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: 10006031
• 负责人: DEEPAK SRIVASTAVA
• 金额: $ 273.12万
• 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/10006031
• 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; 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.

项目摘要/摘要 总体组件 心血管疾病是成人死亡率最常见的原因，先天性心脏缺陷（CHD） 是先天缺陷的最常见形式。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械的失调 有助于CHD和心力衰竭。 TF网络的核心成员的强迫表达足以 重新编程非肌细胞以用于再生医学目的的心肌细胞样细胞，表明是 用于确定细胞命运的组合代码。由于正在发现关键TF的全基因组角色，因此 在高级DNA组织中对其功能的概念理解正在出现。证据表明 DNA的三维组织促进了基因组基因座的激活或表达，已提高 问题如何涉及TF和染色质重塑复合物的合作蛋白 - 蛋白质相互作用 参加此过程。我们已经整合了一个多学科的发展心脏病专家团队， 计算生物学家和系统生物学家，具有CRISPR/CAS9基因组工程专业知识 人IPS细胞，研究如何通过TFS和染色质远程调节基因组以控制 心脏基因表达和命运。我们在本提案中检验的具体假设，其中涉及 核心心脏TF相互作用以协调调节心脏基因的组合 表达如下：1）心脏TFS GATA4和TBX5以特定于谱系的方式与 核孔复合物调节3D基因组结构和随后的转录输出； 2） 该特定的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的相互作用，心脏形态发生和谱系决定的方面； 3） 与GATA4，TBX5和BAF60C相互作用的MEF2C-甲状腺素复合物招募了转录 复杂受到上游信号传导和心肌素维的影响，以调节心脏基因表达。 为了解决这些问题，我们将独特的专业知识纳入了蛋白质 - 蛋白质相互作用的研究 以及通过高级蛋白质组学核心进行翻译后修饰；分析复合物的能力 PPI，DNA结合和转录输出的数据集与转录调节器有关 先进的生物信息学核心；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 引起疾病的突变以揭示控制正常和异常的潜在机制和范例 心脏病发生。这里开发的综合知识将使能够清楚地阅读转录 用于确定心脏细胞脂肪和分化的“代码”，可以利用CHD的干预措施 用于再生医学。