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Nucleome Dynamics during Retinal Development
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DOI：10.1016/j.neuron.2019.08.002.png)
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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.
Keyword:
NON-SYNDROMIC MICROPHTHALMIA/ANOPHTHALMIA
GENE-EXPRESSION
HOMEOBOX GENE
GENOME
MUTATIONS
CELLS
CHX10
ARCHITECTURE
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PRINCIPLES
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IF:
15
论文数:
1.4W
被引数:
9.9W
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