Maternal transcription factors shaping early embryonic chromatin landscape

项目总结： 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受精卵 基因转录，在‘时间和空间’--以确保适当的细胞分化程序，是一个主要的 生物学中的一道题。这一过程的关键是转录因子(TF)的子集的活性，这些转录因子位于 通过与顺式基因的组合相互作用来控制基因表达的调控体系中的高级成员 包括增强器、绝缘器和消音器的监管模块(CRM)。DNA序列基序存在于 基因的CRM起着密码的作用，指示哪些基因将在正确的时间被利用，从而激活 特定的基因调控程序。对许多TF的芯片序列分析通常识别出数万个TF 在全基因组范围内，结合某一特定细胞类型的“峰”，但这些位点中似乎只有一小部分是有功能的。如果 那么，需要什么样的机制约束才能适当地调控基因表达呢？这些问题是 从根本上说很重要，但由于需要，在体内使用哺乳动物胚胎是一个很难解决的问题 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，并研究 合子基因组激活(ZGA)。当胚胎从受精卵过渡到多能合子细胞时 胚胎基因组和转录组需要迅速形成三种生殖层细胞命运。 重新编程。在ZGA保留的过程中，母体TF如何集体重新编程基因组 是当前研究的重要领域。我们最近的研究表明，编码狐狸的母体TF网络， SOX和POU型蛋白通过保守的机制将细胞基因组重新编程到 处于胚胎状态。这部分是通过在促进剂上形成增强体复合体来实现的。 靶基因，导致基因周围组蛋白修饰的变化，形成超级增强， 它们集中转录装置并形成相分离的多分子组件 原子核。我们的前提是母性表达的Foxh1及其相互作用的伴侣TF(SOX3和 Pou5f)位于Tf相互作用层级的顶端，不仅标记发育基因 在合子基因表达开始前激活，而且还协调主要的重组 ZGA期间的表生地貌。通过我们努力阐明这些保守的发育 控制多能性的机制，我们的目标是揭示母体TF在调节中的综合作用 ZGA的开始，协调核小体阶段和靶基因上的组蛋白修饰，并形成 染色质的3D架构。我们结合了基因组和成像方法来提供重要的 对驱动基因组激活的统一原则的洞察。 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