Our current understanding of nucleic acid biology indicates that RNA plays a number of diverse roles in cellular processes ranging from protein translation and gene regulation to metabolite sensing and adaptive immunity. Concomitant with this functional diversity, is the rich chemical diversity of cellular RNA. To date, over 100 structurally distinct chemical modifications have been found, including both enzymatic and non-enzymatic modifications of the canonical ribonucleotides; however, there is a major gap in our understanding of how these chemical modifications impact RNA function.
Our goal is to decipher the chemical complexity of cellular RNA. Towards this end, we are developing and employing novel approaches integrating chemistry and biology to investigate the functional significance of RNA modifications and the interplay of RNA chemistry with cellular mechanisms regulating RNA function and integrity. Our studies rely heavily upon synthetic and chemoenzymatic strategies for generating modified nucleic acids, mass spectrometry-based proteomics, and quantitative cellular imaging, and aim to reveal fundamental biological mechanisms maintaining cellular homeostasis.
Chemical approaches to identify ‘readers’ of RNA modifications
Cellular RNA is subject to a diverse array of post-transcriptional modifications. We are interested in understanding the biochemical mechanisms underlying the function of “epitranscriptomic” modifications, a newly characterized class of RNA modifications that occur on mRNA and can regulate gene expression. Towards this end, we have developed a chemical proteomics approach relying upon photocrosslinking and quantitative mass spectrometry-based proteomics to characterize RNA-protein interactions regulated by RNA modifications. We have applied our approach to characterize the protein interactome of N6-methyladenosine (m6A), the most abundant internal modification on eukaryotic mRNA. We are now pursuing the biological functions of newly discovered m6A-regulated protein-RNA interactions.
Cellular response to RNA damage
Cells are constantly exposed to endogenous and exogenous factors that can damage the central carriers of genetic information – DNA and RNA. While cells have sophisticated surveillance mechanisms that identify and repair lesions within DNA, we know very little about the cellular response to RNA damage, despite the findings that RNA damage is: 1) more prevalent than DNA damage, and 2) deleterious to biological processes. RNA lesions can take many forms including oxidation, alkylation, UV photoproducts, abasic sites, and drug modifications. We are interested in understanding how diverse chemical lesions within RNA affect global RNA-protein interactions and impact biological processes. In addition, we are characterizing cellular quality control mechanisms that respond to RNA damage.
RNA trafficking in the cytosol (RNA-protein granules)
We are interested in the mechanisms underlying the assembly dynamics and function of cytosolic RNA-protein granules. These non-membrane bound organelles, which include stress granules and P-bodies, recruit RNA transcripts in response to diverse cellular signals, and have important roles in regulating RNA metabolism. Studies have revealed that granules are composed of characteristic sets of proteins, however their RNA components have remained poorly understood. We are developing new approaches to characterize the incorporation of mRNA transcripts into RNA-protein granules, with a particular emphasis on understanding how epitranscriptomic RNA modifications regulate the accumulation of transcripts in stress granules.