The Rouskin lab investigates co-transcriptional RNA folding at splice sites in cells. A simple model of alternative splicing regulation is that RNA folding can occlude or expose these sequence features thereby promoting or inhibiting splicing. Regulation of human splicing by RNA structure is a long-standing hypothesis, with indirect evidence, and has remained unexplored due to technical limitations. Our goal is to provide quantitative models for RNA folding and RNA-protein interactions that predict cell-type specific and disease-specific alternative splicing on a genome-wide level.
Rouskin and her lab use a small molecule called DMS (dimethyl sulfate) that enters cells rapidly and modifies unpaired adenine and cytosine bases in the RNA. This assay is coupled with high-throughput sequencing such that the DMS-modified bases can be detected either transcriptome-wide or for a selected population of RNA molecules. The methods they develop in the process are widely universal and aimed at determining basic principles through which the chemical properties of RNA have a profound effect on gene expression.
Another area of interest for the Rouskin Lab is Human Immunodeficiency Virus-1 (HIV-1). The HIV-1 virus must express all of its gene products from the same 10-kb single-stranded RNA primary transcript, which undergoes alternative splicing to produce diverse protein products. Despite the critical role of alternative splicing, the mechanisms driving splice-site choice are poorly understood. Previous work on the genome-wide HIV-1 RNA structure in vitro and in virion provided a population average model. Our lab, however, determined the structure of HIV-1 RNA in cells and revealed the importance of alternative conformations assumed by the same RNA sequence in controlling viral gene expression.
Amidst the COVID19 outbreak, the Rouskin lab is currently prioritizing probing the structure of the entire SARS-CoV2 30kb genome in vivo, including structures in the 5’UTR and frameshift element which are important for virus replication and life-cycle. Like many others, Rouskin hopes to contribute towards scientific understanding of this virus and share what she learns as quickly as possible.
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