{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T21:19:06Z","timestamp":1792790346324,"version":"4.5.0"},"posted":{"date-parts":[[2026,7,22]]},"group-title":"Molecular Biology","reference-count":51,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2026,7,22]],"date-time":"2026-07-22T00:00:00Z","timestamp":1784678400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/publicdomain\/zero\/1.0\/"}],"funder":[{"name":"National Cancer Institute","award":["T32CA009582"],"award-info":[{"award-number":["T32CA009582"]}]},{"name":"National Institute of General Medical Sciences","award":["R00GM144688-04"],"award-info":[{"award-number":["R00GM144688-04"]}],"id":[{"id":"https:\/\/ror.org\/04q48ey07","id-type":"ROR","asserted-by":"crossref"}]},{"name":"Intramural Research Program of the NIH, the National Institute of Diabetes and Digestive and Kidney Diseases","award":["DK075132"],"award-info":[{"award-number":["DK075132"]}],"id":[{"id":"https:\/\/ror.org\/00adh9b73","id-type":"ROR","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2026,10,6]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                <jats:sec>\n                  <jats:title>Background<\/jats:title>\n                  <jats:p>Ribosomes stall when they encounter problematic codons or cellular stress that perturbs translation. Stalled ribosomes can lead to the formation of ribosome collisions, also known as disomes, that engage cellular surveillance and stress signaling pathways. How many disomes form during basal conditions and how disome levels change under stress remain poorly understood.<\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We used spike-in normalized Ribo-seq and Disome-seq to quantify transcriptome-wide disome levels. Applying this approach in yeast and human cells, we found that disomes generate approximately 2-10% of all footprints under basal conditions. A high-resolution Disome-seq experiment in human cells identified reproducible disome-forming sites that contribute to the basal level of disome formation in the cell. Exposure of yeast cells to methyl methanesulfonate and human cells to anisomycin increased disome abundance up to four-fold and redistributed collisions in a stress-specific and context-dependent manner.<\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Conclusions<\/jats:title>\n                  <jats:p>These data provide a quantitative, transcriptome-wide framework for measuring disome levels and reveal how translational stress reshapes the landscape of ribosome collisions in cells.<\/jats:p>\n                <\/jats:sec>","DOI":"10.64898\/2026.07.21.739814","type":"posted-content","created":{"date-parts":[[2026,7,22]],"date-time":"2026-07-22T21:05:31Z","timestamp":1784754331000},"source":"Crossref","is-referenced-by-count":1,"title":["Quantitative profiling of basal and stress-induced ribosome collisions"],"prefix":"10.64898","author":[{"given":"James","family":"Marks","sequence":"first","affiliation":[{"name":"Department of Biochemistry, Vanderbilt University, Nashville, TN, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pedro H","family":"Ayres-Galhardo","sequence":"additional","affiliation":[{"name":"Department of Biochemistry, Vanderbilt University, Nashville, TN, USA"},{"name":"Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bavavarshini","family":"Tamilselvam","sequence":"additional","affiliation":[{"name":"Department of Biochemistry, Vanderbilt University, Nashville, TN, USA"},{"name":"Department of Human Genetics, McGill University, Montreal, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexis B","family":"Roberson","sequence":"additional","affiliation":[{"name":"Department of Biochemistry, Vanderbilt University, Nashville, TN, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ruby","family":"Pitts","sequence":"additional","affiliation":[{"name":"Department of Biochemistry, Vanderbilt University, Nashville, TN, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7116-326X","authenticated-orcid":false,"given":"Nicholas R","family":"Guydosh","sequence":"additional","affiliation":[{"name":"National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sezen","family":"Meydan","sequence":"additional","affiliation":[{"name":"Department of Biochemistry, Vanderbilt University, Nashville, TN, USA"},{"name":"Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN, USA"},{"name":"Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2026101001550823000_2026.07.21.739814v2.1","doi-asserted-by":"publisher","DOI":"10.1038\/s41594-019-0331-x"},{"key":"2026101001550823000_2026.07.21.739814v2.2","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2016.05.070"},{"key":"2026101001550823000_2026.07.21.739814v2.3","doi-asserted-by":"publisher","DOI":"10.1261\/rna.2411710"},{"key":"2026101001550823000_2026.07.21.739814v2.4","doi-asserted-by":"publisher","DOI":"10.15252\/embj.2019103365"},{"key":"2026101001550823000_2026.07.21.739814v2.5","doi-asserted-by":"publisher","DOI":"10.1016\/j.molcel.2017.03.003"},{"key":"2026101001550823000_2026.07.21.739814v2.6","doi-asserted-by":"publisher","DOI":"10.1016\/j.celrep.2014.10.042"},{"key":"2026101001550823000_2026.07.21.739814v2.7","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-019-13579-3"},{"key":"2026101001550823000_2026.07.21.739814v2.8","doi-asserted-by":"publisher","DOI":"10.1016\/j.molcel.2018.06.041"},{"key":"2026101001550823000_2026.07.21.739814v2.9","doi-asserted-by":"publisher","DOI":"10.1126\/science.1249749"},{"key":"2026101001550823000_2026.07.21.739814v2.10","doi-asserted-by":"publisher","DOI":"10.1128\/MCB.17.6.3373"},{"key":"2026101001550823000_2026.07.21.739814v2.11","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2020.06.006"},{"key":"2026101001550823000_2026.07.21.739814v2.12","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pbio.2001882"},{"key":"2026101001550823000_2026.07.21.739814v2.13","doi-asserted-by":"crossref","unstructured":"Diamond, P.D. , Sauer, P.V. , Holm, M. , Swanson-Swett, C.J. , Ferguson, L. , Bratset, N.M. , Wienker, G.W. , Sim, J.S. , Adams, H.K. , Kenner, L. , et al. (2026). Context-dependent translation inhibition as a cancer therapeutic modality. Nat Commun 17.","DOI":"10.1038\/s41467-026-69891-2"},{"key":"2026101001550823000_2026.07.21.739814v2.14","doi-asserted-by":"publisher","DOI":"10.1007\/s00294-020-01111-w"},{"key":"2026101001550823000_2026.07.21.739814v2.15","doi-asserted-by":"publisher","DOI":"10.1002\/cbic.202300264"},{"key":"2026101001550823000_2026.07.21.739814v2.16","doi-asserted-by":"publisher","DOI":"10.1038\/s41580-019-0118-2"},{"key":"2026101001550823000_2026.07.21.739814v2.17","doi-asserted-by":"publisher","DOI":"10.1016\/j.molcel.2018.08.037"},{"key":"2026101001550823000_2026.07.21.739814v2.18","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2012.10.044"},{"key":"2026101001550823000_2026.07.21.739814v2.19","doi-asserted-by":"publisher","DOI":"10.1016\/j.molcel.2017.08.019"},{"key":"2026101001550823000_2026.07.21.739814v2.20","doi-asserted-by":"crossref","unstructured":"Ikeuchi, K. , Tesina, P. , Matsuo, Y. , Sugiyama, T. , Cheng, J. , Saeki, Y. , Tanaka, K. , Becker, T. , Beckmann, R. , and Inada, T . (2019). Collided ribosomes form a unique structural interface to induce Hel2-driven quality control pathways. EMBO J 38.","DOI":"10.15252\/embj.2018100276"},{"key":"2026101001550823000_2026.07.21.739814v2.21","doi-asserted-by":"publisher","DOI":"10.1016\/j.molcel.2020.06.010"},{"key":"2026101001550823000_2026.07.21.739814v2.22","doi-asserted-by":"publisher","DOI":"10.1016\/j.molcel.2020.11.033"},{"key":"2026101001550823000_2026.07.21.739814v2.23","doi-asserted-by":"crossref","unstructured":"Pochopien, A.A. , Beckert, B. , Kasvandik, S. , Berninghausen, O. , Beckmann, R. , Tenson, T. , and Wilson, D.N . (2021). Structure of Gcn1 bound to stalled and colliding 80S ribosomes. Proc Natl Acad Sci U S A 118.","DOI":"10.1073\/pnas.2022756118"},{"key":"2026101001550823000_2026.07.21.739814v2.24","doi-asserted-by":"publisher","DOI":"10.1006\/scel.1994.1049"},{"key":"2026101001550823000_2026.07.21.739814v2.25","doi-asserted-by":"crossref","unstructured":"Juszkiewicz, S. , Slodkowicz, G. , Lin, Z. , Freire-Pritchett, P. , Peak-Chew, S.Y. , and Hegde, R.S . (2020). Ribosome collisions trigger cis-acting feedback inhibition of translation initiation. Elife 9.","DOI":"10.7554\/eLife.60038"},{"key":"2026101001550823000_2026.07.21.739814v2.26","doi-asserted-by":"crossref","unstructured":"Sinha, N.K. , Ordureau, A. , Best, K. , Saba, J.A. , Zinshteyn, B. , Sundaramoorthy, E. , Fulzele, A. , Garshott, D.M. , Denk, T. , Thoms, M. , et al. (2020). EDF1 coordinates cellular responses to ribosome collisions. Elife 9.","DOI":"10.7554\/eLife.58828"},{"key":"2026101001550823000_2026.07.21.739814v2.27","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2024.05.018"},{"key":"2026101001550823000_2026.07.21.739814v2.28","doi-asserted-by":"crossref","first-page":"439","DOI":"10.5483\/BMBRep.2021.54.9.097","article-title":"The trinity of ribosome-associated quality control and stress signaling for proteostasis and neuronal physiology","volume":"54","year":"2021","journal-title":"BMB Rep"},{"key":"2026101001550823000_2026.07.21.739814v2.29","doi-asserted-by":"crossref","first-page":"936","DOI":"10.1111\/febs.17217","article-title":"Dysregulated ribosome quality control in human diseases","volume":"292","year":"2025","journal-title":"FEBS J"},{"key":"2026101001550823000_2026.07.21.739814v2.30","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.M808840200"},{"key":"2026101001550823000_2026.07.21.739814v2.31","doi-asserted-by":"publisher","DOI":"10.1101\/gr.257741.119"},{"key":"2026101001550823000_2026.07.21.739814v2.32","doi-asserted-by":"publisher","DOI":"10.1016\/j.celrep.2020.107610"},{"key":"2026101001550823000_2026.07.21.739814v2.33","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-020-02256-0"},{"key":"2026101001550823000_2026.07.21.739814v2.34","doi-asserted-by":"crossref","unstructured":"Kyei-Baffour, E.S. , Bak, J. , Silva, J. , Faller, W.J. , and Alkan, F . (2025). Detecting ribosome collisions with differential rRNA fragment analysis in ribosome profiling data. NAR Genom Bioinform 7, lqaf045.","DOI":"10.1093\/nargab\/lqaf045"},{"key":"2026101001550823000_2026.07.21.739814v2.35","doi-asserted-by":"crossref","first-page":"13056","DOI":"10.1016\/S0021-9258(18)33621-4","article-title":"Import of proteins into mitochondria. Yeast cells grown in the presence of carbonyl cyanide m-chlorophenylhydrazone accumulate massive amounts of some mitochondrial precursor polypeptides","volume":"257","year":"1982","journal-title":"J Biol Chem"},{"key":"2026101001550823000_2026.07.21.739814v2.36","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2014.02.006"},{"key":"2026101001550823000_2026.07.21.739814v2.37","doi-asserted-by":"crossref","first-page":"104047","DOI":"10.1016\/j.xpro.2025.104047","article-title":"Protocol for Disome-seq to identify transcriptome-wide ribosome collisions in yeast cells","volume":"6","year":"2025","journal-title":"STAR Protoc"},{"key":"2026101001550823000_2026.07.21.739814v2.38","doi-asserted-by":"publisher","DOI":"10.1016\/j.ymeth.2017.05.028"},{"key":"2026101001550823000_2026.07.21.739814v2.39","doi-asserted-by":"crossref","first-page":"100168","DOI":"10.1016\/j.xpro.2020.100168","article-title":"Protocol for Disome Profiling to Survey Ribosome Collision in Humans and Zebrafish","volume":"1","year":"2020","journal-title":"STAR Protoc"},{"key":"2026101001550823000_2026.07.21.739814v2.40","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkab036"},{"key":"2026101001550823000_2026.07.21.739814v2.41","doi-asserted-by":"publisher","DOI":"10.1016\/j.celrep.2023.113359"},{"key":"2026101001550823000_2026.07.21.739814v2.42","unstructured":"Guydosh, N.R. (2021). ribofootPrinter: A precision python toolbox for analysis of ribosome profiling data. bioRxiv, 2021.2007.2004.451082."},{"key":"2026101001550823000_2026.07.21.739814v2.43","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.2646"},{"key":"2026101001550823000_2026.07.21.739814v2.44","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-12-35"},{"key":"2026101001550823000_2026.07.21.739814v2.45","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.1754"},{"key":"2026101001550823000_2026.07.21.739814v2.46","doi-asserted-by":"crossref","unstructured":"Shanmuganathan, V. , Schiller, N. , Magoulopoulou, A. , Cheng, J. , Braunger, K. , Cymer, F. , Berninghausen, O. , Beatrix, B. , Kohno, K. , von Heijne, G. , and Beckmann, R. (2019). Structural and mutational analysis of the ribosome-arresting human XBP1u. Elife 8.","DOI":"10.7554\/eLife.46267"},{"key":"2026101001550823000_2026.07.21.739814v2.47","doi-asserted-by":"publisher","DOI":"10.1126\/science.1197142"},{"key":"2026101001550823000_2026.07.21.739814v2.48","doi-asserted-by":"publisher","DOI":"10.1146\/annurev.micro.59.031805.133833"},{"key":"2026101001550823000_2026.07.21.739814v2.49","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-023-02028-1"},{"key":"2026101001550823000_2026.07.21.739814v2.50","doi-asserted-by":"publisher","DOI":"10.1186\/s12864-018-4933-1"},{"key":"2026101001550823000_2026.07.21.739814v2.51","doi-asserted-by":"crossref","first-page":"14593","DOI":"10.1038\/s41598-020-71323-0","article-title":"Insufficiently complex unique-molecular identifiers (UMIs) distort small RNA sequencing","volume":"10","year":"2020","journal-title":"Sci Rep"}],"container-title":[],"original-title":[],"link":[{"URL":"https:\/\/syndication.highwire.org\/content\/doi\/10.64898\/2026.07.21.739814","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,10]],"date-time":"2026-10-10T08:55:19Z","timestamp":1791622519000},"score":1,"resource":{"primary":{"URL":"http:\/\/biorxiv.org\/lookup\/doi\/10.64898\/2026.07.21.739814"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,7,22]]},"references-count":51,"URL":"https:\/\/doi.org\/10.64898\/2026.07.21.739814","relation":{},"subject":[],"published":{"date-parts":[[2026,7,22]]},"subtype":"preprint"}}