The function of NSUN4 (NOP2/Sun RNA methyltransferase 4, Ensembl gene identifier ENSG00000117481) is as follows. Mitochondrial RNA cytosine C(5)-methyltransferase that methylates cytosine to 5-methylcytosine (m5C) in various RNAs, such as rRNAs, mRNAs and some long non-coding RNAs (lncRNAs) (PubMed:21531335, PubMed:23022348, PubMed:39019044). Involved in mitochondrial ribosome small subunit (SSU) maturation by catalyzing methylation of mitochondrial 12S rRNA; the function is independent of MTERFD2/MTERF4 and assembled mitochondrial ribosome large subunit (LSU) (PubMed:21531335, PubMed:23022348). Targeted to LSU by MTERFD2/MTERF4 and probably is involved in a final step in ribosome biogenesis to ensure that SSU and LSU are assembled (PubMed:21531335, PubMed:23022348). In vitro can methylate 16S rRNA of the LSU; the methylation is enhanced by MTERFD/MTERF4 (PubMed:23022348). Also acts as a regulator of innate immunity by marking double-stranded mitochondrial RNAs(mt-dsRNAs) generated in response to stress: catalyzes m5C modification on mitochondrial RNAs, such as a mRNAs and lncRNAs, with a preference for the termini of light-strand lncRNAs, promoting their degradation and cytosolic release (PubMed:39019044). Modified light-strand lncRNAs are then recognized by C1QBP reader and recruited to the mitochondrial degradosome complex, which promotes their degradation (PubMed:39019044). {ECO:0000269|PubMed:21531335, ECO:0000269|PubMed:23022348, ECO:0000269|PubMed:39019044}.