Defining epigenetic mechanisms for embryonic patterning

定义胚胎模式的表观遗传机制

• 批准号: 10376795
• 负责人: Shelby Alexander Blythe
• 金额: $ 32.3万
• 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/10376795
• 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; Regulatory Element; Research; Resources; Role; Shapes; Site; System; Testing; Therapeutic; Time; United States National Institutes of Health; biological systems; epigenetic regulation; exhaustion; gene regulatory network; 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.

项目总结： 开发计划编码了塑造染色质景观和推动大规模 组织中的过渡，但这些变化被整合到萌芽状态的机制-- 租约系统仍不清楚。指导果蝇胚胎最初形成模式的遗传程序 已经得到了详尽的表征，许多顺式调节元件通过转录因子-PAT- 胚胎已被鉴定出来。然而，直到最近，该领域才能够测量到时间的变化。 充分敏感地观察到这些机构是动态的和 在发展中发挥关键但未得到重视的作用。顺式调控元件在其染色质中不是静态的 状态，而不是将可访问性和修改状态作为在开发过程中进行的函数来更改 心理程序。干扰染色质状态的时间进程会扰乱胚胎的模式。 该项目旨在确定图案系统如何编排表观遗传状态的变化，以进一步低于- 让我们来看看这对胚胎发生的调控逻辑有何贡献。该项目的目标是评估 染色质调节状态对模型基因调控网络运行的影响。 并详细地研究了网络的一个组成部分Pio-Pio-Pio的作用机制。 从不开放染色质状态。中心假设是调控网络使用转录因子 其主要作用是调节可访问性状态，这使网络能够产生更复杂的 来自一组有限的输入因素的模式。这个项目是合理的，因为果蝇 系统为进行时间分辨的全基因组转录测量提供了无与伦比的资源 占有率和染色质可及性，此外还允许这些基因的操纵 用于在发育过程中全面检查动态染色质状态的组件 相关监管网络。第一个目标将通过使用时间分辨芯片和atac-seq来确定。 野生型和突变型胚胎染色质可及性对ALL结合部位选择的影响 转录因子在模型基因调控网络中运行。第二个目标将通过 结合生物化学、遗传学和基因组学方法研究先驱者的分子机制。 ING染色质可由网络的一个组件访问。第三个目标将通过使用 遗传学和基因组学胚胎如何决定某些调控元件的适用期 授予可访问性。这一建议的意义源于对深化认识的创新 在发育中更广泛的调控网络框架内的基因调控的表观遗传机制- 为了阐明驱动细胞命运决定的新的调控策略。因为深层次的进化- 保护从果蝇到人类的大多数发育调节因子，该项目还将 确定在发育和疾病过程中可能调节染色质可及性的因素。