| Literature DB >> 31493975 |
Jackie L Norrie1, Marybeth S Lupo1, Beisi Xu2, Issam Al Diri1, Marc Valentine3, Daniel Putnam2, Lyra Griffiths1, Jiakun Zhang1, Dianna Johnson4, John Easton2, Ying Shao2, Victoria Honnell1, Sharon Frase5, Shondra Miller6, Valerie Stewart1, Xin Zhou2, Xiang Chen7, Michael A Dyer8.
Abstract
More than 8,000 genes are turned on or off as progenitor cells produce the 7 classes of retinal cell types during development. Thousands of enhancers are also active in the developing retinae, many having features of cell- and developmental stage-specific activity. We studied dynamic changes in the 3D chromatin landscape important for precisely orchestrated changes in gene expression during retinal development by ultra-deep in situ Hi-C analysis on murine retinae. We identified developmental-stage-specific changes in chromatin compartments and enhancer-promoter interactions. We developed a machine learning-based algorithm to map euchromatin and heterochromatin domains genome-wide and overlaid it with chromatin compartments identified by Hi-C. Single-cell ATAC-seq and RNA-seq were integrated with our Hi-C and previous ChIP-seq data to identify cell- and developmental-stage-specific super-enhancers (SEs). We identified a bipolar neuron-specific core regulatory circuit SE upstream of Vsx2, whose deletion in mice led to the loss of bipolar neurons.Entities:
Keywords: Hi-C; Vsx2; bipolar neuron; core regulatory circuit; euchromatin; heterochromatin; machine learning; nucleome; retina; super-enhancer
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Year: 2019 PMID： 31493975 PMCID： PMC6842117 DOI： 10.1016/j.neuron.2019.08.002
Source DB: PubMed Journal: Neuron ISSN： 0896-6273 Impact factor: 17.173