Topological characterization of human and mouse M⁵C epitranscriptome revealed by bisulfite sequencing

Background. Compared with the well-studied 5-methylcytosine (m⁵C) in DNA, the role and topology of epitranscriptome m⁵C remain insufficiently characterized. Results. Through analyzing transcriptome-wide m⁵C distribution in human and mouse, we show that the m⁵C modification is significantly enriched at 5′ untranslated regions (5′UTRs) of mRNA in human and mouse. With a comparative analysis of the mRNA and DNA methylome, we demonstrate that, like DNA methylation, transcriptome m⁵C methylation exhibits a strong clustering effect. Surprisingly, an inverse correlation between mRNA and DNA m⁵C methylation is observed at CpG sites. Further analysis reveals that RNA m⁵C methylation level is positively correlated with both RNA expression and RNA half-life. We also observed that the methylation level of mitochondrial RNAs is significantly higher than RNAs transcribed from the nuclear genome. Conclusions. This study provides an in-depth topological characterization of transcriptome-wide m⁵C modification by associating RNA m⁵C methylation patterns with transcriptional expression, DNA methylations, RNA stabilities, and mitochondrial genome.