Mechanisms of Gene Regulatory Network Evolution

基因调控网络进化机制

• 批准号: 1911723
• 负责人: Marc Halfon
• 金额: $ 110.65万
• 依托单位: SUNY at Buffalo
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-09-15 至 2024-08-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1911723&HistoricalAwards=false
• 关键词: Mechanisms; Gene; Regulatory; Network; Evolution

Animal development requires the activity of tightly coordinated programs of gene expression, known as "gene regulatory networks." Changes in these networks, which can occur at the level of DNA sequences that regulate genes, or of regulatory proteins that bind to these sequences, are important mediators of evolution. This project investigates in detail a poorly-understood set of evolutionary mechanisms in which a gene regulatory network's activity is shifted to a new tissue, and a different network appears to take over its role in the old tissue. The research focuses on nervous system development in the embryos of mosquitoes and fruit flies, taking advantage of two highly tractable research organisms with a mature selection of experimental tools, along with novel computational methods the investigators have developed for identifying gene regulatory sequences. The results will provide insight into how regulatory networks evolve and will build a foundation for in-depth functional analysis of the consequences of such evolution, over a greater evolutionary distance than has been possible in most previous studies. As an added impact, the work will lead to increased knowledge of the developmental biology of the Zika, dengue, and yellow fever vector mosquito Aedes aegypti and generate new tools and resources for the study and experimental manipulation of this important organism. The project will also support training of scientists at the graduate, undergraduate, and high school levels. Aspects of the project will form the basis for a new research program for local (city) high school students, centered around genetic model organisms.Gene regulatory networks (GRNs) are composed of transcription factors (TFs) and cis-regulatory modules (CRMs, 'enhancers'). This project will interrogate a novel mode of GRN evolution using the mosquito Aedes aegypti. In this "repeal, replace, and redeploy" mode of evolution, a GRN functioning in the embryonic nervous system midline in the fly Drosophila and other insects (the "Sim GRN") has been "redeployed" to lateral regions in A. aegypti while "repealed" from and potentially "replaced" in the midline. The altered gene expression observed in A. aegypti appears to be the result of trans-dependent redeployment of the GRN, stemming from cis-mediated changes in the expression of key regulatory TFs. This includes in particular the "master" TF Sim, which in the nervous systems of all other studied insects is confined to the midline. The current project investigates the molecular details of how GRN evolution has occurred. Specific aims are to: (1) Characterize the development of the late A. aegypti embryonic central nervous system with respect to cell identities and molecular markers in both medial and lateral regions. (2) Perform reciprocal transgenic analysis in D. melanogaster and A. aegypti of CRMs from both species which regulate genes of the Sim GRN. Orthologous pairs of CRMs will be identified using the PI's SCRMshaw algorithm. (3) Identify the specific mechanisms leading to the evolved patterns of gene expression using a combination of genetics, ectopic gene expression, and mutagenesis of regulatory sequences to define specific cis- and trans- regulatory changes between the two species.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.

动物的发育需要紧密协调的基因表达程序，称为“基因调控网络”。这些网络的变化，可能发生在调节基因的DNA序列水平上，或与这些序列结合的调节蛋白水平上，是进化的重要媒介。该项目详细研究了一套鲜为人知的进化机制，其中一个基因调控网络的活动转移到一个新的组织，而另一个不同的网络似乎接管了它在旧组织中的作用。这项研究的重点是蚊子和果蝇胚胎的神经系统发育，利用了两种高度易处理的研究生物，拥有成熟的实验工具选择，以及研究人员开发的用于识别基因调控序列的新型计算方法。研究结果将提供调控网络如何进化的见解，并将为深入分析这种进化的后果奠定基础，在更大的进化距离上，比大多数以前的研究都可能实现。作为一个额外的影响，这项工作将导致增加对寨卡病毒、登革热和黄热病媒介埃及伊蚊的发育生物学的了解，并为研究和实验操纵这一重要生物体提供新的工具和资源。该项目还将支持对研究生、本科生和高中水平的科学家进行培训。该项目的一些方面将成为当地（城市）高中生的一个新的研究计划的基础，该计划以遗传模式生物为中心。基因调控网络（grn）由转录因子（TFs）和顺式调控模块（CRMs）组成。该项目将利用埃及伊蚊研究GRN进化的新模式。在这种“废除、替换和重新部署”的进化模式中，在果蝇和其他昆虫的胚胎神经系统中线（“Sim GRN”）中起作用的GRN被“重新部署”到埃及伊蚊的侧边区域，而在中线被“废除”并可能被“取代”。在埃及伊蚊中观察到的基因表达改变似乎是GRN的反式依赖重新部署的结果，源于顺式介导的关键调节性tf表达的变化。这尤其包括“大师”TF Sim，在所有其他被研究的昆虫的神经系统中，它被限制在中线。目前的项目调查了GRN进化发生的分子细节。具体目的是：(1)表征晚期埃及伊蚊胚胎中枢神经系统的发育，包括细胞身份和内侧和外侧区域的分子标记。(2)对调节Sim GRN基因的两个物种的CRMs进行互反转基因分析。将使用PI的SCRMshaw算法识别同源的crm对。(3)结合遗传学、异位基因表达和调控序列的突变，确定导致基因表达进化模式的具体机制，以确定两种物种之间特定的顺式和反式调控变化。该奖项反映了美国国家科学基金会的法定使命，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。