Mechanisms of Gene Regulatory Network Evolution

动物的发育需要紧密协调的基因表达程序的活动，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，或者发生在与这些序列结合的调节蛋白水平上，是进化的重要介质。该项目详细研究了一组尚不清楚的进化机制，其中基因调控网络的活性转移到新组织，而不同的网络似乎接管了其在旧组织中的作用。这项研究的重点是蚊子和果蝇胚胎中的神经系统发育，利用两种高度易处理的研究生物，采用成熟的实验工具，沿着研究人员开发的用于识别基因调控序列的新计算方法。研究结果将提供监管网络如何演变的洞察力，并将建立一个深入的功能分析的基础，这种演变的后果，在一个更大的进化距离比以往大多数研究都可能。作为一个额外的影响，这项工作将增加对寨卡病毒，登革热和黄热病媒介蚊子埃及伊蚊的发育生物学的了解，并为这种重要生物的研究和实验操作产生新的工具和资源。该项目还将支持对研究生、本科生和高中科学家的培训。该项目的各个方面将为当地（城市）高中学生的新研究计划奠定基础，以遗传模式生物为中心。基因调控网络（GRNs）由转录因子（TF）和顺式调控模块（CRM，“增强子”）组成。该项目将使用埃及伊蚊询问GRN进化的新模式。在这种“废除、取代和重新部署”的进化模式中，果蝇和其他昆虫胚胎神经系统中线中的GRN功能（“Sim GRN”）已经被“重新部署”到A.埃及，而从中线“废除”和潜在的“取代”。在A. aegypti似乎是GRN的反式依赖性重新部署的结果，源于关键调节TF表达的顺式介导的变化。这特别包括“主”TF Sim，在所有其他研究的昆虫的神经系统中，TF Sim仅限于中线。目前的项目研究GRN进化如何发生的分子细节。具体的目的是：（1）表征晚期A。埃及胚胎中枢神经系统的细胞身份和分子标记在内侧和外侧区域。(2)在D. melanogaster和A.埃及的CRM从这两个物种的调节基因的西姆GRN。将使用PI的SCRMshaw算法识别CRM的正交对。(3)利用遗传学、异位基因表达和调控序列诱变的组合来确定导致基因表达进化模式的特定机制，以确定两个物种之间特定的顺式和反式调控变化。该奖项反映了NSF的法定使命，并通过使用基金会的智力价值和更广泛的影响审查标准进行评估，被认为值得支持。

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.