bioRxiv preprint doi: https://doi.org/10.1101/710061; this version posted May 5, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Transcriptome-wide sites of collided ribosomes reveal principles of translational pausing Alaaddin Bulak Arpata, Ang´elicaLiechtia, Mara De Matosa, Ren´eDreosa, Peggy Janicha,b, David Gatfielda,∗ aCenter for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland bpresent address: Krebsliga Schweiz, 3001 Bern, Switzerland Abstract Translation initiation is the major regulatory step defining the rate of protein production from an mRNA. Meanwhile, the impact of non-uniform ribosomal elongation rates is largely unknown. Using a modified ribosome profiling protocol based on footprints from two closely packed ribosomes (dis- omes), we have mapped ribosomal collisions transcriptome-wide in mouse liver. We uncover that the stacking of an elongating onto a paused ribosome occurs frequently and scales with translation rate, trapping ∼10% of translating ribosomes in the disome state. A distinct class of pause sites, indepen- dent of translation rate, is indicative of deterministic pausing signals. Pause site association with specific amino acids, peptide motifs and nascent polypeptide structure, is suggestive of programmed pausing as a widespread mechanism associated with protein folding. Evolutionary conservation at disome sites indicates functional relevance of translational pausing. Collectively, our disome profiling approach allows unique insights into gene regulation occurring at the step of translation elongation. ∗Lead Contact: Email address:
[email protected] (David Gatfield) bioRxiv preprint doi: https://doi.org/10.1101/710061; this version posted May 5, 2020.