Defining epigenetic mechanisms for embryonic patterning

定义胚胎模式的表观遗传机制

• 批准号: 10211456
• 负责人: Shelby Alexander Blythe
• 金额: $ 32.6万
• 依托单位: NORTHWESTERN UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-04-01 至 2026-03-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10211456
• 关键词: ATAC-seq; Adult; Affinity Chromatography; Automobile Driving; Binding; Binding Sites; Biochemical Genetics; Biological; Cells; ChIP-seq; Chromatin; Chromatin Remodeling Factor; Competence; Complex; Development; Disease; Drosophila genus; Embryo; Embryonic Development; Enhancers; Ensure; Epigenetic Process; Event; Gene Expression Regulation; Genetic; Genetic Transcription; Genome; Genomic approach; Genomics; Goals; Grant; Human; Individual; Instruction; Knowledge; Learning; Logic; Maps; Mass Spectrum Analysis; Measurement; Measures; Mission; Modeling; Modification; Molecular; Nature; NuRD complex; Operating System; Organism; Output; Pattern; Play; Process; Regulator Genes; Regulatory Element; Research; Resources; Role; Shapes; Site; System; Testing; Therapeutic; Time; United States National Institutes of Health; biological systems; epigenetic regulation; exhaustion; genetic approach; genetic manipulation; genome-wide; innovation; loss of function; mutant; novel; operation; prevent; programs; recruit; regenerative biology; regenerative therapy; stem; stem cell biology; stem cell therapy; time use; transcription factor

Project Summary: The developmental program encodes mechanisms that shape the chromatin landscape and drive large-scale transitions in its organization, but the mechanisms whereby these changes are integrated into embryonic pat- terning systems remain unclear. The genetic program that directs the initial patterning of the Drosophila embryo has been exhaustively characterized, and many of the cis-regulatory elements whereby transcription factors pat- tern the embryo have been identified. However, only recently has the field been able to measure changes in chro- matin accessibility and occupancy with sufficient sensitivity to observe that these mechanisms are dynamic and play critical yet underappreciated roles in development. Cis-regulatory elements are not static in their chromatin state but instead change accessibility and modification status as a function of progression through the develop- mental program. Interfering with the temporal progression of chromatin states disrupts embryonic patterning. This project seeks to identify how patterning systems choreograph changes in epigenetic state to further under- stand how this contributes to the regulatory logic of embryogenesis. The objective of this project is to evaluate the impact of regulated chromatin states on the operation of a model gene regulatory network critical for Dro- sophila segmentation, and to investigate in detail the mechanism whereby one component of the network pio- neers open chromatin states. The central hypothesis is that regulatory networks employ transcription factors whose primary role is to modulate accessibility states, and that this enables networks to generate more complex patterns from a limited set of input factors. This project is justified through the rationale that the Drosophila system provides unmatched resources for performing time-resolved genome-wide measurements of transcrip- tion factor occupancy and chromatin accessibility in addition to allowing for the genetic manipulation of these components for the comprehensive examination of dynamic chromatin states in the context of a developmentally relevant regulatory network. The first aim will determine through the use of time-resolved ChIP- and ATAC-seq on wild-type and mutant embryos the influence of chromatin accessibility on the binding site selection for all transcription factors operating within a model gene regulatory network. The second aim will focus through the use of a combination of biochemical, genetic, and genomic approaches on the molecular mechanism for pioneer- ing chromatin accessibility by one component of the network. The third aim will investigate through the use of genetics and genomics how the embryo determines a period of competence for certain regulatory elements to be granted accessibility. The significance of this proposal stems from the innovation to further the understanding of epigenetic mechanisms of gene regulation within the broader framework of regulatory networks in develop- ment in order to elucidate novel regulatory strategies for driving cell fate decisions. Because of the deep evolu- tionary conservation of most developmental regulators from Drosophila to human, this project additionally will identify factors that may function to modulate chromatin accessibility in both development and disease.

项目摘要： 发展计划编码塑造染色质景观并大规模驱动的机制 组织中的过渡，但是这些变化被整合到胚胎的机制 Terning系统尚不清楚。指导果蝇胚胎初始图案的遗传程序 已经详尽地表征了，许多顺式调节元素，这些元素的转录因子被提示 已经确定了胚胎。但是，直到最近，该领域才能够衡量CHRO的变化 Matin的可访问性和占用率具有足够的敏感性，可以观察到这些机制是动态的，并且 扮演关键但不被忽视的发展角色。顺式调节元素在其染色质中不静态 声明，而是改变可访问性和修改状态，这是通过发展的函数 心理计划。干扰染色质状态的时间进展会破坏胚胎模式。 该项目旨在确定模式系统的编排如何在表观遗传状态下变化，以进一步了解 立场如何有助于胚胎发生的调节逻辑。该项目的目的是评估 受调节的染色质状态对模型基因调节网络的运行的影响至关重要 Sophila分割，并详细研究网络pio-一个组成部分的机制 NEERS开放染色质状态。中心假设是监管网络采用转录因子 其主要作用是调节可访问性状态，并且该网络能够生成更复杂的 来自有限的输入因素的模式。通过果蝇的理由证明了这个项目是合理的 系统提供了无与伦比的资源来执行跨基因组全基因组的测量 除了允许对这些操纵的基因操纵之外 在发育中对动态染色质态进行全面检查的组件 相关的监管网络。第一个目标将通过使用时间分辨的芯片和ATAC-SEQ来确定 在野生型和突变胚胎上，染色质可及性对所有人的结合位点选择的影响 在模型基因调节网络中运行的转录因子。第二个目标将集中在 使用生化，遗传和基因组方法的结合在先驱分子机制上 由网络的一个组成部分添加染色质访问性。第三个目标将通过使用 遗传学和基因组学如何确定某些调节元素的能力时期 授予可访问性。该提案的意义源于创新以进一步的理解 基因调节的表观遗传机制在更广泛的调节网络框架内 为了阐明驱动细胞命运决策的新型监管策略。因为深 从果蝇到人类的大多数发育监管机构的保存，此项目还将 确定可能在发育和疾病中调节染色质可及性的因素。