Mechanism of Chromatin Organization and Dynamics in Development

染色质组织机制和发育动力学

• 批准号: 8229591
• 负责人: Xiaole Shirley Liu
• 金额: $ 26.02万
• 依托单位: DANA-FARBER CANCER INST
• 依托单位国家: 美国
• 财政年份: 2012
• 资助国家: 美国
• 起止时间: 2012-03-01 至 2014-02-28
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8229591
• 关键词: Address; Affect; Animal Model; Awareness; Binding; Bioinformatics; Biology; Cell Differentiation process; Cells; ChIP-seq; Chromatin; Collaborations; Computational Biology; DNA; DNA Sequence; Data; Development; Developmental Biology; Disease; Embryo; Embryonic Development; Enhancers; Ensure; Epigenetic Process; Event; Fertilization; Foundations; Future; Gene Activation; Gene Expression; Gene Expression Regulation; Genes; Genetic Transcription; Genome; Genomics; Goals; Histones; Human Development; Maintenance; Maps; Methylation; Modeling; Nucleosomes; Pattern; Physiology; Play; Polymerase; Positioning Attribute; RNA; RNA Polymerase II; Regenerative Medicine; Regulation; Relative (related person); Resolution; Role; Staging; System; Time; Transcript; Transcription Coactivator; Transcription Elongation; Transcription Initiation; Zebrafish; cell type; chromatin remodeling; genome-wide; histone modification; in vivo; insight; pluripotency; promoter; research study; success; transcription factor

DESCRIPTION (provided by applicant): The establishment and maintenance of epigenetic profiles play an important role in the regulation of gene expression in development, physiology, and diseases. Our proposal focuses on understanding how promoter and enhancer histone marks influence nucleosome positioning in vivo, and how in turn they are influenced by transcription. The model organism zebrafish is a unique vertebrate system to address these questions. Before the maternal-zygotic transition (MZT), the genome of early zebrafish embryos is not transcribed and is not occupied by histone marks such as H3K4me3 or H3K27me3. This system therefore allows the study of the transition from a non-transcribed to a transcribed genome. Moreover, large numbers of stage-synchronized embryos can be collected for genomics experiments. We propose to use RNA-seq, Pol II and histone mark ChIP-seq, and nucleosome-seq before, during, and after the onset of transcription during zebrafish MZT to answer the following questions: (1) which genes are maternally loaded versus zygotically expressed in zebrafish early embryonic development? (2) when are different histone marks established at different promoters and enhancers, how are promoter and enhancer marks related and how are they related to the presence of maternally loaded versus zygotically expressed transcription factors? (3) What is the effect of intrinsic DNA sequence, histone mark establishment, Pol II binding, transcription initiation and elongation on nucleosome positioning in vivo? Collectively, the project will provide insights into the interrelationship between gene regulation and the establishment and maintenance of epigenetic profiles in embryonic development. PUBLIC HEALTH RELEVANCE: Epigenetic regulation plays a central role in human development, physiology, and disease. However, little is known about when, where and how epigenetic profiles are established and maintained in early embryonic development in vertebrate systems. We propose to use zebrafish embryos during early development to understand two important aspects of epigenetic regulation - the relative timing and coordination pattern of histone mark establishment, and the positioning of nucleosomes during the onset of transcription. Insights from these experiments will not only help understand gene regulation and epigenetic establishment of pluripotency in early embryonic development, but will also inform studies on directed cell differentiation, reprogramming, and regenerative medicine.

描述（由申请人提供）：表观遗传图谱的建立和维护在发育、生理和疾病中基因表达的调节中发挥着重要作用。我们的建议重点是了解启动子和增强子组蛋白标记如何影响体内核小体定位，以及它们如何受到转录的影响。模式生物斑马鱼是解决这些问题的独特脊椎动物系统。在母本-合子转变 (MZT) 之前，早期斑马鱼胚胎的基因组不进行转录，也不被 H3K4me3 或 H3K27me3 等组蛋白标记占据。因此，该系统允许研究从非转录基因组到转录基因组的转变。此外，还可以收集大量阶段同步胚胎用于基因组学实验。我们建议在斑马鱼 MZT 转录开始之前、期间和之后使用 RNA-seq、Pol II 和组蛋白标记 ChIP-seq 以及核小体-seq 来回答以下问题：(1) 哪些基因是母源加载的，哪些基因是合子加载的在斑马鱼早期胚胎发育中表达？ (2) 不同的组蛋白标记何时在不同的启动子和增强子上建立，启动子和增强子标记如何相关，以及它们与母源负载转录因子和合子表达转录因子的存在如何相关？ (3) 内在DNA序列、组蛋白标记建立、Pol II结合、转录起始和延伸对体内核小体定位有何影响？总的来说，该项目将深入了解胚胎发育中基因调控与表观遗传图谱的建立和维护之间的相互关系。 公共卫生相关性：表观遗传调控在人类发育、生理和疾病中发挥着核心作用。然而，对于脊椎动物系统早期胚胎发育中表观遗传图谱的建立和维持的时间、地点和方式，人们知之甚少。我们建议在早期发育过程中使用斑马鱼胚胎来了解表观遗传调控的两个重要方面——组蛋白标记建立的相对时间和协调模式，以及转录开始期间核小体的定位。这些实验的见解不仅有助于了解早期胚胎发育中多能性的基因调控和表观遗传建立，而且还将为定向细胞分化、重编程和再生医学的研究提供信息。