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

基本信息

批准号：
10353368
负责人：
Ken W.Y. Cho
金额：
$ 40.27万
依托单位：
UNIVERSITY OF CALIFORNIA-IRVINE
依托单位国家：
美国
项目类别：
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

项目摘要

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

项目概要：早期胚胎基因组如何通过一系列渐进的表观遗传修饰控制合子基因转录，无论是在“时间和空间”上——以确保适当的细胞分化程序，是一个主要的这个过程的关键是转录因子 (TF) 子集的活性，它们位于位于调控层级的高位，通过与顺式的组合相互作用来控制基因表达调控模块 (CRM)，包括存在于 DNA 序列基序中的增强子、绝缘子和沉默子。基因的 CRM 作为代码来决定在正确的时间使用哪些基因，从而激活许多 TF 的特定基因调控程序的 ChIP-seq 分析通常可识别数以万计的 TF。对于给定的细胞类型，在全基因组范围内结合“峰”，但这些位点中只有一小部分似乎具有功能。那么，正确调控基因表达需要哪些机制约束呢？由于需要，使用哺乳动物胚胎在体内解决这一问题非常重要，但这是一个困难的问题针对相对大量的胚胎，在众多实验方案中进行基因组规模分析。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，并检查以下事件：合子基因组激活（ZGA），即胚胎从受精卵转变为多能合子细胞。产生三种生殖层细胞的命运，胚胎基因组和转录组需要快速母体 TF 如何在 ZGA 期间集体重新编程基因组仍然是一个问题。我们最近的研究表明，编码 Fox 的母体 TF 网络是当前研究的一个重要领域。 Sox 和 Pou 型蛋白通过保守机制将细胞基因组重新编程为这部分是通过增强子上的增强体复合物形成的。靶基因，导致基因周围的组蛋白修饰发生变化，形成超增强，其集中转录装置并在我们的前提是母系表达的 Foxh1 及其相互作用的伙伴 TF（Sox3 和）。 Pou5f）在 TF 相互作用层次结构的顶部发挥作用，不仅标记发育基因在合子基因表达开始之前激活，而且还协调主要重组通过我们的努力来阐明这些保守的发育过程中的表观遗传景观。控制多能性的机制，我们的目标是揭示母体 TF 在调节中的整体作用 ZGA 的开始，协调核小体定相和靶基因上的组蛋白修饰，并塑造我们结合基因组和成像方法来提供重要的染色质 3D 结构。深入了解驱动基因组激活的统一原则。 1