Maternal transcription factors shaping early embryonic chromatin landscape

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"-以确保适当的细胞分化程序，是一个主要的 生物学中的问题这一过程的关键是转录因子（TF）的一个子集的活性，这些转录因子位于 在调控层次中处于高位，通过与顺式- 调节模块（CRM）包括增强子、绝缘子和沉默子。DNA序列基序存在于 基因的标准物质作为一种编码，指示哪些基因在正确的时间被利用，从而激活 特定的基因调控程序。许多TF的ChIP-seq分析通常鉴定出数万个TF， 结合"峰"，对于一个给定的细胞类型，但只有一小部分这些网站似乎是功能性的。如果 那么，需要什么样的机制约束来适当地调节基因表达呢？这些问题都是 这是一个非常重要的问题，但由于需要使用哺乳动物胚胎在体内解决这个问题是困难的。 用于在众多实验方案中进行基因组规模分析的相对大量的胚胎。 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）。当胚胎从受精卵转变为多能合子细胞时 胚胎基因组和转录组需要迅速地 重新编程在ZGA期间，母体TF如何共同重新编程基因组仍然是一个问题。 是当前研究的重要领域。我们最近的工作表明，编码Fox的母体TF网络， Sox和Pou型蛋白通过保守的机制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体复合物来实现的。 靶向基因，导致基因周围的组蛋白修饰发生变化，并形成超级增强， 其集中转录装置并在细胞中形成相分离的多分子组装体， 原子核我们的前提是，母系表达的Foxh 1及其相互作用伙伴TF（Sox 3和Sox 4）， Pou5f）在TF相互作用的层次结构的顶部起作用，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 ZGA期间的表观遗传景观。通过我们的努力来阐明这些保守的发展 控制多能性的机制，我们的目标是揭示母体TF在调节多能性中的整合作用。 ZGA的开始，协调靶基因上的核小体定相和组蛋白修饰，以及 染色质的三维结构。我们联合收割机结合基因组和成像方法， 深入了解驱动基因组激活的统一原则。 1

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