title: An integrative analysis of post-translational histone modifications in the marine diatom Phaeodactylum tricornutum.
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.
authors.affiliation: Ecology and Evolutionary Biology Section, Institut de Biologie de l'École Normale Supérieure (IBENS), CNRS UMR8197 INSERM U1024, 46 rue d'Ulm, 75005, Paris, France. alaguraj.v@gmail.com.|Present address: BESE Division, Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia. alaguraj.v@gmail.com.
authors.forename: Alaguraj
authors.initials: A
authors.lastname: Veluchamy
authors.affiliation: Ecology and Evolutionary Biology Section, Institut de Biologie de l'École Normale Supérieure (IBENS), CNRS UMR8197 INSERM U1024, 46 rue d'Ulm, 75005, Paris, France. rastogi@biologie.ens.fr.
authors.forename: Achal
authors.initials: A
authors.lastname: Rastogi
authors.affiliation: Ecology and Evolutionary Biology Section, Institut de Biologie de l'École Normale Supérieure (IBENS), CNRS UMR8197 INSERM U1024, 46 rue d'Ulm, 75005, Paris, France. 23swlx@gmail.com.|Present address: State key lab of Marine Environmental Science, Xiamen University, Xiamen, 361005, China. 23swlx@gmail.com.
authors.forename: Xin
authors.initials: X
authors.lastname: Lin
authors.affiliation: Institut Curie, PSL Research University, Centre de Recherche, Laboratoire de Spectrométrie de Masse Protéomique, 26 rue d'Ulm, 75248, Cedex 05 Paris, France. Berangere.Lombard@curie.fr.
authors.forename: Bérangère
authors.initials: B
authors.lastname: Lombard
authors.affiliation: Ecology and Evolutionary Biology Section, Institut de Biologie de l'École Normale Supérieure (IBENS), CNRS UMR8197 INSERM U1024, 46 rue d'Ulm, 75005, Paris, France. murik@biologie.ens.fr.
authors.forename: Omer
authors.initials: O
authors.lastname: Murik
authors.affiliation: Ecology and Evolutionary Biology Section, Institut de Biologie de l'École Normale Supérieure (IBENS), CNRS UMR8197 INSERM U1024, 46 rue d'Ulm, 75005, Paris, France. ythomas@biologie.ens.fr.
authors.forename: Yann
authors.initials: Y
authors.lastname: Thomas
authors.affiliation: Institut Curie, PSL Research University, Centre de Recherche, Laboratoire de Spectrométrie de Masse Protéomique, 26 rue d'Ulm, 75248, Cedex 05 Paris, France. florent.dingli@curie.fr.
authors.forename: Florent
authors.initials: F
authors.lastname: Dingli
authors.affiliation: Institute for Genome Sciences (IGS), University of Maryland School of Medicine, Baltimore, MD, 21201, USA. rivabros2@gmail.com.|Present address: Instituto de Biotecnología, CICVyA, Instituto Nacional de Tecnología Agropecuaria (INTA Castelar), CC 25, Castelar, B1712WAA, Argentina. rivabros2@gmail.com.
authors.forename: Maximo
authors.initials: M
authors.lastname: Rivarola
authors.affiliation: Institute for Genome Sciences (IGS), University of Maryland School of Medicine, Baltimore, MD, 21201, USA. sott@som.umaryland.edu.
authors.forename: Sandra
authors.initials: S
authors.lastname: Ott
authors.affiliation: Institute for Genome Sciences (IGS), University of Maryland School of Medicine, Baltimore, MD, 21201, USA. xyliu@som.umaryland.edu.
authors.forename: Xinyue
authors.initials: X
authors.lastname: Liu
authors.affiliation: Institute for Genome Sciences (IGS), University of Maryland School of Medicine, Baltimore, MD, 21201, USA. YSun@som.umaryland.edu.
authors.forename: Yezhou
authors.initials: Y
authors.lastname: Sun
authors.affiliation: Institute for Genome Sciences (IGS), University of Maryland School of Medicine, Baltimore, MD, 21201, USA. pdrabinowicz@gmail.com.
authors.forename: Pablo D
authors.initials: PD
authors.lastname: Rabinowicz
authors.affiliation: J. Craig Venter Institute, 10355 Science Center Drive, San Diego, CA, 92121, USA. jmccarth@jcvi.org.
authors.forename: James
authors.initials: J
authors.lastname: McCarthy
authors.affiliation: J. Craig Venter Institute, 10355 Science Center Drive, San Diego, CA, 92121, USA. aallen@ucsd.edu.|Scripps Institution of Oceanography, Integrative Oceanography Division, University of California, San Diego, CA, 92093, USA. aallen@ucsd.edu.
authors.forename: Andrew E
authors.initials: AE
authors.lastname: Allen
authors.affiliation: Institut Curie, PSL Research University, Centre de Recherche, Laboratoire de Spectrométrie de Masse Protéomique, 26 rue d'Ulm, 75248, Cedex 05 Paris, France. Damarys.Loew@curie.fr.
authors.forename: Damarys
authors.initials: D
authors.lastname: Loew
authors.affiliation: Ecology and Evolutionary Biology Section, Institut de Biologie de l'École Normale Supérieure (IBENS), CNRS UMR8197 INSERM U1024, 46 rue d'Ulm, 75005, Paris, France. cbowler@biologie.ens.fr.
authors.forename: Chris
authors.initials: C
authors.lastname: Bowler
authors.affiliation: Ecology and Evolutionary Biology Section, Institut de Biologie de l'École Normale Supérieure (IBENS), CNRS UMR8197 INSERM U1024, 46 rue d'Ulm, 75005, Paris, France. leila.tirichine@ens.fr.
authors.forename: Leïla
authors.initials: L
authors.lastname: Tirichine
mesh_terms: D002843:Chromatin / Q000378:metabolism; D017377:Diatoms / Q000235:genetics / Q000378:metabolism*; D015870:Gene Expression; D023281:Genomics; D042421:Histone Code; D006657:Histones / Q000378:metabolism*; D013058:Mass Spectrometry; D009566:Nitrates / Q000378:metabolism; D009707:Nucleosomes / Q000378:metabolism; D011499:Protein Processing, Post-Translational
chemical_list: D002843:Chromatin; D006657:Histones; D009566:Nitrates; D009707:Nucleosomes