Chemical Approaches to Decipher Transcription and RNA Metabolism

Gene expression involves complex processes and determines cell fate and physiological functions. Dysfunction of gene expression regulation is associated with human diseases. Coupled with the next-generation sequencing, small-molecule probes and nucleic acid analogs have been widely involved in interrogating gene expression and its regulatory mechanisms in a high-throughput manner. Although powerful, existing techniques have different limitations, and the current chemical toolbox still needs to be expanded. My doctoral work focus on the development and applications of a novel chemical probe, N3-kethoxal, which reacts specifically with guanine in single-stranded regions of DNA and RNA. I showed that N3-kethoxal serves as a versatile tool that helps to profile RNA secondary structures, RNA-RNA interactions, and transcription dynamics. I also show that METTL4-mediated DNA N6-methyldeoxyadenosine (6mA) modification accumulates in mammalian mitochondrial DNA (mtDNA). 6mA attenuates mitochondrial activity by repressing mtDNA transcription and replication.