RNA is heavily modified with chemical marks, which add an additional layer of control of gene expression. Several of the most abundant modifications, including pseudouridine, inosine, and N6-methyladenosine, have yet to be fully investigated regarding their selective installation, function, dynamic regulation, and relation with innate immunity. Our lab is endeavoring to answer these questions by combining cutting-edge biochemical, genetic, and bioinformatic tools.
1. Biogenesis and function of the Pseudouridine Modification
Pseudouridine is one of the most abundant modified nucleotides in RNA and is found in various types of RNA, including tRNA, rRNA, mRNA, and non-coding RNAs. It is catalyzed by either standalone enzymes or H/ACA snoRNA-dependent RNP complexes. Pseudouridine synthases are linked to human diseases such as neurodevelopmental disorders, mitochondrial myopathy and sideroblastic anemia (MLASA), dyskeratosis congenita, and various cancers. Our lab recently developed a robust tool to label and map this modification transcriptome-wide. We aim to leverage existing tools and develop new ones to address the following questions: 1) What are associations of RNA pseudouridinylation with human diseases and what is its potential as a clinical biomarker? 2) Are there any reader proteins involved in the function of pseudouridine? and 3) Can we further modulate the properties of the modified RNA through targeting pseudouridine?
2. Dynamic Regulation of m6A modifications in neuronal development
Recent studies show that RNA modifications, including m6A, Ψ, and inosine, are particularly abundant in the brain and m6A has been demonstrated to play crucial roles in neuronal development, a process requiring precise spatial and temporal regulation of RNA expression. Understanding the detailed mechanism of how m6A and other modifications contribute to this process necessitates dissecting its location specific and real-time regulations. However, current methods to profile RNA modifications normally use RNAs isolated from bulk cells, lacking the resolution to study modifications at specific subcellular locations or in real-time. To address these challenges, we aim to develop new tools to probe dynamics of RNA modifications within living cells, in order to provide deeper insights into the molecular mechanism of how modifications are involved in neurodevelopment and associated diseases.
3. Roles of RNA Modifications in innate immunity
A few RNA modifications, including Inosine and pseudouridine, have been implicated in marking self-RNA and distinguishing it from invading virus RNAs, thereby preventing inappropriate activation of innate immune response in unaffected cells. We are conducting hypothesis driven research aiming to build a more clear crosstalk between specific RNA modifications and innate immune suppression and identify novel players and mechanisms within these pathways.