An integrative analysis of post-translational histone modifications in the marine diatom Phaeodactylum tricornutum
Type
ArticleAuthors
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
KAUST Department
Biological and Environmental Sciences and Engineering (BESE) DivisionDesert Agriculture Initiative
Date
2015-05-19Online Publication Date
2015-05-20Print Publication Date
2015-12Permanent link to this record
http://hdl.handle.net/10754/594094
Metadata
Show full item recordAbstract
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.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 and Business Media LLCJournal
Genome BiologyPubMed ID
25990474PubMed Central ID
PMC4504042ae974a485f413a2113503eed53cd6c53
10.1186/s13059-015-0671-8
Scopus Count
Except where otherwise noted, this item's license is described as This is an Open Access article distributed under the terms of the Creative Commons Attribution License , which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited.
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