Over 100 types of distinct modifications are known to be catalyzed post-transcriptionally across different classes of RNA. Currently, we lack a comprehensive understanding of which of these modifications even occurs in mRNA, a critical first step towards dissecting function and mechanism. We are developing experimental methodologies coupled with analytic pipelines for quantifying, mapping and characterizing an array of modifications in mRNA.
mRNAs have a complex post-transcriptional life cycle, including processing, export, localization, translation and degradation. Which of these steps are impacted by RNA modifications? We will systematically address these questions, using diverse approaches at various scales, ranging from massively parallel reporter assays, allowing simultaneous interrogation of thousands of variants differing in their modification states, to careful interrogation of individual sites in vivo.
How do modifications on RNA exert their effect? We will systematically address the question of how, mechanistically, RNA modifications exert their effect. Do they recruit specific 'readers' to the modification? Do they alter the secondary structure of the RNA? Do they modulate the genetic code? We will utilize genomic, biochemical and computational strategies to address these questions, to reveal the cellular machinery underlying the decoding of RNA modifications.