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

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.