Stimulation of stop codon readthrough: frequent presence of an extended 3' RNA structural element

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dc.contributor.author Firth, Andrew E.
dc.contributor.author Wills, Norma M.
dc.contributor.author Gesteland, Raymond F.
dc.contributor.author Atkins, John F.
dc.date.accessioned 2017-11-14T13:24:31Z
dc.date.available 2017-11-14T13:24:31Z
dc.date.issued 2011
dc.identifier.citation Firth, A. E., Wills, N. M., Gesteland, R. F. and Atkins, J. F. (2011) 'Stimulation of stop codon readthrough: frequent presence of an extended 3′ RNA structural element', Nucleic Acids Research, 39(15), pp. 6679-6691. doi: 10.1093/nar/gkr224 en
dc.identifier.volume 39
dc.identifier.issued 15
dc.identifier.startpage 6679
dc.identifier.endpage 6691
dc.identifier.issn 0305-1048
dc.identifier.uri http://hdl.handle.net/10468/5023
dc.identifier.doi 10.1093/nar/gkr224
dc.description.abstract In Sindbis, Venezuelan equine encephalitis and related alphaviruses, the polymerase is translated as a fusion with other non-structural proteins via readthrough of a UGA stop codon. Surprisingly, earlier work reported that the signal for efficient readthrough comprises a single cytidine residue 3'-adjacent to the UGA. However, analysis of variability at synonymous sites revealed strikingly enhanced conservation within the similar to 150 nt 3'-adjacent to the UGA, and RNA folding algorithms revealed the potential for a phylogenetically conserved stem-loop structure in the same region. Mutational analysis of the predicted structure demonstrated that the stem-loop increases readthrough by up to 10-fold. The same computational analysis indicated that similar RNA structures are likely to be relevant to readthrough in certain plant virus genera, notably Furovirus, Pomovirus, Tobravirus, Pecluvirus and Benyvirus, as well as the Drosophilia gene kelch. These results suggest that 3' RNA stimulatory structures feature in a much larger proportion of readthrough cases than previously anticipated, and provide a new criterion for assessing the large number of cellular readthrough candidates that are currently being revealed by comparative sequence analysis. en
dc.description.sponsorship Wellcome Trust (088789); National Institutes of Health (R01 GM079523) en
dc.format.mimetype application/pdf en
dc.language.iso en en
dc.publisher Oxford University Press en
dc.relation.uri https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkr224
dc.rights © 2011, the Authors. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. en
dc.rights.uri http://creativecommons.org/licenses/by-nc/2.5
dc.subject Murine leukemia virus en
dc.subject Opal termination codon en
dc.subject Read-through en
dc.subject Sindbis virus en
dc.subject Translational termination en
dc.subject Immediately downstream en
dc.subject Nucleotide sequence en
dc.subject Aphid transmission en
dc.subject Recoding signals en
dc.subject Gene-expression en
dc.title Stimulation of stop codon readthrough: frequent presence of an extended 3' RNA structural element en
dc.type Article (peer-reviewed) en
dc.internal.authorcontactother John F. Atkins, Biochemistry, University College Cork , Cork, Ireland T: +353-21-490-3000. E: j.atkins@ucc.ie en
dc.internal.availability Full text available en
dc.description.version Published Version en
dc.internal.rssid 108083256
dc.contributor.funder National Institutes of Health
dc.contributor.funder Science Foundation Ireland
dc.contributor.funder Wellcome Trust
dc.description.status Peer reviewed en
dc.identifier.journaltitle Nucleic Acids Research en
dc.internal.IRISemailaddress j.atkins@ucc.ie en
dc.relation.project info:eu-repo/grantAgreement/SFI/SFI Principal Investigator Programme (PI)/08/IN.1/B1889/IE/Altered Genetic Code Readout/


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© 2011, the Authors. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. Except where otherwise noted, this item's license is described as © 2011, the Authors. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
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