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

Autor: Ferrández Peral, Luis, 1991, Zhan, Xiaoyu, Alvarez-Estape, Marina, Chiva, Cristina, Esteller Cucala, Paula, García Pérez, Raquel, 1989, Julià, Eva, Lizano González, Esther, 1974, Fornas Carreño, Oscar, Sabidó Aguadé, Eduard, 1981, Li, Qiye, Marquès i Bonet, Tomàs, 1975, Juan, David, Zhang, Guojie
Přispěvatelé: Chinese Academy of Sciences, International Science & Technology Cooperation (China), Carlsberg Foundation, Villum Fonden, Fundación 'la Caixa', Centre for Genomic Regulation, Universidad Pompeu Fabra, Instituto de Salud Carlos III, European Commission, Generalitat de Catalunya, European Research Council, Ministerio de Economía y Competitividad (España), Agencia Estatal de Investigación (España), National Institutes of Health (US)
Jazyk: angličtina
Rok vydání: 2022
Předmět:
Zdroj: Dipòsit Digital de Documents de la UAB
Universitat Autònoma de Barcelona
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 2022, ' Transcriptome innovations in primates revealed by single-molecule long-read sequencing ', Genome Research, vol. 32, no. 8, pp. 1448-1462 . https://doi.org/10.1101/gr.276395.121
DOI: 10.1101/gr.276395.121
Popis: 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. changes in alternative splicing in genes involved in immune response as an important target of recent regulatory divergence in primates.
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).
Databáze: OpenAIRE
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