Promoted Read-through and Mutation Against Pseudouridine-CMC By An Evolved Reverse Transcriptase

Pseudouridine (Y) is an abundant chemical modification that plays critical roles in cellular RNA metabolism and functions, and in RNA therapeutic applications. Transcriptome-wide mapping technologies present major advantages in discovering the functional contexts and crucial effector proteins of Y. Current mapping strategies for Ys are limited in identifying Ys at base-resolution within consecutive uridine sequence contexts where Y occurs frequently. Here we report “Mut-Y-seq” that utilities a recently evolved reverse transcriptase (“RT-1306”) coupled with the selective labeling of Y by the CMC treatment to identify Ys in mRNAs and non-coding RNAs from human cells. We showed that RT-1306 showed significantly promoted read-through and mutation signatures against the CMC-Y adduct; the mutation signatures generated by RT-1306 can discern the position of Y in consecutive uridine sequence contexts. We quantitatively characterized the Y-identification efficiencies by Mut-Y-seq under variable chemical treatment conditions by the receiver operating characteristic curve analysis and revealed the presence of potential false positive discoveries generated by side-reactions on unmodified uridines. Finally, the intersection of sites identified by orthogonal chemical treatments (i.e. CMC and bisulfite) produced a high-confidence list of Y sites in mRNAs and non-ribosomal long non-coding RNAs from HEK-293T cells. This report presents datasets for biological functional studies of endogenous Y sites, and sheds light on the combination of the reverse transcriptase engineering and selective chemical reactions for further expanding the toolkit for studying RNA chemical modifications. transcriptome-wide mapping of pseudouridines in RNAs extracted from HEK-293T cells with CMC treatment and evolved