Defining epigenetic mechanisms for embryonic patterning

定义胚胎模式的表观遗传机制

• 批准号: 10592352
• 负责人: Shelby Alexander Blythe
• 金额: $ 32.22万
• 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/10592352
• 关键词: ATAC-seq; Adult; Affinity Chromatography; Automobile Driving; Binding; Binding Sites; Biochemical; 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; Organism; Output; Pattern; Play; Process; Regulatory Element; Research; Resources; Role; Shapes; Site; System; Testing; Therapeutic; Time; United States National Institutes of Health; biological systems; domain mapping; epigenetic regulation; 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.

项目概要： 发育程序编码形成染色质景观并驱动大规模细胞凋亡的机制。 在其组织中的过渡，但这些变化被整合到胚胎的机制， 终止系统仍不清楚。指导果蝇胚胎初始模式的遗传程序 已经被详尽地描述，许多转录因子的顺式调节元件， 胚胎已被鉴定。然而，直到最近，该领域才能够测量叶绿素的变化， 以足够的灵敏度来观察这些机制是动态的， 在发展中发挥着关键但未得到充分重视的作用。顺式调控元件在染色质中不是静止的 状态，而是改变可访问性和修改状态，作为通过开发的进展的函数， 心理程序干扰染色质状态的时间进程会破坏胚胎的模式。 该项目旨在确定模式化系统如何编排表观遗传状态的变化，以进一步了解 这对胚胎发育的调控逻辑有何贡献。该项目的目标是评估 调控的染色质状态对Dro关键的模型基因调控网络的运作的影响， sophila分割，并详细调查的机制，其中一个组成部分的网络pio- neers neers开放chromatin染色质state状态.核心假设是调控网络利用转录因子 其主要作用是调节可访问性状态，这使网络能够生成更复杂的 从有限的一组输入因素中提取模式。这个项目是合理的，因为果蝇 系统提供了无与伦比的资源，用于执行转录的时间分辨全基因组测量， 除了允许对这些基因进行遗传操作之外， 的动态染色质状态的全面检查的组件在一个发展的背景下， 相关监管网络。第一个目标将通过使用时间分辨的ChIP-和ATAC-seq 在野生型和突变体胚胎上，染色质可及性对所有结合位点选择的影响 在模型基因调控网络内操作的转录因子。第二个目标将集中在 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， 通过网络的一个组成部分改变染色质的可接近性。第三个目标是通过使用 遗传学和基因组学胚胎如何决定某些调控元件的能力， 授予无障碍。这一建议的意义源于创新，以进一步认识 在更广泛的调控网络框架内的基因调控的表观遗传机制， 目的是阐明驱动细胞命运决定的新调控策略。由于深层次的进化- 从果蝇到人类的大多数发育调节因子的进一步保护，该项目还将 鉴定可能在发育和疾病中调节染色质可及性的因素。