ARID1A-dependent maintenance of H3.3 is required for repressive CHD4-ZMYND8 chromatin interactions at super-enhancers [12Z_CHD4_ChIP]. ARID1A-dependent maintenance of H3.3 is required for repressive CHD4-ZMYND8 chromatin interactions at super-enhancers [12Z_CHD4_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 CHD4 binding by chromatin immunoprecipitation followed by sequencing (ChIP-seq).

背景：SWI/SNF（BAF）染色质重塑复合物（SWI/SNF (BAF) chromatin remodeling complexes）可通过提升多种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的活性。此外，已知该复合物可通过调控组蛋白翻译后修饰与核小体组成，对表观基因组的功能进行调控，但目前学界对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是部分哺乳动物SWI/SNF染色质重塑复合物的核心亚基，与源自子宫内膜的恶性肿瘤及良性疾病密切相关。
结果：通过对人子宫内膜异位上皮细胞进行全基因组分析，本研究发现超过半数的ARID1A结合位点均带有组蛋白变体H3.3的修饰标记，其中包括超级增强子（super-enhancers）等活性调控元件。敲低ARID1A会导致ARID1A结合的活性调控元件区域出现H3.3的耗竭，同时经典组蛋白H3.1/H3.2的富集水平上升，且H3.3会伴随向基因区域发生重新分布。ARID1A与阻遏性染色质重塑因子CHD4（NuRD）的互作与H3.3存在关联，且ARID1A是CHD4被招募至H3.3区域所必需的。ZMYND8可与CHD4发生互作，以抑制ARID1A、CHD4与ZMYND8共同结合的、带有H3.3+ H4K16ac+标记的超级增强子的一部分，这些增强子位于调控细胞外基质、细胞运动、黏附以及上皮间质转化（epithelial-to-mesenchymal transition）的基因附近。此外，上述基因表达变化在人子宫内膜异位囊肿中也可被观测到。
结论：本研究证实，携带ARID1A的BAF复合物对于维持活性调控元件（如超级增强子）处的组蛋白变体H3.3水平至关重要，而该功能也是其他染色质重塑因子发挥生理相关活性所必需的。
整体实验设计：本研究通过染色质免疫共沉淀测序（chromatin immunoprecipitation followed by sequencing, ChIP-seq），对人12Z子宫内膜异位上皮细胞的全基因组CHD4结合情况进行了检测。