Remodeling of the interphase chromatin domain structures in embryonic stem cells by targeted placement of human-specific regulatory loci

Abstract

Genome-wide proximity placement analysis of diverse families of human-specific genomic regulatory loci (HSGRL) identified topologically-associating domains (TADs) that are significantly enriched for HSGRL and termed rapidly-evolving in humans TADs (revTADs; Genome Biol Evol. 2016 8; 2774-88). Here, human-specific genomic features of pluripotency regulatory networks in hESC have been analyzed. The primary focus was on identification of human-specific elements of the interphase chromatin architecture of TADs responsible for transcriptional regulatory control of the NANOG, POU5F1, and POU3F2 genes. Comparative analyses of the four adjacent TADs spanning ~3.3 Mb NANOG locus-associated genomic region were carried-out to highlight primate-specific genomic features. Lastly, the putative mechanisms of the genome-wide regulatory effects of human-specific NANOG-binding sites (HSNBS) on expression of genes implicated in the fetal and adult brain development have been examined. Acquisition of primate-specific regulatory loci appears to rewire TADs exerting transcriptional control on pluripotency regulators, revealing a genomic placement pattern consistent with the enhanced regulatory impact of NANOG in primates. Proximity placement analysis of HSNBS identified a large expression signature in the human fetal neocortex temporal lobe comprising 4,957 genes, which appear to retain acquired in the embryo expression changes for many years of human brain development and maintain highly concordant expression profiles in the neocortex and prefrontal cortex regions of adult human brain. Collectively, reported herein observations indicate that genomic elements of pluripotency regulatory circuitry associated with HSNBS, specifically proteins of the classical NurD chromatin remodeling complex, contribute to transcriptional regulation of a large set of genes implicated in development and function of human brain.\n\nList of abbreviations5hmC, 5-Hydromethylcytosine\n\nCTCF, CCCTC-binding factor\n\nDHS, DNase hypersensitivity sites\n\nFHSRR, fixed human-specific regulatory regions\n\nGRNs, genomic regulatory networks\n\nHAR, human accelerated regions\n\nhCONDEL, human-specific conserved deletions\n\nhESC, human embryonic stem cells\n\nHSGRL, human-specific genomic regulatory loci\n\nHSNBS, human-specific NANOG-binding sites\n\nHSTFBS, human-specific transcription factor-binding sites\n\nLAD, lamina-associated domain\n\nLINE, long interspersed nuclear element\n\nlncRNA, long non-coding RNA\n\nLTR, long terminal repeat\n\nMADE, methylation-associated DNA editing\n\nmC, methylcytosine\n\nmESC, mouse embryonic stem cells\n\nNANOG, Nanog homeobox\n\nnt, nucleotide\n\nPOU5F1, POU class 5 homeobox 1\n\nPSDS, partial strand displacement state\n\nTAD, topologically associating domains\n\nTE, transposable elements\n\nTF, transcription factor\n\nTSC, triple-stranded complex\n\nTSS, transcription start sites\n\nSE, super-enhancers\n\nSED, super-enhancer domains\n\nsncRNA, small non coding RNA