Chemical Genomics Paradigm for Epigentic Regulation

描述（由申请人提供）：人类基因组对生理和环境刺激的基因表达是由DNA和DNA包装组蛋白以及转录因子的化学修饰决定的。这个高度复杂的生物系统通过大量不同的表观遗传修饰组合来运作，这使得我们无法用现有工具对其基本机制进行充分的研究。一个典型的例子是干细胞生物学，其中自我更新和分化之间的平衡是其染色质结构如何制定不同的转录程序来指导多能细胞行为的核心。Yamanaka利用四种转录因子Oct3/4、Sox2、Klf4和c-Myc （OSKM）将体细胞重编程为诱导多能干细胞，强调了基因转录对细胞命运的最终控制。然而，在干细胞自我更新和分化过程中，OSKM因子如何改变细胞的表观基因组，以及它们自身的表达如何受到控制，这些问题尚未得到解答。表观遗传修饰的功能效应是通过结合表观基因组读取器来实现的，如转录和染色质调节因子中存在的乙酰赖氨酸结合溴域和甲基赖氨酸结合色域。与RNA干扰或基因敲除需要去除整个蛋白质及其所有相互作用不同，小分子抑制剂（化学探针）可以去除内源性多结构域蛋白质中的单个相互作用，从而为复杂生物系统的时间扰动提供了更精细的工具。在这个多学科研究项目中，我们将为干细胞生物学中起作用的一组溴域和色域开发高亲和力和选择性的化学探针，这些化学探针可以单独（即单目标探针）或作为生物途径中的一组（即多目标探针）。我们的研究使用了一套连贯的结构/化学生物学和染色质/干细胞生物学方法，这些方法是由我们具有多学科专业知识的主要研究人员开发的。我们还将开发一个表观基因组阅读器知识库，以帮助目标分析，设计，生产和验证新的化学探针。为了实现这些目标，我们将实现以下三个具体目标：(1)基于表观遗传功能的表观基因组读取器目标分析；(2)利用目标结构导向策略开发探针；(3)干细胞生物学中基因转录调控功能背景下的探针验证。

DESCRIPTION (provided by applicant): Gene expression of the human genome in response to physiological and environmental stimuli is dictated by chemical modifications of the DNA and the DNA-packing histones, as well as transcription factors. This highly complex biological system that operates with a large number and different combinations of epigenetic modifications has defied our full investigation of its basic mechanisms with existing tools. A prime example is the biology of stem cell in which a balance between self-renewal and differentiation lies at the heart of how its chromatin structure enacts different transcriptional programs to instruct pluripotent cell behavior. Yamanaka's reprogramming of somatic cells to induced pluripotent stem cells using four transcription factors Oct3/4, Sox2, Klf4 and c-Myc (OSKM) highlights the ultimate control of cell fate by gene transcription. However, the questions on how the OSKM factors transform the cell's epigenome and how their own expression are controlled during stem cell self-renewal and differentiation are yet to be answered. The functional effects of epigenetic modifications are realized by the binding of epigenome readers such as the acetyl-lysine binding bromodomain and the methyl-lysine binding chromodomain that are present in transcription and chromatin regulators. Unlike RNA interference or gene knockout that entails the removal of an entire protein along with all its interactions, a small-molecule inhibitor (chemical probe) could remove a single interaction in a multi-domain protein in its endogenous form, thus providing a much finer tool for the temporal perturbation of the complex biological system. In this multidisciplinary research project, we will develop high affinity and selective chemical probes for a selected group of bromodomains and chromodomains that function in stem cell biology, either individually (i.e. single-target probes) or as a group in a biological pathway (i.e. multi-target probes). Our study uses a coherent set of structural/chemical biology and chromatin/stem cell biology methods being developed by our key investigators with multidisciplinary expertise. We will also develop an Epigenome Reader KnowledgeBase to aid target profiling, design, production and validation of new chemical probes. To attain these goals, we will achieve the following three specific aims: (1) Target profiling of epigenome readers based on their epigenetic functions; (2) Probe development using target structure-guided strategy; and (3) Probe validation in a functional context of gene transcriptional regulation in stem cell biology.