{"PubmedArticle":{"MedlineCitation":{"@attributes":{"Status":"MEDLINE","Owner":"NLM","IndexingMethod":"Manual"},"PMID":{"@attributes":{"Version":"1"},"@text":"33766917"},"DateCompleted":{"Year":"2021","Month":"10","Day":"26"},"DateRevised":{"Year":"2021","Month":"10","Day":"26"},"Article":{"@attributes":{"PubModel":"Print"},"Journal":{"ISSN":{"@attributes":{"IssnType":"Electronic"},"@text":"1091-6490"},"JournalIssue":{"@attributes":{"CitedMedium":"Internet"},"Volume":"118","Issue":"13","PubDate":{"Year":"2021","Month":"Mar","Day":"30"}},"Title":"Proceedings of the National Academy of Sciences of the United States of America","ISOAbbreviation":"Proc Natl Acad Sci U S A"},"ArticleTitle":"<i>Drosophila<\/i> Fezf functions as a transcriptional repressor to direct layer-specific synaptic connectivity in the fly visual system.","ELocationID":[{"@attributes":{"EIdType":"pii","ValidYN":"Y"},"@text":"e2025530118"},{"@attributes":{"EIdType":"doi","ValidYN":"Y"},"@text":"10.1073\/pnas.2025530118"}],"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."],"CopyrightInformation":"Copyright \u00a9 2021 the Author(s). Published by PNAS."},"AuthorList":{"@attributes":{"CompleteYN":"Y"},"Author":[{"@attributes":{"ValidYN":"Y"},"LastName":"Santiago","ForeName":"Ivan J","Initials":"IJ","AffiliationInfo":[{"Affiliation":"Department of Neurobiology, Harvard Medical School, Boston, MA 02115."}]},{"@attributes":{"ValidYN":"Y"},"LastName":"Zhang","ForeName":"Dawei","Initials":"D","AffiliationInfo":[{"Affiliation":"Department of Neurobiology, Harvard Medical School, Boston, MA 02115."}]},{"@attributes":{"ValidYN":"Y"},"LastName":"Saras","ForeName":"Arunesh","Initials":"A","AffiliationInfo":[{"Affiliation":"Department of Neurobiology, Harvard Medical School, Boston, MA 02115."}]},{"@attributes":{"ValidYN":"Y"},"LastName":"Pontillo","ForeName":"Nicholas","Initials":"N","AffiliationInfo":[{"Affiliation":"Department of Neurobiology, Harvard Medical School, Boston, MA 02115."}]},{"@attributes":{"ValidYN":"Y"},"LastName":"Xu","ForeName":"Chundi","Initials":"C","Identifier":[{"@attributes":{"Source":"ORCID"},"@text":"0000-0002-1056-8893"}],"AffiliationInfo":[{"Affiliation":"Department of Neurobiology, Harvard Medical School, Boston, MA 02115."}]},{"@attributes":{"ValidYN":"Y"},"LastName":"Chen","ForeName":"Xiaoting","Initials":"X","AffiliationInfo":[{"Affiliation":"Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229."}]},{"@attributes":{"ValidYN":"Y"},"LastName":"Weirauch","ForeName":"Matthew T","Initials":"MT","AffiliationInfo":[{"Affiliation":"Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229."},{"Affiliation":"Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229."},{"Affiliation":"Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229."},{"Affiliation":"Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45267."}]},{"@attributes":{"ValidYN":"Y"},"LastName":"Mistry","ForeName":"Meeta","Initials":"M","Identifier":[{"@attributes":{"Source":"ORCID"},"@text":"0000-0002-5830-9479"}],"AffiliationInfo":[{"Affiliation":"Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115."}]},{"@attributes":{"ValidYN":"Y"},"LastName":"Ginty","ForeName":"David D","Initials":"DD","AffiliationInfo":[{"Affiliation":"HHMI, Harvard Medical School, Boston, MA 02115 david_ginty@hms.harvard.edu Jing_Peng@hms.harvard.edu."}]},{"@attributes":{"ValidYN":"Y"},"LastName":"Pecot","ForeName":"Matthew Y","Initials":"MY","AffiliationInfo":[{"Affiliation":"Department of Neurobiology, Harvard Medical School, Boston, MA 02115."}]},{"@attributes":{"ValidYN":"Y"},"LastName":"Peng","ForeName":"Jing","Initials":"J","Identifier":[{"@attributes":{"Source":"ORCID"},"@text":"0000-0003-2762-7148"}],"AffiliationInfo":[{"Affiliation":"Department of Neurobiology, Harvard Medical School, Boston, MA 02115; david_ginty@hms.harvard.edu Jing_Peng@hms.harvard.edu."}]}]},"Language":["eng"],"GrantList":{"@attributes":{"CompleteYN":"Y"},"Grant":[{"GrantID":"R01 NS099068","Acronym":"NS","Agency":"NINDS NIH HHS","Country":"United States"},{"GrantID":"R01 NS103905","Acronym":"NS","Agency":"NINDS NIH HHS","Country":"United States"}]},"PublicationTypeList":{"PublicationType":[{"@attributes":{"UI":"D016428"},"@text":"Journal Article"},{"@attributes":{"UI":"D052061"},"@text":"Research Support, N.I.H., Extramural"}]}},"MedlineJournalInfo":{"Country":"United States","MedlineTA":"Proc Natl Acad Sci U S A","NlmUniqueID":"7505876","ISSNLinking":"0027-8424"},"ChemicalList":{"Chemical":[{"RegistryNumber":"0","NameOfSubstance":{"@attributes":{"UI":"D029721"},"@text":"Drosophila Proteins"}},{"RegistryNumber":"0","NameOfSubstance":{"@attributes":{"UI":"D012097"},"@text":"Repressor Proteins"}},{"RegistryNumber":"0","NameOfSubstance":{"@attributes":{"UI":"D014157"},"@text":"Transcription Factors"}},{"RegistryNumber":"0","NameOfSubstance":{"@attributes":{"UI":"C547809"},"@text":"erm protein, Drosophila"}},{"RegistryNumber":"0","NameOfSubstance":{"@attributes":{"UI":"C074838"},"@text":"slp1 protein, Drosophila"}}]},"CitationSubset":["IM"],"MeshHeadingList":{"MeshHeading":[{"DescriptorName":{"@attributes":{"UI":"D000818","MajorTopicYN":"N"},"@text":"Animals"}},{"DescriptorName":{"@attributes":{"UI":"D029721","MajorTopicYN":"N"},"@text":"Drosophila Proteins"},"QualifierName":[{"@attributes":{"UI":"Q000235","MajorTopicYN":"Y"},"@text":"genetics"},{"@attributes":{"UI":"Q000378","MajorTopicYN":"Y"},"@text":"metabolism"}]},{"DescriptorName":{"@attributes":{"UI":"D004331","MajorTopicYN":"N"},"@text":"Drosophila melanogaster"},"QualifierName":[{"@attributes":{"UI":"Q000235","MajorTopicYN":"N"},"@text":"genetics"},{"@attributes":{"UI":"Q000254","MajorTopicYN":"Y"},"@text":"growth & development"}]},{"DescriptorName":{"@attributes":{"UI":"D018507","MajorTopicYN":"Y"},"@text":"Gene Expression Regulation, Developmental"}},{"DescriptorName":{"@attributes":{"UI":"D009474","MajorTopicYN":"N"},"@text":"Neurons"},"QualifierName":[{"@attributes":{"UI":"Q000378","MajorTopicYN":"N"},"@text":"metabolism"},{"@attributes":{"UI":"Q000502","MajorTopicYN":"Y"},"@text":"physiology"}]},{"DescriptorName":{"@attributes":{"UI":"D017354","MajorTopicYN":"N"},"@text":"Point Mutation"}},{"DescriptorName":{"@attributes":{"UI":"D012097","MajorTopicYN":"N"},"@text":"Repressor Proteins"},"QualifierName":[{"@attributes":{"UI":"Q000235","MajorTopicYN":"N"},"@text":"genetics"},{"@attributes":{"UI":"Q000378","MajorTopicYN":"Y"},"@text":"metabolism"}]},{"DescriptorName":{"@attributes":{"UI":"D013569","MajorTopicYN":"N"},"@text":"Synapses"},"QualifierName":[{"@attributes":{"UI":"Q000502","MajorTopicYN":"Y"},"@text":"physiology"}]},{"DescriptorName":{"@attributes":{"UI":"D014157","MajorTopicYN":"N"},"@text":"Transcription Factors"},"QualifierName":[{"@attributes":{"UI":"Q000235","MajorTopicYN":"Y"},"@text":"genetics"},{"@attributes":{"UI":"Q000378","MajorTopicYN":"Y"},"@text":"metabolism"}]},{"DescriptorName":{"@attributes":{"UI":"D014795","MajorTopicYN":"N"},"@text":"Visual Pathways"},"QualifierName":[{"@attributes":{"UI":"Q000166","MajorTopicYN":"N"},"@text":"cytology"},{"@attributes":{"UI":"Q000254","MajorTopicYN":"Y"},"@text":"growth & development"}]}]},"KeywordList":[{"@attributes":{"Owner":"NOTNLM"},"Keyword":[{"@attributes":{"MajorTopicYN":"N"},"@text":"dFezf"},{"@attributes":{"MajorTopicYN":"N"},"@text":"growth cone"},{"@attributes":{"MajorTopicYN":"N"},"@text":"laminar organization"},{"@attributes":{"MajorTopicYN":"N"},"@text":"neural connectivity"},{"@attributes":{"MajorTopicYN":"N"},"@text":"transcription"}]}],"CoiStatement":"The authors declare no competing interest."},"PubmedData":{"History":{"PubMedPubDate":[{"@attributes":{"PubStatus":"entrez"},"Year":"2021","Month":"3","Day":"26","Hour":"6","Minute":"14"},{"@attributes":{"PubStatus":"pubmed"},"Year":"2021","Month":"3","Day":"27","Hour":"6","Minute":"0"},{"@attributes":{"PubStatus":"medline"},"Year":"2021","Month":"10","Day":"27","Hour":"6","Minute":"0"},{"@attributes":{"PubStatus":"pmc-release"},"Year":"2021","Month":"3","Day":"25"}]},"PublicationStatus":"ppublish","ArticleIdList":{"ArticleId":[{"@attributes":{"IdType":"pubmed"},"@text":"33766917"},{"@attributes":{"IdType":"pmc"},"@text":"PMC8020669"},{"@attributes":{"IdType":"doi"},"@text":"10.1073\/pnas.2025530118"},{"@attributes":{"IdType":"pii"},"@text":"2025530118"}]},"ReferenceList":[{"Reference":[{"Citation":"Wang I. E., Clandinin T. R., The influence of wiring economy on nervous system evolution. Curr. Biol. 26, R1101\u2013R1108 (2016).","ArticleIdList":{"ArticleId":[{"@attributes":{"IdType":"pubmed"},"@text":"27780051"}]}},{"Citation":"Baier H., Synaptic laminae in the visual system: Molecular mechanisms forming layers of perception. Annu. Rev. Cell Dev. Biol. 29, 385\u2013416 (2013).","ArticleIdList":{"ArticleId":[{"@attributes":{"IdType":"pubmed"},"@text":"24099086"}]}},{"Citation":"Azeredo da Silveira R., Roska B., Cell types, circuits, computation. Curr. Opin. Neurobiol. 21, 664\u2013671 (2011).","ArticleIdList":{"ArticleId":[{"@attributes":{"IdType":"pubmed"},"@text":"21641794"}]}},{"Citation":"Clark D. A., Demb J. B., Parallel computations in insect and mammalian visual motion processing. Curr. Biol. 26, R1062\u2013R1072 (2016).","ArticleIdList":{"ArticleId":[{"@attributes":{"IdType":"pmc"},"@text":"PMC5108051"},{"@attributes":{"IdType":"pubmed"},"@text":"27780048"}]}},{"Citation":"Nassi J. J., Callaway E. M., Parallel processing strategies of the primate visual system. Nat. Rev. Neurosci. 10, 360\u2013372 (2009).","ArticleIdList":{"ArticleId":[{"@attributes":{"IdType":"pmc"},"@text":"PMC2771435"},{"@attributes":{"IdType":"pubmed"},"@text":"19352403"}]}},{"Citation":"Roska B., Werblin F., Vertical interactions across ten parallel, stacked representations in the mammalian retina. Nature 410, 583\u2013587 (2001).","ArticleIdList":{"ArticleId":[{"@attributes":{"IdType":"pubmed"},"@text":"11279496"}]}},{"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\u2013769 (2013).","ArticleIdList":{"ArticleId":[{"@attributes":{"IdType":"pmc"},"@text":"PMC3876965"},{"@attributes":{"IdType":"pubmed"},"@text":"24105342"}]}},{"Citation":"Todd A. J., Neuronal circuitry for pain processing in the dorsal horn. Nat. Rev. Neurosci. 11, 823\u2013836 (2010).","ArticleIdList":{"ArticleId":[{"@attributes":{"IdType":"pmc"},"@text":"PMC3277941"},{"@attributes":{"IdType":"pubmed"},"@text":"21068766"}]}},{"Citation":"Sanes J. R., Zipursky S. L., Design principles of insect and vertebrate visual systems. Neuron 66, 15\u201336 (2010).","ArticleIdList":{"ArticleId":[{"@attributes":{"IdType":"pmc"},"@text":"PMC2871012"},{"@attributes":{"IdType":"pubmed"},"@text":"20399726"}]}},{"Citation":"Pecot M. Y., et al., Multiple interactions control synaptic layer specificity in the Drosophila visual system. Neuron 77, 299\u2013310 (2013).","ArticleIdList":{"ArticleId":[{"@attributes":{"IdType":"pmc"},"@text":"PMC3684158"},{"@attributes":{"IdType":"pubmed"},"@text":"23352166"}]}},{"Citation":"Tan L., et al., Ig superfamily ligand and receptor pairs expressed in synaptic partners in Drosophila. Cell 163, 1756\u20131769 (2015).","ArticleIdList":{"ArticleId":[{"@attributes":{"IdType":"pmc"},"@text":"PMC4804707"},{"@attributes":{"IdType":"pubmed"},"@text":"26687360"}]}},{"Citation":"Peng J., et al., <i>Drosophila<\/i> Fezf coordinates laminar-specific connectivity through cell-intrinsic and cell-extrinsic mechanisms. eLife\n7, e33962 (2018).","ArticleIdList":{"ArticleId":[{"@attributes":{"IdType":"pmc"},"@text":"PMC5854465"},{"@attributes":{"IdType":"pubmed"},"@text":"29513217"}]}},{"Citation":"Lee T., Luo L., Mosaic analysis with a repressible cell marker for studies of gene function in neuronal morphogenesis. Neuron 22, 451\u2013461 (1999).","ArticleIdList":{"ArticleId":[{"@attributes":{"IdType":"pubmed"},"@text":"10197526"}]}},{"Citation":"Lyne R., et al., FlyMine: An integrated database for Drosophila and Anopheles genomics. Genome Biol. 8, R129 (2007).","ArticleIdList":{"ArticleId":[{"@attributes":{"IdType":"pmc"},"@text":"PMC2323218"},{"@attributes":{"IdType":"pubmed"},"@text":"17615057"}]}},{"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\u20131218 (2013).","ArticleIdList":{"ArticleId":[{"@attributes":{"IdType":"pmc"},"@text":"PMC3959825"},{"@attributes":{"IdType":"pubmed"},"@text":"24097267"}]}},{"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\u2013D117 (2011).","ArticleIdList":{"ArticleId":[{"@attributes":{"IdType":"pmc"},"@text":"PMC3013762"},{"@attributes":{"IdType":"pubmed"},"@text":"21097781"}]}},{"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\u20132814 (1998).","ArticleIdList":{"ArticleId":[{"@attributes":{"IdType":"pmc"},"@text":"PMC110659"},{"@attributes":{"IdType":"pubmed"},"@text":"9566899"}]}},{"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\u20134123 (1987).","ArticleIdList":{"ArticleId":[{"@attributes":{"IdType":"pmc"},"@text":"PMC553894"},{"@attributes":{"IdType":"pubmed"},"@text":"16453817"}]}},{"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\u201310720 (2005).","ArticleIdList":{"ArticleId":[{"@attributes":{"IdType":"pmc"},"@text":"PMC1316973"},{"@attributes":{"IdType":"pubmed"},"@text":"16314497"}]}},{"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\u2013226 (2012).","ArticleIdList":{"ArticleId":[{"@attributes":{"IdType":"pubmed"},"@text":"22803940"}]}},{"Citation":"Janssens D. H., et al., Earmuff restricts progenitor cell potential by attenuating the competence to respond to self-renewal factors. Development 141, 1036\u20131046 (2014).","ArticleIdList":{"ArticleId":[{"@attributes":{"IdType":"pmc"},"@text":"PMC3929404"},{"@attributes":{"IdType":"pubmed"},"@text":"24550111"}]}},{"Citation":"Port F., Bullock S. L., Augmenting CRISPR applications in Drosophila with tRNA-flanked sgRNAs. Nat. Methods 13, 852\u2013854 (2016).","ArticleIdList":{"ArticleId":[{"@attributes":{"IdType":"pmc"},"@text":"PMC5215823"},{"@attributes":{"IdType":"pubmed"},"@text":"27595403"}]}},{"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\u20131051 (1992).","ArticleIdList":{"ArticleId":[{"@attributes":{"IdType":"pubmed"},"@text":"1317319"}]}},{"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\u2013116 (1996).","ArticleIdList":{"ArticleId":[{"@attributes":{"IdType":"pubmed"},"@text":"8660881"}]}},{"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\u201324 (2013).","ArticleIdList":{"ArticleId":[{"@attributes":{"IdType":"pubmed"},"@text":"23665475"}]}},{"Citation":"Sato A., Tomlinson A., Dorsal-ventral midline signaling in the developing Drosophila eye. Development 134, 659\u2013667 (2007).","ArticleIdList":{"ArticleId":[{"@attributes":{"IdType":"pubmed"},"@text":"17215299"}]}},{"Citation":"Wang F., et al., RNAscope: A novel in situ RNA analysis platform for formalin-fixed, paraffin-embedded tissues. J. Mol. Diagn. 14, 22\u201329 (2012).","ArticleIdList":{"ArticleId":[{"@attributes":{"IdType":"pmc"},"@text":"PMC3338343"},{"@attributes":{"IdType":"pubmed"},"@text":"22166544"}]}},{"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\u2013475 (1989)."},{"Citation":"Nern A., Zhu Y., Zipursky S. L., Local N-cadherin interactions mediate distinct steps in the targeting of lamina neurons. Neuron 58, 34\u201341 (2008).","ArticleIdList":{"ArticleId":[{"@attributes":{"IdType":"pmc"},"@text":"PMC2692379"},{"@attributes":{"IdType":"pubmed"},"@text":"18400161"}]}},{"Citation":"Hirata T., et al., Zinc-finger genes Fez and Fez-like function in the establishment of diencephalon subdivisions. Development 133, 3993\u20134004 (2006).","ArticleIdList":{"ArticleId":[{"@attributes":{"IdType":"pubmed"},"@text":"16971467"}]}},{"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\u2013135 (2010).","ArticleIdList":{"ArticleId":[{"@attributes":{"IdType":"pmc"},"@text":"PMC6699514"},{"@attributes":{"IdType":"pubmed"},"@text":"20152183"}]}},{"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\u201310948 (2012).","ArticleIdList":{"ArticleId":[{"@attributes":{"IdType":"pmc"},"@text":"PMC3478895"},{"@attributes":{"IdType":"pubmed"},"@text":"22875928"}]}},{"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\u2013474.e6 (2020).","ArticleIdList":{"ArticleId":[{"@attributes":{"IdType":"pmc"},"@text":"PMC7007373"},{"@attributes":{"IdType":"pubmed"},"@text":"31812516"}]}},{"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\u2013223 (2009).","ArticleIdList":{"ArticleId":[{"@attributes":{"IdType":"pmc"},"@text":"PMC2790811"},{"@attributes":{"IdType":"pubmed"},"@text":"19180090"}]}},{"Citation":"Picelli S., et al., Full-length RNA-seq from single cells using Smart-seq2. Nat. Protoc. 9, 171\u2013181 (2014).","ArticleIdList":{"ArticleId":[{"@attributes":{"IdType":"pubmed"},"@text":"24385147"}]}},{"Citation":"Dobin A., et al., STAR: Ultrafast universal RNA-seq aligner. Bioinformatics 29, 15\u201321 (2013).","ArticleIdList":{"ArticleId":[{"@attributes":{"IdType":"pmc"},"@text":"PMC3530905"},{"@attributes":{"IdType":"pubmed"},"@text":"23104886"}]}},{"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\u2013419 (2017).","ArticleIdList":{"ArticleId":[{"@attributes":{"IdType":"pmc"},"@text":"PMC5600148"},{"@attributes":{"IdType":"pubmed"},"@text":"28263959"}]}},{"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).","ArticleIdList":{"ArticleId":[{"@attributes":{"IdType":"pmc"},"@text":"PMC4712774"},{"@attributes":{"IdType":"pubmed"},"@text":"26925227"}]}},{"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).","ArticleIdList":{"ArticleId":[{"@attributes":{"IdType":"pmc"},"@text":"PMC4302049"},{"@attributes":{"IdType":"pubmed"},"@text":"25516281"}]}},{"Citation":"Didion J. P., Martin M., Collins F. S., Atropos: Specific, sensitive, and speedy trimming of sequencing reads. PeerJ 5, e3720 (2017).","ArticleIdList":{"ArticleId":[{"@attributes":{"IdType":"pmc"},"@text":"PMC5581536"},{"@attributes":{"IdType":"pubmed"},"@text":"28875074"}]}},{"Citation":"Langmead B., Salzberg S. L., Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357\u2013359 (2012).","ArticleIdList":{"ArticleId":[{"@attributes":{"IdType":"pmc"},"@text":"PMC3322381"},{"@attributes":{"IdType":"pubmed"},"@text":"22388286"}]}},{"Citation":"Zhang Y., et al., Model-based analysis of ChIP-seq (MACS). Genome Biol. 9, R137 (2008).","ArticleIdList":{"ArticleId":[{"@attributes":{"IdType":"pmc"},"@text":"PMC2592715"},{"@attributes":{"IdType":"pubmed"},"@text":"18798982"}]}},{"Citation":"Yu G., Wang L. G., He Q. Y., ChIPseeker: An R\/bioconductor package for ChIP peak annotation, comparison and visualization. Bioinformatics 31, 2382\u20132383 (2015).","ArticleIdList":{"ArticleId":[{"@attributes":{"IdType":"pubmed"},"@text":"25765347"}]}},{"Citation":"Lambert S. A., et al., Similarity regression predicts evolution of transcription factor sequence specificity. Nat. Genet. 51, 981\u2013989 (2019).","ArticleIdList":{"ArticleId":[{"@attributes":{"IdType":"pubmed"},"@text":"31133749"}]}},{"Citation":"Stormo G. D., DNA binding sites: Representation and discovery. Bioinformatics 16, 16\u201323 (2000).","ArticleIdList":{"ArticleId":[{"@attributes":{"IdType":"pubmed"},"@text":"10812473"}]}},{"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\u2013985 (2008).","ArticleIdList":{"ArticleId":[{"@attributes":{"IdType":"pmc"},"@text":"PMC2630283"},{"@attributes":{"IdType":"pubmed"},"@text":"18817735"}]}},{"Citation":"Peng J., Drosophila Fezf functions as a transcriptional repressor to direct layer specific synaptic connectivity in the fly visual system.\nGene Expression Omnibus (GEO). https:\/\/www.ncbi.nlm.nih.gov\/geo\/query\/acc.cgi?acc=GSE163311. Deposited 16 December 2020.","ArticleIdList":{"ArticleId":[{"@attributes":{"IdType":"pmc"},"@text":"PMC8020669"},{"@attributes":{"IdType":"pubmed"},"@text":"33766917"}]}}]}]}}}