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; Thomas, Yann; Dingli, Florent; Rivarola, Maximo Lisandro; Ott, Sandra; Liu, Xinyue; Sun, Yezhou; Rabinowicz, Pablo D.; McCarthy, James; Allen, Andrew E.; Loew, Damarys; Bowler, Chris; Tirichine, Leïla
- 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 Stramenopiles, which include the diatoms. 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 histones of the marine diatom Phaeodactylum tricornutum, 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.
Instituto de Biotecnología
Fil: Veluchamy, Alaguraj. Centre National de la Recherche Scientifique. Institut de Biologie de l’École Normale Supérieure. Ecology and Evolutionary Biology Section; Francia. King Abdullah University of Science and Technology. BESE Division. Center for Desert Agriculture; Arabia Saudita
Fil: Rastogi, Achal. Centre National de la Recherche Scientifique. Institut de Biologie de l’École Normale Supérieure. Ecology and Evolutionary Biology Section; Francia
Fil: Lin, Xin. Centre National de la Recherche Scientifique. Institut de Biologie de l’École Normale Supérieure. Ecology and Evolutionary Biology Section; Francia. Xiamen University. State key lab of Marine Environmental Science; China
Fil: Lombard, Bérangère. Institut Curie PSL Research University. Centre de Recherche. Laboratoire de Spectrométrie de Masse Protéomique; Francia
Fil: Murik, Omer. Centre National de la Recherche Scientifique. Institut de Biologie de l’École Normale Supérieure. Ecology and Evolutionary Biology Section; Francia
Fil: Thomas, Yann. Centre National de la Recherche Scientifique. Institut de Biologie de l’École Normale Supérieure. Ecology and Evolutionary Biology Section; Francia
Fil: Dingli, Florent. Institut Curie PSL Research University. Centre de Recherche. Laboratoire de Spectrométrie de Masse Protéomique; Francia
Fil: Rivarola, Maximo Lisandro. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. University of Maryland School of Medicine. Institute for Genome Sciences; Estados Unidos
Fil: Ott, Sandra. University of Maryland School of Medicine. Institute for Genome Sciences; Estados Unidos
Fil: Liu, Xinyue. University of Maryland School of Medicine. Institute for Genome Sciences; Estados Unidos
Fil: Sun, Yezhou. University of Maryland School of Medicine. Institute for Genome Sciences; Estados Unidos
Fil: Rabinowicz, Pablo D. University of Maryland School of Medicine. Institute for Genome Sciences; Estados Unidos
Fil: McCarthy, James. J. Craig Venter Institute; Estados Unidos
Fil: Allen, Andrew E. J. Craig Venter Institute; Estados Unidos. University of California. Integrative Oceanography Division. Scripps Institution of Oceanography; Estados Unidos
Fil: Loew, Damarys. Institut Curie PSL Research University. Centre de Recherche. Laboratoire de Spectrométrie de Masse Protéomique; Francia
Fil: Bowler, Chris. Centre National de la Recherche Scientifique. Institut de Biologie de l’École Normale Supérieure. Ecology and Evolutionary Biology Section; Francia
Fil: Tirichine, Leïla. Centre National de la Recherche Scientifique. Institut de Biologie de l’École Normale Supérieure. Ecology and Evolutionary Biology Section; Francia - Fuente
- Genome biology 16 : 102.(2015)
- Materia
-
Bacillariophyceae
Histonas
Histones
Phaeodactylum Tricornutum
Diatomea Marina
Marine Diatom - Nivel de accesibilidad
- acceso abierto
- Condiciones de uso
- http://creativecommons.org/licenses/by-nc-sa/4.0/
- Repositorio
.jpg)
- Institución
- Instituto Nacional de Tecnología Agropecuaria
- OAI Identificador
- oai:localhost:20.500.12123/4557
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An integrative analysis of post-translational histone modifications in the marine diatom Phaeodactylum tricornutumVeluchamy, AlagurajRastogi, AchalLin, XinLombard, BérangèreMurik, OmerThomas, YannDingli, FlorentRivarola, Maximo LisandroOtt, SandraLiu, XinyueSun, YezhouRabinowicz, Pablo D.McCarthy, JamesAllen, Andrew E.Loew, DamarysBowler, ChrisTirichine, LeïlaBacillariophyceaeHistonasHistonesPhaeodactylum TricornutumDiatomea MarinaMarine DiatomBackground: 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 Stramenopiles, which include the diatoms. 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 histones of the marine diatom Phaeodactylum tricornutum, 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.Instituto de BiotecnologíaFil: Veluchamy, Alaguraj. Centre National de la Recherche Scientifique. Institut de Biologie de l’École Normale Supérieure. Ecology and Evolutionary Biology Section; Francia. King Abdullah University of Science and Technology. BESE Division. Center for Desert Agriculture; Arabia SauditaFil: Rastogi, Achal. Centre National de la Recherche Scientifique. Institut de Biologie de l’École Normale Supérieure. Ecology and Evolutionary Biology Section; FranciaFil: Lin, Xin. Centre National de la Recherche Scientifique. Institut de Biologie de l’École Normale Supérieure. Ecology and Evolutionary Biology Section; Francia. Xiamen University. State key lab of Marine Environmental Science; ChinaFil: Lombard, Bérangère. Institut Curie PSL Research University. Centre de Recherche. Laboratoire de Spectrométrie de Masse Protéomique; FranciaFil: Murik, Omer. Centre National de la Recherche Scientifique. Institut de Biologie de l’École Normale Supérieure. Ecology and Evolutionary Biology Section; FranciaFil: Thomas, Yann. Centre National de la Recherche Scientifique. Institut de Biologie de l’École Normale Supérieure. Ecology and Evolutionary Biology Section; FranciaFil: Dingli, Florent. Institut Curie PSL Research University. Centre de Recherche. Laboratoire de Spectrométrie de Masse Protéomique; FranciaFil: Rivarola, Maximo Lisandro. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. University of Maryland School of Medicine. Institute for Genome Sciences; Estados UnidosFil: Ott, Sandra. University of Maryland School of Medicine. Institute for Genome Sciences; Estados UnidosFil: Liu, Xinyue. University of Maryland School of Medicine. Institute for Genome Sciences; Estados UnidosFil: Sun, Yezhou. University of Maryland School of Medicine. Institute for Genome Sciences; Estados UnidosFil: Rabinowicz, Pablo D. University of Maryland School of Medicine. Institute for Genome Sciences; Estados UnidosFil: McCarthy, James. J. Craig Venter Institute; Estados UnidosFil: Allen, Andrew E. J. Craig Venter Institute; Estados Unidos. University of California. Integrative Oceanography Division. Scripps Institution of Oceanography; Estados UnidosFil: Loew, Damarys. Institut Curie PSL Research University. Centre de Recherche. Laboratoire de Spectrométrie de Masse Protéomique; FranciaFil: Bowler, Chris. Centre National de la Recherche Scientifique. Institut de Biologie de l’École Normale Supérieure. Ecology and Evolutionary Biology Section; FranciaFil: Tirichine, Leïla. Centre National de la Recherche Scientifique. Institut de Biologie de l’École Normale Supérieure. Ecology and Evolutionary Biology Section; FranciaBioMed Central2019-03-08T13:12:21Z2019-03-08T13:12:21Z2015info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfhttp://hdl.handle.net/20.500.12123/4557https://genomebiology.biomedcentral.com/articles/10.1186/s13059-015-0671-81474-760Xhttps://doi.org/10.1186/s13059-015-0671-8Genome biology 16 : 102.(2015)reponame:INTA Digital (INTA)instname:Instituto Nacional de Tecnología Agropecuariaenginfo:eu-repo/semantics/openAccesshttp://creativecommons.org/licenses/by-nc-sa/4.0/Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)2025-09-29T13:44:35Zoai:localhost:20.500.12123/4557instacron:INTAInstitucionalhttp://repositorio.inta.gob.ar/Organismo científico-tecnológicoNo correspondehttp://repositorio.inta.gob.ar/oai/requesttripaldi.nicolas@inta.gob.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:l2025-09-29 13:44:35.824INTA Digital (INTA) - Instituto Nacional de Tecnología Agropecuariafalse |
| 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 Bacillariophyceae Histonas Histones Phaeodactylum Tricornutum Diatomea Marina Marine Diatom |
| 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 Thomas, Yann Dingli, Florent Rivarola, Maximo Lisandro Ott, Sandra Liu, Xinyue Sun, Yezhou Rabinowicz, Pablo D. McCarthy, James Allen, Andrew E. Loew, Damarys Bowler, Chris Tirichine, Leïla |
| author |
Veluchamy, Alaguraj |
| author_facet |
Veluchamy, Alaguraj Rastogi, Achal Lin, Xin Lombard, Bérangère Murik, Omer Thomas, Yann Dingli, Florent Rivarola, Maximo Lisandro Ott, Sandra Liu, Xinyue Sun, Yezhou Rabinowicz, Pablo D. McCarthy, James Allen, Andrew E. Loew, Damarys Bowler, Chris Tirichine, Leïla |
| author_role |
author |
| author2 |
Rastogi, Achal Lin, Xin Lombard, Bérangère Murik, Omer Thomas, Yann Dingli, Florent Rivarola, Maximo Lisandro Ott, Sandra Liu, Xinyue Sun, Yezhou Rabinowicz, Pablo D. McCarthy, James Allen, Andrew E. Loew, Damarys Bowler, Chris Tirichine, Leïla |
| author2_role |
author author author author author author author author author author author author author author author author |
| dc.subject.none.fl_str_mv |
Bacillariophyceae Histonas Histones Phaeodactylum Tricornutum Diatomea Marina Marine Diatom |
| topic |
Bacillariophyceae Histonas Histones Phaeodactylum Tricornutum Diatomea Marina Marine Diatom |
| 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 Stramenopiles, which include the diatoms. 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 histones of the marine diatom Phaeodactylum tricornutum, 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. Instituto de Biotecnología Fil: Veluchamy, Alaguraj. Centre National de la Recherche Scientifique. Institut de Biologie de l’École Normale Supérieure. Ecology and Evolutionary Biology Section; Francia. King Abdullah University of Science and Technology. BESE Division. Center for Desert Agriculture; Arabia Saudita Fil: Rastogi, Achal. Centre National de la Recherche Scientifique. Institut de Biologie de l’École Normale Supérieure. Ecology and Evolutionary Biology Section; Francia Fil: Lin, Xin. Centre National de la Recherche Scientifique. Institut de Biologie de l’École Normale Supérieure. Ecology and Evolutionary Biology Section; Francia. Xiamen University. State key lab of Marine Environmental Science; China Fil: Lombard, Bérangère. Institut Curie PSL Research University. Centre de Recherche. Laboratoire de Spectrométrie de Masse Protéomique; Francia Fil: Murik, Omer. Centre National de la Recherche Scientifique. Institut de Biologie de l’École Normale Supérieure. Ecology and Evolutionary Biology Section; Francia Fil: Thomas, Yann. Centre National de la Recherche Scientifique. Institut de Biologie de l’École Normale Supérieure. Ecology and Evolutionary Biology Section; Francia Fil: Dingli, Florent. Institut Curie PSL Research University. Centre de Recherche. Laboratoire de Spectrométrie de Masse Protéomique; Francia Fil: Rivarola, Maximo Lisandro. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. University of Maryland School of Medicine. Institute for Genome Sciences; Estados Unidos Fil: Ott, Sandra. University of Maryland School of Medicine. Institute for Genome Sciences; Estados Unidos Fil: Liu, Xinyue. University of Maryland School of Medicine. Institute for Genome Sciences; Estados Unidos Fil: Sun, Yezhou. University of Maryland School of Medicine. Institute for Genome Sciences; Estados Unidos Fil: Rabinowicz, Pablo D. University of Maryland School of Medicine. Institute for Genome Sciences; Estados Unidos Fil: McCarthy, James. J. Craig Venter Institute; Estados Unidos Fil: Allen, Andrew E. J. Craig Venter Institute; Estados Unidos. University of California. Integrative Oceanography Division. Scripps Institution of Oceanography; Estados Unidos Fil: Loew, Damarys. Institut Curie PSL Research University. Centre de Recherche. Laboratoire de Spectrométrie de Masse Protéomique; Francia Fil: Bowler, Chris. Centre National de la Recherche Scientifique. Institut de Biologie de l’École Normale Supérieure. Ecology and Evolutionary Biology Section; Francia Fil: Tirichine, Leïla. Centre National de la Recherche Scientifique. Institut de Biologie de l’École Normale Supérieure. Ecology and Evolutionary Biology Section; 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 Stramenopiles, which include the diatoms. 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 histones of the marine diatom Phaeodactylum tricornutum, 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 |
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2015 2019-03-08T13:12:21Z 2019-03-08T13:12:21Z |
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article |
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publishedVersion |
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| url |
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BioMed Central |
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BioMed Central |
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