Long-range chromatin interactions in mouse embryonic stem cells identified by ChIA-PET [ChIA-PET]

The pluripotent state of embryonic stem cells (ESCs) is produced by active transcription of cell identity genes and repression of genes encoding lineage-specifying developmental regulators. Here we use large ESC cohesin ChIA-PET datasets and other genomic data to identify the local chromosomal structures at both active and repressed genes across the genome. The results show that super-enhancer driven cell identity genes generally occur within large loops that are connected through CTCF-CTCF interaction sites occupied by cohesin. Smc1 ChIA-PET data from wild type murine embryonic stem cells V6.5 were generated by deep sequencing using Illumina Hi-Seq 2000.

胚胎干细胞（embryonic stem cells，ESCs）的多能状态，依赖于细胞身份基因的活跃转录与编码谱系特异性发育调控因子的基因的沉默。本研究借助大规模胚胎干细胞黏连蛋白（cohesin）ChIA-PET数据集及其他基因组学数据，在全基因组范围内鉴定活跃基因与沉默基因的局部染色体结构。研究结果显示，由超级增强子驱动的细胞身份基因，通常位于由黏连蛋白占据的CCCTC结合因子（CTCF）-CTCF相互作用位点所连接的大型染色质环内。本研究采用Illumina Hi-Seq 2000平台开展深度测序，获取了野生型小鼠胚胎干细胞V6.5的Smc1蛋白ChIA-PET数据集。