Evolutionary and functional impact of common polymorphic inversions in the human genome
Inversions are one type of structural variants linked to phenotypic differences and adaptation in multiple organisms. However, there is still very little information about polymorphic inversions in the human genome due to the difficulty of their detection. Here, we develop a new high-throughput genotyping method based on probe hybridization and amplification, and we perform a complete study of 45 common human inversions of 0.1-415 kb. Most inversions promoted by homologous recombination occur recurrently in humans and great apes and they are not tagged by SNPs. Furthermore, there is an enrichment of inversions showing signatures of positive or balancing selection, diverse functional effects, such as gene disruption and gene-expression changes, or association with phenotypic traits. Therefore, our results indicate that the genome is more dynamic than previously thought and that human inversions have important functional and evolutionary consequences, making possible to determine for the first time their contribution to complex traits.
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Nature Publishing Group
2019-09-17
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Subjects: | Gene expression profiling, Genome evolution, Population genetics, Structural variation, |
Online Access: | http://hdl.handle.net/10261/207204 http://dx.doi.org/10.13039/501100000781 http://dx.doi.org/10.13039/501100003329 http://dx.doi.org/10.13039/501100000780 http://dx.doi.org/10.13039/501100002809 http://dx.doi.org/10.13039/501100011104 http://dx.doi.org/10.13039/501100001871 |
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dig-ibe-es-10261-2072042021-12-28T16:10:16Z Evolutionary and functional impact of common polymorphic inversions in the human genome Giner-Delgado, Carla Villatoro, Sergi Lerga-Jaso, Jon Gayà-Vidal, Magdalena Oliva, Meritxell Castellano, David Pantano, Lorena Bitarello, B.D. Izquierdo, David Noguera, Isaac Olalde, Iñigo Delprat, Alejandra Blancher, Antoine Lalueza-Fox, Carles Esko, Tonu O'Reilly, Paul F. Andrés, Aida M. Ferretti, Luca García-Puig, Marta Cáceres, Mario European Research Council Ministerio de Economía y Competitividad (España) European Commission Generalitat de Catalunya Universidad Autónoma de Barcelona La Caixa Fundação para a Ciência e a Tecnologia (Portugal) Gene expression profiling Genome evolution Population genetics Structural variation Inversions are one type of structural variants linked to phenotypic differences and adaptation in multiple organisms. However, there is still very little information about polymorphic inversions in the human genome due to the difficulty of their detection. Here, we develop a new high-throughput genotyping method based on probe hybridization and amplification, and we perform a complete study of 45 common human inversions of 0.1-415 kb. Most inversions promoted by homologous recombination occur recurrently in humans and great apes and they are not tagged by SNPs. Furthermore, there is an enrichment of inversions showing signatures of positive or balancing selection, diverse functional effects, such as gene disruption and gene-expression changes, or association with phenotypic traits. Therefore, our results indicate that the genome is more dynamic than previously thought and that human inversions have important functional and evolutionary consequences, making possible to determine for the first time their contribution to complex traits. This work was supported by research grants ERC Starting Grant 243212 (INVFEST) from the European Research Council under the European Union Seventh Research Framework Programme (FP7), BFU2013-42649-P and BFU2016-77244-R funded by the Agencia Estatal de Investigación (AEI, Spain) and the European Regional Development Fund (FEDER, EU), and 2014-SGR-1346 and 2017-SGR-1379 from the Generalitat de Catalunya (Spain) to M.C., a PIF PhD fellowship from the Universitat Autònoma de Barcelona (Spain) to C.G.D., a La Caixa Doctoral fellowship to J.L.J., and a FPI PhD fellowship from the Ministerio de Economía y Competitividad (Spain) to M.O. and I.N. M.G.V. was supported in part by POCI-01-0145-FEDER-006821 funded through the Operational Programme for Competitiveness Factors (COMPETE, EU) and UID/BIA/50027/2013 from the Foundation for Science and Technology (FCT, Portugal). 2020-04-13T07:36:13Z 2020-04-13T07:36:13Z 2019-09-17 2020-04-13T07:36:13Z artículo http://purl.org/coar/resource_type/c_6501 doi: 10.1038/s41467-019-12173-x e-issn: 2041-1723 Nature Communications 10: 4222 (2019) http://hdl.handle.net/10261/207204 10.1038/s41467-019-12173-x http://dx.doi.org/10.13039/501100000781 http://dx.doi.org/10.13039/501100003329 http://dx.doi.org/10.13039/501100000780 http://dx.doi.org/10.13039/501100002809 http://dx.doi.org/10.13039/501100011104 http://dx.doi.org/10.13039/501100001871 31530810 #PLACEHOLDER_PARENT_METADATA_VALUE# #PLACEHOLDER_PARENT_METADATA_VALUE# #PLACEHOLDER_PARENT_METADATA_VALUE# info:eu-repo/grantAgreement/EC/FP7/243212 info:eu-repo/grantAgreement/MINECO/Plan Estatal de Investigación Científica y Técnica y de Innovación 2013-2016/BFU2013-42649-P info:eu-repo/grantAgreement/MINECO/Plan Estatal de Investigación Científica y Técnica y de Innovación 2013-2016/BFU2016-77244-R Publisher's version http://doi.org/10.1038/s41467-019-12173-x Sí open Nature Publishing Group |
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Gene expression profiling Genome evolution Population genetics Structural variation Gene expression profiling Genome evolution Population genetics Structural variation |
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Gene expression profiling Genome evolution Population genetics Structural variation Gene expression profiling Genome evolution Population genetics Structural variation Giner-Delgado, Carla Villatoro, Sergi Lerga-Jaso, Jon Gayà-Vidal, Magdalena Oliva, Meritxell Castellano, David Pantano, Lorena Bitarello, B.D. Izquierdo, David Noguera, Isaac Olalde, Iñigo Delprat, Alejandra Blancher, Antoine Lalueza-Fox, Carles Esko, Tonu O'Reilly, Paul F. Andrés, Aida M. Ferretti, Luca García-Puig, Marta Cáceres, Mario Evolutionary and functional impact of common polymorphic inversions in the human genome |
description |
Inversions are one type of structural variants linked to phenotypic differences and adaptation in multiple organisms. However, there is still very little information about polymorphic inversions in the human genome due to the difficulty of their detection. Here, we develop a new high-throughput genotyping method based on probe hybridization and amplification, and we perform a complete study of 45 common human inversions of 0.1-415 kb. Most inversions promoted by homologous recombination occur recurrently in humans and great apes and they are not tagged by SNPs. Furthermore, there is an enrichment of inversions showing signatures of positive or balancing selection, diverse functional effects, such as gene disruption and gene-expression changes, or association with phenotypic traits. Therefore, our results indicate that the genome is more dynamic than previously thought and that human inversions have important functional and evolutionary consequences, making possible to determine for the first time their contribution to complex traits. |
author2 |
European Research Council |
author_facet |
European Research Council Giner-Delgado, Carla Villatoro, Sergi Lerga-Jaso, Jon Gayà-Vidal, Magdalena Oliva, Meritxell Castellano, David Pantano, Lorena Bitarello, B.D. Izquierdo, David Noguera, Isaac Olalde, Iñigo Delprat, Alejandra Blancher, Antoine Lalueza-Fox, Carles Esko, Tonu O'Reilly, Paul F. Andrés, Aida M. Ferretti, Luca García-Puig, Marta Cáceres, Mario |
format |
artículo |
topic_facet |
Gene expression profiling Genome evolution Population genetics Structural variation |
author |
Giner-Delgado, Carla Villatoro, Sergi Lerga-Jaso, Jon Gayà-Vidal, Magdalena Oliva, Meritxell Castellano, David Pantano, Lorena Bitarello, B.D. Izquierdo, David Noguera, Isaac Olalde, Iñigo Delprat, Alejandra Blancher, Antoine Lalueza-Fox, Carles Esko, Tonu O'Reilly, Paul F. Andrés, Aida M. Ferretti, Luca García-Puig, Marta Cáceres, Mario |
author_sort |
Giner-Delgado, Carla |
title |
Evolutionary and functional impact of common polymorphic inversions in the human genome |
title_short |
Evolutionary and functional impact of common polymorphic inversions in the human genome |
title_full |
Evolutionary and functional impact of common polymorphic inversions in the human genome |
title_fullStr |
Evolutionary and functional impact of common polymorphic inversions in the human genome |
title_full_unstemmed |
Evolutionary and functional impact of common polymorphic inversions in the human genome |
title_sort |
evolutionary and functional impact of common polymorphic inversions in the human genome |
publisher |
Nature Publishing Group |
publishDate |
2019-09-17 |
url |
http://hdl.handle.net/10261/207204 http://dx.doi.org/10.13039/501100000781 http://dx.doi.org/10.13039/501100003329 http://dx.doi.org/10.13039/501100000780 http://dx.doi.org/10.13039/501100002809 http://dx.doi.org/10.13039/501100011104 http://dx.doi.org/10.13039/501100001871 |
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