An integrative analysis of post-translational histone modifications in the marine diatom Phaeodactylum tricornutum

Autores
Veluchamy, Alaguraj; Rastogi, Achal; Lin, Xin; Lombard, Bérangère; Murik, Omer; Yann, Thomas; Dingli, Florent; Rivarola, Maximo Lisandro; Ott, Sandra; Liu, Xinyue; Sun, Yezhou; Rabinowicz, Pablo D.; McCarthy, James; Allen, Andrew E.; Loew, Damarys; Bowler, Chris; Tirichine, Leila
Año de publicación
2015
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Background: Nucleosomes are the building blocks of chromatin where gene regulation takes place. Chromatin landscapes have been profiled for several species, providing insights into the fundamental mechanisms of chromatin-mediated transcriptional regulation of gene expression. However, knowledge is missing for several major and deep-branching eukaryotic groups, such as the marine model diatom Phaeodactylum tricornutum. Diatoms are highly diverse and ubiquitous species of phytoplankton that play a key role in global biogeochemical cycles. Dissecting chromatin-mediated regulation of genes in diatoms will help understand the ecological success of these organisms in contemporary oceans.Results: Here, we use high resolution mass spectrometry to identify a full repertoire of post-translational modifications on P. tricornutum histones, including eight novel modifications. We map five histone marks coupled with expression data and show that P. tricornutum displays both unique and broadly conserved chromatin features, reflecting the chimeric nature of its genome. Combinatorial analysis of histone marks and DNA methylation demonstrates the presence of an epigenetic code defining activating or repressive chromatin states. We further profile three specific histone marks under conditions of nitrate depletion and show that the histone code is dynamic and targets specific sets of genes.Conclusions: This study is the first genome-wide characterization of the histone code from a stramenopile and a marine phytoplankton. The work represents an important initial step for understanding the evolutionary history of chromatin and how epigenetic modifications affect gene expression in response to environmental cues in marine environments.
Fil: Veluchamy, Alaguraj. King Abdullah University of Science and Technology; Arabia Saudita. Centre National de la Recherche Scientifique; Francia
Fil: Rastogi, Achal. Centre National de la Recherche Scientifique; Francia
Fil: Lin, Xin. Centre National de la Recherche Scientifique; Francia. Xiamen University; China
Fil: Lombard, Bérangère. PSL Research University ; Francia
Fil: Murik, Omer. Centre National de la Recherche Scientifique; Francia
Fil: Yann, Thomas. Centre National de la Recherche Scientifique; Francia
Fil: Dingli, Florent. PSL Research University ; Francia
Fil: Rivarola, Maximo Lisandro. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. University of Maryland; Estados Unidos
Fil: Ott, Sandra. University of Maryland; Estados Unidos
Fil: Liu, Xinyue. University of Maryland; Estados Unidos
Fil: Sun, Yezhou. University of Maryland; Estados Unidos
Fil: Rabinowicz, Pablo D.. University of Maryland; Estados Unidos
Fil: McCarthy, James. Instituto J. Craig Venter; Estados Unidos
Fil: Allen, Andrew E.. Instituto J. Craig Venter; Estados Unidos. University of California; Estados Unidos
Fil: Loew, Damarys. PSL Research University; Francia
Fil: Bowler, Chris. Centre National de la Recherche Scientifique; Francia
Fil: Tirichine, Leila. Centre National de la Recherche Scientifique; Francia
Materia
EPIGENOMICA
GENOMICA
TRANSCRIPTOMICA
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:11336/111731
Acceder
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oai_identifier_str oai:ri.conicet.gov.ar:11336/111731
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling An integrative analysis of post-translational histone modifications in the marine diatom Phaeodactylum tricornutumVeluchamy, AlagurajRastogi, AchalLin, XinLombard, BérangèreMurik, OmerYann, ThomasDingli, FlorentRivarola, Maximo LisandroOtt, SandraLiu, XinyueSun, YezhouRabinowicz, Pablo D.McCarthy, JamesAllen, Andrew E.Loew, DamarysBowler, ChrisTirichine, LeilaEPIGENOMICAGENOMICATRANSCRIPTOMICAhttps://purl.org/becyt/ford/1.2https://purl.org/becyt/ford/1Background: Nucleosomes are the building blocks of chromatin where gene regulation takes place. Chromatin landscapes have been profiled for several species, providing insights into the fundamental mechanisms of chromatin-mediated transcriptional regulation of gene expression. However, knowledge is missing for several major and deep-branching eukaryotic groups, such as the marine model diatom Phaeodactylum tricornutum. Diatoms are highly diverse and ubiquitous species of phytoplankton that play a key role in global biogeochemical cycles. Dissecting chromatin-mediated regulation of genes in diatoms will help understand the ecological success of these organisms in contemporary oceans.Results: Here, we use high resolution mass spectrometry to identify a full repertoire of post-translational modifications on P. tricornutum histones, including eight novel modifications. We map five histone marks coupled with expression data and show that P. tricornutum displays both unique and broadly conserved chromatin features, reflecting the chimeric nature of its genome. Combinatorial analysis of histone marks and DNA methylation demonstrates the presence of an epigenetic code defining activating or repressive chromatin states. We further profile three specific histone marks under conditions of nitrate depletion and show that the histone code is dynamic and targets specific sets of genes.Conclusions: This study is the first genome-wide characterization of the histone code from a stramenopile and a marine phytoplankton. The work represents an important initial step for understanding the evolutionary history of chromatin and how epigenetic modifications affect gene expression in response to environmental cues in marine environments.Fil: Veluchamy, Alaguraj. King Abdullah University of Science and Technology; Arabia Saudita. Centre National de la Recherche Scientifique; FranciaFil: Rastogi, Achal. Centre National de la Recherche Scientifique; FranciaFil: Lin, Xin. Centre National de la Recherche Scientifique; Francia. Xiamen University; ChinaFil: Lombard, Bérangère. PSL Research University ; FranciaFil: Murik, Omer. Centre National de la Recherche Scientifique; FranciaFil: Yann, Thomas. Centre National de la Recherche Scientifique; FranciaFil: Dingli, Florent. PSL Research University ; FranciaFil: Rivarola, Maximo Lisandro. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. University of Maryland; Estados UnidosFil: Ott, Sandra. University of Maryland; Estados UnidosFil: Liu, Xinyue. University of Maryland; Estados UnidosFil: Sun, Yezhou. University of Maryland; Estados UnidosFil: Rabinowicz, Pablo D.. University of Maryland; Estados UnidosFil: McCarthy, James. Instituto J. Craig Venter; Estados UnidosFil: Allen, Andrew E.. Instituto J. Craig Venter; Estados Unidos. University of California; Estados UnidosFil: Loew, Damarys. PSL Research University; FranciaFil: Bowler, Chris. Centre National de la Recherche Scientifique; FranciaFil: Tirichine, Leila. Centre National de la Recherche Scientifique; FranciaBioMed Central2015-05info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/111731Veluchamy, Alaguraj; Rastogi, Achal; Lin, Xin; Lombard, Bérangère; Murik, Omer; et al.; An integrative analysis of post-translational histone modifications in the marine diatom Phaeodactylum tricornutum; BioMed Central; Genome Biology; 16; 1; 5-2015; 1-181474-760XCONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://genomebiology.biomedcentral.com/articles/10.1186/s13059-015-0671-8info:eu-repo/semantics/altIdentifier/doi/10.1186/s13059-015-0671-8info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-29T09:32:52Zoai:ri.conicet.gov.ar:11336/111731instacron: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:34982025-09-29 09:32:52.871CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv An integrative analysis of post-translational histone modifications in the marine diatom Phaeodactylum tricornutum
title An integrative analysis of post-translational histone modifications in the marine diatom Phaeodactylum tricornutum
spellingShingle An integrative analysis of post-translational histone modifications in the marine diatom Phaeodactylum tricornutum
Veluchamy, Alaguraj
EPIGENOMICA
GENOMICA
TRANSCRIPTOMICA
title_short An integrative analysis of post-translational histone modifications in the marine diatom Phaeodactylum tricornutum
title_full An integrative analysis of post-translational histone modifications in the marine diatom Phaeodactylum tricornutum
title_fullStr An integrative analysis of post-translational histone modifications in the marine diatom Phaeodactylum tricornutum
title_full_unstemmed An integrative analysis of post-translational histone modifications in the marine diatom Phaeodactylum tricornutum
title_sort An integrative analysis of post-translational histone modifications in the marine diatom Phaeodactylum tricornutum
dc.creator.none.fl_str_mv Veluchamy, Alaguraj
Rastogi, Achal
Lin, Xin
Lombard, Bérangère
Murik, Omer
Yann, Thomas
Dingli, Florent
Rivarola, Maximo Lisandro
Ott, Sandra
Liu, Xinyue
Sun, Yezhou
Rabinowicz, Pablo D.
McCarthy, James
Allen, Andrew E.
Loew, Damarys
Bowler, Chris
Tirichine, Leila
author Veluchamy, Alaguraj
author_facet Veluchamy, Alaguraj
Rastogi, Achal
Lin, Xin
Lombard, Bérangère
Murik, Omer
Yann, Thomas
Dingli, Florent
Rivarola, Maximo Lisandro
Ott, Sandra
Liu, Xinyue
Sun, Yezhou
Rabinowicz, Pablo D.
McCarthy, James
Allen, Andrew E.
Loew, Damarys
Bowler, Chris
Tirichine, Leila
author_role author
author2 Rastogi, Achal
Lin, Xin
Lombard, Bérangère
Murik, Omer
Yann, Thomas
Dingli, Florent
Rivarola, Maximo Lisandro
Ott, Sandra
Liu, Xinyue
Sun, Yezhou
Rabinowicz, Pablo D.
McCarthy, James
Allen, Andrew E.
Loew, Damarys
Bowler, Chris
Tirichine, Leila
author2_role author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
dc.subject.none.fl_str_mv EPIGENOMICA
GENOMICA
TRANSCRIPTOMICA
topic EPIGENOMICA
GENOMICA
TRANSCRIPTOMICA
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.2
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv Background: Nucleosomes are the building blocks of chromatin where gene regulation takes place. Chromatin landscapes have been profiled for several species, providing insights into the fundamental mechanisms of chromatin-mediated transcriptional regulation of gene expression. However, knowledge is missing for several major and deep-branching eukaryotic groups, such as the marine model diatom Phaeodactylum tricornutum. Diatoms are highly diverse and ubiquitous species of phytoplankton that play a key role in global biogeochemical cycles. Dissecting chromatin-mediated regulation of genes in diatoms will help understand the ecological success of these organisms in contemporary oceans.Results: Here, we use high resolution mass spectrometry to identify a full repertoire of post-translational modifications on P. tricornutum histones, including eight novel modifications. We map five histone marks coupled with expression data and show that P. tricornutum displays both unique and broadly conserved chromatin features, reflecting the chimeric nature of its genome. Combinatorial analysis of histone marks and DNA methylation demonstrates the presence of an epigenetic code defining activating or repressive chromatin states. We further profile three specific histone marks under conditions of nitrate depletion and show that the histone code is dynamic and targets specific sets of genes.Conclusions: This study is the first genome-wide characterization of the histone code from a stramenopile and a marine phytoplankton. The work represents an important initial step for understanding the evolutionary history of chromatin and how epigenetic modifications affect gene expression in response to environmental cues in marine environments.
Fil: Veluchamy, Alaguraj. King Abdullah University of Science and Technology; Arabia Saudita. Centre National de la Recherche Scientifique; Francia
Fil: Rastogi, Achal. Centre National de la Recherche Scientifique; Francia
Fil: Lin, Xin. Centre National de la Recherche Scientifique; Francia. Xiamen University; China
Fil: Lombard, Bérangère. PSL Research University ; Francia
Fil: Murik, Omer. Centre National de la Recherche Scientifique; Francia
Fil: Yann, Thomas. Centre National de la Recherche Scientifique; Francia
Fil: Dingli, Florent. PSL Research University ; Francia
Fil: Rivarola, Maximo Lisandro. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. University of Maryland; Estados Unidos
Fil: Ott, Sandra. University of Maryland; Estados Unidos
Fil: Liu, Xinyue. University of Maryland; Estados Unidos
Fil: Sun, Yezhou. University of Maryland; Estados Unidos
Fil: Rabinowicz, Pablo D.. University of Maryland; Estados Unidos
Fil: McCarthy, James. Instituto J. Craig Venter; Estados Unidos
Fil: Allen, Andrew E.. Instituto J. Craig Venter; Estados Unidos. University of California; Estados Unidos
Fil: Loew, Damarys. PSL Research University; Francia
Fil: Bowler, Chris. Centre National de la Recherche Scientifique; Francia
Fil: Tirichine, Leila. Centre National de la Recherche Scientifique; Francia
description Background: Nucleosomes are the building blocks of chromatin where gene regulation takes place. Chromatin landscapes have been profiled for several species, providing insights into the fundamental mechanisms of chromatin-mediated transcriptional regulation of gene expression. However, knowledge is missing for several major and deep-branching eukaryotic groups, such as the marine model diatom Phaeodactylum tricornutum. Diatoms are highly diverse and ubiquitous species of phytoplankton that play a key role in global biogeochemical cycles. Dissecting chromatin-mediated regulation of genes in diatoms will help understand the ecological success of these organisms in contemporary oceans.Results: Here, we use high resolution mass spectrometry to identify a full repertoire of post-translational modifications on P. tricornutum histones, including eight novel modifications. We map five histone marks coupled with expression data and show that P. tricornutum displays both unique and broadly conserved chromatin features, reflecting the chimeric nature of its genome. Combinatorial analysis of histone marks and DNA methylation demonstrates the presence of an epigenetic code defining activating or repressive chromatin states. We further profile three specific histone marks under conditions of nitrate depletion and show that the histone code is dynamic and targets specific sets of genes.Conclusions: This study is the first genome-wide characterization of the histone code from a stramenopile and a marine phytoplankton. The work represents an important initial step for understanding the evolutionary history of chromatin and how epigenetic modifications affect gene expression in response to environmental cues in marine environments.
publishDate 2015
dc.date.none.fl_str_mv 2015-05
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/11336/111731
Veluchamy, Alaguraj; Rastogi, Achal; Lin, Xin; Lombard, Bérangère; Murik, Omer; et al.; An integrative analysis of post-translational histone modifications in the marine diatom Phaeodactylum tricornutum; BioMed Central; Genome Biology; 16; 1; 5-2015; 1-18
1474-760X
CONICET Digital
CONICET
url http://hdl.handle.net/11336/111731
identifier_str_mv Veluchamy, Alaguraj; Rastogi, Achal; Lin, Xin; Lombard, Bérangère; Murik, Omer; et al.; An integrative analysis of post-translational histone modifications in the marine diatom Phaeodactylum tricornutum; BioMed Central; Genome Biology; 16; 1; 5-2015; 1-18
1474-760X
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/url/https://genomebiology.biomedcentral.com/articles/10.1186/s13059-015-0671-8
info:eu-repo/semantics/altIdentifier/doi/10.1186/s13059-015-0671-8
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
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score 13.070432

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