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.