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Series GSE22276 Query DataSets for GSE22276
Status Public on Feb 02, 2011
Title Genome-wide maps of histone modifications in Arabidopsis thaliana
Organism Arabidopsis thaliana
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by array
Summary Histone acetylation and methylation regulate gene expression in eukaryotes, but their effects on the transcriptome of a multicellular organism and on the transcriptomic divergence between species are still poorly understood. Here we present the first genome-wide 1-bp resolution maps of histone acetylation, histone methylation and core histone in Arabidopsis thaliana and a comprehensive analysis of these maps and gene expression data in A. thaliana, A. arenosa and allotetraploids. H3K9 acetylation (H3K9ac) and H3K4 trimethylation (H3K4me3) are correlated, and their high densities near transcriptional start sites determine constitutive expression of genes involved in translation. In contrast, broad distributions of these modifications toward coding regions determine expression variation, especially in genes involved in photosynthesis, carbohydrate metabolism, and defense responses. A dispersed distribution of H3K27me3 and depletion of H3K9ac and H3K4me3 are associated with developmentally repressed genes. Finally, genes affected by histone deacetylase mutation and species divergence tend to show high expression variation. In conclusion, changes in histone acetylation and methylation modulate developmental and environmental gene expression variation within and between species.
Overall design ChIP-Seq: Identification of distribution of H3K9ac, H3K4me3 and H3 in Arabidopsis thaliana leaf.

Expression: Gene expression in the histone deacetylase 1 mutant was generated using t-DNA insertion. mRNA expressions in leaf and flower of the AtHD1 mutant were compared with those of the wild type plants. We conducted 8 replicates of dual-channel microarrays, including 4 biological replicates and individual dye swaps.
Contributor(s) Ha M, Ng DW, Li W, Chen ZJ, Tian L
Citation(s) 21324879
Submission date Jun 10, 2010
Last update date May 15, 2019
Contact name Misook Ha
Phone 7732795900
Organization name National Heart Lung Blood Institute
Lab Laboratory of Epigenome Biology
Street address NIH
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
Platforms (2)
GPL5680 Arabidopsis thaliana 26k 70-mer spotted oligoarray
GPL9062 Illumina Genome Analyzer (Arabidopsis thaliana)
Samples (20)
GSM554339 H3K9ac_ChIPseq
GSM554340 H3K4me3_ChIPSeq
GSM554341 H3_ChIPseq
SRA SRP002650
BioProject PRJNA128717

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Supplementary file Size Download File type/resource
GSE22276_RAW.tar 105.2 Mb (http)(custom) TAR (of BED, GPR)
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA
Processed data included within Sample table

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