Investigating the role of prion-mediated epigenetic regulation in yeast using an integrative approach of multi-omics

Northwestern University At Chicago, Evanston IL

Investigators

Abstract

Yeast prions are unusual genetic elements in the budding yeast, S. cerevisiae, transmitted as inheritable protein conformations. Due to its simplicity and amenability, yeast has become a powerful model system for studying prion biology. Multiple prion elements can co-exist in a single yeast cell, making it crucial to understand how they interact and how their interactions affect yeast cell biology. This project aims to examine how the Swi1 prion interacts with another yeast prion, Mot3, and how such prion-prion interactions affect yeast global transcription and protein-homeostasis. The proposed research program will serve as a platform to train graduate students and summer undergraduate interns. An outreach program will be established to connect Chicago-area underrepresented high school students at the Illinois Math and Science Academy with the Li research laboratory at the Feinberg School of Medicine, Northwestern University. This includes a one-day per week lab activity during the academic year and an eight-week long summer program. The ultimate broader impact is to propel disadvantaged youth in the Chicago area towards further science education and potentially to a science-oriented career. The protein determinant of the [SWI+] prion is Swi1, a subunit of the SWI/SNF chromatin remodeling complex, and the protein determinant of the [MOT3+] prion is Mot3, a transcription repressor. Both Swi1 and Mot3 are transcriptional modulators affecting yeast multicellularity. A single yeast cell can harbor both [SWI+] and [MOT3+], providing an excellent platform to study prion-prion interactions. The specific objectives of this project include: 1) Identify prion-specific changes in transcriptome and cell-to-cell heterogeneity using the technology of high-throughput single-cell RNA-sequencing. 2) Examine the genomic occupancies of important transcriptional modulators and epigenetic marks that are functionally linked to [SWI+] and/or [MOT3+] through the CUT&RUN-sequencing methodology. 3) Investigate prion-specific changes in proteomics and post-translational modifications using multiplex-labeling proteomics. The results from the proposed study will provide valuable insights into the interaction between the [SWI+] and [MOT3+] prions and their impact on global transcription and proteostasis. 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.