An integrative analysis of post-translational histone modifications in the marine diatom Phaeodactylum tricornutum
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...
| Autores principales: | , , , , , , , , , , , , , , , , |
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| Formato: | Artículo |
| Lenguaje: | Inglés |
| Publicado: |
BioMed Central
2019
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| Materias: | |
| Acceso en línea: | http://hdl.handle.net/20.500.12123/4557 https://genomebiology.biomedcentral.com/articles/10.1186/s13059-015-0671-8 https://doi.org/10.1186/s13059-015-0671-8 |
| _version_ | 1855483455857491968 |
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| author | 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_browse | Allen, Andrew E. Bowler, Chris Dingli, Florent Lin, Xin Liu, Xinyue Loew, Damarys Lombard, Bérangère McCarthy, James Murik, Omer Ott, Sandra Rabinowicz, Pablo D. Rastogi, Achal Rivarola, Maximo Lisandro Sun, Yezhou Thomas, Yann Tirichine, Leïla 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_sort | Veluchamy, Alaguraj |
| collection | INTA Digital |
| 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. |
| format | Artículo |
| id | INTA4557 |
| institution | Instituto Nacional de Tecnología Agropecuaria (INTA -Argentina) |
| language | Inglés |
| publishDate | 2019 |
| publishDateRange | 2019 |
| publishDateSort | 2019 |
| publisher | BioMed Central |
| publisherStr | BioMed Central |
| record_format | dspace |
| spelling | INTA45572019-03-08T13:16:41Z An integrative analysis of post-translational histone modifications in the marine diatom Phaeodactylum tricornutum 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 Bacillariophyceae Histonas Histones Phaeodactylum Tricornutum Diatomea Marina Marine Diatom 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 2019-03-08T13:12:21Z 2019-03-08T13:12:21Z 2015 info:ar-repo/semantics/artículo info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion http://hdl.handle.net/20.500.12123/4557 https://genomebiology.biomedcentral.com/articles/10.1186/s13059-015-0671-8 1474-760X https://doi.org/10.1186/s13059-015-0671-8 eng info:eu-repo/semantics/openAccess http://creativecommons.org/licenses/by-nc-sa/4.0/ Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) application/pdf BioMed Central Genome biology 16 : 102.(2015) |
| spellingShingle | Bacillariophyceae Histonas Histones Phaeodactylum Tricornutum Diatomea Marina Marine Diatom 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 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 |
| 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_short | An integrative analysis of post-translational histone modifications in the marine diatom Phaeodactylum tricornutum |
| title_sort | integrative analysis of post translational histone modifications in the marine diatom phaeodactylum tricornutum |
| topic | Bacillariophyceae Histonas Histones Phaeodactylum Tricornutum Diatomea Marina Marine Diatom |
| url | http://hdl.handle.net/20.500.12123/4557 https://genomebiology.biomedcentral.com/articles/10.1186/s13059-015-0671-8 https://doi.org/10.1186/s13059-015-0671-8 |
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