Generation of a genomic tiling array of the human Major Histocompatibility Complex (MHC) and its application for DNA methylation analysis

Autores
Tomazou, Eleni M; Rakyan, Vardhman K; Lefebvre, Gregory; Andrews, Robert; Ellis, Peter; Jackson, David K; Langford, Cordelia; Francis, Matthew D; Bäckdahl, Liselotte; Miretti, Marcos Mateo; Coggill, Penny; Ottaviani, Diego; Sheer, Denise; Murrell, Adele; Beck, Stephan G.
Año de publicación
2008
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Background: The major histocompatibility complex (MHC) is essential for human immunity and is highly associated with common diseases, including cancer. While the genetics of the MHC has been studied intensively for many decades, very little is known about the epigenetics of this most polymorphic and disease-associated region of the genome. Methods: To facilitate comprehensive epigenetic analyses of this region, we have generated a genomic tiling array of 2 Kb resolution covering the entire 4 Mb MHC region. The array has been designed to be compatible with chromatin immunoprecipitation (ChIP), methylated DNA immunoprecipitation (MeDIP), array comparative genomic hybridization (aCGH) and expression profiling, including of non-coding RNAs. The array comprises 7832 features, consisting of two replicates of both forward and reverse strands of MHC amplicons and appropriate controls. Results: Using MeDIP, we demonstrate the application of the MHC array for DNA methylation profiling and the identification of tissue-specific differentially methylated regions (tDMRs). Based on the analysis of two tissues and two cell types, we identified 90 tDMRs within the MHC and describe their characterisation. Conclusion: A tiling array covering the MHC region was developed and validated. Its successful application for DNA methylation profiling indicates that this array represents a useful tool for molecular analyses of the MHC in the context of medical genomics.
Fil: Tomazou, Eleni M. Wellcome Trust Sanger Institute; Reino Unido
Fil: Rakyan, Vardhman K. Institute of Cell and Molecular Science; Reino Unido
Fil: Lefebvre, Gregory. Wellcome Trust Sanger Institute; Reino Unido
Fil: Andrews, Robert. Wellcome Trust Sanger Institute; Reino Unido
Fil: Ellis, Peter. Wellcome Trust Sanger Institute; Reino Unido
Fil: Jackson, David K. Wellcome Trust Sanger Institute; Reino Unido
Fil: Langford, Cordelia. Wellcome Trust Sanger Institute; Reino Unido
Fil: Francis, Matthew D. Wellcome Trust Sanger Institute; Reino Unido
Fil: Bäckdahl, Liselotte. University College London; Reino Unido
Fil: Miretti, Marcos Mateo. Wellcome Trust Sanger Institute; Reino Unido. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Instituto de Biología Subtropical. Instituto de Biología Subtropical - Nodo Posadas | Universidad Nacional de Misiones. Instituto de Biología Subtropical. Instituto de Biología Subtropical - Nodo Posadas; Argentina
Fil: Coggill, Penny. Wellcome Trust Sanger Institute; Reino Unido
Fil: Ottaviani, Diego. London Research Institute; Reino Unido. London School of Medicine and Dentistry; Reino Unido
Fil: Sheer, Denise. London School of Medicine and Dentistry; Reino Unido
Fil: Murrell, Adele. Cambridge Research Institute; Reino Unido
Fil: Beck, Stephan G.. University College London; Reino Unido
Materia
HUMAN MAJOR HISTOCOMPATIBILITY
HLA
GENOMIC ARRAY
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/113919
Acceder
id CONICETDig_7ed8ebdb63b107e1564701812079f213
oai_identifier_str oai:ri.conicet.gov.ar:11336/113919
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling Generation of a genomic tiling array of the human Major Histocompatibility Complex (MHC) and its application for DNA methylation analysisTomazou, Eleni MRakyan, Vardhman KLefebvre, GregoryAndrews, RobertEllis, PeterJackson, David KLangford, CordeliaFrancis, Matthew DBäckdahl, LiselotteMiretti, Marcos MateoCoggill, PennyOttaviani, DiegoSheer, DeniseMurrell, AdeleBeck, Stephan G.HUMAN MAJOR HISTOCOMPATIBILITYHLAGENOMIC ARRAYhttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1Background: The major histocompatibility complex (MHC) is essential for human immunity and is highly associated with common diseases, including cancer. While the genetics of the MHC has been studied intensively for many decades, very little is known about the epigenetics of this most polymorphic and disease-associated region of the genome. Methods: To facilitate comprehensive epigenetic analyses of this region, we have generated a genomic tiling array of 2 Kb resolution covering the entire 4 Mb MHC region. The array has been designed to be compatible with chromatin immunoprecipitation (ChIP), methylated DNA immunoprecipitation (MeDIP), array comparative genomic hybridization (aCGH) and expression profiling, including of non-coding RNAs. The array comprises 7832 features, consisting of two replicates of both forward and reverse strands of MHC amplicons and appropriate controls. Results: Using MeDIP, we demonstrate the application of the MHC array for DNA methylation profiling and the identification of tissue-specific differentially methylated regions (tDMRs). Based on the analysis of two tissues and two cell types, we identified 90 tDMRs within the MHC and describe their characterisation. Conclusion: A tiling array covering the MHC region was developed and validated. Its successful application for DNA methylation profiling indicates that this array represents a useful tool for molecular analyses of the MHC in the context of medical genomics.Fil: Tomazou, Eleni M. Wellcome Trust Sanger Institute; Reino UnidoFil: Rakyan, Vardhman K. Institute of Cell and Molecular Science; Reino UnidoFil: Lefebvre, Gregory. Wellcome Trust Sanger Institute; Reino UnidoFil: Andrews, Robert. Wellcome Trust Sanger Institute; Reino UnidoFil: Ellis, Peter. Wellcome Trust Sanger Institute; Reino UnidoFil: Jackson, David K. Wellcome Trust Sanger Institute; Reino UnidoFil: Langford, Cordelia. Wellcome Trust Sanger Institute; Reino UnidoFil: Francis, Matthew D. Wellcome Trust Sanger Institute; Reino UnidoFil: Bäckdahl, Liselotte. University College London; Reino UnidoFil: Miretti, Marcos Mateo. Wellcome Trust Sanger Institute; Reino Unido. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Instituto de Biología Subtropical. Instituto de Biología Subtropical - Nodo Posadas | Universidad Nacional de Misiones. Instituto de Biología Subtropical. Instituto de Biología Subtropical - Nodo Posadas; ArgentinaFil: Coggill, Penny. Wellcome Trust Sanger Institute; Reino UnidoFil: Ottaviani, Diego. London Research Institute; Reino Unido. London School of Medicine and Dentistry; Reino UnidoFil: Sheer, Denise. London School of Medicine and Dentistry; Reino UnidoFil: Murrell, Adele. Cambridge Research Institute; Reino UnidoFil: Beck, Stephan G.. University College London; Reino UnidoBioMed Central2008-05info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/113919Tomazou, Eleni M; Rakyan, Vardhman K; Lefebvre, Gregory; Andrews, Robert; Ellis, Peter; et al.; Generation of a genomic tiling array of the human Major Histocompatibility Complex (MHC) and its application for DNA methylation analysis; BioMed Central; Bmc Medical Genomics; 1; 19; 5-2008; 1-161755-8794CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/doi/10.1186/1755-8794-1-19info:eu-repo/semantics/altIdentifier/url/https://bmcmedgenomics.biomedcentral.com/articles/10.1186/1755-8794-1-19info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-03T10:06:19Zoai:ri.conicet.gov.ar:11336/113919instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-09-03 10:06:19.617CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Generation of a genomic tiling array of the human Major Histocompatibility Complex (MHC) and its application for DNA methylation analysis
title Generation of a genomic tiling array of the human Major Histocompatibility Complex (MHC) and its application for DNA methylation analysis
spellingShingle Generation of a genomic tiling array of the human Major Histocompatibility Complex (MHC) and its application for DNA methylation analysis
Tomazou, Eleni M
HUMAN MAJOR HISTOCOMPATIBILITY
HLA
GENOMIC ARRAY
title_short Generation of a genomic tiling array of the human Major Histocompatibility Complex (MHC) and its application for DNA methylation analysis
title_full Generation of a genomic tiling array of the human Major Histocompatibility Complex (MHC) and its application for DNA methylation analysis
title_fullStr Generation of a genomic tiling array of the human Major Histocompatibility Complex (MHC) and its application for DNA methylation analysis
title_full_unstemmed Generation of a genomic tiling array of the human Major Histocompatibility Complex (MHC) and its application for DNA methylation analysis
title_sort Generation of a genomic tiling array of the human Major Histocompatibility Complex (MHC) and its application for DNA methylation analysis
dc.creator.none.fl_str_mv Tomazou, Eleni M
Rakyan, Vardhman K
Lefebvre, Gregory
Andrews, Robert
Ellis, Peter
Jackson, David K
Langford, Cordelia
Francis, Matthew D
Bäckdahl, Liselotte
Miretti, Marcos Mateo
Coggill, Penny
Ottaviani, Diego
Sheer, Denise
Murrell, Adele
Beck, Stephan G.
author Tomazou, Eleni M
author_facet Tomazou, Eleni M
Rakyan, Vardhman K
Lefebvre, Gregory
Andrews, Robert
Ellis, Peter
Jackson, David K
Langford, Cordelia
Francis, Matthew D
Bäckdahl, Liselotte
Miretti, Marcos Mateo
Coggill, Penny
Ottaviani, Diego
Sheer, Denise
Murrell, Adele
Beck, Stephan G.
author_role author
author2 Rakyan, Vardhman K
Lefebvre, Gregory
Andrews, Robert
Ellis, Peter
Jackson, David K
Langford, Cordelia
Francis, Matthew D
Bäckdahl, Liselotte
Miretti, Marcos Mateo
Coggill, Penny
Ottaviani, Diego
Sheer, Denise
Murrell, Adele
Beck, Stephan G.
author2_role author
author
author
author
author
author
author
author
author
author
author
author
author
author
dc.subject.none.fl_str_mv HUMAN MAJOR HISTOCOMPATIBILITY
HLA
GENOMIC ARRAY
topic HUMAN MAJOR HISTOCOMPATIBILITY
HLA
GENOMIC ARRAY
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv Background: The major histocompatibility complex (MHC) is essential for human immunity and is highly associated with common diseases, including cancer. While the genetics of the MHC has been studied intensively for many decades, very little is known about the epigenetics of this most polymorphic and disease-associated region of the genome. Methods: To facilitate comprehensive epigenetic analyses of this region, we have generated a genomic tiling array of 2 Kb resolution covering the entire 4 Mb MHC region. The array has been designed to be compatible with chromatin immunoprecipitation (ChIP), methylated DNA immunoprecipitation (MeDIP), array comparative genomic hybridization (aCGH) and expression profiling, including of non-coding RNAs. The array comprises 7832 features, consisting of two replicates of both forward and reverse strands of MHC amplicons and appropriate controls. Results: Using MeDIP, we demonstrate the application of the MHC array for DNA methylation profiling and the identification of tissue-specific differentially methylated regions (tDMRs). Based on the analysis of two tissues and two cell types, we identified 90 tDMRs within the MHC and describe their characterisation. Conclusion: A tiling array covering the MHC region was developed and validated. Its successful application for DNA methylation profiling indicates that this array represents a useful tool for molecular analyses of the MHC in the context of medical genomics.
Fil: Tomazou, Eleni M. Wellcome Trust Sanger Institute; Reino Unido
Fil: Rakyan, Vardhman K. Institute of Cell and Molecular Science; Reino Unido
Fil: Lefebvre, Gregory. Wellcome Trust Sanger Institute; Reino Unido
Fil: Andrews, Robert. Wellcome Trust Sanger Institute; Reino Unido
Fil: Ellis, Peter. Wellcome Trust Sanger Institute; Reino Unido
Fil: Jackson, David K. Wellcome Trust Sanger Institute; Reino Unido
Fil: Langford, Cordelia. Wellcome Trust Sanger Institute; Reino Unido
Fil: Francis, Matthew D. Wellcome Trust Sanger Institute; Reino Unido
Fil: Bäckdahl, Liselotte. University College London; Reino Unido
Fil: Miretti, Marcos Mateo. Wellcome Trust Sanger Institute; Reino Unido. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Instituto de Biología Subtropical. Instituto de Biología Subtropical - Nodo Posadas | Universidad Nacional de Misiones. Instituto de Biología Subtropical. Instituto de Biología Subtropical - Nodo Posadas; Argentina
Fil: Coggill, Penny. Wellcome Trust Sanger Institute; Reino Unido
Fil: Ottaviani, Diego. London Research Institute; Reino Unido. London School of Medicine and Dentistry; Reino Unido
Fil: Sheer, Denise. London School of Medicine and Dentistry; Reino Unido
Fil: Murrell, Adele. Cambridge Research Institute; Reino Unido
Fil: Beck, Stephan G.. University College London; Reino Unido
description Background: The major histocompatibility complex (MHC) is essential for human immunity and is highly associated with common diseases, including cancer. While the genetics of the MHC has been studied intensively for many decades, very little is known about the epigenetics of this most polymorphic and disease-associated region of the genome. Methods: To facilitate comprehensive epigenetic analyses of this region, we have generated a genomic tiling array of 2 Kb resolution covering the entire 4 Mb MHC region. The array has been designed to be compatible with chromatin immunoprecipitation (ChIP), methylated DNA immunoprecipitation (MeDIP), array comparative genomic hybridization (aCGH) and expression profiling, including of non-coding RNAs. The array comprises 7832 features, consisting of two replicates of both forward and reverse strands of MHC amplicons and appropriate controls. Results: Using MeDIP, we demonstrate the application of the MHC array for DNA methylation profiling and the identification of tissue-specific differentially methylated regions (tDMRs). Based on the analysis of two tissues and two cell types, we identified 90 tDMRs within the MHC and describe their characterisation. Conclusion: A tiling array covering the MHC region was developed and validated. Its successful application for DNA methylation profiling indicates that this array represents a useful tool for molecular analyses of the MHC in the context of medical genomics.
publishDate 2008
dc.date.none.fl_str_mv 2008-05
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/11336/113919
Tomazou, Eleni M; Rakyan, Vardhman K; Lefebvre, Gregory; Andrews, Robert; Ellis, Peter; et al.; Generation of a genomic tiling array of the human Major Histocompatibility Complex (MHC) and its application for DNA methylation analysis; BioMed Central; Bmc Medical Genomics; 1; 19; 5-2008; 1-16
1755-8794
CONICET Digital
CONICET
url http://hdl.handle.net/11336/113919
identifier_str_mv Tomazou, Eleni M; Rakyan, Vardhman K; Lefebvre, Gregory; Andrews, Robert; Ellis, Peter; et al.; Generation of a genomic tiling array of the human Major Histocompatibility Complex (MHC) and its application for DNA methylation analysis; BioMed Central; Bmc Medical Genomics; 1; 19; 5-2008; 1-16
1755-8794
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/doi/10.1186/1755-8794-1-19
info:eu-repo/semantics/altIdentifier/url/https://bmcmedgenomics.biomedcentral.com/articles/10.1186/1755-8794-1-19
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv BioMed Central
publisher.none.fl_str_mv BioMed Central
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
instname:Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
collection CONICET Digital (CONICET)
instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
repository.name.fl_str_mv CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
_version_ 1842269953449787392
score 13.13397

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