CDK-Mediator and FBXL19 cooperate in the induction of developmental genes by promoting regulatory interactions [Native ChIP-seq]. CDK-Mediator and FBXL19 cooperate in the induction of developmental genes by promoting regulatory interactions [Native ChIP-seq]

Appropriate developmental gene regulation relies on the capacity of gene promoters to integrate inputs from distal regulatory elements, yet how this is achieved remains poorly understood. In embryonic stem cells (ESCs), a subset of silent developmental gene promoters are primed for activation by FBXL19, a CpG island binding protein, through its capacity to recruit CDK-Mediator. How mechanistically these proteins function together to prime genes for activation during differentiation is unknown. Here we discover that in mouse ESCs FBXL19 and CDK-Mediator support long-range interactions between silent gene promoters that rely on FBXL19 for their induction during differentiation and gene regulatory elements. During gene induction, these distal regulatory elements behave in an atypical manner, in that the majority do not acquire histone H3 lysine 27 acetylation and no longer interact with their target gene promoter following gene activation. Despite these atypical features, we demonstrate by targeted deletions that these distal elements are required for appropriate gene induction during differentiation. Together these discoveries demonstrate that CpG-island associated gene promoters can prime genes for activation by communicating with atypical distal gene regulatory elements to achieve appropriate gene expression. Overall design: E14 mouse embryonic stem cells were profiled for H3K4me1 using native ChIP-seq before and after RA treatment

发育基因的精准调控依赖于基因启动子整合远端调控元件输入信号的能力，但其具体实现机制至今仍不甚明晰。在胚胎干细胞（ESCs）中，一类沉默的发育基因启动子可通过FBXL19——一种CpG岛结合蛋白——招募CDK-Mediator的特性，被预激活以启动后续激活程序。目前学界尚不明确这些蛋白质在细胞分化过程中如何协同作用，为基因激活做好预准备。
本研究在小鼠胚胎干细胞中发现，FBXL19与CDK-Mediator可介导那些依赖FBXL19以在分化过程中实现诱导表达的沉默基因启动子，与远端调控元件之间形成长距离相互作用。在基因诱导过程中，这类远端调控元件呈现非典型行为：绝大多数不会获得组蛋白H3赖氨酸27乙酰化修饰，且在基因激活后不再与其靶基因启动子发生相互作用。
尽管存在这些非典型特征，我们通过靶向敲除实验证实，这些远端调控元件对于细胞分化过程中基因的正常诱导表达是必需的。综上，本研究表明，与CpG岛相关的基因启动子可通过与非典型远端基因调控元件进行通信，为基因激活做好预准备，从而实现恰当的基因表达调控。
整体实验设计：采用原生染色质免疫沉淀测序（native ChIP-seq），检测E14小鼠胚胎干细胞在视黄酸（RA）处理前后的组蛋白H3赖氨酸4单甲基化（H3K4me1）谱型。