RNA methylation plays a significant regulatory role in various of physiological activities and it has gradually become a hotspot of epigenetics in the past decade. 2′-O-methyladenosine (Am), 2′-O-methylguanosine (Gm),2′-O-methylcytidine (Cm),2′-O-methyluridine (Um),N 6-methyladenosine (m6A), N 1-methylguanosine (m1G),5-methylcytidine (m5C),and 5-methyluridine (m5U) are representative 2′-O-methylation and base-methylation modified epigenetic marks of RNA. 5-Methylcytosine (5mC), a modified nucleobase derived from cytosine, is present in both DNA and RNA molecules. 5mC in DNA is an essential epigenetic mark associated with gene silencing and genome stability during embryonic development. 5mC in ribonucleoside, called 5-methylcytidine (m5C), is involved in structural stability, aminoacylation and codon recognition of tRNA. In rRNA, m5C affects translational fidelity and tRNA recognition. m5C-modified nucleobase also have been identified in mRNA and other non-coding RNA but the biological functions are still unclear. m5C is detected not only in tissues and cells but also in urine. It is reported that the levels of m5C change in urine or tissues from patients with various diseases such as bladder, breast and colon cancers.