Transcriptome-wide mapping reveals a diverse dihydrouridine landscape including mRNA
Fig 2
D-seq identifies known and novel dihydrouridine sites in structured ncRNAs.
(A) Plots of cDNA end positions in Dus2 target tRNA ProAGG and Dus2, Dus4 target tRNA ArgCCG. D Peaks are highlighted. X scale in RPM and Y scale in bp. (B) Summary of known tRNA D positions and corresponding DUS. (C) Plots of cDNA end positions in snR5, snR13, and snR46 snoRNAs. D peaks are highlighted. TSS (transcription start site) of snR5. X scale in RPM and Y scale in bp. (D) snoRNA Ds occur primarily in stem-loop structures that resemble tRNA D loops. Plot of median DMS-induced mutation rate in 25 nt window flanking D site. Red trace is median DMS reactivity flanking D positions. Black dots are median DMS reactivity for randomly selected set of background positions. Blue trace is p-value for difference in DMS reactivity for sequences flanking D or background sites. (E) D sites occur in stem-loop structures of 16 H/ACA and 7 C/D box snoRNAs. The data underlying this figure can be found in S1 and S2 Tables. DMS, dimethyl sulfate; D-seq, dihydrouridine sequencing; ncRNA, non-coding RNA; snoRNA, small nucleolar RNA; TSS, transcription start site.