Using ChAP-MS to Study Macromolecular Chromatin Composition during Transcription

描述（由申请人提供）：染色体是真核细胞中组成最多样化的结构之一。大量的大分子蛋白相互作用必须正确地发生在染色质上，以驱动染色体生物学的功能方面，如基因转录、DNA复制、重组、修复和姐妹染色单体分离。重要的是，PTM状态的不必要改变和调节染色质代谢的酶机制的缺陷与包括癌症在内的多种表观遗传疾病有关。然而，分析蛋白质组装如何在体内与染色质相互作用以指导这些活动仍然是一个重大挑战，因为它们的关联具有时间和动态性质。在过去的6年里，Taverna和Tackett实验室在染色质背景下对大分子蛋白相互作用的体内分析一直是主要的合作重点。同时，利用我们小组的互补技能，我们开发了新的工具来明确识别染色质上大分子复合物的蛋白质-蛋白质相互作用。最重要的是，我们的共同努力最近达到了一种称为质谱染色质亲和纯化或chapp - ms的技术的发展。chapp - ms提供了一个独特的1 kb染色体片段的富集，用于大分子蛋白相互作用和相关组蛋白翻译后修饰的位点特异性鉴定。在人类细胞中建立chapp - ms将使我们能够前所未有地深入了解哺乳动物的转录调控以及人类疾病中的表观遗传失调，以及治疗方法的潜在作用机制。在这一提议中，我们假设chapp - ms可以适用于人类细胞培养和组织，为体内大分子蛋白相互作用的分析提供一种新的工具。我们的短期目标是将chapm - ms应用于人类细胞系和组织，而我们的长期目标是将其应用于动物模型，如小鼠，并使用chapm - ms在整个染色体上进行分析。为了验证我们的假设并朝着我们的短期目标努力，我们将追求以下三个目标：(1)开发和应用chapp - ms来分析哺乳动物细胞系中活跃转录基因的大分子染色质组成；(2)开发chapp - ms的反义富集程序；(3)多重chapp - ms在哺乳动物细胞和组织中的应用。

DESCRIPTION (provided by applicant): One of the most compositionally diverse structures in a eukaryotic cell is a chromosome. A multitude of macromolecular protein interactions must properly occur on chromatin to drive functional aspects of chromosome biology like gene transcription, DNA replication, recombination, repair, and sister chromatid segregation. Importantly, unwanted alterations in PTM states and defects in the enzymatic machineries that regulate chromatin metabolism are linked to a wide variety of illnesses and diseases that are epigenetic in scope, including cancer. However, analyzing how protein assemblies interact in vivo with chromatin to direct these activities remains a significant challenge due to the temporal and dynamic nature of their associations. The in vivo analysis of macromolecular protein interactions in the context of chromatin has been a primary collaborative focus of the Taverna and Tackett laboratories for the last 6 years. Together, using the complementary skill sets of our groups, we have developed novel tools to unambiguously identify protein- protein interactions of macromolecular complexes on chromatin. Most importantly, our combined efforts recently culminated in the development of a technique termed Chromatin Affinity Purification with Mass Spectrometry or ChAP-MS. ChAP-MS provides for the enrichment of a unique 1 kb section of a chromosome for site-specific identification of macromolecular protein interactions and associated histone posttranslational modifications. The establishment of ChAP-MS in human cells will permit unprecedented insight into mammalian transcription regulation as well as epigenetic disregulation in human disease, and potentially mechanisms of action for therapeutics. In this proposal, we hypothesize that ChAP-MS can be adapted to human cell culture and tissues to provide a novel tool for the analysis of in vivo macromolecular protein interactions. Our short-term goal is to apply ChAP-MS to human cell lines and tissues, while our long-term goal is to move development into animal models like mice and to use ChAP-MS to profile across an entire chromosome. To test our hypothesis and work towards our short term goal, we will pursue the following three Aims: (1) Develop and Apply ChAP-MS for the analysis of macromolecular chromatin composition at actively transcribing genes in mammalian cell lines, (2) Develop an antisense enrichment procedure for ChAP-MS and (3) Application of Multiplex ChAP-MS in mammalian cells and tissues.