title: Widespread occurrence of 5-methylcytosine in human coding and non-coding RNA.
abstract: The modified base 5-methylcytosine (m(5)C) is well studied in DNA, but investigations of its prevalence in cellular RNA have been largely confined to tRNA and rRNA. In animals, the two m(5)C methyltransferases NSUN2 and TRDMT1 are known to modify specific tRNAs and have roles in the control of cell growth and differentiation. To map modified cytosine sites across a human transcriptome, we coupled bisulfite conversion of cellular RNA with next-generation sequencing. We confirmed 21 of the 28 previously known m(5)C sites in human tRNAs and identified 234 novel tRNA candidate sites, mostly in anticipated structural positions. Surprisingly, we discovered 10,275 sites in mRNAs and other non-coding RNAs. We observed that distribution of modified cytosines between RNA types was not random; within mRNAs they were enriched in the untranslated regions and near Argonaute binding regions. We also identified five new sites modified by NSUN2, broadening its known substrate range to another tRNA, the RPPH1 subunit of RNase P and two mRNAs. Our data demonstrates the widespread presence of modified cytosines throughout coding and non-coding sequences in a transcriptome, suggesting a broader role of this modification in the post-transcriptional control of cellular RNA function.
authors.affiliation: Molecular Genetics Division, Victor Chang Cardiac Research Institute, Darlinghurst, Sydney, NSW, 2010, Australia.
authors.forename: Jeffrey E
authors.initials: JE
authors.lastname: Squires
authors.forename: Hardip R
authors.initials: HR
authors.lastname: Patel
authors.forename: Marco
authors.initials: M
authors.lastname: Nousch
authors.forename: Tennille
authors.initials: T
authors.lastname: Sibbritt
authors.forename: David T
authors.initials: DT
authors.lastname: Humphreys
authors.forename: Brian J
authors.initials: BJ
authors.lastname: Parker
authors.forename: Catherine M
authors.initials: CM
authors.lastname: Suter
authors.forename: Thomas
authors.initials: T
authors.lastname: Preiss
mesh_terms: D044503:5-Methylcytosine / Q000032:analysis* / Q000378:metabolism; D004248:DNA (Cytosine-5-)-Methyltransferases / Q000378:metabolism; D006367:HeLa Cells; D006801:Humans; D008780:Methyltransferases / Q000378:metabolism; D012333:RNA, Messenger / Q000737:chemistry*; D012335:RNA, Ribosomal / Q000737:chemistry; D012343:RNA, Transfer / Q000737:chemistry; D022661:RNA, Untranslated / Q000737:chemistry*; D017423:Sequence Analysis, RNA; D059467:Transcriptome
chemical_list: D012333:RNA, Messenger; D012335:RNA, Ribosomal; D022661:RNA, Untranslated; D044503:5-Methylcytosine; D012343:RNA, Transfer; D008780:Methyltransferases; C515610:NSUN2 protein, human; D004248:DNA (Cytosine-5-)-Methyltransferases; C112218:TRDMT1 protein, human