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dc.contributor.authorCarvunis, Anne-Ruxandra
dc.contributor.authorRolland, Thomas
dc.contributor.authorWapinski, Ilan
dc.contributor.authorCalderwood, Michael A.
dc.contributor.authorYildirim, Muhammed A.
dc.contributor.authorSimonis, Nicolas
dc.contributor.authorCharloteaux, Benoit
dc.contributor.authorBarbette, Justin
dc.contributor.authorSanthanam, Balaji
dc.contributor.authorBrar, Gloria A.
dc.contributor.authorWeissman, Jonathan S.
dc.contributor.authorRegev, Aviv
dc.contributor.authorThierry-Mieg, Nicolas
dc.contributor.authorCusick, Michael E.
dc.contributor.authorVidal, Marc
dc.contributor.authorHidalgo, Cesar A.
dc.date.accessioned2013-08-14T13:04:16Z
dc.date.available2013-08-14T13:04:16Z
dc.date.issued2012-06
dc.date.submitted2011-11
dc.identifier.issn0028-0836
dc.identifier.issn1476-4687
dc.identifier.urihttp://hdl.handle.net/1721.1/79845
dc.descriptionAuthor manuscript; available in PMC 2013 January 19.en_US
dc.description.abstractNovel protein-coding genes can arise either through re-organization of pre-existing genes or de novo. Processes involving re-organization of pre-existing genes, notably after gene duplication, have been extensively described. In contrast, de novo gene birth remains poorly understood, mainly because translation of sequences devoid of genes, or ‘non-genic’ sequences, is expected to produce insignificant polypeptides rather than proteins with specific biological functions. Here we formalize an evolutionary model according to which functional genes evolve de novo through transitory proto-genes generated by widespread translational activity in non-genic sequences. Testing this model at the genome scale in Saccharomyces cerevisiae, we detect translation of hundreds of short species-specific open reading frames (ORFs) located in non-genic sequences. These translation events seem to provide adaptive potential, as suggested by their differential regulation upon stress and by signatures of retention by natural selection. In line with our model, we establish that S. cerevisiae ORFs can be placed within an evolutionary continuum ranging from non-genic sequences to genes. We identify ~1,900 candidate proto-genes among S. cerevisiae ORFs and find that de novo gene birth from such a reservoir may be more prevalent than sporadic gene duplication. Our work illustrates that evolution exploits seemingly dispensable sequences to generate adaptive functional innovation.en_US
dc.description.sponsorshipBurroughs Wellcome Fund (Career Award at the Scientific Interface)en_US
dc.description.sponsorshipHoward Hughes Medical Instituteen_US
dc.description.sponsorshipNational Institutes of Health (U.S.) (Pioneer Award)en_US
dc.language.isoen_US
dc.publisherNature Publishing Groupen_US
dc.relation.isversionofhttp://dx.doi.org/10.1038/nature11184en_US
dc.rightsArticle is made available in accordance with the publisher's policy and may be subject to US copyright law. Please refer to the publisher's site for terms of use.en_US
dc.rights.urien_US
dc.sourcePMCen_US
dc.titleProto-genes and de novo gene birthen_US
dc.typeArticleen_US
dc.identifier.citationCarvunis, Anne-Ruxandra, Thomas Rolland, Ilan Wapinski, Michael A. Calderwood, Muhammed A. Yildirim, Nicolas Simonis, Benoit Charloteaux, et al. “Proto-genes and de novo gene birth.” Nature 487, no. 7407 (June 24, 2012): 370-374.en_US
dc.contributor.departmentmove to dc.description.sponsorshipen_US
dc.contributor.departmentMassachusetts Institute of Technology. Department of Biologyen_US
dc.contributor.departmentMassachusetts Institute of Technology. Media Laboratoryen_US
dc.contributor.departmentProgram in Media Arts and Sciences (Massachusetts Institute of Technology)en_US
dc.contributor.mitauthorHidalgo, Cesar A.en_US
dc.contributor.mitauthorRegev, Aviven_US
dc.relation.journalNatureen_US
dc.eprint.versionAuthor's final manuscripten_US
dc.type.urihttp://purl.org/eprint/type/JournalArticleen_US
eprint.statushttp://purl.org/eprint/status/PeerRevieweden_US
dspace.orderedauthorsCarvunis, Anne-Ruxandra; Rolland, Thomas; Wapinski, Ilan; Calderwood, Michael A.; Yildirim, Muhammed A.; Simonis, Nicolas; Charloteaux, Benoit; Hidalgo, César A.; Barbette, Justin; Santhanam, Balaji; Brar, Gloria A.; Weissman, Jonathan S.; Regev, Aviv; Thierry-Mieg, Nicolas; Cusick, Michael E.; Vidal, Marcen_US
dc.identifier.orcidhttps://orcid.org/0000-0002-6031-5982
dc.identifier.orcidhttps://orcid.org/0000-0001-8567-2049
mit.licensePUBLISHER_POLICYen_US


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