A dual role for CDK-Mediator in controlling Polycomb-dependent topology and priming genes for induction [Hi-C]. 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. Overall design: 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正常发育至关重要。据推测，该过程依赖于能够实现基因启动子与其他调控元件间通信的调控机制。在胚胎干细胞（embryonic stem cells, ESCs）中，已有研究表明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，同时为分化过程中的基因诱导激活做好预准备。本研究发现，CDK-MED在ESCs中对全基因组整体组织的贡献微乎其微，但有趣的是，其在调控由多梳抑制复合物（Polycomb repressive complexes, PRCs）结合的非活性基因调控元件之间的相互作用时，发挥着特定且不可或缺的作用。这类相互作用由CDK-MED介导，但依赖于经典PRC1（canonical PRC1）。然而，通过功能分离实验，本研究揭示：CDK-MED与经典PRC1（cPRC1）在构建长程相互作用中的协同作用，并非用于为分化过程中的基因诱导激活做好预准备。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模块可支持核心Mediator与基因启动子的结合，从而助力基因激活。实验整体设计：在可条件性敲除CDK-MED复合物的Med13/13l fl/fl ESCs中，检测多梳蛋白（经典PRC1与H3K27me3）、CDK-Mediator（CDK8）以及核心Mediator（MED14）的全基因组分布谱；在可条件性敲除经典PRC1的Pcgf4-/-Pcgf2 fl/fl ESCs中，检测CDK-Mediator（CDK8）的全基因组分布谱。