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Gene fusions derived by transcriptional readthrough are driven by segmental duplication in human

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dc.contributor.author McCartney, Ann M.
dc.contributor.author Hyland, Edel M.
dc.contributor.author Cormican, Paul
dc.contributor.author Moran, Raymond J.
dc.contributor.author Webb, Andrew E.
dc.contributor.author Lee, Kate D.
dc.contributor.author Hernández Rodríguez, Jéssica, 1983-
dc.contributor.author Prado Martínez, Javier, 1987-
dc.contributor.author Creevey, Christopher J.
dc.contributor.author Aspden, Julie L.
dc.contributor.author McInerney, James O.
dc.contributor.author Marquès i Bonet, Tomàs, 1975-
dc.contributor.author O'Connell, Mary J.
dc.date.accessioned 2020-03-26T13:57:47Z
dc.date.available 2020-03-26T13:57:47Z
dc.date.issued 2019
dc.identifier.citation McCartney AM, Hyland EM, Cormican P, Moran RJ, Webb AE, Lee KD, Hernandez-Rodriguez J, Prado-Martinez J, Creevey CJ, Aspden JL, McInerney JO, Marques-Bonet T, O'Connell MJ. Gene fusions derived by transcriptional readthrough are driven by segmental duplication in human. Genome Biol Evol. 2019; 11(9):2678-90. DOI: 10.1093/gbe/evz163
dc.identifier.issn 1759-6653
dc.identifier.uri http://hdl.handle.net/10230/44054
dc.description.abstract Gene fusion occurs when two or more individual genes with independent open reading frames becoming juxtaposed under the same open reading frame creating a new fused gene. A small number of gene fusions described in detail have been associated with novel functions, for example, the hominid-specific PIPSL gene, TNFSF12, and the TWE-PRIL gene family. We use Sequence Similarity Networks and species level comparisons of great ape genomes to identify 45 new genes that have emerged by transcriptional readthrough, that is, transcription-derived gene fusion. For 35 of these putative gene fusions, we have been able to assess available RNAseq data to determine whether there are reads that map to each breakpoint. A total of 29 of the putative gene fusions had annotated transcripts (9/29 of which are human-specific). We carried out RT-qPCR in a range of human tissues (placenta, lung, liver, brain, and testes) and found that 23 of the putative gene fusion events were expressed in at least one tissue. Examining the available ribosome foot-printing data, we find evidence for translation of three of the fused genes in human. Finally, we find enrichment for transcription-derived gene fusions in regions of known segmental duplication in human. Together, our results implicate chromosomal structural variation brought about by segmental duplication with the emergence of novel transcripts and translated protein products.
dc.description.sponsorship The authors would like to thank the following funding agencies: Irish Research Council (IRC) to AMMC (RS/2012/466), Pierse Trust fund, and Orla Benson scholarships to A.M.M.C. 250 Great Minds University of Leeds Fellowship to M.J.O'.C.,IRC to R.J.M. (GOIPG/2014/306), and the Irish Centre for High End Computing (ICHEC) for computational resources. TMB is supported by BFU2017-86471-P (MINECO/FEDER, UE), U01 MH106874 grant, Howard Hughes International Early Career, Obra Social “La Caixa” and Secretaria d'Universitats i Recerca and CERCA Programme del Departament d'Economia i Coneixement de la Generalitat de Catalunya (GRC 2017 SGR 880).
dc.format.mimetype application/pdf
dc.language.iso eng
dc.publisher Oxford University Press
dc.relation.ispartof Genome Biol Evol. 2019; 11(9):2678-90
dc.rights © The Author(s) 2019. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
dc.rights.uri http://creativecommons.org/licenses/by/4.0/
dc.title Gene fusions derived by transcriptional readthrough are driven by segmental duplication in human
dc.type info:eu-repo/semantics/article
dc.identifier.doi http://dx.doi.org/10.1093/gbe/evz163
dc.subject.keyword Great Ape Comparative genomics
dc.subject.keyword Mechanisms of protein-coding evolution
dc.subject.keyword Novel genes
dc.subject.keyword Segmental duplication
dc.subject.keyword Sequence similarity networks
dc.subject.keyword Transcriptional readthrough
dc.relation.projectID info:eu-repo/grantAgreement/ES/2PE/BFU2017-86471-P
dc.rights.accessRights info:eu-repo/semantics/openAccess
dc.type.version info:eu-repo/semantics/publishedVersion

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