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

Handle URI:
http://hdl.handle.net/10754/594094
Title:
An integrative analysis of post-translational histone modifications in the marine diatom Phaeodactylum tricornutum
Authors:
Veluchamy, Alaguraj; Rastogi, Achal; Lin, Xin; Lombard, Bérangère; Murik, Omer; Thomas, Yann; Dingli, Florent; Rivarola, Maximo; Ott, Sandra; Liu, Xinyue; Sun, Yezhou; Rabinowicz, Pablo D.; McCarthy, James; Allen, Andrew E.; Loew, Damarys; Bowler, Chris; Tirichine, Leïla
Abstract:
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. © 2015 Veluchamy et al.
KAUST Department:
Biological and Environmental Sciences and Engineering (BESE) Division; Center for Desert Agriculture
Citation:
Veluchamy A, Rastogi A, Lin X, Lombard B, Murik O, et al. (2015) An integrative analysis of post-translational histone modifications in the marine diatom Phaeodactylum tricornutum. Genome Biology 16. Available: http://dx.doi.org/10.1186/s13059-015-0671-8.
Publisher:
Springer Science + Business Media
Journal:
Genome Biology
Issue Date:
20-May-2015
DOI:
10.1186/s13059-015-0671-8
PubMed ID:
25990474
PubMed Central ID:
PMC4504042
Type:
Article
ISSN:
1465-6906
Appears in Collections:
Articles; Center for Desert Agriculture; Biological and Environmental Sciences and Engineering (BESE) Division

Full metadata record

DC FieldValue Language
dc.contributor.authorVeluchamy, Alagurajen
dc.contributor.authorRastogi, Achalen
dc.contributor.authorLin, Xinen
dc.contributor.authorLombard, Bérangèreen
dc.contributor.authorMurik, Omeren
dc.contributor.authorThomas, Yannen
dc.contributor.authorDingli, Florenten
dc.contributor.authorRivarola, Maximoen
dc.contributor.authorOtt, Sandraen
dc.contributor.authorLiu, Xinyueen
dc.contributor.authorSun, Yezhouen
dc.contributor.authorRabinowicz, Pablo D.en
dc.contributor.authorMcCarthy, Jamesen
dc.contributor.authorAllen, Andrew E.en
dc.contributor.authorLoew, Damarysen
dc.contributor.authorBowler, Chrisen
dc.contributor.authorTirichine, Leïlaen
dc.date.accessioned2016-01-19T13:21:30Zen
dc.date.available2016-01-19T13:21:30Zen
dc.date.issued2015-05-20en
dc.identifier.citationVeluchamy A, Rastogi A, Lin X, Lombard B, Murik O, et al. (2015) An integrative analysis of post-translational histone modifications in the marine diatom Phaeodactylum tricornutum. Genome Biology 16. Available: http://dx.doi.org/10.1186/s13059-015-0671-8.en
dc.identifier.issn1465-6906en
dc.identifier.pmid25990474en
dc.identifier.doi10.1186/s13059-015-0671-8en
dc.identifier.urihttp://hdl.handle.net/10754/594094en
dc.description.abstractBackground: 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. © 2015 Veluchamy et al.en
dc.publisherSpringer Science + Business Mediaen
dc.titleAn integrative analysis of post-translational histone modifications in the marine diatom Phaeodactylum tricornutumen
dc.typeArticleen
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Divisionen
dc.contributor.departmentCenter for Desert Agricultureen
dc.identifier.journalGenome Biologyen
dc.identifier.pmcidPMC4504042en
dc.contributor.institutionEcology and Evolutionary Biology Section, Institut de Biologie de l'École Normale Supérieure (IBENS), CNRS UMR8197 INSERM U1024, 46 rue d'Ulm, Paris, 75005 Franceen
dc.contributor.institutionInstitut Curie, PSL Research University, Centre de Recherche, Laboratoire de Spectrométrie de Masse Protéomique, 26 rue d'Ulm, Cedex 05 Paris, 75248 Franceen
dc.contributor.institutionInstitute for Genome Sciences (IGS), University of Maryland School of Medicine, Baltimore, MD, 21201 USAen
dc.contributor.institutionJ. Craig Venter Institute, 10355 Science Center Drive, San Diego, CA, 92121 USAen
dc.contributor.institutionScripps Institution of Oceanography, Integrative Oceanography Division, University of California, San Diego, CA, 92093 USAen
dc.contributor.institutionState key lab of Marine Environmental Science, Xiamen University, Xiamen, 361005 Chinaen
dc.contributor.institutionInstituto de Biotecnología, CICVyA, Instituto Nacional de Tecnología Agropecuaria (INTA Castelar), CC 25, Castelar, B1712WAA Argentinaen
kaust.authorVeluchamy, Alagurajen

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