Transcriptome innovations in primates revealed by single-molecule long-read sequencing

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  • dc.contributor.author Ferrández Peral, Luis, 1991-
  • dc.contributor.author Zhan, Xiaoyu
  • dc.contributor.author Zhan, Xiaoyu
  • dc.contributor.author Alvarez-Estape, Marina
  • dc.contributor.author Chiva, Cristina
  • dc.contributor.author Esteller Cucala, Paula
  • dc.contributor.author García Pérez, Raquel, 1989-
  • dc.contributor.author Julià, Eva
  • dc.contributor.author Lizano González, Esther, 1974-
  • dc.contributor.author Fornas Carreño, Oscar
  • dc.contributor.author Sabidó Aguadé, Eduard, 1981-
  • dc.contributor.author Li, Qiye
  • dc.contributor.author Marquès i Bonet, Tomàs, 1975-
  • dc.contributor.author Juan, David
  • dc.contributor.author Zhang, Guojie
  • dc.date.accessioned 2022-10-24T06:25:28Z
  • dc.date.available 2022-10-24T06:25:28Z
  • dc.date.issued 2022
  • dc.description.abstract Transcriptomic diversity greatly contributes to the fundamentals of disease, lineage-specific biology, and environmental adaptation. However, much of the actual isoform repertoire contributing to shaping primate evolution remains unknown. Here, we combined deep long- and short-read sequencing complemented with mass spectrometry proteomics in a panel of lymphoblastoid cell lines (LCLs) from human, three other great apes, and rhesus macaque, producing the largest full-length isoform catalog in primates to date. Around half of the captured isoforms are not annotated in their reference genomes, significantly expanding the gene models in primates. Furthermore, our comparative analyses unveil hundreds of transcriptomic innovations and isoform usage changes related to immune function and immunological disorders. The confluence of these evolutionary innovations with signals of positive selection and their limited impact in the proteome points to changes in alternative splicing in genes involved in immune response as an important target of recent regulatory divergence in primates.
  • dc.description.sponsorship This work was supported by the Strategic Priority Research Program of the Chinese Academy of Sciences (XDB31020000); National Key R&D Program of China (China's Ministry of Science and Technology [MoST]) grant 2018YFC1406901; the International Partnership Program of the Chinese Academy of Sciences (no. 152453KYSB20170002); the Carlsberg Foundation (CF16-0663); the Villum Foundation (no. 25900) to G.Z.; and the La Caixa Foundation (ID 100010434) Fellowship Code LCF/BQ/DE16/11570011 (L.F.-P.). The Center for Genomic Regulation (CRG) / Universitat Pompeu Fabra (UPF) Proteomics Unit is part of the Spanish Infrastructure for Omics Technologies (National Map of Unique Scientific and Technical Infrastructures [ICTS] OmicsTech) and a member of the ProteoRed PRB3 Consortium, which is supported by grant PT17/0019 of the PE I + D + i 2013–2016 from the Instituto de Salud Carlos III (ISCIII), European Regional Development Fund (ERDF), and “Secretaria d'Universitats i Recerca del Departament d'Economia i Coneixement de la Generalitat de Catalunya” (2017SGR595). T.M.-B. is supported by funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (grant agreement no. 864203), BFU2017-86471-P (MINECO/FEDER, UE); “Unidad de Excelencia María de Maeztu,” funded by the Agencia Estatal de Investigación (AEI) (CEX2018-000792-M); Howard Hughes International Early Career; National Institutes of Health 1R01HG010898-01A1; and Secretaria d'Universitats i Recerca and Centres de Recerca de Catalunya (CERCA) Programme del Departament d'Economia i Coneixement de la Generalitat de Catalunya (GRC 2017 SGR 880).
  • dc.format.mimetype application/pdf
  • dc.identifier.citation Ferrández-Peral L, Zhan X, Alvarez-Estape M, Chiva C, Esteller-Cucala P, García-Pérez R, Julià E, Lizano E, Fornas Ò, Sabidó E, Li Q, Marquès-Bonet T, Juan D, Zhang G. Transcriptome innovations in primates revealed by single-molecule long-read sequencing. Genome Res. 2022 Jul 15;32(8):1448-62. DOI: 10.1101/gr.276395.121
  • dc.identifier.doi http://dx.doi.org/10.1101/gr.276395.121
  • dc.identifier.issn 1088-9051
  • dc.identifier.uri http://hdl.handle.net/10230/54542
  • dc.language.iso eng
  • dc.publisher Cold Spring Harbor Laboratory Press (CSHL Press)
  • dc.relation.ispartof Genome Res. 2022 Jul 15;32(8):1448-62
  • dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/864203
  • dc.relation.projectID info:eu-repo/grantAgreement/ES/2PE/BFU2017-86471-P
  • dc.rights © 2022 Ferrández-Peral et al.; Published by Cold Spring Harbor Laboratory Press. This article, published in Genome Research, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/.
  • dc.rights.accessRights info:eu-repo/semantics/openAccess
  • dc.rights.uri http://creativecommons.org/licenses/by/4.0/
  • dc.title Transcriptome innovations in primates revealed by single-molecule long-read sequencing
  • dc.type info:eu-repo/semantics/article
  • dc.type.version info:eu-repo/semantics/publishedVersion

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