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，但其具体实现机制仍不甚明晰。在胚胎干细胞（embryonic stem cells, ESCs）中，一类沉默的发育基因启动子可通过CpG岛（CpG island）结合蛋白FBXL19招募CDK-Mediator复合物，获得激活预编程。目前这些蛋白协同作用，在细胞分化过程中为基因激活预编程的具体分子机制仍未明确。本研究在小鼠胚胎干细胞中发现，FBXL19与CDK-Mediator可介导那些在分化过程中依赖FBXL19完成诱导的沉默基因启动子，与基因调控元件之间形成长距离相互作用。在基因诱导过程中，这些远端调控元件表现出非典型特征：绝大多数既不会获得组蛋白H3赖氨酸27乙酰化修饰，在基因激活后也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，通过靶向缺失实验我们证实，这些远端元件对于分化过程中正常的基因诱导是必需的。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，实现恰当的基因表达，从而为基因激活完成预编程。 整体实验设计：分别在视黄酸（retinoic acid, RA）处理前后，采用天然染色质免疫共沉淀测序（native ChIP-seq）技术，对E14小鼠胚胎干细胞的H3K4me1组蛋白修饰进行检测分析。