Arabidopsis thaliana
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA90713 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Testing the hypothesis that cytosine methylation and histone deacetylation regulate an overlapping set of genes. Keywords: other
2004-08-06 | GSE1612 | GEO
Project description:Blocking histone deacetylation with trichostatin A (TSA) or blocking cytosine methylation using 5-aza-2'-deoxycytosine (aza-dC) can derepress silenced genes in multicellular eukaryotes, including animals and plants. We questioned whether DNA methylation and histone deacetylation overlap in the regulation of endogenous plant genes by monitoring changes in expression of ~7800 Arabidopsis thaliana genes following treatment with azadC, TSA, or both chemicals together. RNA levels for ~4% of the genes were reproducibly changed 3-fold or more by at least one treatment. Distinct subsets of genes are up-regulated or down-regulated in response to aza-dC, TSA, or simultaneous treatment with both chemicals, with little overlap among subsets. Surprisingly, the microarray data indicate that TSA and aza-dC are often antagonistic rather than synergistic in their effects. Analysis of green fluorescent protein transgenic plants confirmed this finding, showing that TSA can block the up-regulation of silenced green fluorescent protein transgenes in response to aza-dC or a ddm1 (decrease in DNA methylation 1) mutation. Our results indicate that global inhibition of DNA methylation or histone deacetylation has complex, nonredundant effects for the majority of responsive genes and suggest that activation of some genes requires one or more TSA-sensitive deacetylation events in addition to cytosine demethylation.
2007-05-10 | E-SMDB-4105 | biostudies-arrayexpress
Project description:Cytosine methylation at CpCpG sites triggers accumulation of non-CpG methylation in gene bodies
| PRJNA354264 | ENA
Project description:To understand the roles of DNA methylation and histone deacetylation in plant gene network that controls plant tolerance to freezing treatment, we used Affymetrix GeneChips ATH-121501 to analysis. For microarray analysis, Arabidopsis (ecotype Columbia) seedlings grew in four types of sterile growth medium: no any other modifying agents, added 7g/ml 0.5 M aza-dC in water (DNA methylation inhibitor), added TSA in methanol (histone deacetylation inhibitor), both aza-dC and TSA, all for 16 day in growth chamber (16-h day length at 70% relative humidity, 23 °C) , then all seedlings were cold treated at 0 °C for 24 h in growth chamber (16-h day length at 70% relative humidity). A total of 3305 genes expression were statistically analysized. Our study provides some clues that the transcript levels of some cold-responsive genes regulated by DNA methylation and histone deacetylation. This will be valuable for understanding gene regulation by epigenetic modifications under freezing stress. Keywords: Cold Stress response, DNA methylation, histone deacetylation
2015-01-20 | GSE63131 | GEO
Project description:Expression data from the Arabidopsis with freezing treatment following the inhibitors of DNA methylation and histone deacetylation
| PRJNA266764 | ENA
Project description:To understand the roles of DNA methylation and histone deacetylation in plant gene network that controls plant tolerance to freezing treatment, we used Affymetrix GeneChips ATH-121501 to analysis. For microarray analysis, Arabidopsis (ecotype Columbia) seedlings grew in four types of sterile growth medium: no any other modifying agents, added 7g/ml 0.5 M aza-dC in water (DNA methylation inhibitor), added TSA in methanol (histone deacetylation inhibitor), both aza-dC and TSA, all for 16 day in growth chamber (16-h day length at 70% relative humidity, 23 M-BM-0C) , then all seedlings were cold treated at 0 M-BM-0C for 24 h in growth chamber (16-h day length at 70% relative humidity). A total of 3305 genes expression were statistically analysized. Our study provides some clues that the transcript levels of some cold-responsive genes regulated by DNA methylation and histone deacetylation. This will be valuable for understanding gene regulation by epigenetic modifications under freezing stress. Keywords: Cold Stress response, DNA methylation, histone deacetylation Three replicates for aza-dc and TSA treatment, and two replicates for Mock and both aza-dc and TSA treatment. All samples were treated 0M-BM-0C 24h.
2015-01-20 | E-GEOD-63131 | biostudies-arrayexpress
Project description:Powerdress Mediated Histone Deacetylation Is Essential For Thermomorphogenesis In Arabidopsis Thaliana
| PRJNA395465 | ENA
Project description:Bioinformatics powered correlative analysis of epigenomic patterns is an effective method to help derive biological hypotheses that can be tested genetically or biochemically. To accommodate the variety and complexity of epigenomic and transcriptomic patterns, ANchored COrrelative Patterns (ANCORP) was developed as a platform to integrate and intuitively visualize a large number of genome-wide profiles. With global profiles of 9 histone modifications mapped by ChIP-seq and a strand-specific RNA-seq dataset, we have applied the ANCORP-genetics pipeline for hypothesis building and testing in order to understand how global transcription may be regulated by epigenetic pathways such as histone modifications. It was found that intragenic antisense RNAs were depleted from genes with strong gene-body H3K36me2 mark and cytosine methylation enrichments but were significantly overrepresented in H3K4me3/H3K27me3 bivalent genes. Moreover, gene body H3K36me2 and DNA methylation anti-correlated with multiple active chromatin marks including H3K4me2/3, H3K9Ac and H3K18Ac. These observations lead us to hypothesize that H3K36me2 and DNA methylation may synergistically repress active chromatin marks in gene bodies and subsequently inhibit transcription of the antisense strand. Mutant analyses revealed that Polymerase Associated Factors (PAF) may be universally required for modulating NAT abundance whereas the role for the 5mC and H3K36me marks are more locus specific. H3K36me and PAF may either repress or permit the accumulation NATs depending on the chromatin state context in a particular transcription unit. Interestingly, the activation of antisense RNA in sdg8-2 or elf8-1 mutants does not associate with any increase of histone marks in gene bodies that are known to correlate with gene activation. Our results suggest that ANCORP-genetics is an effective approach to uncover epigenetic regulatory mechanisms by leveraging on the rapid advances in sequencing technologies and the resultant wealth of genome-wide information.
2011-06-06 | GSE28398 | GEO
Project description:Using acetylated histone H3 ChIP-seq, we reveal that the histone H3 acetylation level is gradually increased on the neural gene loci while decreased on the neural-inhibitory gene loci during mouse ESC neural differentiation. By overlapping with the targets of HDAC1 ChIP-seq, we identify Nodal as a target gene repressed by histone deacetylation. Thus, our study reveals an intrinsic mechanism that epigenetic histone deacetylation ensures neural fate commitment by restricting Nodal signaling. Examination of HDAC1 in differentiated day 2 cells and acetylated histone H3 in day 2, day 4 and day 6 cells.
2015-02-19 | E-GEOD-66025 | biostudies-arrayexpress
Project description:Identification of a complex functioning in histone H3 deacetylation and flowering in Arabidopsis
| PRJNA700810 | ENA