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Analysis of a Model Developmental Gene Regulatory Network

模型发育基因调控网络分析

基本信息

批准号：
2004952
负责人：
Charles Ettensohn
金额：
$ 120万
依托单位：
Carnegie-Mellon University
依托单位国家：
美国
项目类别：
Continuing Grant
财政年份：
2020
资助国家：
美国
起止时间：
2020-09-01 至 2025-08-31
项目状态：
未结题

来源：
https://www.nsf.gov/awardsearch/showAward?AWD_ID=2004952&HistoricalAwards=false
关键词：
Analysis Model Developmental Gene Regulatory

项目摘要

Multicellular organisms arise from a single cell- a fertilized egg- through a process known as embryonic development. During this process, repeated cell divisions create an embryo composed of many cells. These cells gradually take on distinct functions and organize themselves into tissues and organs. Understanding development is of great scientific importance, as this is the process by which new generations of multicellular organisms arise. Moreover, during earth’s history, modifications to developmental programs have produced the diverse animal morphologies we see in nature. Lastly, failures of human development have profound societal impacts, and any appreciation of the causes of such dysregulation must begin with an understanding of the mechanisms that ordinarily operate during development. Remarkably, the entire blueprint for embryonic development is contained in the DNA sequence of the genome. A central challenge of modern biology is to explain how this genomic information is “decoded” to control the process of embryogenesis. This research project addresses that question. It exploits new methods (and undergraduate researchers) for examining the physical structure of genomic DNA, for monitoring when and where in the embryo various genes are working, and for dissecting interactions among these genes. The work will shed light on the mechanisms by which the information contained in the genome is deciphered during the transformation of a single cell into an organism, and will form a foundation for development of a digital atlas of echinoderm development. A hallmark of animal development is the gradual emergence of anatomy, as represented by the many different cell types of the mature organism and their organization into distinct tissues and organs. The emergence of anatomy during embryonic development (morphogenesis) requires specialized cell and tissue behaviors that are driven by differential gene expression. Systems level approaches have revealed that programs of differential gene expression are controlled by complex networks of transcription factors and non-coding DNA sequences to which they bind. Such gene regulatory networks (GRNs) are powerful tools for analyzing the genetic control and evolution of development. To understand the genotype-to-phenotype transformation it will therefore be important to link GRNs to morphogenesis. The overarching goal of this work is to uncover the detailed architecture of a model GRN and elucidate its control of crucial downstream effectors that drive morphogenesis. It leverages a GRN that drives a suite of spectacular behaviors by skeleton-forming primary mesenchyme cells (PMCs) of the sea urchin embryo. The project combines “top-down” and “bottom-up” approaches. The former uses gene knockdowns and gene expression profiling to elucidate the regulatory topology of the network. The latter uses chromatin accessibility profiling and eRNA analysis to identify cis-regulatory DNA sequences that control morphogenetic effector genes, and then applies transcription factor footprinting, mutagenesis, and transgenic reporter assays to dissect these sequences and bootstrap into the upstream network circuitry. Lastly, the project extends a successful gene knockdown screen to identify and characterize key morphogenetic effectors. With respect to Broader Impacts, this project involves undergraduate researchers, outreach to high school students and teachers, and the development of a digital atlas of echinoderm development.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

多细胞生物起源于一个单细胞-受精卵-通过一个称为胚胎发育的过程。在这个过程中，重复的细胞分裂产生了由许多细胞组成的胚胎。这些细胞逐渐承担不同的功能，并组织成组织和器官。了解发育具有重要的科学意义，因为这是新一代多细胞生物产生的过程。此外，在地球的历史上，对发育程序的修改产生了我们在自然界中看到的各种动物形态。最后，人类发展的失败会产生深远的社会影响，任何对这种失调原因的认识都必须开始于对发展过程中通常运作的机制的理解。值得注意的是，胚胎发育的整个蓝图包含在基因组的DNA序列中。现代生物学的一个核心挑战是解释这些基因组信息是如何“解码”以控制胚胎发生过程的。这个研究项目解决了这个问题。它利用新的方法（和本科生研究人员）来检查基因组DNA的物理结构，监测胚胎中各种基因的工作时间和位置，以及解剖这些基因之间的相互作用。这项工作将揭示基因组中包含的信息在单细胞转化为生物体过程中被破译的机制，并将为开发棘皮动物发育的数字图谱奠定基础。动物发育的一个标志是解剖学的逐渐出现，表现为成熟生物体的许多不同细胞类型及其组织成不同的组织和器官。胚胎发育（形态发生）过程中解剖学的出现需要由差异基因表达驱动的特殊细胞和组织行为。系统水平的方法已经揭示了差异基因表达的程序是由转录因子和它们所结合的非编码DNA序列的复杂网络控制的。这种基因调控网络（GRNs）是分析发育的遗传控制和进化的有力工具。因此，为了理解基因型到表型的转化，将GRNs与形态发生联系起来是很重要的。这项工作的总体目标是揭示模型GRN的详细架构，并阐明其对驱动形态发生的关键下游效应子的控制。它利用GRN驱动一系列壮观的行为，通过海胆胚胎的成膜初级间充质细胞（PMC）。该项目结合了“自上而下”和“自下而上”的方法。前者使用基因敲除和基因表达谱来阐明网络的调控拓扑结构。后者使用染色质可及性分析和eRNA分析来鉴定控制形态发生效应基因的顺式调控DNA序列，然后应用转录因子足迹法、诱变和转基因报告基因测定来解剖这些序列并引导进入上游网络电路。最后，该项目扩展了一个成功的基因敲除筛选，以确定和表征关键的形态发生效应。关于更广泛的影响，该项目涉及本科生研究人员，向高中学生和教师推广，并开发棘皮动物发育的数字地图集。该奖项反映了NSF的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。