ARID1A-dependent maintenance of H3.3 is required for repressive CHD4-ZMYND8 chromatin interactions at super-enhancers [12Z_ZMYND8_ChIP]. ARID1A-dependent maintenance of H3.3 is required for repressive CHD4-ZMYND8 chromatin interactions at super-enhancers [12Z_ZMYND8_ChIP]

Background: SWI/SNF (BAF) chromatin remodeling complexes regulate lineage-specific enhancer activity by promoting accessibility for diverse DNA-binding factors and chromatin regulators. Additionally, they are known to modulate the function of the epigenome through regulation of histone post-translational modifications and nucleosome composition, although the way SWI/SNF complexes govern the epigenome remains poorly understood. Here, we investigate the function of ARID1A, a subunit of certain mammalian SWI/SNF chromatin remodeling complexes associated with malignancies and benign diseases originating from the uterine endometrium. Results: Through genome-wide analysis of human endometriotic epithelial cells, we show that more than half of ARID1A binding sites are marked by the variant histone H3.3, including active regulatory elements such as super-enhancers. ARID1A knockdown leads to H3.3 depletion and gain of canonical H3.1/3.2 at ARID1A-bound active regulatory elements, and a concomitant redistribution of H3.3 towards genic elements. ARID1A interactions with the repressive chromatin remodeler CHD4 (NuRD) are associated with H3.3, and ARID1A is required for CHD4 recruitment to H3.3. ZMYND8 interacts with CHD4 to suppress a subset of ARID1A, CHD4, and ZMYND8 co-bound, H3.3+ H4K16ac+ super-enhancers near genes governing extracellular matrix, motility, adhesion, and epithelial-to-mesenchymal transition. Moreover, these gene expression alterations are observed in human endometriomas. Conclusions: These studies demonstrate that ARID1A-containing BAF complexes are required for maintenance of the histone variant H3.3 at active regulatory elements, such as super-enhancers, and this function is required for the physiologically relevant activities of alternative chromatin remodelers. Overall design: Human 12Z endometriotic epithelial cells were measured for genome-wide ZMYND8 binding by chromatin immunoprecipitation followed by sequencing (ChIP-seq).

背景：SWI/SNF（BAF）染色质重塑复合物通过促进多种DNA结合因子与染色质调控因子的染色质可及性，调控谱系特异性增强子活性。此外，已知其可通过调控组蛋白翻译后修饰与核小体组成，调节表观基因组功能，但目前对SWI/SNF复合物如何调控表观基因组的机制仍知之甚少。本研究针对ARID1A展开功能探究——ARID1A是部分与子宫子宫内膜来源的恶性肿瘤及良性疾病相关的哺乳动物SWI/SNF染色质重塑复合物的亚基。
结果：通过对人子宫内膜异位上皮细胞开展全基因组分析，本研究发现超过半数的ARID1A结合位点存在组蛋白变体H3.3标记，其中包括超级增强子等活性调控元件。ARID1A基因敲低会导致ARID1A结合的活性调控元件处出现H3.3耗竭与经典组蛋白H3.1/3.2的富集，并伴随H3.3向基因元件的重新分布。ARID1A与抑制性染色质重塑因子CHD4（NuRD复合物）的互作与H3.3相关，且ARID1A是CHD4招募至H3.3位点所必需的。ZMYND8与CHD4互作，可抑制ARID1A、CHD4与ZMYND8共结合的、H3.3阳性且H4K16乙酰化阳性的超级增强子子集，这些增强子邻近调控细胞外基质、细胞迁移、细胞黏附以及上皮间质转化的基因。此外，在人子宫内膜异位囊肿中可观测到此类基因表达改变。
结论：本研究证实，携带ARID1A的BAF复合物对于维持超级增强子等活性调控元件处的组蛋白变体H3.3水平至关重要，且该功能是替代性染色质重塑因子发挥生理相关活性所必需的。
实验整体设计：通过染色质免疫共沉淀测序（ChIP-seq），对人12Z子宫内膜异位上皮细胞开展全基因组水平的ZMYND8结合位点检测。