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. E14 mouse embryonic stem cells were profiled for H3K4me1 using native ChIP-seq before and after RA treatment

恰当的发育基因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，被预激活以响应后续激活。目前学界尚未明确这些蛋白质在分化过程中协同预激活基因的具体分子机制。本研究在小鼠胚胎干细胞中发现，FBXL19与CDK-Mediator可介导一类在分化过程中依赖FBXL19完成诱导的沉默基因启动子，与其远端调控元件之间形成长距离相互作用。在基因诱导阶段，这类远端调控元件表现出非典型特征：绝大多数不会发生组蛋白H3赖氨酸27乙酰化（H3K27ac），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性，我们通过靶向敲除实验证实，这类远端调控元件对于分化过程中正常的基因诱导不可或缺。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调控元件进行通信，实现基因的预激活以达成恰当的基因表达模式。本研究采用天然染色质免疫共沉淀测序（native ChIP-seq）技术，对经视黄酸（RA）处理前后的E14小鼠胚胎干细胞的组蛋白H3赖氨酸4单甲基化（H3K4me1）进行了检测分析。