Cell-type-specific translational regulation by human DUS enzymes [iCLIP]

Dihydrouridine is an abundant and evolutionary conserved modified nucleoside present on tRNA, but characterization and functional studies of individual modification sites and associated DUS writer enzymes in mammals is lacking. Here we use a chemical probing strategy, RNABPP-PS, to identify 5-chlorouridine as a general activity-based probe for human DUS enzymes. We map D modifications using mechanism-based RNA-protein crosslinking and also through chemical reactivity and mutational profiling to reveal the landscape of D modification sites on human tRNAs. Further, we knockout individual DUS genes in two model human cell lines to investigate their regulation of tRNA expression levels and codon-specific translation elongation. We show that whereas D modifications are present across most tRNA species, loss of D only perturbs the translational function of a subset of tRNAs in a cell-type-specific manner. Our work provides powerful chemical strategies for investigating D and DUS enzymes in diverse biological systems and provides insight into the role of a ubiquitous tRNA modification in translational regulation. iCLIP sequencing samples of 5-ClUrd-treated 3xFLAG-DUS1L cells, 2 biological replicates with 2 untreated replicates and iCLIP sequencing samples of 5-ClUrd-treated 3xFLAG-DUS2L cells, 2 biological replicates with 2 untreated replicates