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Histone modifications in the marine diatom Phaeodactylum tricornutum

ABSTRACT: Genome wide mapping of five histone marks (H3K4me2, H3K9me2, H3K9me3, H3K27me3 and H3AcK9/14) as well as nucleosome occupancy was generated by chromatin immunoprecipitation followed by deep sequencing. To gain insights into the dynamic nature of the P. tricornutum epigenome in response to an environmental cue, we analyzed the impact of nitrate depletion. We specifically examined three histone modifications (H3K4me2, H3K9/14Ac and H3K9me3) using Chip-seq.

ORGANISM(S): Phaeodactylum tricornutum

PROVIDER: GSE68513 | GEO | 2015/05/05

SECONDARY ACCESSION(S): PRJNA282957

REPOSITORIES: GEO

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Histone modifications in the marine diatom Phaeodactylum tricornutum

Project description:Genome wide mapping of five histone marks (H3K4me2, H3K9me2, H3K9me3, H3K27me3 and H3AcK9/14) as well as nucleosome occupancy was generated by chromatin immunoprecipitation followed by deep sequencing. To gain insights into the dynamic nature of the P. tricornutum epigenome in response to an environmental cue, we analyzed the impact of nitrate depletion. We specifically examined three histone modifications (H3K4me2, H3K9/14Ac and H3K9me3) using Chip-seq. Examination of 5 different histone modifications.

2015-05-05 | E-GEOD-68513 | biostudies-arrayexpress

Transcriptional response of the marine pennate diatom Phaeodactylum tricornutum to Fe limitation

Project description:Diatoms, which are responsible for up to 40% of the 45 to 50 billion metric tons of organic carbon production each year in the sea, are particularly sensitive to Fe stress. Here we describe the transcriptional response of the pennate diatom Phaeodactylum tricornutum to Fe limitation using a partial genome microarray based on EST and genome sequence data. Processes carried out by components rich in Fe, such as photosynthesis, mitochondrial electron transport and nitrate assimilation are down-regulated to cope with the reduced cellular iron quota. This retrenchment is compensated by nitrogen (N) and carbon (C) reallocation from protein and storage carbohydrate degradation, adaptations to chlorophyll biosynthesis and pigment metabolism, removal of excess electron s by mitochondrial alternative oxidase (AOX), augmented Fe-independent oxidative stress responses, and sensitized iron capture mechanisms. Keywords: Marine phytoplankton, pinnate diatom Wild-type Phaeodactylum tricornutum was grown under Fe replete (10,000 nM) and Fe limiting (5nM) conditions. Partial genome gene expression analysis of iron-inducible genes was conducted using a two-color competitive hybridization microarray.

2010-05-27 | E-GEOD-8675 | biostudies-arrayexpress

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

Project 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.

2015-05-08 | PXD002148 | Pride

Mapping of H3K4me3 in the model diatom Phaeodactylum tricornutum

Project description:Chromatin organization in Phaeodactylum tricornutum

2019-11-15 | GSE139676 | GEO

Transcriptional response of the marine pennate diatom Phaeodactylum tricornutum to Fe limitation

2008-01-01 | GSE8675 | GEO

Gene silencing in the marine diatom Phaeodactylum tricornutum.

Project description: Not available

| S-EPMC2724275 | biostudies-literature

Early nutrient starvation response of the diatom Phaeodactylum tricornutum

Project description:An experiment was performed to determine the similarities on the RNA level between different conditions where cell division stops in the diatom Phaeodactylum tricornutum. Many of these conditions also increase the accumulation of lipids within the cell or impair photosynthesis. The different metabolic responses were evaluated and the dataset was mined for potential transcriptional regulators of these changes. The experimental setup was as follows: Cells from the pennate diatom Phaeodactylum tricornutum were grown in ESAW medium under continous fluorescent light at 21C in baffled shakeflasks. Exponentially growing cells were harvested by centrifugation and washed twice in 21gr/L NaCL to remove nutrients. Cells were subsequently resuspended in the five different media/conditions (control, darkness, no nitrate, no phosphate, nocodazole).

2015-12-07 | E-MTAB-4096 | biostudies-arrayexpress

Analysis of the α-1,3 fucosyltransferase gene funtion in diatom Phaeodactylum tricornutum

Project description:Anylasis of the α-1,3 fucosyltransferase gene function in diatom Phaeodactylum tricornutum

2022-10-03 | GSE214570 | GEO

An Integrated Analysis of Molecular Acclimation to High Light in the Marine Diatom Phaeodactylum tricornutum

Project description:Photosynthetic diatoms are exposed to rapid and unpredictable changes in irradiance and spectral quality, and must be able to adapt their light harvesting systems to varying light conditions. Molecular mechanisms behind light acclimation in diatoms are largely unknown. We set out to investigate the mechanisms of high light acclimation in Phaeodactylum tricornutum using an integrated approach involving global transcriptional profiling, metabolite profiling and variable fluorescence technique. Algae cultures were acclimated to low light (LL), after which the cultures were transferred to high light (HL). Molecular, metabolic and physiological responses were studied at time points 0.5 h, 3 h, 6 h, 12 h, 24 h and 48 h after transfer to HL conditions. The integrated results indicate that the acclimation mechanisms in diatoms can be divided into an initial response phase (0.5 h), an intermediate acclimation phase (3-12 h) and a late acclimation phase (12-48 h). The initial phase is recognized by strong and rapid regulation of genes encoding proteins involved in photosynthesis, pigment metabolism and reactive oxygen species (ROS) scavenging systems. A significant increase in light protecting metabolites occur together with the induction of transcriptional processes involved in protection of cellular structures at this early phase. During the following phases, the metabolite profiling display a pronounced decrease in light harvesting pigments, whereas the variable fluorescence measurements show that the photosynthetic capacity increases strongly during the late acclimation phase. We show that P. tricornutum is capable of swift and efficient execution of photoprotective mechanisms, followed by changes in the composition of the photosynthetic machinery that enable the diatoms to utilize the excess energy available in HL. Central molecular players in light protection and acclimation to high irradiances have been identified.

2009-11-06 | GSE17237 | GEO

Regulatory mechanism of diurnal fluctuated laminarin in diatom Phaeodactylum tricornutum

Project description:Diatoms played an essential role in marine primary productivity. Polysaccharide chrysolaminarin and neutral lipid, mainly TAG, were necessary carbon fixation in diatom Phaeodactylum tricornutum. Our study speculated on the metabolism pathway of chrysolaminarin, fatty acid, fatty acid β-oxidation and TAG. Transcriptional levels coordinated with carbon fixation metabolism pathway were conjoint analysis in this study.

2022-08-03 | GSE210141 | GEO

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