Regulatory roles of the epitranscriptome and RNA structurome during vertebrate development

项目摘要/摘要(与原始申请中提交的相同) 在所有动物中，母体到受精卵的转变允许将单个受精卵所需的信息转移到 发育成成熟的生物体。受精后，母体程序由母系遗传组成 MRNAs和蛋白质，驱动细胞发育，并被合子程序取代。因为这一过渡 主要发生在转录沉默的胚胎中，它严重依赖于转录后调控。未能做到 适当地调节母系遗传的mRNAs通常会导致发育停滞或异常。近期 研究表明，母体的mRNAs被RNA修饰，统称为 “表位转录组”，与不同的mRNA命运相关。此外，我们和其他人进行了全球分析 在母体到受精卵的转变过程中的mRNA结构动态，并确定了许多区域 在这一基本过程中，结构发生了重塑，其中许多影响了mRNA的衰变。这些研究 提示RNA修饰和动态RNA结构正在成为基因表达的关键调控因素 在母体到受精卵的转变过程中。然而，外延的详细景观说明了这一点和动态 在母体向合子的转变过程中，RNA结构及其在基因调控中的作用仍然很少 明白了。此外，RNA修饰和结构相互影响以调节RNA功能，但是 关于它们在脊椎动物发育过程中如何相互作用来控制基因表达，人们知之甚少。初级阶段 我的实验室的目标是了解表位转录组和RNA结构是如何介导基因调控网络的， 单独和合作，在脊椎动物的发育过程中，以及它们的功能障碍如何促进发育 缺陷或疾病。在这里，我们假设RNA修饰和结构与反式因子相互作用 参与推动脊椎动物发育的转录后调控格局。为了测试这一点 假设，我们将结合斑马鱼--一种脊椎动物体内发育的模型--及其遗传工具箱 通过创新的多重组学方法。在接下来的五年里，我们将检查本地转录组以 在母体到受精卵的转变过程中，生成表位编码组的全球但详细的图谱，并进行研究 具体的RNA修饰如何影响基因表达。我们还将破译动态形成的RNA折叠 并分析它们对RNA调控的影响。我们将确定相互作用的跨因子 RNA修饰和感兴趣的结构，并研究它们功能丧失对基因的影响 表达与脊椎动物的发育。最后，我们将研究RNA修饰和结构是如何 合作调节转录后调控。成功完成这些调查将极大地 增加关于RNA修饰和结构如何协调转录后反应的现有知识 调节，并将扩大我们对塑造脊椎动物发育的分子机制的理解。

PROJECT SUMMARY/ABSTRACT (as submitted in original application) In all animals, the maternal-to-zygotic transition allows the transfer of information required for a single zygote to develop into a mature organism. After fertilization, the maternal program, composed of maternally-inherited mRNAs and proteins, drives cellular development and is replaced by the zygotic program. Because this transition occurs primarily in a transcriptionally silent embryo, it relies heavily on post-transcriptional regulation. Failure to properly regulate maternally-inherited mRNAs generally leads to developmental arrest or abnormalities. Recent studies have shown that maternal mRNAs are decorated with RNA modifications, collectively known as the ‘epitranscriptome’, that correlate with different mRNA fates. Moreover, we and others performed global analyses of mRNA structure dynamics during the maternal-to-zygotic transition and identified numerous regions that are structurally remodeled during this fundamental process, many of which impact mRNA decay. These studies suggest that RNA modifications and dynamic RNA structures are emerging as key regulators of gene expression during the maternal-to-zygotic transition. However, the detailed landscape of the epitranscriptome and dynamic RNA structures, and their roles in gene regulation during the maternal-to-zygotic transition remain poorly understood. Furthermore, RNA modifications and structures affect one another to regulate RNA functions, but little is known about how they interact to control gene expression during vertebrate development. The primary goal of my lab is to understand how the epitranscriptome and RNA structures mediate gene regulatory networks, separately and cooperatively, during vertebrate development and how their dysfunction promotes developmental defects or diseases. Here, we hypothesize that RNA modifications and structures interact with trans-factors to participate in the post-transcriptional regulatory landscape driving vertebrate development. To test this hypothesis, we will combine zebrafish —an in vivo model of vertebrate development— and its genetic toolbox with innovative multi-omics approaches. Over the next five years, we will inspect the native transcriptome to generate global, yet detailed, maps of the epitranscriptome during the maternal-to-zygotic transition, and study how specific RNA modifications impact gene expression. We will also decipher the RNA folds formed by dynamic regions of the transcriptome and analyze their effect on RNA regulation. We will identify trans-factors interacting with RNA modifications and structures of interest and study the consequences of their loss-of-function on gene expression and vertebrate development. Finally, we will examine how RNA modifications and structures cooperate to modulate post-transcriptional regulation. Successful completion of these investigations will greatly increase the existing knowledge of how RNA modifications and structures orchestrate post-transcriptional regulation, and will expand our understanding of the molecular mechanisms shaping vertebrate development.