Uncovering the regulatory DNA logic of the Drosophila innate immune response

许多生物过程，从早期发育到免疫反应，都依赖于基因组的“非编码”部分，研究人员对此还有很多要了解。生物体的DNA可以分为两类：编码DNA，它具有如何构建蛋白质的方向-细胞的分子机器，以及非编码DNA，它具有许多功能，包括何时，何地以及应该构建多少蛋白质的指令。人类基因组的大部分是非编码DNA，其正常功能对生命至关重要。该项目旨在破译一些规则，这些规则在先天免疫反应中控制非编码DNA对感染的功能，并将这些规则与其他生物过程所需的非编码DNA进行比较。成功将为科学家提供关于非编码DNA如何协调免疫反应的具体信息，并更深入地了解基因组的大部分功能。研究生和本科生都将参加这项工作并接受培训。该项目还包括一个更广泛的影响计划，以提高生物学本科生和研究生的定量素养，这将使他们更好地为越来越需要定量技能的现代工作做好准备。几乎每一个生物过程，从发育到免疫，都受到基因调控网络（GRN）的控制，这是一个控制基因表达的信号分子和转录因子的网络。多年的工作已经揭示了调控DNA的序列，例如启动子和增强子，如何指定GRN的功能。这项工作主要集中在发展的GRNs，这是唯一的限制进化：选择有利于GRNs，尽管扰动驱动一个定型的发展计划。为了解释哪些发育GRNs的原则转化为较少研究的非发育GRNs，这些GRNs具有不同的功能并受到不同的进化压力，该项目将研究果蝇先天免疫GRN。目的1：利用等位基因特异性RNA-seq技术，研究D.黑腹线这些数据将允许鉴定其表达变异由调控DNA的变化驱动的基因。将使用不同感染条件比较表达变化的模式。在目标2中，将使用体内和体外功能基因组学测定来鉴定免疫应答增强子并产生这些增强子的序列-功能模型。进一步的实验将验证和完善增强子功能的模型。该项目还包括一个计划，实施基于问题的学习的数字识字组件到一个大的，本科班，这将提高生物学生的定量技能，并传播给他人使用。这个奖项反映了NSF的法定使命，并已被认为是值得通过评估使用基金会的智力价值和更广泛的影响审查标准的支持。

Many biological processes, from early development to the immune response, rely on the “non-coding” part of the genome, about which researchers have much to learn. An organism’s DNA can be separated into two categories: coding DNA, which has the directions for how to build proteins – the molecular machines of the cell, and non-coding DNA, which has many functions including the instructions for when, where, and how much protein should be built. The majority of the human genome is non-coding DNA, and its proper functioning is essential for life. This project aims to decipher some of the rules that govern function of non-coding DNA in the innate immune response to infection and to compare these rules to non-coding DNA needed for other biological processes. Success will give scientists specific information about how non-coding DNA orchestrates the immune response and a deeper understanding about how a large part of the genome functions in general. Both graduate and undergraduate students will participate and be trained in the work. This project also includes a broader impacts plan to improve quantitative literacy among biology undergraduate and graduate students, which will better equip them for modern jobs that increasingly require quantitative skills.Virtually every biological process, from development to immunity, is controlled by a gene regulatory network (GRN), a network of signaling molecules and transcription factors that control gene expression. Years of work have uncovered how the sequence of regulatory DNA, e.g. promoters and enhancers, can specify a GRN’s function. This work largely has focused on developmental GRNs, which are uniquely constrained by evolution: selection favors GRNs that drive a stereotyped developmental program in spite of perturbations. To decipher which principles of developmental GRNs translate to lesser studied non-developmental GRNs, which have diverse functions and are subject to different evolutionary pressures, this project will study the Drosophila innate immunity GRN. In Aim 1, allele-specific RNA-seq will be used to characterize the natural variation in transcriptional response to infection between D. melanogaster lines. These data will allow the identification of genes whose expression variation is driven by changes in regulatory DNA. Comparisons of the pattern of expression variation using different infection conditions will be made. In Aim 2, in vivo and in vitro functional genomics assays will be used to identify immune-responsive enhancers and to generate sequence-to-function models of these enhancers. Additional experiments will validate and refine the models of enhancer function. The project also includes a plan to implement problem-based learning of numerical literacy components into a large, undergraduate class, which will improve the quantitive skills of biology students and be disseminated for use by others.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.