Abstract
BackgroundNucleosomes 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.ResultsHere, 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.ConclusionsThis 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-015-0671-8) contains supplementary material, which is available to authorized users.
Highlights
Nucleosomes are the building blocks of chromatin where gene regulation takes place
Most post-translational modification (PTM) are on the protruding N-terminal tails, a substantial number of modified sites were detected on the globular domains (Fig. 1a; Additional file 2)
Several arginine methylases are encoded in the P. tricornutum genome [19], methylation of arginine was not detected, which might be due to its low abundance
Summary
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. Histones are one of the most highly conserved groups of proteins throughout evolution, highlighting their important role in living organisms. They have been found in almost all eukaryotes so far examined, and they are not found in bacteria, they do occur in some Archaea [5], indicating their ancient origin. They have been extensively studied in several model organisms, including human, Drosophila, yeast and Arabidopsis. Little is known about their role in genome organization in phylogenetically distant groups of eukaryotes beyond the Opisthokonta (including metazoans and fungi) and the Archaeplastida (higher plants, green and red algae)
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