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

许多生物体会根据环境的变化而改变它们的生理机能，这种现象被称为可塑性。其中一些变化可能是有益的，帮助生物体在不利的条件下生存。但其他变化可能代价高昂或具有破坏性，如果条件足够恶劣，最终可能导致死亡。在测量生理可塑性的普通实验中，通常不可能确定哪些变化是有益的，哪些是有害的。这阻碍了理解可能促进或限制对变化环境的反应的生理机制。这项研究探讨了低温如何影响转录，这是合成新蛋白质过程中的关键步骤。通过比较经常遇到非常寒冷的温度（远低于冰点）的温带蝇类和很少遇到寒冷温度的热带蝇类的低温反应，研究人员将确定哪些过程有利于在寒冷环境中持续生存。这项研究还将尝试量化转录的低温极限，并测试当果蝇经历新的环境时，这些极限是否会进化。本研究将与本科阶段的生物学教育相结合。研究人员将开发一种基于课程的本科生研究体验（CURE），让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获得研究的机会往往较少；CURE将有目的地鼓励广泛参与，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为细胞、组织或整个生物体生理如何在不同环境中发生变化提供了广泛使用且相对全面的快照。然而，在常用的实验设计中，不可能推断出任何特定转录物丰度的变化对性能和最终适应性是否有有益或有害的影响。由于无法区分新转录和转录物降解对转录物丰度的影响，量化转录物差异表达的常用方法受到进一步限制。因此，调控转录组环境反应的转录动力学在很大程度上仍然是未知的。本研究将比较低温暴露下复制温带和热带起源的果蝇物种中新形成的转录本的概况。结合染色质相关RNA片段的测序和溴胺标记的新转录物与标准信使RNA测序，研究小组将1)确定与低温适应相关的新转录或转录物降解率的推定有益变化，2)在比较框架中表征转录动力学的反应规范。该研究将通过开发实验室练习与本科教育相结合，允许本科生使用转基因果蝇品系测试个体基因在热适应中的作用。该CURE将与科罗拉多大学丹佛分校的持续努力相结合，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还将建立一个透明报告结果的数据库，这将有助于热生物学领域的候选基因测试。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。

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.