Characterization and evolution of the novel gene family FAM90A in primates originated by multiple duplication and rearrangement events

Genomic plasticity of human chromosome 8p23.1 region is highly influenced by two groups of complex segmental duplications (SDs), termed REPD and REPP, that mediate different kinds of rearrangements. Part of the difficulty to explain the wide range of phenotypes associated with 8p23.1 rearrangements...

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Autores: Bosch Pagès, Nina, Cáceres Aguilar, Mario, Cardone, Maria Francesca, Carreras, Anna, Ballana Guix, Ester, Rocchi, Mariano, Armengol i Dulcet, Lluís, Estivill, Xavier, 1955-
Tipo de recurso: artículo
Estado:Versión aceptada para publicación
Fecha de publicación:2007
País:España
Institución:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
Repositorio:Recercat. Dipósit de la Recerca de Catalunya
OAI Identifier:oai:recercat.cat:10230/16488
Acceso en línea:http://hdl.handle.net/10230/16488
http://dx.doi.org/10.1093/hmg/ddm209
Access Level:acceso abierto
Palabra clave:Genoma humà
Genètica evolutiva
Cromosomes
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spelling Characterization and evolution of the novel gene family FAM90A in primates originated by multiple duplication and rearrangement eventsBosch Pagès, NinaCáceres Aguilar, MarioCardone, Maria FrancescaCarreras, AnnaBallana Guix, EsterRocchi, MarianoArmengol i Dulcet, LluísEstivill, Xavier, 1955-Genoma humàGenètica evolutivaCromosomesGenomic plasticity of human chromosome 8p23.1 region is highly influenced by two groups of complex segmental duplications (SDs), termed REPD and REPP, that mediate different kinds of rearrangements. Part of the difficulty to explain the wide range of phenotypes associated with 8p23.1 rearrangements is that REPP and REPD are not yet well characterized, probably due to their polymorphic status. Here, we describe a novel primate-specific gene family, named FAM90A (family with sequence similarity 90), found within these SDs. According to the current human reference sequence assembly, the FAM90A family includes 24 members along 8p23.1 region plus a single member on chromosome 12p13.31, showing copy number variation (CNV) between individuals. These genes can be classified into subfamilies I and II, which differ in their upstream and 5′-untranslated region sequences, but both share the same open reading frame and are ubiquitously expressed. Sequence analysis and comparative fluorescence in situ hybridization studies showed that FAM90A subfamily II suffered a big expansion in the hominoid lineage, whereas subfamily I members were likely generated sometime around the divergence of orangutan and African great apes by a fusion process. In addition, the analysis of the Ka/Ks ratios provides evidence of functional constraint of some FAM90A genes in all species. The characterization of the FAM90A gene family contributes to a better understanding of the structural polymorphism of the human 8p23.1 region and constitutes a good example of how SDs, CNVs and rearrangements within themselves can promote the formation of new gene sequences with potential functional consequences.Oxford University Press201220122007info:eu-repo/semantics/articleinfo:eu-repo/semantics/acceptedVersionapplication/pdfapplication/pdfhttp://hdl.handle.net/10230/16488http://dx.doi.org/10.1093/hmg/ddm209reponame:Recercat. Dipósit de la Recerca de Catalunyainstname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)InglésHuman Molecular Genetics. 2007;16(21):2572-82© 2007 Oxford University Press. This is a pre-copy-editing, author-produced PDF of an article accepted for publication in Human Molecular Genetics following peer review. The definitive publisher-authenticated version Cáceres M, Cardone MF, Carreras A, Ballana E, Rocchi M, Armengol L, Estivill X. Characterization and evolution of the novel gene family FAM90A in primates originated by multiple duplication and rearrangement events. Hum. Mol. Genet. 2007; 16(21): 2572-82 is available online at: http://hmg.oxfordjournals.org/content/16/21/2572info:eu-repo/semantics/openAccessoai:recercat.cat:10230/164882026-05-29T05:05:01Z
dc.title.none.fl_str_mv Characterization and evolution of the novel gene family FAM90A in primates originated by multiple duplication and rearrangement events
title Characterization and evolution of the novel gene family FAM90A in primates originated by multiple duplication and rearrangement events
spellingShingle Characterization and evolution of the novel gene family FAM90A in primates originated by multiple duplication and rearrangement events
Bosch Pagès, Nina
Genoma humà
Genètica evolutiva
Cromosomes
title_short Characterization and evolution of the novel gene family FAM90A in primates originated by multiple duplication and rearrangement events
title_full Characterization and evolution of the novel gene family FAM90A in primates originated by multiple duplication and rearrangement events
title_fullStr Characterization and evolution of the novel gene family FAM90A in primates originated by multiple duplication and rearrangement events
title_full_unstemmed Characterization and evolution of the novel gene family FAM90A in primates originated by multiple duplication and rearrangement events
title_sort Characterization and evolution of the novel gene family FAM90A in primates originated by multiple duplication and rearrangement events
dc.creator.none.fl_str_mv Bosch Pagès, Nina
Cáceres Aguilar, Mario
Cardone, Maria Francesca
Carreras, Anna
Ballana Guix, Ester
Rocchi, Mariano
Armengol i Dulcet, Lluís
Estivill, Xavier, 1955-
author Bosch Pagès, Nina
author_facet Bosch Pagès, Nina
Cáceres Aguilar, Mario
Cardone, Maria Francesca
Carreras, Anna
Ballana Guix, Ester
Rocchi, Mariano
Armengol i Dulcet, Lluís
Estivill, Xavier, 1955-
author_role author
author2 Cáceres Aguilar, Mario
Cardone, Maria Francesca
Carreras, Anna
Ballana Guix, Ester
Rocchi, Mariano
Armengol i Dulcet, Lluís
Estivill, Xavier, 1955-
author2_role author
author
author
author
author
author
author
dc.subject.none.fl_str_mv Genoma humà
Genètica evolutiva
Cromosomes
topic Genoma humà
Genètica evolutiva
Cromosomes
description Genomic plasticity of human chromosome 8p23.1 region is highly influenced by two groups of complex segmental duplications (SDs), termed REPD and REPP, that mediate different kinds of rearrangements. Part of the difficulty to explain the wide range of phenotypes associated with 8p23.1 rearrangements is that REPP and REPD are not yet well characterized, probably due to their polymorphic status. Here, we describe a novel primate-specific gene family, named FAM90A (family with sequence similarity 90), found within these SDs. According to the current human reference sequence assembly, the FAM90A family includes 24 members along 8p23.1 region plus a single member on chromosome 12p13.31, showing copy number variation (CNV) between individuals. These genes can be classified into subfamilies I and II, which differ in their upstream and 5′-untranslated region sequences, but both share the same open reading frame and are ubiquitously expressed. Sequence analysis and comparative fluorescence in situ hybridization studies showed that FAM90A subfamily II suffered a big expansion in the hominoid lineage, whereas subfamily I members were likely generated sometime around the divergence of orangutan and African great apes by a fusion process. In addition, the analysis of the Ka/Ks ratios provides evidence of functional constraint of some FAM90A genes in all species. The characterization of the FAM90A gene family contributes to a better understanding of the structural polymorphism of the human 8p23.1 region and constitutes a good example of how SDs, CNVs and rearrangements within themselves can promote the formation of new gene sequences with potential functional consequences.
publishDate 2007
dc.date.none.fl_str_mv 2007
2012
2012
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/acceptedVersion
format article
status_str acceptedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10230/16488
http://dx.doi.org/10.1093/hmg/ddm209
url http://hdl.handle.net/10230/16488
http://dx.doi.org/10.1093/hmg/ddm209
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv Human Molecular Genetics. 2007;16(21):2572-82
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv Oxford University Press
publisher.none.fl_str_mv Oxford University Press
dc.source.none.fl_str_mv reponame:Recercat. Dipósit de la Recerca de Catalunya
instname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
instname_str Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
reponame_str Recercat. Dipósit de la Recerca de Catalunya
collection Recercat. Dipósit de la Recerca de Catalunya
repository.name.fl_str_mv
repository.mail.fl_str_mv
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