A Mediator-cohesin axis controls heterochromatin domain formation [RNA-seq]

The genome consists of regions of transcriptionally active euchromatin and more silent heterochromatin. We reveal that the formation of heterochromatin domains requires cohesin turnover on DNA. Stabilization of cohesin on DNA through depletion of its release factor WAPL leads to a near-complete loss of heterochromatin domains. The Mediator CDK module controls heterochromatin in an opposing manner. Loss of this module leads to an almost binary partition of the genome into dense H3K9me3 domains, and regions devoid of H3K9me3 spanning the rest of the genome. By restricting the degree of heterochromatinization, the Mediator CDK module creates a transcription-permissive context that enables gene expression within heterochromatin domains. WAPL deficiency prevents the formation of heterochromatin domains, thus allowing for gene expression even in the absence of the Mediator CDK module. We propose that heterochromatin is controlled by two opposing activities, in which the Mediator CDK module and cohesin turnover must be balanced to enable the correct distribution of epigenetic marks to ensure proper gene expression. Overall design: RNA-seq

基因组包含转录活跃的常染色质（euchromatin）区域与转录沉默程度更高的异染色质（heterochromatin）区域。本研究发现，异染色质结构域的形成依赖于DNA上黏连蛋白（cohesin）的周转过程。通过敲低黏连蛋白的释放因子WAPL以稳定DNA结合的黏连蛋白，会导致异染色质结构域近乎完全消失。中介体CDK模块（Mediator CDK module）以相反的方式调控异染色质：该模块的缺失会使基因组几乎发生二元划分，一类为密集的组蛋白H3赖氨酸9三甲基化（H3K9me3）结构域，另一类则为基因组其余区域缺乏H3K9me3修饰的区段。中介体CDK模块通过限制异染色质化程度，营造出转录允许的微环境，使得异染色质结构域内部也可进行基因表达。WAPL缺陷会阻碍异染色质结构域的形成，即便在中介体CDK模块缺失的情况下，仍可允许基因表达。我们提出，异染色质受两种相互拮抗的活性调控：必须平衡中介体CDK模块与黏连蛋白周转过程，才能实现表观遗传标记的正确分布，进而保障正常的基因表达。整体实验设计：RNA测序（RNA-seq）