ArticleNeuron2019
Single-Cell RNA-Seq Analysis of Retinal Development Identifies NFI Factors as Regulating Mitotic Exit and Late-Born Cell Specification.
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Article in Neuron, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 309 papers.
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309 citing papers in PubMed, 603 citations in OpenAlex.
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- Article
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249 more citing papers are in PubMed but not listed here.
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Authors and funding
14 authors at 5 institutions in 1 country.
Brian S ClarkSolomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
Genevieve L Stein-O'BrienSolomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Oncology, Division of Biostatistics and Bioinformatics, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; McKusick-Nathans Institute for Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Institute for Data Intensive Engineering and Science, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
Fion ShiauSolomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
Gabrielle H CannonSolomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; McKusick-Nathans Institute for Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
Emily Davis-MarcisakDepartment of Oncology, Division of Biostatistics and Bioinformatics, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; McKusick-Nathans Institute for Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
Thomas ShermanDepartment of Oncology, Division of Biostatistics and Bioinformatics, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
Clayton P SantiagoSolomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
Thanh V HoangSolomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
Fatemeh RajaiiDepartment of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
Rebecca E James-EspositoSolomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
Richard M GronostajskiDepartment of Biochemistry, Genetics, Genomics and Bioinformatics Graduate Program, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY 14203, USA.
Elana J FertigDepartment of Oncology, Division of Biostatistics and Bioinformatics, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Institute for Data Intensive Engineering and Science, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Institute for Computational Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Mathematical Institute for Data Science, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Applied Mathematics and Statistics, Johns Hopkins University, Baltimore, MD 21205, USA; Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
Loyal A GoffSolomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; McKusick-Nathans Institute for Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Kavli Neuroscience Discovery Institute, Johns Hopkins University, Baltimore, MD 21205, USA.
Seth BlackshawSolomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Kavli Neuroscience Discovery Institute, Johns Hopkins University, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Center for Human Systems Biology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA. Electronic address: sblack@jhmi.edu.
Johns Hopkins Medicine · USJohns Hopkins University · USDiscovery Institute · USSidney Kimmel Comprehensive Cancer Center · USUniversity at Buffalo, State University of New York · US
Funding
Murine Mutagenesis CoreP30NS050274 · NINDS · JOHNS HOPKINS UNIVERSITY · PI KOLODKIN, ALEX L · 2005 to 2020
$10.9MPredoctoral Training Program in Human GeneticsT32GM007814 · NIGMS · JOHNS HOPKINS UNIVERSITY · PI VALLE, DAVID · 1985 to 2021
$10.6MTranscriptional regulation of retinal cell differentiation and functionR01EY020560 · NEI · JOHNS HOPKINS UNIVERSITY · PI BLACKSHAW, SETH · 2011 to 2021
$4.4MIntegrating bioinformatics into multiscale models for hepatocellular carcinomaU01CA212007 · NCI · JOHNS HOPKINS UNIVERSITY · PI EWALD, ANDREW JOSEF, FERTIG, ELANA · 2018 to 2022
$3.2MComparative transcriptomic and epigenomic analyses of Muller glia reprogrammingU01EY027267 · NEI · UNIVERSITY OF NOTRE DAME · PI BLACKSHAW, SETH, HYDE, DAVID R · 2016 to 2019
$3.0MDynamical Models of Cetuximab Resistance in HNSCC Based on Serial Genomics DataR01CA177669 · NCI · JOHNS HOPKINS UNIVERSITY · PI FERTIG, ELANA · 2014 to 2019
$1.8MIdentification of pathways involved in orbital adipogenesis using functional genomicsK08EY027093 · NEI · JOHNS HOPKINS UNIVERSITY · PI RAJAII, FATEMEH · 2016 to 2020
$862kIdentification of the molecular mechanisms mediating intrinsic control of retinal progenitor competenceR00EY027844 · NEI · WASHINGTON UNIVERSITY · PI CLARK, BRIAN S · 2019 to 2021
$739kIdentification of the molecular mechanisms mediating intrinsic control of retinal progenitor competenceK99EY027844 · NEI · JOHNS HOPKINS UNIVERSITY · PI CLARK, BRIAN S · 2017 to 2018
$205kRegulation of Retinal Progenitor Cell Competence by Long noncoding RNAsF32EY024201 · NEI · JOHNS HOPKINS UNIVERSITY · PI CLARK, BRIAN S · 2014 to 2016
$164kNCI NIH HHS R01 CA177669NCI NIH HHS U01 CA212007NEI NIH HHS F32 EY024201NEI NIH HHS K08 EY027093NEI NIH HHS K99 EY027844NEI NIH HHS R00 EY027844NEI NIH HHS R01 EY020560NEI NIH HHS U01 EY027267NIGMS NIH HHS T32 GM007814NINDS NIH HHS P30 NS050274
Abstract
Precise temporal control of gene expression in neuronal progenitors is necessary for correct regulation of neurogenesis and cell fate specification. However, the cellular heterogeneity of the developing CNS has posed a major obstacle to identifying the gene regulatory networks that control these processes. To address this, we used single-cell RNA sequencing to profile ten developmental stages encompassing the full course of retinal neurogenesis. This allowed us to comprehensively characterize changes in gene expression that occur during initiation of neurogenesis, changes in developmental competence, and specification and differentiation of each major retinal cell type. We identify the NFI transcription factors (Nfia, Nfib, and Nfix) as selectively expressed in late retinal progenitor cells and show that they control bipolar interneuron and Müller glia cell fate specification and promote proliferative quiescence.
Indexed as
AnimalsCell ProliferationEpendymoglial CellsGene Expression Regulation, DevelopmentalInterneuronsMiceMitosisNeural Stem CellsNeurogenesisNFI Transcription FactorsRetinaRetinal NeuronsRNA-SeqSingle-Cell AnalysisNfia protein, mouseNfib protein, mouseNFI Transcription FactorsNfix protein, mousecell fateCoGAPSdevelopmentMüller glianeural progenitorneurogenesisphotoreceptorproliferationretinascRNA-seqsingle-cell RNA-sequencing
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