BioProject

Gene regulatory networks (GRNs), consisting of transcription factors and their target cis-regulatory sequences, control neurogenesis and cell fate specification in the developing central nervous system, but their organization is poorly characterized. More...

Gene regulatory networks (GRNs), consisting of transcription factors and their target cis-regulatory sequences, control neurogenesis and cell fate specification in the developing central nervous system, but their organization is poorly characterized. In this study, we performed integrated scRNA-seq and scATAC-seq analysis from both mouse and human retina to profile dynamic changes in gene expression, chromatin accessibility and transcription factor footprinting during retinal neurogenesis and gliogenesis. We identified multiple interconnected, evolutionarily-conserved GRNs consisting of cell type-specific transcription factors that both activate expression of genes within their own network and often inhibit expression of genes in other networks. These GRNs control state transitions within primary retinal progenitors that underlie temporal patterning, regulate the transition from primary to neurogenic progenitors, and drive specification of each major retinal cell type. We confirmed the prediction of this analysis that the NFI transcription factors Nfia, Nfib, and Nfix selectively activate expression of genes that promote late-stage temporal identity in primary retinal progenitors. We also used GRNs to identify additional transcription factors that selectively promote (Insm1/2) and inhibit (Tbx3, Tcf7l1/2) rod photoreceptor specification in postnatal retina. This study provides an inventory of cis- and trans-acting factors that control retinal development, identifies transcription factors that control the temporal identity of retinal progenitors and cell fate specification, and will potentially help guide cell-based therapies aimed at replacing retinal neurons lost due to disease. Overall design: [scATAC-seq_whole retina] To comprehensively profile dynamic changes in chromatin accessibility across the full course of retinogenesis, we conducted scATAC-seq analysis using the 10x Genomics Chromium platform on dissociated cell nuclei from whole mouse retina at 11 timepoints: embryonic (E) day 11, 12, 14, 16, and 18, as well as postnatal (P) day 0, 2, 5, 8, 11 and 14. [scATACseq_electroporation] We used ex vivo electroporation to overexpress human homologues of NFIA/B/X in E14 retina, and then profiled changes in gene expression and chromatin accessibility in primary RPCs at E16 using scATAC-seq. In parallel, we performed similar analysis in P2 and P14 Nfia/b/x cKO retina [ChIPseq] We used ex vivo electroporation to overexpress human homologues of NFIA/B/X in E14 retina, and then profiled changes in gene expression and chromatin accessibility in primary RPCs at E16 and P0 using scRNA-seq. In parallel, we performed similar analysis in P2 and P14 Nfia/b/x cKO retina [scRNAseq] We used ex vivo electroporation to overexpress human homologues of NFIA/B/X in E14 retina, and then profiled changes in gene expression and chromatin accessibility in primary RPCs at E16 and P0 using scRNA-seq. In parallel, we performed similar analysis in P2 and P14 Nfia/b/x cKO retina Less...