Highlights d There are dynamic changes in chromatin compartments and looping during retinogenesis d Euchromatin and heterochromatin localization can be predicted by machine learning d Vsx2 has a cell-type-and stage-specific core regulatory circuit super-enhancer d Vsx2 core regulatory circuit super-enhancer deletion eliminates bipolar neurons

The nuclei of rod photoreceptors in mice and other nocturnal species have an unusual inverted chromatin structure: the heterochromatin is centrally located to help focus light and improve photosensitivity. To better understand this unique nuclear organization, we performed ultra-deep Hi-C analysis on murine retina at 3 stages of development and on purified rod photoreceptors. Predicted looping interactions from the Hi-C data were validated with fluorescence in situ hybridization (FISH). We discovered that a subset of retinal genes that are important for retinal development, cancer, and stress response are localized to the facultative heterochromatin domain. We also used machine learning to develop an algorithm based on our chromatin Hidden Markov Modeling (chromHMM) of retinal development to predict heterochromatin domains and study their dynamics during retinogenesis. FISH data for 264 genomic loci were used to train and validate the algorithm. The integrated data were then used to identify a developmental stage-and cell type-specific core regulatory circuit super-enhancer (CRC-SE) upstream of the Vsx2 gene, which is required for bipolar neuron expression. Deletion of the Vsx2 CRC-SE in mice led to the loss of bipolar neurons in the retina.We have previously analyzed DNA methylation [whole-genome bisulfite sequencing (WGBS)], histone modifications [chromatin immunoprecipitation with DNA sequencing (ChIPseq) for 8 marks], chromatin accessibility [assay for transposase-accessible chromatin using sequencing (ATAC-seq)], and transcriptional regulation through enhancer interactions (Brd4, CTCF, RNA-PolII, and ChIP-seq) in detail on the developing murine retina 1 . By integrating those data with RNA-seq data, we identified putative developmental stage-and cell typespecific enhancers, superenhancers, and CRC-SEs 1,2 . Many of those regulatory elements are

No abstract