A dual role for CDK-Mediator in controlling Polycomb-dependent topology and priming genes for induction [Hi-C]

Precise control of gene expression is essential for normal development. This is thought to rely on mechanisms that enable communication between gene promoters and other regulatory elements. In embryonic stem cells (ESCs) the CDK-Mediator (CDK-MED) complex has been reported to topologically link gene regulatory elements to enable gene expression and also prime genes for induction during differentiation. Here we discover that CDK-MED contributes little to overall genome organisation in ESCs, but interestingly has a specific and essential role in controlling interactions between inactive gene regulatory elements bound by the Polycomb repressive complexes (PRCs). These interactions are facilitated by CDK-MED but rely on canonical PRC1. However, through separation of function experiments, we reveal that the collaboration between CDK-MED and cPRC1 in creating long-range interactions does not function to prime genes for induction during differentiation. Instead, we discover that priming relies on a topology-independent mechanism whereby the CDK module supports core Mediator engagement with gene promoters to support gene activation. Pofile of genomic distribution of Polycomb (canonical PRC1 and H3K27me3), CDK-Mediator (CDK8) and core Mediator (MED14) was profiled in Med13/13l fl/fl ESCs, in which the CDK-Mediator can be conditionally depleted. Pofile of genomic distribution of CDK-Mediator (CDK8) was profiled in Pcgf4-/-Pcgf2 fl/fl ESCs, in which the canonical PRC1 can be conditionally depleted.

精准调控基因表达对于生物体正常发育至关重要。现有研究表明，该过程依赖于能够实现基因启动子与其他调控元件之间通讯的分子机制。已有研究报道，在胚胎干细胞（embryonic stem cells, ESCs）中，CDK-中介体（CDK-Mediator, CDK-MED）复合物可通过拓扑连接基因调控元件以介导基因表达，并为分化过程中的基因诱导预作准备。本研究发现，在ESCs中，CDK-MED复合物对整体基因组组织的贡献甚微，但值得关注的是，其在调控由多梳抑制复合体（Polycomb repressive complexes, PRCs）结合的非活性基因调控元件之间的相互作用方面，发挥着特异性且不可或缺的作用。该类相互作用由CDK-MED复合物介导，但依赖于经典多梳抑制复合体1（canonical PRC1）。然而，通过功能分离实验，我们揭示：CDK-MED与cPRC1协同形成远程相互作用的功能，并非用于在分化过程中为基因诱导预作准备。与之相反，本研究发现基因预激活依赖于一种不依赖于拓扑结构的机制：即CDK亚模块可支持核心中介体与基因启动子结合，从而介导基因激活。我们在可条件性敲除CDK-MED复合物的Med13/13l fl/fl胚胎干细胞中，对多梳蛋白（经典PRC1与组蛋白H3第27位三甲基化（H3K27me3））、CDK-中介体（CDK8）以及核心中介体（MED14）的基因组分布特征进行了分析。此外，我们在可条件性敲除经典PRC1的Pcgf4-/-Pcgf2 fl/fl胚胎干细胞中，对CDK-中介体（CDK8）的基因组分布特征进行了分析。