Dynamics of DNA Methylation in Recent Human and Great Ape Evolution
DNA methylation is an epigenetic modification involved in regulatory processes such as cell differentiation during development, X-chromosome inactivation, genomic imprinting and susceptibility to complex disease. However, the dynamics of DNA methylation changes between humans and their closest relatives are still poorly understood. We performed a comparative analysis of CpG methylation patterns between 9 humans and 23 primate samples including all species of great apes (chimpanzee, bonobo, gorilla and orangutan) using Illumina Methylation450 bead arrays. Our analysis identified ∼800 genes with significantly altered methylation patterns among the great apes, including ∼170 genes with a methylation pattern unique to human. Some of these are known to be involved in developmental and neurological features, suggesting that epigenetic changes have been frequent during recent human and primate evolution. We identified a significant positive relationship between the rate of coding variation and alterations of methylation at the promoter level, indicative of co-occurrence between evolution of protein sequence and gene regulation. In contrast, and supporting the idea that many phenotypic differences between humans and great apes are not due to amino acid differences, our analysis also identified 184 genes that are perfectly conserved at protein level between human and chimpanzee, yet show significant epigenetic differences between these two species. We conclude that epigenetic alterations are an important force during primate evolution and have been under-explored in evolutionary comparative genomics. © 2013 Hernando-Herraez et al.
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2013-09-05
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Online Access: | http://hdl.handle.net/10261/112417 http://dx.doi.org/10.13039/501100000781 http://dx.doi.org/10.13039/501100000780 http://dx.doi.org/10.13039/501100002809 http://dx.doi.org/10.13039/501100004837 http://dx.doi.org/10.13039/501100003339 http://dx.doi.org/10.13039/100000957 |
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dig-ibe-es-10261-1124172021-12-28T16:16:26Z Dynamics of DNA Methylation in Recent Human and Great Ape Evolution Hernando-Herraez, Irene Prado-Martinez, Javier Garg, Paras Fernández-Callejo, Marcos Heyn, Holger Hvilsom, Christina Navarro, Arcadi Esteller, Manel Sharp, Andrew J. Marqués-Bonet, Tomàs European Research Council European Commission Generalitat de Catalunya Zoo de Barcelona Ministerio de Ciencia e Innovación (España) Alzheimer's Association Consejo Superior de Investigaciones Científicas (España) DNA methylation is an epigenetic modification involved in regulatory processes such as cell differentiation during development, X-chromosome inactivation, genomic imprinting and susceptibility to complex disease. However, the dynamics of DNA methylation changes between humans and their closest relatives are still poorly understood. We performed a comparative analysis of CpG methylation patterns between 9 humans and 23 primate samples including all species of great apes (chimpanzee, bonobo, gorilla and orangutan) using Illumina Methylation450 bead arrays. Our analysis identified ∼800 genes with significantly altered methylation patterns among the great apes, including ∼170 genes with a methylation pattern unique to human. Some of these are known to be involved in developmental and neurological features, suggesting that epigenetic changes have been frequent during recent human and primate evolution. We identified a significant positive relationship between the rate of coding variation and alterations of methylation at the promoter level, indicative of co-occurrence between evolution of protein sequence and gene regulation. In contrast, and supporting the idea that many phenotypic differences between humans and great apes are not due to amino acid differences, our analysis also identified 184 genes that are perfectly conserved at protein level between human and chimpanzee, yet show significant epigenetic differences between these two species. We conclude that epigenetic alterations are an important force during primate evolution and have been under-explored in evolutionary comparative genomics. © 2013 Hernando-Herraez et al. TMB is supported by the European Research Council (ERC Starting Grant, StG_20091118) and the Spanish Government (BFU2011-28549). AJS is supported by NIH grants 1R01DA033660, 1R01HG006696, and a grant from the Alzheimer's Association (2012ALZNIRG69983). IHH is supported by the European Social Fund, AGAUR (Generalitat de Catalunya, Spain) and the Spanish National Research Council (CSIC). We also thank the Spanish Government for the grant BFU2009-13409-C02-02 to AN and the Barcelona Zoo (Ajuntament de Barcelona) for an award to JPM. Peer Reviewed 2015-03-16T11:35:43Z 2015-03-16T11:35:43Z 2013-09-05 2015-03-16T11:35:43Z artículo http://purl.org/coar/resource_type/c_6501 doi: 10.1371/journal.pgen.1003763 issn: 1553-7390 PLoS Genetics 9(9): e1003763 (2013) http://hdl.handle.net/10261/112417 10.1371/journal.pgen.1003763 http://dx.doi.org/10.13039/501100000781 http://dx.doi.org/10.13039/501100000780 http://dx.doi.org/10.13039/501100002809 http://dx.doi.org/10.13039/501100004837 http://dx.doi.org/10.13039/501100003339 http://dx.doi.org/10.13039/100000957 24039605 Publisher's version http://dx.doi.org/10.1371/journal.pgen.1003763 Sí open Public Library of Science |
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DNA methylation is an epigenetic modification involved in regulatory processes such as cell differentiation during development, X-chromosome inactivation, genomic imprinting and susceptibility to complex disease. However, the dynamics of DNA methylation changes between humans and their closest relatives are still poorly understood. We performed a comparative analysis of CpG methylation patterns between 9 humans and 23 primate samples including all species of great apes (chimpanzee, bonobo, gorilla and orangutan) using Illumina Methylation450 bead arrays. Our analysis identified ∼800 genes with significantly altered methylation patterns among the great apes, including ∼170 genes with a methylation pattern unique to human. Some of these are known to be involved in developmental and neurological features, suggesting that epigenetic changes have been frequent during recent human and primate evolution. We identified a significant positive relationship between the rate of coding variation and alterations of methylation at the promoter level, indicative of co-occurrence between evolution of protein sequence and gene regulation. In contrast, and supporting the idea that many phenotypic differences between humans and great apes are not due to amino acid differences, our analysis also identified 184 genes that are perfectly conserved at protein level between human and chimpanzee, yet show significant epigenetic differences between these two species. We conclude that epigenetic alterations are an important force during primate evolution and have been under-explored in evolutionary comparative genomics. © 2013 Hernando-Herraez et al. |
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European Research Council |
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European Research Council Hernando-Herraez, Irene Prado-Martinez, Javier Garg, Paras Fernández-Callejo, Marcos Heyn, Holger Hvilsom, Christina Navarro, Arcadi Esteller, Manel Sharp, Andrew J. Marqués-Bonet, Tomàs |
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Hernando-Herraez, Irene Prado-Martinez, Javier Garg, Paras Fernández-Callejo, Marcos Heyn, Holger Hvilsom, Christina Navarro, Arcadi Esteller, Manel Sharp, Andrew J. Marqués-Bonet, Tomàs |
spellingShingle |
Hernando-Herraez, Irene Prado-Martinez, Javier Garg, Paras Fernández-Callejo, Marcos Heyn, Holger Hvilsom, Christina Navarro, Arcadi Esteller, Manel Sharp, Andrew J. Marqués-Bonet, Tomàs Dynamics of DNA Methylation in Recent Human and Great Ape Evolution |
author_sort |
Hernando-Herraez, Irene |
title |
Dynamics of DNA Methylation in Recent Human and Great Ape Evolution |
title_short |
Dynamics of DNA Methylation in Recent Human and Great Ape Evolution |
title_full |
Dynamics of DNA Methylation in Recent Human and Great Ape Evolution |
title_fullStr |
Dynamics of DNA Methylation in Recent Human and Great Ape Evolution |
title_full_unstemmed |
Dynamics of DNA Methylation in Recent Human and Great Ape Evolution |
title_sort |
dynamics of dna methylation in recent human and great ape evolution |
publisher |
Public Library of Science |
publishDate |
2013-09-05 |
url |
http://hdl.handle.net/10261/112417 http://dx.doi.org/10.13039/501100000781 http://dx.doi.org/10.13039/501100000780 http://dx.doi.org/10.13039/501100002809 http://dx.doi.org/10.13039/501100004837 http://dx.doi.org/10.13039/501100003339 http://dx.doi.org/10.13039/100000957 |
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