PXD002148

PXD002148 is an original dataset announced via ProteomeXchange.

Title	An integrative analysis of post-translational histone modifications in the marine diatom Phaeodactylum tricornutum
Description	Nucleosomes are the building blocks of chromatin where gene regulation takes place. Chromatin landscapes have been profiled for several species, providing insights into the understanding of fundamental mechanisms of chromatin-mediated transcriptional regulation of gene expression. However, knowledge is missing from 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. 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 active 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. 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.
HostingRepository	PRIDE
AnnounceDate	2015-05-08
AnnouncementXML	Submission_2015-06-01_03:40:17.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD002148
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Guillaume Arras
SpeciesList	scientific name: Phaeodactylum tricornutum (strain CCAP 1055/1); NCBI TaxID: 556484;
ModificationList	Oxidation; Dimethyl; Trimethyl; GlyGly; Propionyl; Methyl; Acetyl; Carbamidomethyl
Instrument	LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2015-05-06 08:41:23	ID requested
1	2015-05-08 10:57:12	announced
⏵ 2	2015-06-01 03:40:18	announced	Updated publication reference for PubMed record(s): 25990474.

Veluchamy A, Rastogi A, Lin X, Lombard B, Murik O, Thomas Y, Dingli F, Rivarola M, Ott S, Liu X, Sun Y, Rabinowicz PD, McCarthy J, Allen AE, Loew D, Bowler C, Tirichine L, An integrative analysis of post-translational histone modifications in the marine diatom Phaeodactylum tricornutum. Genome Biol, 16(1):102(2015) [pubmed]

submitter keyword: Phaeodactylum tricornutum, epigenetics, histone modifications, H3K27me3, evolution

Damarys Loew
contact affiliation	LSMP Institut Curie FRANCE
contact email	damarys.loew@curie.fr
lab head
Guillaume Arras
contact affiliation	Institut Curie
contact email	guillaume.arras@curie.fr
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD002148
     1. Label: PRIDE project
     2. Name: An integrative analysis of post-translational histone modifications in the marine diatom Phaeodactylum tricornutum