RNA, which conveys genetic information from DNA to protein, is heavily modified with over 170 types of chemical marks. These modifications significantly enhance the diversity and complexity of RNA molecules, adding 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. There are 13 pseudouridine synthases in human, each with different specificities. 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 new robust tool to map this modification transcriptome-wide. We aim to leverage existing tools and develop new ones to address the following questions regarding pseudouridine and other modifications: Why do cells require such a diverse array of writing machinery for a single type of modification? What are the specific substrates for each of the 13 writer proteins within the cells? How do these writer proteins recognize their respective substrates? Which snoRNAs pseudouridylate which pseudouridine modifications in mRNA? What roles does pseudouridine play in messenger RNA, particularly in the non-coding regions and at sense codons? Are there any reader proteins involved in the function of pseudouridine? Can we further modulate the properties of the modified RNA?
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, are indicated to play important roles in innate immunity. How are RNA modifications spatially and temporally regulated in cells? How do modifications respond to immune stimulation, and how does this process contribute to the cellular defense mechanism during viral infection? We will investigate these mechanisms in detail.