MajorTopicYN="N">Point Mutation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D012097" MajorTopicYN="N">Repressor Proteins</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D013569" MajorTopicYN="N">Synapses</DescriptorName><QualifierName UI="Q000502" MajorTopicYN="Y">physiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D014157" MajorTopicYN="N">Transcription Factors</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D014795" MajorTopicYN="N">Visual Pathways</DescriptorName><QualifierName UI="Q000166" MajorTopicYN="N">cytology</QualifierName><QualifierName UI="Q000254" MajorTopicYN="Y">growth &amp; development</QualifierName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">dFezf</Keyword><Keyword MajorTopicYN="N">growth cone</Keyword><Keyword MajorTopicYN="N">laminar organization</Keyword><Keyword MajorTopicYN="N">neural connectivity</Keyword><Keyword MajorTopicYN="N">transcription</Keyword></KeywordList><CoiStatement>The authors declare no competing interest.</CoiStatement></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="entrez"><Year>2021</Year><Month>3</Month><Day>26</Day><Hour>6</Hour><Minute>14</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2021</Year><Month>3</Month><Day>27</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2021</Year><Month>10</Month><Day>27</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pmc-release"><Year>2021</Year><Month>3</Month><Day>25</Day></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">33766917</ArticleId><ArticleId IdType="pmc">PMC8020669</ArticleId><ArticleId IdType="doi">10.1073/pnas.2025530118</ArticleId><ArticleId IdType="pii">2025530118</ArticleId></ArticleIdList><ReferenceList><Reference><Citation>Wang I. E., Clandinin T. R., The influence of wiring economy on nervous system evolution. Curr. Biol. 26, R1101&#x2013;R1108 (2016).</Citation><ArticleIdList><ArticleId IdType="pubmed">27780051</ArticleId></ArticleIdList></Reference><Reference><Citation>Baier H., Synaptic laminae in the visual system: Molecular mechanisms forming layers of perception. Annu. Rev. Cell Dev. Biol. 29, 385&#x2013;416 (2013).</Citation><ArticleIdList><ArticleId IdType="pubmed">24099086</ArticleId></ArticleIdList></Reference><Reference><Citation>Azeredo da Silveira R., Roska B., Cell types, circuits, computation. Curr. Opin. Neurobiol. 21, 664&#x2013;671 (2011).</Citation><ArticleIdList><ArticleId IdType="pubmed">21641794</ArticleId></ArticleIdList></Reference><Reference><Citation>Clark D. A., Demb J. B., Parallel computations in insect and mammalian visual motion processing. Curr. Biol. 26, R1062&#x2013;R1072 (2016).</Citation><ArticleIdList><ArticleId IdType="pmc">PMC5108051</ArticleId><ArticleId IdType="pubmed">27780048</ArticleId></ArticleIdList></Reference><Reference><Citation>Nassi J. J., Callaway E. M., Parallel processing strategies of the primate visual system. Nat. Rev. Neurosci. 10, 360&#x2013;372 (2009).</Citation><ArticleIdList><ArticleId IdType="pmc">PMC2771435</ArticleId><ArticleId IdType="pubmed">19352403</ArticleId></ArticleIdList></Reference><Reference><Citation>Roska B., Werblin F., Vertical interactions across ten parallel, stacked representations in the mammalian retina. Nature 410, 583&#x2013;587 (2001).</Citation><ArticleIdList><ArticleId IdType="pubmed">11279496</ArticleId></ArticleIdList></Reference><Reference><Citation>Greig L. C., Woodworth M. B., Galazo M. J., Padmanabhan H., Macklis J. D., Molecular logic of neocortical projection neuron specification, development and diversity. Nat. Rev. Neurosci. 14, 755&#x2013;769 (2013).</Citation><ArticleIdList><ArticleId IdType="pmc">PMC3876965</ArticleId><ArticleId IdType="pubmed">24105342</ArticleId></ArticleIdList></Reference><Reference><Citation>Todd A. J., Neuronal circuitry for pain processing in the dorsal horn. Nat. Rev. Neurosci. 11, 823&#x2013;836 (2010).</Citation><ArticleIdList><ArticleId IdType="pmc">PMC3277941</ArticleId><ArticleId IdType="pubmed">21068766</ArticleId></ArticleIdList></Reference><Reference><Citation>Sanes J. R., Zipursky S. L., Design principles of insect and vertebrate visual systems. Neuron 66, 15&#x2013;36 (2010).</Citation><ArticleIdList><ArticleId IdType="pmc">PMC2871012</ArticleId><ArticleId IdType="pubmed">20399726</ArticleId></ArticleIdList></Reference><Reference><Citation>Pecot M. Y., et al., Multiple interactions control synaptic layer specificity in the Drosophila visual system. Neuron 77, 299&#x2013;310 (2013).</Citation><ArticleIdList><ArticleId IdType="pmc">PMC3684158</ArticleId><ArticleId IdType="pubmed">23352166</ArticleId></ArticleIdList></Reference><Reference><Citation>Tan L., et al., Ig superfamily ligand and receptor pairs expressed in synaptic partners in Drosophila. Cell 163, 1756&#x2013;1769 (2015).</Citation><ArticleIdList><ArticleId IdType="pmc">PMC4804707</ArticleId><ArticleId IdType="pubmed">26687360</ArticleId></ArticleIdList></Reference><Reference><Citation>Peng J., et al., <i>Drosophila</i> Fezf coordinates laminar-specific connectivity through cell-intrinsic and cell-extrinsic mechanisms. eLife
7, e33962 (2018).</Citation><ArticleIdList><ArticleId IdType="pmc">PMC5854465</ArticleId><ArticleId IdType="pubmed">29513217</ArticleId></ArticleIdList></Reference><Reference><Citation>Lee T., Luo L., Mosaic analysis with a repressible cell marker for studies of gene function in neuronal morphogenesis. Neuron 22, 451&#x2013;461 (1999).</Citation><ArticleIdList><ArticleId IdType="pubmed">10197526</ArticleId></ArticleIdList></Reference><Reference><Citation>Lyne R., et al., FlyMine: An integrated database for Drosophila and Anopheles genomics. Genome Biol. 8, R129 (2007).</Citation><ArticleIdList><ArticleId IdType="pmc">PMC2323218</ArticleId><ArticleId IdType="pubmed">17615057</ArticleId></ArticleIdList></Reference><Reference><Citation>Buenrostro J. D., Giresi P. G., Zaba L. C., Chang H. Y., Greenleaf W. J., Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat. Methods 10, 1213&#x2013;1218 (2013).</Citation><ArticleIdList><ArticleId IdType="pmc">PMC3959825</ArticleId><ArticleId IdType="pubmed">24097267</ArticleId></ArticleIdList></Reference><Reference><Citation>Zhu L. J., et al., FlyFactorSurvey: A database of Drosophila transcription factor binding specificities determined using the bacterial one-hybrid system. Nucleic Acids Res. 39, D111&#x2013;D117 (2011).</Citation><ArticleIdList><ArticleId IdType="pmc">PMC3013762</ArticleId><ArticleId IdType="pubmed">21097781</ArticleId></ArticleIdList></Reference><Reference><Citation>Tolkunova E. N., Fujioka M., Kobayashi M., Deka D., Jaynes J. B., Two distinct types of repression domain in engrailed: One interacts with the groucho corepressor and is preferentially active on integrated target genes. Mol. Cell. Biol. 18, 2804&#x2013;2814 (1998).</Citation><ArticleIdList><ArticleId IdType="pmc">PMC110659</ArticleId><ArticleId IdType="pubmed">9566899</ArticleId></ArticleIdList></Reference><Reference><Citation>Knust E., Tietze K., Campos-Ortega J. A., Molecular analysis of the neurogenic locus enhancer of split of Drosophila melanogaster. EMBO J. 6, 4113&#x2013;4123 (1987).</Citation><ArticleIdList><ArticleId IdType="pmc">PMC553894</ArticleId><ArticleId IdType="pubmed">16453817</ArticleId></ArticleIdList></Reference><Reference><Citation>Goldstein R. E., et al., An eh1-like motif in odd-skipped mediates recruitment of Groucho and repression in vivo. Mol. Cell. Biol. 25, 10711&#x2013;10720 (2005).</Citation><ArticleIdList><ArticleId IdType="pmc">PMC1316973</ArticleId><ArticleId IdType="pubmed">16314497</ArticleId></ArticleIdList></Reference><Reference><Citation>Razin S. V., Borunova V. V., Maksimenko O. G., Kantidze O. L., Cys2His2 zinc finger protein family: Classification, functions, and major members. Biochemistry (Mosc.) 77, 217&#x2013;226 (2012).</Citation><ArticleIdList><ArticleId IdType="pubmed">22803940</ArticleId></ArticleIdList></Reference><Reference><Citation>Janssens D. H., et al., Earmuff restricts progenitor cell potential by attenuating the competence to respond to self-renewal factors. Development 141, 1036&#x2013;1046 (2014).</Citation><ArticleIdList><ArticleId IdType="pmc">PMC3929404</ArticleId><ArticleId IdType="pubmed">24550111</ArticleId></ArticleIdList></Reference><Reference><Citation>Port F., Bullock S. L., Augmenting CRISPR applications in Drosophila with tRNA-flanked sgRNAs. Nat. Methods 13, 852&#x2013;854 (2016).</Citation><ArticleIdList><ArticleId IdType="pmc">PMC5215823</ArticleId><ArticleId IdType="pubmed">27595403</ArticleId></ArticleIdList></Reference><Reference><Citation>Grossniklaus U., Pearson R. K., Gehring W. J., The Drosophila sloppy paired locus encodes two proteins involved in segmentation that show homology to mammalian transcription factors. Genes Dev. 6, 1030&#x2013;1051 (1992).</Citation><ArticleIdList><ArticleId IdType="pubmed">1317319</ArticleId></ArticleIdList></Reference><Reference><Citation>Park M., Wu X., Golden K., Axelrod J. D., Bodmer R., The wingless signaling pathway is directly involved in Drosophila heart development. Dev. Biol. 177, 104&#x2013;116 (1996).</Citation><ArticleIdList><ArticleId IdType="pubmed">8660881</ArticleId></ArticleIdList></Reference><Reference><Citation>Suzuki T., Kaido M., Takayama R., Sato M., A temporal mechanism that produces neuronal diversity in the Drosophila visual center. Dev. Biol. 380, 12&#x2013;24 (2013).</Citation><ArticleIdList><ArticleId IdType="pubmed">23665475</ArticleId></ArticleIdList></Reference><Reference><Citation>Sato A., Tomlinson A., Dorsal-ventral midline signaling in the developing Drosophila eye. Development 134, 659&#x2013;667 (2007).</Citation><ArticleIdList><ArticleId IdType="pubmed">17215299</ArticleId></ArticleIdList></Reference><Reference><Citation>Wang F., et al., RNAscope: A novel in situ RNA analysis platform for formalin-fixed, paraffin-embedded tissues. J. Mol. Diagn. 14, 22&#x2013;29 (2012).</Citation><ArticleIdList><ArticleId IdType="pmc">PMC3338343</ArticleId><ArticleId IdType="pubmed">22166544</ArticleId></ArticleIdList></Reference><Reference><Citation>Fischbach K. F., Dittrich A. P. M., The optic lobe of Drosophila melanogaster. I. A Golgi analysis of wild-type structure. Cell Tissue Res. 258, 441&#x2013;475 (1989).</Citation></Reference><Reference><Citation>Nern A., Zhu Y., Zipursky S. L., Local N-cadherin interactions mediate distinct steps in the targeting of lamina neurons. Neuron 58, 34&#x2013;41 (2008).</Citation><ArticleIdList><ArticleId IdType="pmc">PMC2692379</ArticleId><ArticleId IdType="pubmed">18400161</ArticleId></ArticleIdList></Reference><Reference><Citation>Hirata T., et al., Zinc-finger genes Fez and Fez-like function in the establishment of diencephalon subdivisions. Development 133, 3993&#x2013;4004 (2006).</Citation><ArticleIdList><ArticleId IdType="pubmed">16971467</ArticleId></ArticleIdList></Reference><Reference><Citation>Weng M., Golden K. L., Lee C. Y., dFezf/Earmuff maintains the restricted developmental potential of intermediate neural progenitors in Drosophila. Dev. Cell 18, 126&#x2013;135 (2010).</Citation><ArticleIdList><ArticleId IdType="pmc">PMC6699514</ArticleId><ArticleId IdType="pubmed">20152183</ArticleId></ArticleIdList></Reference><Reference><Citation>Yang N., Dong Z., Guo S., Fezf2 regulates multilineage neuronal differentiation through activating basic helix-loop-helix and homeodomain genes in the zebrafish ventral forebrain. J. Neurosci. 32, 10940&#x2013;10948 (2012).</Citation><ArticleIdList><ArticleId IdType="pmc">PMC3478895</ArticleId><ArticleId IdType="pubmed">22875928</ArticleId></ArticleIdList></Reference><Reference><Citation>Peng Y. R., et al., Binary fate choice between closely related interneuronal types is determined by a Fezf1-dependent postmitotic transcriptional switch. Neuron 105, 464&#x2013;474.e6 (2020).</Citation><ArticleIdList><ArticleId IdType="pmc">PMC7007373</ArticleId><ArticleId IdType="pubmed">31812516</ArticleId></ArticleIdList></Reference><Reference><Citation>Sharan S. K., Thomason L. C., Kuznetsov S. G., Court D. L., Recombineering: A homologous recombination-based method of genetic engineering. Nat. Protoc. 4, 206&#x2013;223 (2009).</Citation><ArticleIdList><ArticleId IdType="pmc">PMC2790811</ArticleId><ArticleId IdType="pubmed">19180090</ArticleId></ArticleIdList></Reference><Reference><Citation>Picelli S., et al., Full-length RNA-seq from single cells using Smart-seq2. Nat. Protoc. 9, 171&#x2013;181 (2014).</Citation><ArticleIdList><ArticleId IdType="pubmed">24385147</ArticleId></ArticleIdList></Reference><Reference><Citation>Dobin A., et al., STAR: Ultrafast universal RNA-seq aligner. Bioinformatics 29, 15&#x2013;21 (2013).</Citation><ArticleIdList><ArticleId IdType="pmc">PMC3530905</ArticleId><ArticleId IdType="pubmed">23104886</ArticleId></ArticleIdList></Reference><Reference><Citation>Patro R., Duggal G., Love M. I., Irizarry R. A., Kingsford C., Salmon provides fast and bias-aware quantification of transcript expression. Nat. Methods 14, 417&#x2013;419 (2017).</Citation><ArticleIdList><ArticleId IdType="pmc">PMC5600148</ArticleId><ArticleId IdType="pubmed">28263959</ArticleId></ArticleIdList></Reference><Reference><Citation>Soneson C., Love M. I., Robinson M. D., Differential analyses for RNA-seq: Transcript-level estimates improve gene-level inferences. F1000 Res. 4, 1521 (2015).</Citation><ArticleIdList><ArticleId IdType="pmc">PMC4712774</ArticleId><ArticleId IdType="pubmed">26925227</ArticleId></ArticleIdList></Reference><Reference><Citation>Love M. I., Huber W., Anders S., Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).</Citation><ArticleIdList><ArticleId IdType="pmc">PMC4302049</ArticleId><ArticleId IdType="pubmed">25516281</ArticleId></ArticleIdList></Reference><Reference><Citation>Didion J. P., Martin M., Collins F. S., Atropos: Specific, sensitive, and speedy trimming of sequencing reads. PeerJ 5, e3720 (2017).</Citation><ArticleIdList><ArticleId IdType="pmc">PMC5581536</ArticleId><ArticleId IdType="pubmed">28875074</ArticleId></ArticleIdList></Reference><Reference><Citation>Langmead B., Salzberg S. L., Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357&#x2013;359 (2012).</Citation><ArticleIdList><ArticleId IdType="pmc">PMC3322381</ArticleId><ArticleId IdType="pubmed">22388286</ArticleId></ArticleIdList></Reference><Reference><Citation>Zhang Y., et al., Model-based analysis of ChIP-seq (MACS). Genome Biol. 9, R137 (2008).</Citation><ArticleIdList><ArticleId IdType="pmc">PMC2592715</ArticleId><ArticleId IdType="pubmed">18798982</ArticleId></ArticleIdList></Reference><Reference><Citation>Yu G., Wang L. G., He Q. Y., ChIPseeker: An R/bioconductor package for ChIP peak annotation, comparison and visualization. Bioinformatics 31, 2382&#x2013;2383 (2015).</Citation><ArticleIdList><ArticleId IdType="pubmed">25765347</ArticleId></ArticleIdList></Reference><Reference><Citation>Lambert S. A., et al., Similarity regression predicts evolution of transcription factor sequence specificity. Nat. Genet. 51, 981&#x2013;989 (2019).</Citation><ArticleIdList><ArticleId IdType="pubmed">31133749</ArticleId></ArticleIdList></Reference><Reference><Citation>Stormo G. D., DNA binding sites: Representation and discovery. Bioinformatics 16, 16&#x2013;23 (2000).</Citation><ArticleIdList><ArticleId IdType="pubmed">10812473</ArticleId></ArticleIdList></Reference><Reference><Citation>Kurusu M., et al., A screen of cell-surface molecules identifies leucine-rich repeat proteins as key mediators of synaptic target selection. Neuron 59, 972&#x2013;985 (2008).</Citation><ArticleIdList><ArticleId IdType="pmc">PMC2630283</ArticleId><ArticleId IdType="pubmed">18817735</ArticleId></ArticleIdList></Reference><Reference><Citation>Peng J., Drosophila Fezf functions as a transcriptional repressor to direct layer specific synaptic connectivity in the fly visual system.
Gene Expression Omnibus (GEO). https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE163311. Deposited 16 December 2020.</Citation><ArticleIdList><ArticleId IdType="pmc">PMC8020669</ArticleId><ArticleId IdType="pubmed">33766917</ArticleId></ArticleIdList></Reference></ReferenceList></PubmedData></PubmedArticle></PubmedArticleSet>