Systems Analysis of Cardiac Chromatin Structure

心脏染色质结构的系统分析

• 批准号: 9091598
• 负责人: Thomas M. Vondriska
• 金额: $ 38.5万
• 依托单位: UNIVERSITY OF CALIFORNIA LOS ANGELES
• 依托单位国家: 美国
• 财政年份: 2012
• 资助国家: 美国
• 起止时间: 2012-07-24 至 2018-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9091598
• 关键词: Adult; Affect; Binding Proteins; Binding Sites; Biological Models; Cardiac; Cardiac Myocytes; Cardiac development; Cardiovascular Diseases; Cell Nucleus; Cell Size; Cell Survival; Cells; ChIP-seq; Chromatin; Chromatin Modeling; Chromatin Structure; Clinical; Complex; Computer Analysis; CpG Islands; DNA Sequence; DNA-Directed RNA Polymerase; Data; Development; Dimensions; Disease; Embryo; Enhancers; Environment; Enzymes; Event; Exons; Family; Family member; Figs - dietary; Fishes; Fluorescent in Situ Hybridization; Future; Gene Activation; Gene Expression; Gene Expression Process; Generations; Genes; Genome; Genomics; Goals; Grant; HMGB Proteins; Health; Heart; Heart Diseases; Heart failure; Higher Order Chromatin Structure; Histone H1; Histone H1(s); Histones; Human; Individual; Injury; Intercistronic Region; Interphase; Introns; Length; Linker DNA; Measurement; Microscopy; Mitosis; Morphology; Mus; Muscle Cells; Nucleosomes; Phenotype; Play; Post-Translational Protein Processing; Process; Protein Family; Protein Isoforms; Proteins; Proteomics; Publishing; Regulation; Resolution; Role; SPT6 Protein; Site; Small Interfering RNA; Specificity; Stimulus; Structure; System; Systems Analysis; Testing; Variant; Vertebral column; Work; Zebrafish; base; chromatin immunoprecipitation; chromatin remodeling; fetal; genome-wide; in vivo; insight; interest; knock-down; loss of function; microscopic imaging; mouse development; mouse model; novel; overexpression; pressure; response; screening; text searching; transcription factor

DESCRIPTION (provided by applicant): What the interphase genome looks like in vivo is unknown. Advances in sequencing over the last decade have provided new insight into sequence variants (and their expression); yet how the genome is organized in three dimensions, apart from the well-described machinations of mitosis, is only beginning to be understood. Adult cardiac myocytes reside primarily in interphase but are capable of large-scale changes in gene expression. Transcription factors, histone modifying enzymes and RNA polymerase complexes play a central role in the process of global gene expression; however, an equally important and less explored factor is endogenous chromatin structure. To be transcribed, a gene's local environment must be accessible for protein binding. The objective of this grant is to understand how this phenomenon is integrated on a genome- wide scale: how is the genome appropriately poised to have the right genes on and off under basal conditions, and what are the mechanisms that globally reorganize chromatin following a stimulus (e.g. during disease)? Heart failure involves large-scale gene expression changes, including reactivation of genes normally silenced during development. Our data from an in vivo mouse model of pressure overload show alterations in abundance and localization of chromatin structural proteins from the linker histone H1 and high mobility group (HMG) B families, and indicate that heart failure is associated with global reprogramming of the chromatin environment for gene activation. We seek to discover universal principles for how HMGs and linker histones control bulk chromatin rearrangement and global gene expression; therefore, we will employ zebrafish, isolated myocytes and mouse hearts as model systems. Our unifying hypothesis is that global reorganization of chromatin structure during heart failure is the result of systematic changes in the abundance, genomic localization, and protein interactions among chromatin structural proteins. We will examine how linker histones and HMGs establish the higher order structure of the genome in the cardiac nucleus and how they dynamically repackage chromatin in disease. We will use gain/loss-of-function approaches combined with super resolution STED microscopy (image chromatin packing), chromatin immunoprecipitation and DNA sequencing (localize proteins across the genome) and proteomics (determine proteins necessary for targeting). Our short-term goal is to understand the role of HMGs and linker histones in cardiac phenotype. The long-term goal is to develop an understanding of how HMGs, linker histones and other chromatin structural proteins coordinate genomic structure to facilitate specificity in gene expression. The significance in the basic realm is to develop an integrated model of chromatin packing. The significance to the clinical realm is to provide a mechanistic basis for how the genome is reprogrammed with disease, such that future therapies can target specific chromatin remodeling events.

描述（由申请人提供）：间期基因组在体内的样子是未知的。在过去的十年中，测序的进步为序列变异（及其表达）提供了新的见解;然而，除了有丝分裂的精心描述之外，基因组如何在三维空间中组织，才刚刚开始被理解。成人心肌细胞主要存在于间期，但能够大规模的基因表达的变化。转录因子、组蛋白修饰酶和RNA聚合酶复合体在全球基因表达过程中发挥着核心作用;然而，一个同样重要且较少探索的因素是内源性染色质结构。为了转录，基因的局部环境必须便于蛋白质结合。这项资助的目的是了解这种现象是如何在全基因组范围内整合的：基因组如何在基础条件下适当地保持正确的基因开启和关闭，以及在刺激后（例如，在疾病期间）全局重组染色质的机制是什么？ 心力衰竭涉及大规模的基因表达变化，包括在发育过程中通常沉默的基因的重新激活。我们的数据从体内小鼠模型的压力超负荷显示改变的丰度和本地化的染色质结构蛋白的连接组蛋白H1和高迁移率族（HMG）B家族，并表明，心力衰竭与全球重编程的染色质环境的基因激活。我们寻求发现HMG和连接组蛋白如何控制大量染色质重排和全球基因表达的普遍原则，因此，我们将采用斑马鱼，分离的肌细胞和小鼠心脏作为模型系统。 我们统一的假设是，在心力衰竭的染色质结构的全球重组是系统的变化的结果，在丰度，基因组定位，染色质结构蛋白之间的蛋白质相互作用。我们将研究连接组蛋白和HMG如何建立心核基因组的高级结构，以及它们如何在疾病中动态重新包装染色质。我们将使用获得/丧失功能的方法结合超分辨率STED显微镜（图像染色质包装），染色质免疫沉淀和DNA测序（定位整个基因组中的蛋白质）和蛋白质组学（确定靶向所需的蛋白质）。我们的短期目标是了解HMG和连接组蛋白在心脏表型中的作用。长期目标是了解HMG，连接组蛋白和其他染色质结构蛋白如何协调基因组结构，以促进基因表达的特异性。在基础领域的意义是建立一个完整的染色质包装模型。对临床领域的意义是为基因组如何随着疾病重新编程提供机制基础，使得未来的疗法可以靶向特定的染色质重塑事件。