RNA cytosine C(5)-methyltransferase that methylates cytosine to 5-methylcytosine (m5C) in various RNAs, such as tRNAs, mRNAs and some long non-coding RNAs (lncRNAs). Involved in various processes, such as epidermal stem cell differentiation, testis differentiation and maternal to zygotic transition during early development: acts by increasing protein synthesis; cytosine C(5)-methylation promoting tRNA stability and preventing mRNA decay. Methylates cytosine to 5-methylcytosine (m5C) at positions 34 and 48 of intron-containing tRNA(Leu)(CAA) precursors, and at positions 48, 49 and 50 of tRNA(Gly)(GCC) precursors. tRNA methylation is required generation of RNA fragments derived from tRNAs (tRFs). Also mediates C(5)-methylation of mitochondrial tRNAs. Catalyzes cytosine C(5)-methylation of mRNAs, leading to stabilize them and prevent mRNA decay. Cytosine C(5)-methylation of mRNAs also regulates mRNA export. Also mediates cytosine C(5)-methylation of non-coding RNAs, such as vault RNAs (vtRNAs), promoting their processing into regulatory small RNAs. Required for proper spindle assembly and chromosome segregation, independently of its methyltransferase activity. cytidine(48) in tRNA + S-adenosyl-L-methionine = 5-methylcytidine(48) in tRNA + H(+) + S-adenosyl-L-homocysteine cytidine(49) in tRNA + S-adenosyl-L-methionine = 5-methylcytidine(49) in tRNA + H(+) + S-adenosyl-L-homocysteine cytidine(50) in tRNA + S-adenosyl-L-methionine = 5-methylcytidine(50) in tRNA + H(+) + S-adenosyl-L-homocysteine cytidine(34) in tRNA precursor + S-adenosyl-L-methionine = 5-methylcytidine(34) in tRNA precursor + H(+) + S-adenosyl-L-homocysteine a cytidine in mRNA + S-adenosyl-L-methionine = a 5-methylcytidine in mRNA + H(+) + S-adenosyl-L-homocysteine Belongs to the class I-like SAM-binding methyltransferase superfamily. RsmB/NOP family. TRM4 subfamily.