BET inhibition disrupts transcription but retains enhancer-promoter contact [Capture-C]. BET inhibition disrupts transcription but retains enhancer-promoter contact [Capture-C]

Enhancers are DNA sequences that enable complex temporal and tissue-specific regulation of genes in higher eukaryotes. Although it is not entirely clear how enhancer-promoter interactions can increase gene expression, this proximity has been observed in multiple systems at multiple loci and is thought to be essential for the maintenance of gene expression. Bromodomain and Extra-Terminal domain (BET) and Mediator proteins have been shown capable of forming phase condensates and are thought to be essential for super-enhancer function. Here, we show that targeting of cells with inhibitors of BET proteins or pharmacological degradation of BET protein Bromodomain-containing protein 4 (BRD4) has a strong impact on transcription but very little impact on enhancer-promoter interactions. Dissolving phase condensates reduces BRD4 and Mediator binding at enhancers and can also strongly affect gene transcription, without disrupting enhancer-promoter interactions. These results suggest that activation of transcription and maintenance of enhancer-promoter interactions are separable events. Our findings further indicate that enhancer-promoter interactions are not dependent on high levels of BRD4 and Mediator, and are likely maintained by a complex set of factors including additional activator complexes and, at some sites, CTCF and cohesin. Overall design: Next generation Capture-C

增强子（enhancer）是一类可介导高等真核生物基因进行复杂时空特异性与组织特异性调控的DNA序列。目前学界尚未完全明确增强子-启动子相互作用提升基因表达的具体机制，但这种邻近关联已在多个系统、多个基因座中被观测到，且被认为对维持基因表达至关重要。溴结构域与额外末端结构域（Bromodomain and Extra-Terminal domain, BET）蛋白及中介体（Mediator）蛋白已被证实可形成相分离凝聚体，且被认为是超级增强子发挥功能的必需组分。本研究显示，采用BET蛋白抑制剂处理细胞，或对BET家族蛋白中的含溴结构域蛋白4（Bromodomain-containing protein 4, BRD4）进行药物降解，会对基因转录产生显著影响，但对增强子-启动子相互作用几乎无作用。解离相分离凝聚体会降低增强子区域的BRD4与中介体结合水平，同时也能强烈影响基因转录，但不会破坏增强子-启动子相互作用。上述结果表明，转录激活与增强子-启动子相互作用的维持是两个可分离的独立过程。本研究进一步指出，增强子-启动子相互作用并不依赖于高水平的BRD4与中介体蛋白，其维持可能依赖于包括其他激活复合物在内的复杂因子网络，在部分位点还涉及CTCF与黏连蛋白（cohesin）。整体实验设计：新一代捕获测序（Capture-C）