Exploring evidence of non-coding RNA translation with Trips-Viz and GWIPS-Viz browsers

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dc.contributor.authorZaheed, Oza
dc.contributor.authorKiniry, Stephen J.
dc.contributor.authorBaranov, Pavel V.
dc.contributor.authorDean, Kellie
dc.contributor.funderScience Foundation Irelanden
dc.contributor.funderIrish Research Councilen
dc.contributor.funderRussian Science Foundationen
dc.date.accessioned2022-07-19T14:33:38Z
dc.date.available2022-07-19T14:33:38Z
dc.date.issued2021-08
dc.date.updated2022-07-19T14:04:03Z
dc.description.abstractDetection of translation in so-called non-coding RNA provides an opportunity for identification of novel bioactive peptides and microproteins. The main methods used for these purposes are ribosome profiling and mass spectrometry. A number of publicly available datasets already exist for a substantial number of different cell types grown under various conditions, and public data mining is an attractive strategy for identification of translation in non-coding RNAs. Since the analysis of publicly available data requires intensive data processing, several data resources have been created recently for exploring processed publicly available data, such as OpenProt, GWIPS-viz, and Trips-Viz. In this work we provide a detailed demonstration of how to use the latter two tools for exploring experimental evidence for translation of RNAs hitherto classified as non-coding. For this purpose, we use a set of transcripts with substantially different patterns of ribosome footprint distributions. We discuss how certain features of these patterns can be used as evidence for or against genuine translation. During our analysis we concluded that the MTLN mRNA, previously misannotated as lncRNA LINC000116, likely encodes only a short proteoform expressed from shorter RNA transcript variants.en
dc.description.sponsorshipScience Foundation Ireland (Centre for Research Training in Genomics Data Science 18/CRT/6214); Irish Research Council (Government of Ireland Postgraduate Scholarship Programme); Russian Science Foundation (Grant 20-14-00121)en
dc.description.statusPeer revieweden
dc.description.versionPublished Versionen
dc.format.mimetypeapplication/pdfen
dc.identifier.articleid703374en
dc.identifier.citationZaheed, O., Kiniry, S. J., Baranov, P. V. and Dean, Kellie (2021) 'Exploring evidence of non-coding RNA translation with Trips-Viz and GWIPS-Viz browsers', Frontiers In Cell And Developmental Biology, 9, 703374, (17pp). doi: 10.3389/fcell.2021.703374en
dc.identifier.doi10.3389/fcell.2021.703374en
dc.identifier.endpage17en
dc.identifier.issn2296-634X
dc.identifier.journaltitleFrontiers In Cell And Developmental Biologyen
dc.identifier.startpage1en
dc.identifier.urihttps://hdl.handle.net/10468/13377
dc.identifier.volume9en
dc.language.isoenen
dc.publisherFrontiers Media S.A.en
dc.relation.urihttps://doi.org/10.3389/fcell.2021.703374en
dc.rights© 2021 Zaheed, Kiniry, Baranov and Dean. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.en
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/en
dc.subjectRibosome profiling revealsen
dc.subjectHuman genomeen
dc.subjectGeneen
dc.subjectIdentificationen
dc.subjectMicroproteinen
dc.subjectMitoregulinen
dc.subjectMechanismsen
dc.subjectComplexityen
dc.subjectInitiationen
dc.subjectInsightsen
dc.titleExploring evidence of non-coding RNA translation with Trips-Viz and GWIPS-Viz browsersen
dc.typeArticle (peer-reviewed)en
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