Systems Analysis of Cardiac Chromatin Structure

心脏染色质结构的系统分析

• 批准号: 8699830
• 负责人: Thomas M. Vondriska
• 金额: $ 37.73万
• 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 2017-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8699830
• 关键词: Adult; Affect; Binding Sites; Biological Models; Cardiac; Cardiac Myocytes; Cardiovascular Diseases; Cell Nucleus; Cell Size; Cell Survival; Cells; ChIP-seq; Chromatin; Chromatin Modeling; Chromatin Structure; Clinical; Complex; CpG Islands; DNA Sequence; DNA Sequence Rearrangement; 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; Image; 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 Binding; 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; mouse development; mouse model; novel; 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）：体内的相间基因组的外观未知。在过去十年中，测序的进步为序列变体（及其表达）提供了新的见解。然而，除了描述的有丝分裂的阴谋性外，基因组是如何在三个维度上组织的，才刚刚开始被理解。成年心肌细胞主要存在于相间，但基因表达的大规模变化。转录因子，修饰酶的组蛋白和RNA聚合酶复合物在全球基因表达过程中起着核心作用。但是，同样重要且较少的因素是内源性染色质结构。要转录，必须可以访问基因的局部环境以进行蛋白质结合。这笔赠款的目的是了解这种现象是如何在基因组中整合的：基因组如何适当地在基础条件下和关闭基础条件下正确的基因，以及在刺激后全球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重新激活。我们来自压力过载的体内小鼠模型的数据显示，从接头组蛋白H1和高迁移率组（HMG）B家族的染色质结构蛋白的定位变化，并表明心力衰竭与基因激活的染色质环境的全球重编程有关。我们试图发现HMG和接头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理；因此，我们将采用斑马鱼，孤立的肌细胞和小鼠心脏作为模型系统。 我们统一的假设是，心力衰竭期间染色质结构的全球重组是染色质结构蛋白之间丰度，基因组定位和蛋白质相互作用的系统变化的结果。我们将研究如何在心脏核中建立基因组的高阶结构以及它们如何在疾病中动态重新包装染色质。我们将使用功能/功能丧失方法以及超级分辨率STED显微镜（图像染色质填料），染色质免疫沉淀和DNA测序（遍布基因组的蛋白质）和蛋白质组学（确定靶标所需的蛋白质）。我们的短期目标是了解HMG和接头组蛋白在心脏表型中的作用。长期目标是对HMG，接头组蛋白和其他染色质结构蛋白坐标基因组结构的理解，以促进基因表达中的特异性。基本领域的重要性是开发染色质填料的集成模型。对临床领域的意义是为如何用疾病重编程基因组提供机械基础，以便未来的疗法可以针对特定的染色质重塑事件。