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为任何类型的胎儿细胞之间保持微妙的平衡。对表观遗传状态的精确调控，特别是在能够诱导分化的谱系特异性发育调节器上，对于在早期发育过程中维持这种稳定状态至关重要。值得注意的是，这些基因经常被双重标记，既有激活的染色质标记，也有抑制染色质的标记，这是一种独特的染色质结构，称为二价域。然而，尽管人们有强烈的兴趣，但了解控制二价结构域建立和维护的生物学机制仍然是一个难以实现的目标。这项拟议的研究将利用高通量表观基因组学技术发现染色质调节电路在二价基因座上运行。我将使用染色质免疫沉淀和深度测序(CHIP-SEQ)来鉴定与二价基因座结合的染色质调节剂(CR)。然后，我将扰乱小鼠胚胎干细胞中的这些酶，并测量由此导致的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、组蛋白修饰和转录输出相关的功能相互依赖关系。这项研究将大大加深我们对CRS在早期发育中所起的作用的理解，特别是对负责建立、维持和解析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.