Chemical Genomics Paradigm for Epigenetic Regulation

描述(申请人提供)：后基因组生物医学研究的重大挑战是将编码在人类基因组的基因和基因产物中的信息转化为对它们在细胞生理学和病理生理学中的功能的理解，并转化为新的医学方法。然而，我们目前对遗传信息的调节和转导的知识有限，这些遗传信息被认为是由不在基因组DNA序列中编码的可遗传信息控制的--这是表观遗传学的本质。我们研究的长期目标是开发创新的工具和技术，用于人类基因组表观遗传调控的基因组规模研究。最近的研究表明，响应生理和环境刺激的基因激活或沉默是由DNA的化学修饰(即胞嘧啶的甲基化)和染色体上DNA包装的组蛋白的化学修饰(即乙酰化、甲基化、磷酸化和泛素化)决定的。一个统一的模型已经出现，提出了一个嵌入染色质中的“表观遗传密码”，它表示不同的核活动区域，如异染色质形成或转录激活。这个神秘的密码是由染色质修饰酶建立的，并由以修饰敏感的方式与染色质结合的蛋白质解释。甲基-CpG结合域、组蛋白中“读取”乙酰赖氨酸的溴域以及甲基赖氨酸的色素域或PhD指的发现为这一工作假说提供了支持的证据。为了理解控制表观遗传基因调控的基本原理，需要新的方法和创新的工具来研究与表观遗传调控相关的全基因组条件下的染色体蛋白质。为了实现这一目标，我们建议开发一种新的化学基因组学范式，用于基于结构的组蛋白结合蛋白小分子探针的功能设计。这一范式依赖于一套连贯的结构和化学生物学以及分子/细胞染色质生物学的实验和计算方法，这些方法是在专注于该系统研究的关键研究人员的合作下开发的。随着配基设计与表观遗传控制中染色体蛋白质全基因组功能图谱的结合，我们称之为化学表观基因组学。我们预计，从这项研究中出现的新的化学工具和技术将有助于解决诸如组蛋白修饰如何导致染色质在引导基因沉默或激活方面的调节能力等问题。我们的目标是实现以下三个具体目标： 1.组蛋白识别中染色体蛋白结构域的全基因组图谱 2.基于结构的化学探针功能设计 3.组蛋白导向染色质生物学的化学表观基因组学研究 与公共健康相关：人类基因组遗传信息的调节和转导，尽管有近完整的基因组序列信息，但我们目前的知识有限，不仅受DNA序列中编码的信息支配，而且受DNA复杂化学修饰中可遗传的表观遗传信息以及染色体DNA包装组蛋白的支配。在这个项目中，我们建议开发创新的工具和技术，以在基因组水平上产生关于染色体蛋白质结构-功能和机制的大量新知识，并开发新的选择性小分子化学探针，以便能够研究内源形式的染色体蛋白质的生物功能，以及在与表观基因调控有关的生理条件下的一种新的基因组研究范式，我们称之为化学表观基因组学。我们预计，组蛋白导向的染色质生物学的化学表观基因组学研究的新推论将对进一步的研究产生广泛的影响，从对基本人类表观遗传学、干细胞身份和命运的新理解，到针对人类疾病的新表观遗传疗法的新发展。

DESCRIPTION (provided by applicant): The grand challenge in post genomic biomedical research is to translate the information encoded in genes and gene products of the human genome into an understanding of their functions in cellular physiology and patho- physiology, and into new approaches to medicine. However, our current knowledge is limited about the regulation and transduction of the genetic information that is believed to be governed by heritable information not encoded in the genomic DNA sequence - the essence of epigenetics. The long-term goal of our research is to develop innovative tools and technologies for the genomic scale study of epigenetic regulation of the human genome. Recent studies show that gene activation or silencing in response to physiological and environmental stimuli is dictated by chemical modifications of the DNA (i.e. methylation of cytosine) and of the chromosomal DNA-packing histones (i.e. acetylation, methylation, phosphorylation and ubiquitination). A unifying model has emerged to suggest an "epigenetic code" embedded in chromatin that signifies regions of distinct nuclear activities such as heterochromatin formation or transcriptional activation. This enigmatic code is established by chromatin modifying enzymes and interpreted by proteins that bind the chromatin in a modification-sensitive manner. The discovery of the methyl-CpG binding domain, the bromodomain that "reads" acetyl-lysine in histones, and the chromodomain or the PHD finger for methyl-lysine provides supporting evidence for this working hypothesis. To understand the fundamental principles that govern epigenetic gene regulation, new methodologies and innovative tools are needed for genome-wide investigation of chromosomal proteins in physiological conditions as pertained to the epigenetic regulation. Towards this goal, we propose to develop a new chemical genomics paradigm for structure-based functional design of small-molecule probes for histone binding proteins. This paradigm relies on a coherent set of experimental and computational methods of structural and chemical biology, and molecular/cell chromatin biology that are being developed in collaborations among the key investigators focused on the study of this system. As the new paradigm couples ligand design to genome-wide functional profiling of chromosomal proteins in epigenetic control, we term it Chemical Epigenomics. We expect that the new chemical tools and technologies emerging from this study will help address questions such as how histone modifications lead to regulatory capabilities of the chromatin in directing gene silencing or activation. We aim to attain the following three Specific Aims: 1. Genome-wide profiling of chromosomal protein domains in histone recognition 2. Structure-based functional design of chemical probes 3. Chemical epigenomics study of histone-directed chromatin biology PUBLIC HEALTH RELEVANCE: The regulation and transduction of genetic information of the human genome, of which our current knowledge is limited despite the available near complete genome sequence information, is governed by information not only encoded in the DNA sequence, but also by the epigenetic information that is heritable in the complex chemical modifications of the DNA as well as the chromosomal DNA-packing histones. In this project, we propose to develop innovative tools and technologies that are required for the generation of an extremely large amount of new knowledge on structure-function and mechanisms of chromosomal proteins on the genomic scale, and also the means to develop novel selective small-molecule chemical probes to enable investigation of biological functions of chromosomal proteins in their endogenous forms and under physiological conditions as pertained to the epigenetic gene regulation a new genomics research paradigm we term Chemical Epigenomics. We expect that the emerging inferences on the Chemical Epigenomics study of the histone- directed chromatin biology have broad implications on further investigations that range from new understanding of the fundamental human epigenetics, stem cell identity and fate to the new development of novel epigenetic therapies to human disease.