Mechanism of Chromatin Organization and Dynamics in Development

描述（由申请人提供）：表观遗传特征的建立和维持在发育、生理和疾病中的基因表达调控中发挥重要作用。我们的建议侧重于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，以及它们如何反过来受到转录的影响。模式生物斑马鱼是解决这些问题的独特脊椎动物系统。在母合子转换（MZT）之前，早期斑马鱼胚胎的基因组不被转录，也不被组蛋白标记（如H3 K4 me 3或H3 K27 me 3）占据。因此，该系统允许研究从非转录到转录的基因组的转变。此外，可以收集大量阶段同步化的胚胎用于基因组学实验。我们建议使用RNA-seq，Pol II和组蛋白标记ChIP-seq，以及在斑马鱼MZT期间转录开始之前，期间和之后的nucleosome-seq来回答以下问题：（1）哪些基因在斑马鱼早期胚胎发育中是母系负载的，而不是合子表达的？(2)当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是如何相关的，以及它们与母源装载转录因子和合子表达转录因子的存在是如何相关的？(3)内在DNA序列、组蛋白标记的建立、Pol II结合、转录起始和延伸对核小体在体内的定位有什么影响？总的来说，该项目将提供深入了解基因调控和胚胎发育中表观遗传特征的建立和维持之间的相互关系。

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.