mRNA psi profiling using nanopore DRS reveals cell type-specific pseudouridylation

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: May 10, 2024

Abstract Pseudouridine (psi) is one of the most abundant human mRNA modifications generated via psi synthases, including TRUB1 and PUS7 . Nanopore direct RNA sequencing combined with our recently developed tool, Mod- p ID, enables mapping, transcriptome-wide, without chemical derivatization input and/or conversion to cDNA. This method sensitive for detecting differences in positional occupancy across cell types, which can inform understanding impact on gene expression. We sequenced, mapped, compared six immortalized lines derived from diverse tissue types. found that lung-derived cells have highest proportion psi, while liver-derived lowest. Further, we find conserved positions mRNAs produce higher levels protein than expected, suggesting a role translation regulation. Interestingly, identify type-specific sites modification ubiquitously expressed genes. Finally, characterize transcripts multiple these be or type-specific, examples within same motif. Our data suggest contribute regulating trans-acting factors play major driving pseudouridylation.

Language: Английский

Nanopore signal deviations from pseudouridine modifications in RNA are sequence-specific: quantification requires dedicated synthetic controls

Scientific Reports, Journal Year: 2024, Volume and Issue: 14(1)

Published: Sept. 28, 2024

Language: Английский