Maternal transcription factors shaping early embryonic chromatin landscape

母体转录因子塑造早期胚胎染色质景观

• 批准号: 10389644
• 负责人: Ken W.Y. Cho
• 金额: $ 14.9万
• 依托单位: UNIVERSITY OF CALIFORNIA-IRVINE
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-03-01 至 2026-02-28
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10389644
• 关键词: 3-Dimensional; Address; Animals; Architecture; Area; Binding; Biology; Cell Differentiation process; Cell Nucleus; Cells; ChIP-seq; Chromatin; Chromatin Loop; Code; Complex; DNA; DNA Sequence; Deposition; Development; Developmental Gene; Diploidy; Distant; Drosophila genus; Embryo; Embryonic Development; Enhancers; Ensure; Enzymes; Epigenetic Process; Equipment; Event; FOXH1 gene; Fertilization; Foxes; Funding; Gene Activation; Gene Expression; Genes; Genetic; Genetic Enhancer Element; Genetic Transcription; Genome; Genomic approach; Genomics; Germ Layers; Goals; Histones; Human; Methods; Modeling; Modification; Molecular Conformation; Mus; Nuclear; Nucleosomes; Oogenesis; Organism; Output; Phase; Physical condensation; Polymerase; Positioning Attribute; Process; Proteins; RNA; Rana; Regimen; Regulator Genes; Research; Role; Series; Shapes; Site; Structure; System; Testing; Time; Transcriptional Regulation; Work; Xenopus; Zebrafish; base; blastomere structure; cell type; chromosome conformation capture; combinatorial; embryo stage 2; genome-wide; histone modification; imaging approach; in vitro Model; in vivo; insight; interest; meter; nuclear reprogramming; parent grant; pluripotency; programs; promoter; recruit; segregation; single-cell RNA sequencing; transcription factor; transcriptome; zygote

Project Summary: How the early embryonic genome – through a progressive series of epigenetic modifications controls zygotic gene transcription, both in `time and space' – to ensure proper cellular differentiation programs, is a major question in biology. Crucial to this process is the activity of a subset of transcription factors (TFs), which sit high in the regulatory hierarchy to control gene expression through combinatorial interactions with cis- regulatory modules (CRMs) that include enhancers, insulators and silencers. DNA sequence motifs present in the CRMs of genes act as a code to dictate which genes are to be utilized at the right time, and thus activate specific gene regulatory programs. ChIP-seq analysis of many TFs usually identifies tens of thousands of TF binding “peaks,” genomewide, for a given cell type, but only a fraction of these sites appears to be functional. If so, what mechanistic constrains are needed to properly regulate gene expression? These questions are fundamentally important, but a difficult question to address in vivo using mammalian embryos due to the need for relatively large numbers of embryos for genome-scale analyses across numerous experimental regimens. Here we tackle this question by leveraging the strengths of the frog embryo system and examine the events of zygotic genome activation (ZGA). As the embryo transitions from fertilized egg to pluripotent zygotic cells giving rise to three germ layer cell fates, the embryonic genome and transcriptome need to be rapidly reprogrammed. How can maternal TFs collectively reprogram the genome during the ZGA remains an important area for the current research. Our recent work shows that a network of maternal TFs encoding Fox, Sox and Pou type proteins acts through conserved mechanisms to reprogram the cellular genome into the embryonic states. This is in part accomplished by forming enhanceososme complexes on the enhancers of target genes, resulting in changing in histone modifications surrounding genes, and forming super enhances, which concentrate the transcription apparatus and form phase-separated multimolecular assemblies in the nucleus. Our premise is that maternally expressed Foxh1 and its interacting partner TFs (Sox3 and Pou5f) function at the top of a hierarchy of TF interactions to not only mark developmental genes for activation prior to the onset of zygotic gene expression, but also coordinate major reorganization of the epigenetic landscape during ZGA. Through our efforts to elucidate these conserved developmental mechanisms controlling pluripotency, our goal is to uncover the integrative roles of maternal TFs in regulating the onset of ZGA, coordinating nucleosome phasing and histone modifications on target genes, and shaping the 3D architecture of chromatin. We combine both genomic and imaging approaches to provide important insights into the unifying principles that drive genome activation. 1

项目摘要： 早期的胚胎基因组如何通过一系列渐进遗传修饰来控制合子 基因转录，无论是在时间和空间中 - 以确保适当的蜂窝分化程序，都是主要的 生物学问题。对此过程至关重要的是转录因子（TF）的一部分的活性， 在调节层次结构中高度通过与顺式相互作用来控制基因表达 调节模块（CRM），包括增强剂，绝缘子和消音器。 DNA序列基序存在于 基因的CRM充当指定在正确时间使用哪些基因的代码，从而激活 特定的基因调节程序。许多TF的CHIP-seq分析通常可以识别成千上万的TF 对于给定的细胞类型的结合“峰”（全基因组），但只​​有一部分这些位点似乎是功能性的。如果 那么，需要哪些机械约束才能正确调节基因表达？这些问题是 从根本上重要，但由于需要，使用哺乳动物胚胎在体内解决一个困难的问题 对于相对较大的胚胎，用于跨许多实验方案的基因组规模分析。 在这里，我们通过利用青蛙胚胎系统的优势来解决这个问题，并检查 合子基因组激活（ZGA）。随着胚胎从受精卵到多能性粘合细胞的过渡 产生三个生殖层细胞命运，需要快速胚胎基因组和转录组 重编程。在ZGA期间，母体TF如何共同对基因组进行重新编程 当前研究的重要领域。我们最近的工作表明，编码Fox的Modal TF网络， SOX和POU型蛋白质通过配置的机制作用，将细胞基因组重编程为 胚胎状态。这部分是通过在增强子上形成增强剂复合物来完成的 靶基因，导致基因周围的组蛋白修饰变化，并形成超级增强， 在哪个集中到转录设备和形成相位分离的多分子组件 核。我们的前提是主要表达FOXH1及其互动合作伙伴TFS（Sox3和 pou5f）功能在TF相互作用的层次结构的顶部，不仅标记了发展基因的发展基因 在发作之前激活合子基因表达，但也协调重新组织的重新组织 ZGA期间的表观遗传景观。通过我们阐明这些保守发展的努力 控制多能性的机制，我们的目标是揭示Mater TF在调节中的综合作用 ZGA的发作，协调核定量和对目标基因的修改，并塑造 染色质的3D结构。我们结合了基因组和成像方法，以提供重要的 深入了解驱动基因组激活的统一原则。 1