Dynamic landscape and regulation of m⁵C methylation in human tissues

5-methylcytosine (m⁵C) is a prevalent RNA modification that has various impacts on mRNA fate. Here, we generated 30 single-base resolution RNA m⁵C methylomes and revealed the dynamic nature of m⁵C of heart, muscle, lung, esophagus, stomach, pancreas, colon, jejunum, and rectum from 7 adult human individuals using RNA-BisSeq. Based on clustering analysis, the heart and muscle formed one cluster, while the remaining tissues constituted another cluster. Intriguingly, we observed a discrepancy pattern between m⁵C levels and gene expression in these tissues when comparing the m⁵C methylome and transcriptome. Moreover, we identified differences in NSUN2-mediated m⁵C modifications between esophageal paracancerous tissues and healthy individual tissues. Notably, NSUN2 was found to interact with PLXNA1 mRNA, and silencing NSUN2 in esophageal squamous cell carcinoma (ESCC) cells resulted in the downregulation of PLXNA1 expression through an m⁵C-mediated mechanism. Overall, our study provides valuable insights into the m⁵C profile and the relationship between the methylome and transcriptome in human tissues, highlighting the potential role of m⁵C modification as an epitranscriptomic biomarker.