Research
The research of the Chanfreau lab focuses on mechanisms of RNA processing and degradation, using Saccharomyces Cerevisiae, also known as brewer’s yeast, as a model organism. Yeast is a useful organism for studying RNA processing as it’s mechanisms are more simple than in higher eukaryotes. Our lab has several ongoing research projects that are each investigating the underlying principles governing the life cycle of RNA- from transcription to degradation.
Direct RNA Sequencing and RNA Degradation Pathways
RNA degradation can occur through a variety of pathways, which provide efficient mechanisms for rapid control of gene expression. While many canonical RNA degradation pathways have been well characterized, others are poorly understood but still play an important role in gene regulation. In order to study these isoforms that show varying degrees of stability in different cellular contexts, we utilize direct long-read RNA sequencing, as it provides vast amounts of information on both the identity of RNA isoforms and how they are produced and degraded. By utilizing computational and RNA sequencing technologies together, we are able to analyze novel methods of RNA degradation as well as characterize specific factors that play a role in regulating the RNA transcriptome.
Coordination between RNA processing reactions in eukaryotic gene expression
3’-end processing by cleavage and 3 polyadenylation (CPA) and excision of introns by RNA splicing occur co-transcriptionally, which gives the proteins carrying out both processes the opportunity to directly interact. We use RNA sequencing and other approaches to investigate how these processes impact one another, and how deficient transcription termination due to defects in CPA can impact splicing of RNAs.
RNA structures and Gene regulation
RNA secondary structures can impact a variety of processes, including sequestering signals required for splicing or translation, as well as generating cleavage site for endonucleases specific for double-stranded RNAs. We are using a combination of computational RNA folding, RNA-sequencing, and biochemical experiments to determine if changes in RNA secondary structures can influence gene regulation through various mechanisms.
