Loss of Cohesin regulator PDS5A reveals repressive role of Polycomb loops

Polycomb Repressive Complexes 1 and 2 (PRC1, PRC2) are conserved epigenetic regulators that promote transcriptional silencing. PRC1 and PRC2 converge on shared targets, catalyzing repressive histone modifications. In addition, a subset of PRC1/PRC2 targets engage in long-range interactions whose functions in gene silencing are poorly understood. Using a CRISPR screen in mouse embryonic stem cells, we discovered that the cohesin regulator PDS5A links transcriptional silencing by Polycomb and 3D genome organization. PDS5A deletion impairs cohesin unloading and results in derepression of subset of endogenous PRC1/PRC2 target genes. Importantly, derepression is not associated with loss of repressive Polycomb chromatin modifications. Instead, loss of PDS5A leads to aberrant cohesin activity, ectopic insulation sites and specific reduction of ultra-long Polycomb loops. We infer that these loops are important for robust silencing at a subset of Polycomb target genes and that maintenance of cohesin-dependent genome architecture is critical for Polycomb regulation. Overall design: 105 samples in total: 34 ChIP-Seq (17x2 replicates each), 12 RNA-Seq (6x2 replicates each), 6 ATACseq (2x3 replicates each), 43 HiC, 10 ChIPCapture (5x2 replicates each)

多梳抑制复合体1与2（Polycomb Repressive Complexes 1 and 2，PRC1、PRC2）是一类保守的表观遗传调控因子，可介导转录沉默。PRC1与PRC2共同结合于共有靶染色质区域，催化产生抑制性组蛋白修饰。此外，部分PRC1/PRC2靶标参与长距离染色质相互作用，其在基因沉默中的功能目前尚不明晰。本研究通过在小鼠胚胎干细胞中开展CRISPR筛选，发现黏连蛋白调控因子PDS5A可将多梳蛋白介导的转录沉默与三维基因组组织结构建立关联。敲除PDS5A会损伤黏连蛋白的卸载过程，进而导致部分内源性PRC1/PRC2靶基因的表达去抑制。值得注意的是，这种去抑制现象与多梳蛋白染色质抑制性修饰的丢失并无关联。与之相反，PDS5A缺失会引发异常的黏连蛋白活性、异位绝缘子位点的形成，以及超长多梳蛋白染色质环的特异性减少。本研究据此推测，这类染色质环对于部分多梳蛋白靶基因的稳定沉默至关重要，而维持黏连蛋白依赖的基因组三维结构对于多梳蛋白的调控功能不可或缺。整体实验设计：样本总计105份，其中包含34份ChIP-Seq测序样本（每组17份，设置2次生物学重复）、12份RNA-Seq测序样本（每组6份，设置2次生物学重复）、6份ATAC-seq测序样本（每组2份，设置3次生物学重复）、43份Hi-C测序样本，以及10份ChIP捕获测序样本（每组5份，设置2次生物学重复）