Base-resolution m5C profiling across the mammalian transcriptome by bisulfite-free enzyme-assisted chemical labeling approach

5-methylcytosine (m5C) is a prevalent RNA modification crucial for gene expression regulation. However, accurate and sensitive m5C sites identification remains challenging due to severe RNA degradation and reduced sequence complexity during bisulfite sequencing (BS-seq). Here, we report m5C-TAC-seq, a bisulfite-free approach combining TET-assisted m5C-to-f5C oxidation with selective chemical labeling, therefore enabling direct base-resolution m5C detection through pre-enrichment and C-to-T transitions at m5C sites. With m5C-TAC-seq, we comprehensively profiled the m5C methylomes in human and mouse cells, identifying a substantially larger number of confident m5C sites. Through perturbing potential m5C methyltransferases, we deciphered the responsible enzymes for most m5C sites, including the characterization of NSUN5’s involvement in mRNA m5C deposition. Additionally, we characterized m5C dynamics during mESC differentiation. Notably, the mild reaction conditions and preservation of nucleotide composition in m5C-TAC-seq allow m5C detection in chromatin-associated RNAs. The accurate and robust m5C-TAC-seq will advance research into m5C methylation functional investigation. [Display omitted] •m5C-TAC-seq utilizes TET-assisted chemical labeling to induce C-to-T at m5C sites•m5C-TAC-seq achieves comprehensive m5C profiling across the transcriptomes•m5C-TAC-seq identifies m5C dynamics in diverse biological processes•m5C-TAC-seq reveals m5C methylations can be deposited in caRNAs Lu et al. develop m5C-TAC-seq, a bisulfite-free method for single-base-resolution m5C profiling across transcriptomes. The direct detection feature of m5C-TAC-seq enables the identification of low-stoichiometry m5C sites. Additionally, the preservation of nucleotide compositions and the mild reaction conditions in m5C-TAC-seq allow m5C detection in various RNA species, including low-abundance and low-sequence-complexity RNAs.