Uncovering de novo gene birth in yeast using deep transcriptomics
De novo gene origination has been recently established as an important mechanism for the formation of new genes. In organisms with a large genome, intergenic and intronic regions provide plenty of raw material for new transcriptional events to occur, but little is know about how de novo transcripts...
| Authors: | , , , , , , , , |
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| Format: | article |
| Status: | Published version |
| Publication Date: | 2021 |
| Country: | España |
| Institution: | Universitat Pompeu Fabra |
| Repository: | Repositorio Digital de la UPF |
| OAI Identifier: | oai:repositori.upf.edu:10230/46484 |
| Online Access: | http://hdl.handle.net/10230/46484 http://dx.doi.org/10.1038/s41467-021-20911-3 |
| Access Level: | Open access |
| Keyword: | Evolvability Fungal genetics Molecular evolution Transcriptomics |
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Uncovering de novo gene birth in yeast using deep transcriptomicsBlevins, William Robert, 1987-Ruiz Orera, Jorge, 1988-Messeguer, XavierBlasco Moreno, Bernat, 1986-Villanueva Cañas, José Luis, 1984-Espinar, LorenaDíez Antón, Juana, 1962-Carey, Lucas, 1980-Albà Soler, MarEvolvabilityFungal geneticsMolecular evolutionTranscriptomicsDe novo gene origination has been recently established as an important mechanism for the formation of new genes. In organisms with a large genome, intergenic and intronic regions provide plenty of raw material for new transcriptional events to occur, but little is know about how de novo transcripts originate in more densely-packed genomes. Here, we identify 213 de novo originated transcripts in Saccharomyces cerevisiae using deep transcriptomics and genomic synteny information from multiple yeast species grown in two different conditions. We find that about half of the de novo transcripts are expressed from regions which already harbor other genes in the opposite orientation; these transcripts show similar expression changes in response to stress as their overlapping counterparts, and some appear to translate small proteins. Thus, a large fraction of de novo genes in yeast are likely to co-evolve with already existing genes.The work was funded by grants PGC2018-094091-B-I00, BFU2015-65235-P, BFU2015-68351-P, BFU2016-80039-R, TIN2015-69175-C4-3-R and RTI2018-094403-B-C33 from Spanish Government—FEDER (EU), and from grant PT17/0009/0014 from Instituto de Salud Carlos III—FEDER. We also received funding from the “Maria de Maeztu” Programme for Units of Excellence in R&D (MDM-2014-0370) and from Agència de Gestió d’Ajuts Universitaris i de Recerca Generalitat de Catalunya (AGAUR), grants number 2014SGR1121, 2014SGR0974, 2017SGR1054 and 2017SGR01020 and, predoctoral fellowship (FI) to W.R.B.Nature Research202120212021info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionapplication/pdfapplication/pdfhttp://hdl.handle.net/10230/46484http://dx.doi.org/10.1038/s41467-021-20911-3reponame:Repositorio Digital de la UPFinstname:Universitat Pompeu FabraInglésNat Commun. 2021; 12(1):604info:eu-repo/grantAgreement/ES/2PE/PGC2018-094091-B-I00info:eu-repo/grantAgreement/ES/1PE/BFU2015-65235-Pinfo:eu-repo/grantAgreement/ES/1PE/BFU2015-68351-Pinfo:eu-repo/grantAgreement/ES/1PE/BFU2016-80039-R© The Author(s) 2021. 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 license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.http://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/openAccessoai:repositori.upf.edu:10230/464842026-06-12T07:21:37Z |
| dc.title.none.fl_str_mv |
Uncovering de novo gene birth in yeast using deep transcriptomics |
| title |
Uncovering de novo gene birth in yeast using deep transcriptomics |
| spellingShingle |
Uncovering de novo gene birth in yeast using deep transcriptomics Blevins, William Robert, 1987- Evolvability Fungal genetics Molecular evolution Transcriptomics |
| title_short |
Uncovering de novo gene birth in yeast using deep transcriptomics |
| title_full |
Uncovering de novo gene birth in yeast using deep transcriptomics |
| title_fullStr |
Uncovering de novo gene birth in yeast using deep transcriptomics |
| title_full_unstemmed |
Uncovering de novo gene birth in yeast using deep transcriptomics |
| title_sort |
Uncovering de novo gene birth in yeast using deep transcriptomics |
| dc.creator.none.fl_str_mv |
Blevins, William Robert, 1987- Ruiz Orera, Jorge, 1988- Messeguer, Xavier Blasco Moreno, Bernat, 1986- Villanueva Cañas, José Luis, 1984- Espinar, Lorena Díez Antón, Juana, 1962- Carey, Lucas, 1980- Albà Soler, Mar |
| author |
Blevins, William Robert, 1987- |
| author_facet |
Blevins, William Robert, 1987- Ruiz Orera, Jorge, 1988- Messeguer, Xavier Blasco Moreno, Bernat, 1986- Villanueva Cañas, José Luis, 1984- Espinar, Lorena Díez Antón, Juana, 1962- Carey, Lucas, 1980- Albà Soler, Mar |
| author_role |
author |
| author2 |
Ruiz Orera, Jorge, 1988- Messeguer, Xavier Blasco Moreno, Bernat, 1986- Villanueva Cañas, José Luis, 1984- Espinar, Lorena Díez Antón, Juana, 1962- Carey, Lucas, 1980- Albà Soler, Mar |
| author2_role |
author author author author author author author author |
| dc.subject.none.fl_str_mv |
Evolvability Fungal genetics Molecular evolution Transcriptomics |
| topic |
Evolvability Fungal genetics Molecular evolution Transcriptomics |
| description |
De novo gene origination has been recently established as an important mechanism for the formation of new genes. In organisms with a large genome, intergenic and intronic regions provide plenty of raw material for new transcriptional events to occur, but little is know about how de novo transcripts originate in more densely-packed genomes. Here, we identify 213 de novo originated transcripts in Saccharomyces cerevisiae using deep transcriptomics and genomic synteny information from multiple yeast species grown in two different conditions. We find that about half of the de novo transcripts are expressed from regions which already harbor other genes in the opposite orientation; these transcripts show similar expression changes in response to stress as their overlapping counterparts, and some appear to translate small proteins. Thus, a large fraction of de novo genes in yeast are likely to co-evolve with already existing genes. |
| publishDate |
2021 |
| dc.date.none.fl_str_mv |
2021 2021 2021 |
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info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion |
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article |
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publishedVersion |
| dc.identifier.none.fl_str_mv |
http://hdl.handle.net/10230/46484 http://dx.doi.org/10.1038/s41467-021-20911-3 |
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http://hdl.handle.net/10230/46484 http://dx.doi.org/10.1038/s41467-021-20911-3 |
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Inglés |
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Inglés |
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Nat Commun. 2021; 12(1):604 info:eu-repo/grantAgreement/ES/2PE/PGC2018-094091-B-I00 info:eu-repo/grantAgreement/ES/1PE/BFU2015-65235-P info:eu-repo/grantAgreement/ES/1PE/BFU2015-68351-P info:eu-repo/grantAgreement/ES/1PE/BFU2016-80039-R |
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http://creativecommons.org/licenses/by/4.0/ info:eu-repo/semantics/openAccess |
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http://creativecommons.org/licenses/by/4.0/ |
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openAccess |
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application/pdf application/pdf |
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Nature Research |
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Nature Research |
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