Combinatorial Regulation of Gene Networks During Cardiac Development and Disease

心脏发育和疾病过程中基因网络的组合调控

• 批准号: 10245023
• 负责人: DEEPAK SRIVASTAVA
• 金额: $ 273.2万
• 依托单位: J. DAVID GLADSTONE INSTITUTES
• 依托单位国家: 美国
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-09-01 至 2024-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10245023
• 关键词: 3-Dimensional; Address; Adult; Anatomy; Architecture; Bioinformatics; CRISPR/Cas technology; Cardiac; Cardiac Myocytes; Cardiac development; Cardiovascular Diseases; Cells; Chromatin; Chromatin Remodeling Factor; Chromatin Structure; Code; Complex; Congenital Abnormality; Congenital Heart Defects; DNA; DNA Binding; Data Set; Development; Dimerization; GATA4 gene; Gene Expression; Gene Expression Regulation; Genes; Genetic Transcription; Genome; Genome engineering; Genomics; Heart Diseases; Heart failure; Human; Intervention; Knowledge; Location; Morphogenesis; Mutate; Mutation; Nuclear; Nuclear Pore Complex; Nuclear Pore Complex Proteins; Output; Paper; Play; Post-Translational Protein Processing; Process; Program Research Project Grants; Proteins; Proteomics; Publishing; Reading; Regenerative Medicine; Regulation; Repression; Role; Signal Transduction; Specificity; System; Testing; Transcription Factor 3; Transcriptional Regulation; cardiogenesis; causal variant; chromatin remodeling; combinatorial; congenital heart disorder; disease-causing mutation; genome-wide; genomic locus; human disease; induced pluripotent stem cell; interest; member; mortality; multidisciplinary; myocardin; protein protein interaction; recruit; regenerative cell; synergism; transcription factor

PROJECT SUMMARY/ABSTRACT OVERALL COMPONENT Cardiovascular disease is the most common cause of mortality in adults, and congenital heart defects (CHDs) are the most common form of birth defects. An important concept that has emerged in recent years is that dysregulation of cardiac transcription factor (TF) networks and related chromatin remodeling machinery contributes to CHDs and heart failure. Forced expression of the core members of the TF network is sufficient to reprogram non-myocytes into cardiomyocyte-like cells for regenerative medicine purposes, suggesting a combinatorial code for determining cell fate. As genome-wide roles for critical TFs are being discovered, a conceptual understanding of their function in higher order DNA organization is emerging. Evidence that the three-dimensional organization of DNA promotes activation or repression of genomic loci has raised the question of how cooperative protein-protein interactions involving TF and chromatin remodeling complexes participate in this process. We have integrated a multidisciplinary team of developmental cardiologists, computational biologists, and systems biologists, with expertise in CRISPR/Cas9 genome engineering in human iPS cells, to investigate how the genome is regulated by TFs and chromatin remodelers to control cardiac gene expression and fate. The specific hypotheses that we test in this proposal, which involve a combination of core cardiac TFs that interact with one another to coordinately regulate cardiac gene expression, are as follows: 1) that the cardiac TFs GATA4 and TBX5 interact in a lineage-specific fashion with the nuclear pore complex to regulate the 3D genomic architecture and subsequent transcriptional output; 2) that specific BAF chromatin remodeling complexes form dynamically to coordinate regulation of distinct aspects of cardiac morphogenesis and lineage decisions through interaction with cardiac TFs; and 3) that the MEF2C-myocardin complex, which interacts with GATA4, TBX5 and BAF60c, recruits a transcriptional complex influenced by upstream signaling and myocardin dimerization to regulate cardiac gene expression. To address these questions, we have integrated unique expertise in the study of protein-protein interactions and post-translational modifications through the Advanced Proteomics Core; the ability to analyze complex datasets of PPIs, DNA-binding, and transcriptional output related to transcriptional regulators through the Advanced Bioinformatics Core; and the ability to leverage state-of-the-art genome engineering approaches through the Genome Engineering Core. The questions in this proposal will be studied in the context of human disease-causing mutations to reveal underlying mechanisms and paradigms that control normal and abnormal cardiogenesis. The integrated knowledge developed here will enable a clear reading of the transcriptional “code” for cardiac cell fate determination and differentiation that may be leveraged for interventions in CHD and for regenerative medicine.

项目概要/摘要 整体组成 心血管疾病是成人死亡的最常见原因，而先天性心脏缺陷 (CHD) 是最常见的出生缺陷形式。近年来出现的一个重要概念是 心脏转录因子 (TF) 网络和相关染色质重塑机制的失调 导致冠心病和心力衰竭。 TF网络核心成员的强行表达足以 将非心肌细胞重新编程为心肌细胞样细胞以用于再生医学目的，这表明 用于确定细胞命运的组合代码。随着关键转录因子在全基因组范围内的作用不断被发现， 对它们在高阶 DNA 组织中的功能的概念性理解正在出现。有证据表明 DNA 的三维组织促进基因组位点的激活或抑制 涉及 TF 和染色质重塑复合物的蛋白质-蛋白质相互作用如何协同的问题 参与这个过程。我们整合了一支由发育心脏病学家组成的多学科团队， 计算生物学家和系统生物学家，拥有 CRISPR/Cas9 基因组工程方面的专业知识 人类 iPS 细胞，研究基因组如何受 TF 和染色质重塑因子的调控来控制 心脏基因表达和命运。我们在本提案中测试的具体假设涉及 核心心脏 TF 的组合，彼此相互作用以协调调节心脏基因 表达，如下：1）心脏转录因子 GATA4 和 TBX5 以谱系特异性方式与 核孔复合体调节 3D 基因组结构和随后的转录输出； 2） 特定的 BAF 染色质重塑复合物动态形成，以协调不同的调节 通过与心脏 TF 相互作用来了解心脏形态发生和谱系决策的各个方面； 3） MEF2C-心肌素复合物与 GATA4、TBX5 和 BAF60c 相互作用，招募转录因子 复合物受上游信号传导和心肌蛋白二聚化的影响来调节心脏基因表达。 为了解决这些问题，我们整合了蛋白质-蛋白质相互作用研究方面的独特专业知识 以及通过高级蛋白质组学核心进行翻译后修饰；分析复杂的能力 与转录调节因子相关的 PPI、DNA 结合和转录输出数据集 高级生物信息学核心；以及利用最先进的基因组工程方法的能力 通过基因组工程核心。该提案中的问题将在人类的背景下进行研究 致病突变揭示控制正常和异常的潜在机制和范式 心脏发生。这里开发的综合知识将使您能够清晰地阅读转录内容 心肌细胞命运决定和分化的“代码”可用于干预冠心病和 用于再生医学。