Uncovering the regulatory DNA logic of the Drosophila innate immune response

许多生物学过程，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需要了解的地方。生物体的DNA可以分为两类：编码DNA和非编码DNA，编码DNA具有如何构建蛋白质的指令-细胞的分子机器；非编码DNA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控制非编码DNA在对感染的先天免疫反应中功能的规则，并将这些规则与其他生物过程所需的非编码DNA进行比较。成功将使科学家获得关于非编码DNA如何协调免疫反应的具体信息，并更深入地了解很大一部分基因组通常是如何发挥作用的。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，旨在提高生物学本科生和研究生的量化素养，这将使他们更好地为现代工作做好准备，这些工作越来越需要定量技能。实际上，从发育到免疫，每个生物过程都受到基因调控网络(GRN)的控制，GRN是控制基因表达的信号分子和转录因子的网络。多年的工作揭示了调控DNA序列，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育GRN上，它们受到进化的独特限制：尽管存在扰动，但选择有利于驱动刻板印象的发展计划的GRN。为了解释发育GRN的哪些原理翻译成较少研究的非发育GRN，这些非发育GRN具有不同的功能，并受到不同的进化压力，本项目将研究果蝇的天然免疫GRN。在目标1中，等位基因特异的RNA-seq将被用来表征黑腹果蝇品系之间对感染的转录反应的自然差异。这些数据将允许识别其表达变化是由调控DNA的变化驱动的基因。将对不同感染条件下的表达变化模式进行比较。在目标2中，体内和体外功能基因组学分析将用于鉴定免疫反应增强剂，并产生这些增强剂的序列与功能模型。其他实验将验证和提炼增强子功能模型。该项目还包括一项计划，将以问题为基础的数字素养部分的学习应用到一个大的本科生班级中，这将提高生物学学生的量化技能，并将其传播给其他人使用。该奖项反映了NSF的法定使命，并通过使用基金会的智力优势和更广泛的影响审查标准进行评估，被认为值得支持。

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.