Figure 2

A comparison of m⁵C target sites identified by three transcriptome-wide approaches (Additional file1) [[18, 23, 24]]. The bisulfite study identifies the global pattern of m⁵C methylation in the genome, while the AzaIP and miCLIP data shown focus specifically on Nsun2-mediated methylation. (a) Types of transcripts found to be methylated by each technique. (b) Comparison of the genomic locations of individual methylation sites found by each of the three approaches. The Venn diagrams show the overlap between all sites (upper panel), the sites that map to tRNAs (middle panel), and non-tRNA sites (lower panel). (c) Non-tRNA target sites found in at least two of the three studies, which represent high-confidence sites. The genomic location (hg19) of methylated cytosines is given. * = target sites that overlap with tRNA locations. (d) The proportion of miCLIP-identified targets occurring in exons/introns/UTRs of mRNAs, including those sites overlapping with tRNA genes. (e) Genome browser view of the miCLIP-identified SHF mRNA methylation. Predicted methylation sites are indicated by the black peaks. Note that methylation may occur either in an SHF mRNA intron or within a tRNA, which is transcribed from the same genomic DNA strand. (f) miCLIP data showing identified sites within the CTC1 3′ UTR. The CTC1 3′ UTR contains three tRNA genes predicted to be transcribed from the same genomic DNA strand. The miCLIP predicted methylation sites (black peaks) overlapped specifically with these three regions. (g) An example showing that all miCLIP sequence reads, indicated by purple bars, only extend slightly beyond the annotated tRNA genes. It is most likely that these represent extensions only into the 3′ trailer sequences of tRNAs, and that tRNA rather than mRNA methylation is being detected.