Analysis of a Model Developmental Gene Regulatory Network

模型发育基因调控网络分析

• 批准号: 1656580
• 负责人: Charles Ettensohn
• 金额: $ 76.37万
• 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: 2017
• 资助国家: 美国
• 起止时间: 2017-08-01 至 2020-12-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1656580&HistoricalAwards=false
• 关键词: Analysis; Model; Developmental; Gene; Regulatory

Non-Technical ParagraphIn development, multicellular organisms arise from a single cell - a fertilized egg. 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 cardinal scientific importance, as this is the process by which new generations of multicellular organisms arise. 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 genome information is "decoded" to control the process of development. The research project described here addresses this question, using the sea urchin embryo as a convenient experimental model. It examines the genes that encode the formation of the skeleton of these sea creatures through use of new methods to examine the physical structure of genomic DNA, to monitor when and where in the embryo various genes work, and to determine interactions among these genes. The work will shed light on the mechanisms by which the information contained in the genome is deciphered during the development of a single cell into a critical part of these organisms. Technical ParagraphThe central challenge of developmental biology is to link genes to anatomy. The programs of differential gene expression that drive development are largely controlled by complex networks of regulatory genes (i.e., genes that encode transcription factors, or TFs) and the non-coding DNA sequences to which TFs bind. Such gene regulatory networks (GRNs) are powerful tools for analyzing the genetic control and evolution of development. At present, we have a very limited understanding of the connections between GRNs and the processes that directly shape embryonic tissues and organs (morphogenesis). The project described here addresses this question using the sea urchin embryo, a pre-eminent system for both GRN biology and the analysis of morphogenesis. The project leverages one of the most complete GRNs in any developing organism, a GRN that drives a suite of cell behaviors by primary mesenchyme cells (PMCs) and culminates in the formation of the embryonic skeleton. The research plan takes a "top-down" approach to dissect the architecture of an essential subcircuit controlled by Alx1, a key TF in the skeletogenic GRN. These studies utilize gene knockdowns, mRNA overexpression, gene expression profiling, and bioinformatics-based approaches. In parallel, a "bottom-up" approach is taken that uses reporter gene assays to dissect non-coding regulatory DNA sequences that control the transcription of morphogenetic effector genes. This information is used to bootstrap into the upstream network circuitry. Lastly, the project extends a gene knockdown screen to identify and characterize new morphogenetic effectors that have emerged from genome-wide profiling of PMC-enriched transcripts and Alx1 targets.

在发育过程中，多细胞生物起源于一个单细胞-受精卵。 重复的细胞分裂产生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。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被“解码”以控制发育过程的。 这里描述的研究项目解决了这个问题，使用海胆胚胎作为一个方便的实验模型。 它通过使用新方法来检查基因组DNA的物理结构，监测胚胎中各种基因的工作时间和位置，并确定这些基因之间的相互作用，从而检查编码这些海洋生物骨骼形成的基因。这项工作将揭示基因组中包含的信息在单细胞发育成这些生物体的关键部分期间被破译的机制。发育生物学的中心挑战是将基因与解剖学联系起来。驱动发育的差异基因表达程序在很大程度上受调控基因的复杂网络控制（即，编码转录因子或TF的基因）和TF结合的非编码DNA序列。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。目前，我们对GRNs与直接塑造胚胎组织和器官（形态发生）的过程之间的联系了解非常有限。这里描述的项目使用海胆胚胎解决了这个问题，海胆胚胎是GRN生物学和形态发生分析的杰出系统。 该项目利用了任何发育中的生物体中最完整的GRN之一，GRN通过初级间充质细胞（PMC）驱动一系列细胞行为，并最终形成胚胎骨骼。 该研究计划采取“自上而下”的方法来解剖由Alx1控制的重要子回路的结构，Alx1是骨骼生成GRN中的关键TF。 这些研究利用基因敲除、mRNA过表达、基因表达谱和基于生物信息学的方法。 与此同时，采用"自下而上"的方法，使用报告基因测定来剖析控制形态发生效应基因转录的非编码调控DNA序列。 此信息用于引导到上游网络电路中。 最后，该项目扩展了基因敲除筛选，以识别和表征新的形态发生效应子，这些效应子是从富含PMC的转录本和Alx1靶标的全基因组谱中出现的。