Common cell lysis procedures distort ribosome profiling analyses of gene expression

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dc.contributor.authorO'Connell, Aoifeen
dc.contributor.authorFedorova, Alla Den
dc.contributor.authorO'Connor, Patrick B Fen
dc.contributor.authorZhdanov, Alexander Ven
dc.contributor.authorBaranov, Pavel Ven
dc.contributor.authorLoughran, Garyen
dc.contributor.authorAndreev, Dmitry Een
dc.contributor.funderRussian Science Foundationen
dc.contributor.funderScience Foundation Irelanden
dc.contributor.funderIrish Research Councilen
dc.date.accessioned2025-09-18T13:27:09Z
dc.date.available2025-09-18T13:27:09Z
dc.date.issued2025-08-11T00:00:00Zen
dc.description.abstractRibosome profiling is a powerful technique used to study gene expression on a transcriptome-wide scale. It involves sequencing of mRNA fragments protected by ribosomes from ribonuclease digestion. The initial steps commonly involve cell lysis followed by centrifugation and ribonuclease digestion. We find that centrifugation depletes 329 translated mRNAs in HEK293T cells. Many of these mRNAs encode cytoskeleton proteins. This suggests that the expression of a subset of mRNAs may be significantly underestimated in most ribosome profiling experiments. We show that omitting the centrifugation step after cell lysis can resolve this issue.en
dc.description.sponsorshipRussian Science Foundation (Grant 20-14-00121); Irish Research Council (Enterprise Partnership Studentship Award EPSPG/2020/461)en
dc.description.statusPeer revieweden
dc.description.versionPublished Versionen
dc.format.mimetypeapplication/pdfen
dc.identifier.articleid241en
dc.identifier.citationO’Connell, A., Fedorova, A. D., O’Connor, P. B., Zhdanov, A. V., Baranov, P. V., Loughran, G. and Andreev, D. E. (2025) 'Common cell lysis procedures distort ribosome profiling analyses of gene expression', Genome Biology, 26(1), 241 (9pp). https://doi.org/10.1186/s13059-025-03651-1en
dc.identifier.doi10.1186/s13059-025-03651-1en
dc.identifier.eissn40790224en
dc.identifier.endpage9en
dc.identifier.issn40790224en
dc.identifier.issued1en
dc.identifier.journaltitleGenome Biology, 26(1), 241 (9pp).en
dc.identifier.startpage1en
dc.identifier.urihttps://hdl.handle.net/10468/17881
dc.identifier.volume26en
dc.language.isoenen
dc.publisherSpringer Natureen
dc.relation.projectinfo:eu-repo/grantAgreement/SFI/Frontiers for the Future::Awards/20/FFP-A/8929/IE/CHARACTERISATION OF HUMAN mRNA DECODING DIVERSITY./en
dc.rights© 2025, the Authors. Open Access. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. To view a copy of this licence, visit https://creativecommons.org/licenses/by/4.0/en
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/en
dc.subjectCytoskeletonen
dc.subjectGene expressionen
dc.subjectInsoluble fractionen
dc.subjectLysisen
dc.subjectNascent peptideen
dc.subjectPolysome profilingen
dc.subjectRiboseqen
dc.subjectRibosome profilingen
dc.titleCommon cell lysis procedures distort ribosome profiling analyses of gene expressionen
dc.typeArticle (peer-reviewed)en
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