{Reference Type}: Journal Article
{Title}: Nucleome Dynamics during Retinal Development.
{Author}: Norrie JL;Lupo MS;Xu B;Al Diri I;Valentine M;Putnam D;Griffiths L;Zhang J;Johnson D;Easton J;Shao Y;Honnell V;Frase S;Miller S;Stewart V;Zhou X;Chen X;Dyer MA;
{Journal}: Neuron
{Volume}: 104
{Issue}: 3
{Year}: 11 2019 6
{Factor}: 18.688
{DOI}: 10.1016/j.neuron.2019.08.002
{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.