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Publication

Single-Cell RNA-Seq Analysis of Retinal Development Identifies NFI Factors as Regulating Mitotic Exit and Late-Born Cell Specification.

Neuron | 2019

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.

Pubmed ID: 31128945 RIS Download

Research resources used in this publication

Tg(Chx10-EGFP/cre/-ALPP)2Clc (RRID:MGI:3838985) (organism)

Additional research tools detected in this publication

Antibodies used in this publication

Associated grants

Agency: NEI NIH HHS, United States
Id: R01 EY020560
Agency: NIGMS NIH HHS, United States
Id: T32 GM007814
Agency: NEI NIH HHS, United States
Id: U01 EY027267
Agency: NEI NIH HHS, United States
Id: K99 EY027844
Agency: NEI NIH HHS, United States
Id: F32 EY024201
Agency: NCI NIH HHS, United States
Id: R01 CA177669
Agency: NEI NIH HHS, United States
Id: R00 EY027844

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This is a list of tools and resources that we have found mentioned in this publication.

Charles River Laboratories (tool)

RRID:SCR_003792

Commercial organism provider selling mice, rats and other model animals. American corporation specializing in a variety of pre-clinical and clinical laboratory services for the pharmaceutical, medical device and biotechnology industries. It also supplies assorted biomedical products and research and development outsourcing services for use in the pharmaceutical industry. (Wikipedia)

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PRISM (tool)

RRID:SCR_005375

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 5,2022.Tool that predicts interactions between transcription factors and their regulated genes from binding motifs. Understanding vertebrate development requires unraveling the cis-regulatory architecture of gene regulation. PRISM provides accurate genome-wide computational predictions of transcription factor binding sites for the human and mouse genomes, and integrates the predictions with GREAT to provide functional biological context. Together, accurate computational binding site prediction and GREAT produce for each transcription factor: 1. putative binding sites, 2. putative target genes, 3. putative biological roles of the transcription factor, and 4. putative cis-regulatory elements through which the factor regulates each target in each functional role.

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Monocle2 (tool)

RRID:SCR_016339

Software package for analyzing single cell gene expression, classifying and counting cells, performing differential expression analysis between subpopulations of cells, and reconstructing cellular trajcectories. Works well with very large single-cell RNA-Seq experiments containing tens of thousands of cells or more. Used in computational analysis of gene expression data in single cell gene expression studies to profile transcriptional regulation in complex biological processes and highly heterogeneous cell populations.

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