The chromatin regulatory circuitry of bivalent domains

描述（申请人提供）：胚胎干细胞在多能自我更新和定向分化成任何胎儿细胞类型之间保持着微妙的平衡。表观遗传状态的精确调控，特别是谱系特异性发育调控，可以诱导分化，是在早期发育期间维持这种平衡状态的关键。值得注意的是，这些基因通常具有激活和抑制染色质标记的双重标记，这是一种称为二价结构域的独特染色质结构。然而，了解控制二价结构域的建立和维持的生物学机制仍然是一个难以捉摸的目标，尽管有强烈的兴趣。提出的研究将利用高通量表观基因组学技术发现在二价位点上运行的染色质调控电路。我将通过染色质免疫沉淀和深度测序（ChIP-seq）鉴定与二价位点结合的染色质调节因子（CR）。然后，我将干扰小鼠胚胎干细胞中的这些酶，并测量染色质状态和基因表达的变化。将这些数据集整合在一起，我将应用概率图形建模技术来发现与染色质调节因子、组蛋白修饰和转录输出相关的功能相互依赖性。这项研究将大大提高我们对CRs在早期发育中的作用的理解，特别是对建立、维持和解决二价结构域的调控机制的理解。

DESCRIPTION (provided by applicant): Embryonic stem cells maintain a delicate balance between pluripotent self-renewal and directed differentiation into any fetus cell type. Precise regulation of epigenetic state, particularly at lineage-specific developmental regulators which can induce differentiation, is crucial to maintaining this poised state during early development. Remarkably, these genes are often dually marked with both activating and repressive chromatin marks, a unique chromatin structure known as a bivalent domain. Understanding the biological mechanisms governing the setup and maintenance of bivalent domains however, has remained an elusive goal despite intense interest. The proposed research will discover the chromatin regulator circuitry operating at bivalent loci using high-throughput epigenomics technologies. I will identify chromatin regulators (CR) which bind to bivalent loci by using chromatin immunoprecipitation followed by deep sequencing (ChIP-seq). I will then perturb these enzymes in mouse embryonic stem cells and measure the resulting changes in both chromatin state and gene expression. Integrating these datasets together, I will apply probabilistic graphical modeling techniques to discover functional interdependencies relating chromatin regulators, histone modifications, and transcriptional output. This study will substantially enhance our understanding of the role CRs perform in early development, and in particular, the regulatory mechanisms responsible for establishing, maintaining, and resolving bivalent domains.