Mechanism of Chromatin Organization and Dynamics in Development

染色质组织机制和发育动力学

• 批准号: 8431756
• 负责人: Xiaole Shirley Liu
• 金额: $ 20.54万
• 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/8431756
• 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 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; transcriptome sequencing

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.

描述（由申请人提供）：表观遗传特征的建立和维持在调节基因表达中的发育，生理和疾病中起着重要作用。我们的建议着重于了解启动子和增强子组蛋白如何影响体内核小体定位，以及它们如何受到转录影响。斑马鱼模型是一个独特的脊椎动物系统，可以解决这些问题。在母体 - 杂种过渡（MZT）之前，早期斑马鱼胚胎的基因组没有转录，也不会被H3K4ME3或H3K27me3等组蛋白标记所占据。因此，该系统允许研究从非转录到转录基因组的过渡。此外，可以为基因组学实验收集大量分期同步胚胎。我们建议在斑马鱼MZT期间，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，以及核小体seq，以回答以下问题：（1）在Zebrafish的早期胚胎早期发育中具有母体载荷相对于Zygotine thermathernationallation：（1） （2）何时在不同的启动子和增强子上建立不同的组蛋白标记时，启动子和增强子标记如何相关，以及它们与母体负载与合子表达的转录因子的存在如何相关？ （3）固有的DNA序列，组蛋白标记的建立，POL II结合，转录起始和伸长对体内核小体定位的影响是什么？总的来说，该项目将提供有关基因调节与胚胎发育中表观遗传特征的建立和维持之间相互关系的见解。