Ribosome profiling of H9 PUS7KO

Transfer RNA (tRNA)-derived fragments (tRF) are emerging small noncoding (nc) RNAs that, while commonly altered in cancer, have poorly defined roles in tumorigenesis. Here we show that pseudouridylation (Y) of a stem-cell-enriched tRF subtype, mTOG, selectively modulates malignant protein synthesis programs, thereby promoting differentiation of myelodysplastic syndrome (MDS) hematopoietic stem and progenitor cells (HSPC). Building on evidence that mTOG targets the polyadenylate-binding protein cytoplasmic 1 (PABPC1), we employed isotope exchange proteomics to reveal critical interactions between mTOG and functional RNA-recognition motif (RRM) domains in PABPC1. Mechanistically, this hinders the recruitment of the translational co-activator PABPC1-interacting protein 1 (PAIP1)3 and selectively represses translation of transcripts sharing pyrimidine-enriched sequences (PES) in their 5’UTR including 5’ terminal oligopyrimidine tracts (TOP) that encode protein machinery components, and are frequently altered in cancer4. Significantly, mTOG dysregulation leads to aberrant 5’PES mRNA translation in malignant MDS-HSPC and is clinically associated with leukemic transformation and decreased patient survival. Taken together, these results unveil a critical role for tRF and Y in difficult-to-treat subsets of MDS characterized by high risk of progression to acute myeloid leukemia. Evaluation of hESC WT and PUS7-KO translatome using ribosome profiling