CAREER: Beyond differential expression: quantifying transcriptional dynamics and testing for adaptive value of transcriptomic responses at low temperature

许多生物体因环境变化而改变他们的生理，这种现象被称为可塑性。其中一些变化可能是有益的，有助于有机体在不利的条件下坚持下去。但其他变化可能代价高昂或具有破坏性，如果条件足够苛刻，最终可能会导致死亡。在测量生理可塑性的常见类型的实验中，通常无法确定哪些变化是有益的，哪些是无益的。这阻碍了对可能促进或限制对变化环境的反应的生理机制的理解。这项研究探索了低温对转录的影响，转录是合成新蛋白质过程中的关键步骤。通过比较经常遇到极低温度(远低于冰点)的温带苍蝇物种和很少遇到寒冷温度的热带苍蝇物种的低温反应，研究人员将确定哪些过程有利于在寒冷环境中的持久性。这项研究还将试图量化转录的温度下限，并将测试当苍蝇经历新环境时，这些限制是否会进化。这项研究将与本科阶段的生物教育相结合。研究人员将开发基于课程的本科生研究体验(CURE)，允许学生参与真实的研究，作为生物学入门课程的一部分。代表性不足的学生群体往往减少了获得研究机会的机会；治疗方法将有目的地设计，以鼓励广泛参与，并为代表性不足的学生群体提供进一步研究经验的门户。环境诱导的转录组变化提供了广泛使用和相对全面的细胞、组织或整个生物生理如何在环境中变化的快照。然而，在常用的实验设计中，不可能推断任何特定转录的丰富性的变化对表现和最终健康的影响是有益的还是有害的。由于不能区分新转录和转录降解对转录丰度的影响，量化转录本差异表达的常用方法进一步受到限制。因此，调控转录切分环境反应的转录动力学在很大程度上仍然是未知的。这项研究将比较温带和热带起源的果蝇物种在低温暴露期间新形成的转录物的图谱。将染色质相关的RNA组分和溴鼠啶标记的新转录本的测序与标准信使RNA测序相结合，研究小组将1)确定与低温适应相关的新转录或转录本降解率的假定有益变化，以及2)在比较框架中表征转录动力学的反应规范。这项研究将与本科教育相结合，开发实验室练习，允许本科生使用转基因黑腹果蝇品系测试单个基因在热适应中的作用。这一解决办法将与哥伦比亚大学丹佛分校正在进行的努力相结合，以改善代表性不足群体的结果，并增加他们在STEM领域的代表性。CURE还将生成一个透明报告的结果数据库，这将有助于热生物领域的候选基因测试。该奖项反映了NSF的法定使命，并已被认为值得支持，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。

Many organisms change their physiology in response to changing environments, a phenomenon known as plasticity. Some of these changes can be beneficial, helping an organism to persist in unfavorable conditions. But other changes may be costly or damaging and may eventually lead to death if conditions are harsh enough. In common types of experiments that measure physiological plasticity, it is often impossible to identify which changes are beneficial, and which are not. This impedes understanding the physiological mechanism that may facilitate or limit responses to changing environments. This research explores how exposure to low temperatures affects transcription, a critical step in the process of synthesizing new proteins. By comparing low temperature responses of temperate fly species that often encounter very cold temperatures (well below freezing) to tropical fly species that rarely encounter cold temperatures, the investigators will identify which processes are beneficial for persistence in cold environments. The research will also attempt to quantify the lower temperature limits of transcription and will test whether these limits can evolve when flies experience new environments. This research will be integrated with biology education at the undergraduate level. The investigators will develop a Course-Based Undergraduate Research Experience (CURE) allowing students to participate in authentic research as part of an introductory biology course. Underrepresented student groups often have reduced access to research opportunities; the CURE will be purposefully designed to encourage broad participation and to provide a gateway to further research experiences for underrepresented student groups. Environmentally-induced changes in the transcriptome provide a widely used and relatively comprehensive snapshot of how cellular, tissue, or whole organismal physiology changes across environments. However, in commonly used experimental designs it is impossible to infer whether a change in abundance of any particular transcript has beneficial or detrimental effects on performance, and ultimately fitness. Common approaches to quantify differential expression in transcripts are further limited because they cannot distinguish the effects of new transcription and transcript degradation on transcript abundance. Thus, the transcriptional dynamics regulating transcriptomic environmental responses also remain largely unknown. This research will compare profiles of newly formed transcripts during low temperature exposures among replicate temperate- and tropical-origin Drosophila species. Combining sequencing of chromatin-associated RNA fractions and bromouridine-labeled new transcripts with standard messenger RNA sequencing, the research team will 1) identify putatively beneficial changes in new transcription or transcript degradation rates associated with adaptation to low temperature, and 2) characterize reaction norms for transcriptional dynamics in a comparative framework. The research will be integrated with undergraduate education by developing lab exercises that allow undergraduates to test the roles of individual genes in thermal adaptation using transgenically-modified lines of Drosophila melanogaster. This CURE will integrate with ongoing efforts at CU Denver to improve outcomes for underrepresented groups and increase their representation in STEM fields. The CURE will also generate a database of transparently reported results that will contribute to candidate gene testing in the field of thermal biology.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.