Transcriptome architecture across tissues in the pig

Detalhes bibliográficos
Autor(a) principal: Ferraz, Andre L. J. [UNESP]
Data de Publicação: 2008
Outros Autores: Ojeda, Ana, Lopez-Bejar, Manel, Fernandes, Lana T., Castello, Anna, Folch, Josep M., Perez-Enciso, Miguel
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Institucional da UNESP
Texto Completo: http://dx.doi.org/10.1186/1471-2164-9-173
http://hdl.handle.net/11449/42354
Resumo: Background: Artificial selection has resulted in animal breeds with extreme phenotypes. As an organism is made up of many different tissues and organs, each with its own genetic programme, it is pertinent to ask: How relevant is tissue in terms of total transcriptome variability? Which are the genes most distinctly expressed between tissues? Does breed or sex equally affect the transcriptome across tissues?Results: In order to gain insight on these issues, we conducted microarray expression profiling of 16 different tissues from four animals of two extreme pig breeds, Large White and Iberian, two males and two females. Mixed model analysis and neighbor - joining trees showed that tissues with similar developmental origin clustered closer than those with different embryonic origins. Often a sound biological interpretation was possible for overrepresented gene ontology categories within differentially expressed genes between groups of tissues. For instance, an excess of nervous system or muscle development genes were found among tissues of ectoderm or mesoderm origins, respectively. Tissue accounted for similar to 11 times more variability than sex or breed. Nevertheless, we were able to confidently identify genes with differential expression across tissues between breeds (33 genes) and between sexes (19 genes). The genes primarily affected by sex were overall different than those affected by breed or tissue. Interaction with tissue can be important for differentially expressed genes between breeds but not so much for genes whose expression differ between sexes.Conclusion: Embryonic development leaves an enduring footprint on the transcriptome. The interaction in gene x tissue for differentially expressed genes between breeds suggests that animal breeding has targeted differentially each tissue's transcriptome.
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spelling Transcriptome architecture across tissues in the pigBackground: Artificial selection has resulted in animal breeds with extreme phenotypes. As an organism is made up of many different tissues and organs, each with its own genetic programme, it is pertinent to ask: How relevant is tissue in terms of total transcriptome variability? Which are the genes most distinctly expressed between tissues? Does breed or sex equally affect the transcriptome across tissues?Results: In order to gain insight on these issues, we conducted microarray expression profiling of 16 different tissues from four animals of two extreme pig breeds, Large White and Iberian, two males and two females. Mixed model analysis and neighbor - joining trees showed that tissues with similar developmental origin clustered closer than those with different embryonic origins. Often a sound biological interpretation was possible for overrepresented gene ontology categories within differentially expressed genes between groups of tissues. For instance, an excess of nervous system or muscle development genes were found among tissues of ectoderm or mesoderm origins, respectively. Tissue accounted for similar to 11 times more variability than sex or breed. Nevertheless, we were able to confidently identify genes with differential expression across tissues between breeds (33 genes) and between sexes (19 genes). The genes primarily affected by sex were overall different than those affected by breed or tissue. Interaction with tissue can be important for differentially expressed genes between breeds but not so much for genes whose expression differ between sexes.Conclusion: Embryonic development leaves an enduring footprint on the transcriptome. The interaction in gene x tissue for differentially expressed genes between breeds suggests that animal breeding has targeted differentially each tissue's transcriptome.Univ Autonoma Barcelona, Fac Vet, Dept Ciência Anim & Aliments, Bellaterra 08193, SpainUniv Estadual Paulista, Fac Ciencias Agrarias & Vet, UNESP, BR-14884900 Jaboticabal, SP, BrazilUniv Autonoma Barcelona, Fac Vet, Dept Sanit & Anatomia Anim, Bellaterra 08193, SpainUniv Autonoma Barcelona, CReSA, Bellaterra 08193, SpainUniv Autonoma Barcelona, ICREA, Bellaterra 08193, SpainUniv Estadual Paulista, Fac Ciencias Agrarias & Vet, UNESP, BR-14884900 Jaboticabal, SP, BrazilBiomed Central Ltd.Univ Autonoma BarcelonaUniversidade Estadual Paulista (Unesp)Ferraz, Andre L. J. [UNESP]Ojeda, AnaLopez-Bejar, ManelFernandes, Lana T.Castello, AnnaFolch, Josep M.Perez-Enciso, Miguel2014-05-20T15:33:54Z2014-05-20T15:33:54Z2008-04-16info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article20application/pdfhttp://dx.doi.org/10.1186/1471-2164-9-173Bmc Genomics. London: Biomed Central Ltd., v. 9, p. 20, 2008.1471-2164http://hdl.handle.net/11449/4235410.1186/1471-2164-9-173WOS:000255709500001WOS000255709500001.pdfWeb of Sciencereponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengBMC Genomics3.7302,110info:eu-repo/semantics/openAccess2023-12-10T06:21:34Zoai:repositorio.unesp.br:11449/42354Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462024-08-05T19:58:04.742464Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false
dc.title.none.fl_str_mv Transcriptome architecture across tissues in the pig
title Transcriptome architecture across tissues in the pig
spellingShingle Transcriptome architecture across tissues in the pig
Ferraz, Andre L. J. [UNESP]
title_short Transcriptome architecture across tissues in the pig
title_full Transcriptome architecture across tissues in the pig
title_fullStr Transcriptome architecture across tissues in the pig
title_full_unstemmed Transcriptome architecture across tissues in the pig
title_sort Transcriptome architecture across tissues in the pig
author Ferraz, Andre L. J. [UNESP]
author_facet Ferraz, Andre L. J. [UNESP]
Ojeda, Ana
Lopez-Bejar, Manel
Fernandes, Lana T.
Castello, Anna
Folch, Josep M.
Perez-Enciso, Miguel
author_role author
author2 Ojeda, Ana
Lopez-Bejar, Manel
Fernandes, Lana T.
Castello, Anna
Folch, Josep M.
Perez-Enciso, Miguel
author2_role author
author
author
author
author
author
dc.contributor.none.fl_str_mv Univ Autonoma Barcelona
Universidade Estadual Paulista (Unesp)
dc.contributor.author.fl_str_mv Ferraz, Andre L. J. [UNESP]
Ojeda, Ana
Lopez-Bejar, Manel
Fernandes, Lana T.
Castello, Anna
Folch, Josep M.
Perez-Enciso, Miguel
description Background: Artificial selection has resulted in animal breeds with extreme phenotypes. As an organism is made up of many different tissues and organs, each with its own genetic programme, it is pertinent to ask: How relevant is tissue in terms of total transcriptome variability? Which are the genes most distinctly expressed between tissues? Does breed or sex equally affect the transcriptome across tissues?Results: In order to gain insight on these issues, we conducted microarray expression profiling of 16 different tissues from four animals of two extreme pig breeds, Large White and Iberian, two males and two females. Mixed model analysis and neighbor - joining trees showed that tissues with similar developmental origin clustered closer than those with different embryonic origins. Often a sound biological interpretation was possible for overrepresented gene ontology categories within differentially expressed genes between groups of tissues. For instance, an excess of nervous system or muscle development genes were found among tissues of ectoderm or mesoderm origins, respectively. Tissue accounted for similar to 11 times more variability than sex or breed. Nevertheless, we were able to confidently identify genes with differential expression across tissues between breeds (33 genes) and between sexes (19 genes). The genes primarily affected by sex were overall different than those affected by breed or tissue. Interaction with tissue can be important for differentially expressed genes between breeds but not so much for genes whose expression differ between sexes.Conclusion: Embryonic development leaves an enduring footprint on the transcriptome. The interaction in gene x tissue for differentially expressed genes between breeds suggests that animal breeding has targeted differentially each tissue's transcriptome.
publishDate 2008
dc.date.none.fl_str_mv 2008-04-16
2014-05-20T15:33:54Z
2014-05-20T15:33:54Z
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/article
format article
status_str publishedVersion
dc.identifier.uri.fl_str_mv http://dx.doi.org/10.1186/1471-2164-9-173
Bmc Genomics. London: Biomed Central Ltd., v. 9, p. 20, 2008.
1471-2164
http://hdl.handle.net/11449/42354
10.1186/1471-2164-9-173
WOS:000255709500001
WOS000255709500001.pdf
url http://dx.doi.org/10.1186/1471-2164-9-173
http://hdl.handle.net/11449/42354
identifier_str_mv Bmc Genomics. London: Biomed Central Ltd., v. 9, p. 20, 2008.
1471-2164
10.1186/1471-2164-9-173
WOS:000255709500001
WOS000255709500001.pdf
dc.language.iso.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv BMC Genomics
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application/pdf
dc.publisher.none.fl_str_mv Biomed Central Ltd.
publisher.none.fl_str_mv Biomed Central Ltd.
dc.source.none.fl_str_mv Web of Science
reponame:Repositório Institucional da UNESP
instname:Universidade Estadual Paulista (UNESP)
instacron:UNESP
instname_str Universidade Estadual Paulista (UNESP)
instacron_str UNESP
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reponame_str Repositório Institucional da UNESP
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repository.name.fl_str_mv Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)
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