Systems analysis of mouse gastrulation

项目摘要 原肠胚形成是胚胎发生过程中的基本事件，产生三个初级胚 来自多能外胚层的层。为了理解这个复杂的过程，必须使用基于系统的 方法来阐明基因调控网络，控制紧密协调的事件， 在原肠胚形成过程中发生的图案形成、分化和形态发生。在这个应用程序中，我们将 使用复杂的计算工具从头重建调控网络， 小鼠原肠胚形成在我们的初步研究中，我们已经产生了一个基因调控网络（相互作用组） 小鼠外胚层干细胞（EpiSC）使用无偏见的反向工程方法。使用基因表达 从原肠胚形成期小鼠胚胎产生的信号，我们已经询问了EpiSC相互作用组， 鉴定原肠胚形成的候选主调节因子以及顺式调节序列基序和同源物 这些转录因子可能在原肠胚形成期间活跃。根据这些初步 研究结果显示，我们假设我们的系统方法可以识别关键生物学的新型主调节因子 在小鼠原肠胚形成过程中。 我们现在将对控制小鼠的遗传调控网络进行全面分析。 通过三个相关的特定目标：（1）鉴定小鼠外胚层发育过程中的主调节因子 通过无偏系统分析，使用原肠胚形成前后小鼠胚胎的特征， 询问EpiSC相互作用物组以鉴定候选主调节物，然后进行功能分析。 验证研究;（2）通过以下方式分析调节小鼠原肠胚形成的转录网络： 顺式调控基序和同源转录的计算机鉴定和实验验证 可能在原肠胚形成中起作用的因素;（3）对原肠胚形成的调控网络的功能分析。 原肠胚形成通过测试推断的调控网络和生物功能的主调节器使用 来自原肠胚形成缺陷的小鼠突变体的特征，并通过进行功能丧失分析 在小鼠胚胎体内的候选主调节剂。总之，这些研究将提供新的 对胚胎正常发育所必需的中心生物过程的机械见解，以及 其扰动可导致严重的先天性缺陷。

Project Summary Gastrulation is the fundamental event during embryogenesis that generates the three primary germ layers from the pluripotent epiblast. To understand this intricate process, it is essential to use systems-based approaches to elucidate the genetic regulatory network that controls the tightly coordinated events of patterning, differentiation, and morphogenesis that take place during gastrulation. In this application, we will use sophisticated computational tools for the de novo reconstruction of regulatory networks to investigate mouse gastrulation. In our preliminary studies, we have generated a genetic regulatory network (interactome) for mouse epiblast stem cells (EpiSC) using unbiased reverse-engineering approaches. Using gene expression signatures generated from peri-gastrulation mouse embryos, we have interrogated the EpiSC interactome to identify candidate master regulators of gastrulation, as well as cis-regulatory sequence motifs and cognate transcription factors that are likely to be active during gastrulation. Therefore, based on these preliminary findings, we hypothesize that our systems approach can identify novel master regulators of key biological processes during mouse gastrulation. We will now pursue a comprehensive analysis of the genetic regulatory network that governs mouse gastrulation through three linked specific aims: (1) Identification of master regulators of mouse epiblast during gastrulation by unbiased systems analyses using signatures from peri-gastrulation mouse embryos to interrogate the EpiSC interactome for the identification of candidate master regulators, followed by functional validation studies; (2) Analysis of the transcriptional network that regulates mouse gastrulation by computational identification and experimental validation of cis-regulatory motifs and cognate transcription factors that are likely to function in gastrulation; and (3) Functional analyses of the regulatory network for gastrulation by testing the inferred regulatory network and biological functions of master regulators using signatures from mouse mutants that are defective in gastrulation, and by performing loss-of-function analyses of candidate master regulators in mouse embryos in vivo. Taken together, these studies will provide novel mechanistic insights into a central biological process that is essential for proper embryonic development, and whose perturbation can lead to major congenital defects.