Arabidopsis thaliana
Ontology highlight
ABSTRACT:
OTHER RELATED OMICS DATASETS IN: E-GEOD-67777
PROVIDER: PRJNA280870 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR1965000.fastq.gz | Fastqsanger.gz | |||
| SRR1964991.fastq.gz | Fastqsanger.gz | |||
| SRR1965001.fastq.gz | Fastqsanger.gz | |||
| SRR1964992.fastq.gz | Fastqsanger.gz | |||
| SRR1965002.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:A Genome-wide Chronological Study of Gene Expression and Two Histone Modifications, H3K4me3 and H3K9ac, during Developmental Leaf Senescence [ChIP-seq]
| PRJNA280871 | ENA
Project description:The genome-wide abundance of two histone modifications, H3K4me3 and H3K9ac, both associated with actively expressed genes, was monitored in Arabidopsis thaliana leaves at different time points during developmental senescence, along with expression in the form of RNA-seq data. H3K9ac and H3K4me3 marks were highly convergent at all stages of leaf aging, but H3K4me3 marks covered nearly twice the gene area as H3K9ac marks. Genes with the greatest fold-change in expression displayed the largest positively-correlated percent change in coverage for both marks. Most senescence up-regulated genes were pre-marked by H3K4me3 and H3K9ac, but at levels below the whole-genome average, and for these genes, gene expression increased without a significant increase in either histone mark. However, for a subset of genes showing increased or decreased expression, the respective gain or loss of H3K4me3 marks were found to closely match the temporal changes in mRNA abundance. 22% of genes that increased expression during senescence showed accompanying changes in H3K4me3 modification, and they include numerous regulatory genes, which may act as primary response genes. H3K4me3 and H3K9ac were measured on a genome-wide scale using ChIP-seq at different stages of leaf aging.
2015-04-11 | E-GEOD-67776 | biostudies-arrayexpress
Project description:The genome-wide abundance of two histone modifications, H3K4me3 and H3K9ac, both associated with actively expressed genes, was monitored in Arabidopsis thaliana leaves at different time points during developmental senescence, along with expression in the form of RNA-seq data. H3K9ac and H3K4me3 marks were highly convergent at all stages of leaf aging, but H3K4me3 marks covered nearly twice the gene area as H3K9ac marks. Genes with the greatest fold-change in expression displayed the largest positively-correlated percent change in coverage for both marks. Most senescence up-regulated genes were pre-marked by H3K4me3 and H3K9ac, but at levels below the whole-genome average, and for these genes, gene expression increased without a significant increase in either histone mark. However, for a subset of genes showing increased or decreased expression, the respective gain or loss of H3K4me3 marks were found to closely match the temporal changes in mRNA abundance. 22% of genes that increased expression during senescence showed accompanying changes in H3K4me3 modification, and they include numerous regulatory genes, which may act as primary response genes. RNA-seq data at different stages of leaf aging.
2015-04-11 | E-GEOD-67777 | biostudies-arrayexpress
Project description:The genome-wide abundance of two histone modifications, H3K4me3 and H3K9ac, both associated with actively expressed genes, was monitored in Arabidopsis thaliana leaves at different time points during developmental senescence, along with expression in the form of RNA-seq data. H3K9ac and H3K4me3 marks were highly convergent at all stages of leaf aging, but H3K4me3 marks covered nearly twice the gene area as H3K9ac marks. Genes with the greatest fold-change in expression displayed the largest positively-correlated percent change in coverage for both marks. Most senescence up-regulated genes were pre-marked by H3K4me3 and H3K9ac, but at levels below the whole-genome average, and for these genes, gene expression increased without a significant increase in either histone mark. However, for a subset of genes showing increased or decreased expression, the respective gain or loss of H3K4me3 marks were found to closely match the temporal changes in mRNA abundance. 22% of genes that increased expression during senescence showed accompanying changes in H3K4me3 modification, and they include numerous regulatory genes, which may act as primary response genes.
2015-04-11 | GSE67777 | GEO
Project description:The genome-wide abundance of two histone modifications, H3K4me3 and H3K9ac, both associated with actively expressed genes, was monitored in Arabidopsis thaliana leaves at different time points during developmental senescence, along with expression in the form of RNA-seq data. H3K9ac and H3K4me3 marks were highly convergent at all stages of leaf aging, but H3K4me3 marks covered nearly twice the gene area as H3K9ac marks. Genes with the greatest fold-change in expression displayed the largest positively-correlated percent change in coverage for both marks. Most senescence up-regulated genes were pre-marked by H3K4me3 and H3K9ac, but at levels below the whole-genome average, and for these genes, gene expression increased without a significant increase in either histone mark. However, for a subset of genes showing increased or decreased expression, the respective gain or loss of H3K4me3 marks were found to closely match the temporal changes in mRNA abundance. 22% of genes that increased expression during senescence showed accompanying changes in H3K4me3 modification, and they include numerous regulatory genes, which may act as primary response genes.
2015-04-11 | GSE67776 | GEO
Project description: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. 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.
2011-02-02 | E-GEOD-22276 | biostudies-arrayexpress
Project description: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.
2011-02-02 | GSE22276 | GEO
Project description:Nutrient remobilization during leaf senescence nourishes the growing plant. Understanding the regulation of this process is essential for reducing our dependence on nitrogen fertilizers and increasing agricultural sustainability. Our lab is interested in chromatin changes that accompany the transition to leaf senescence. Previously, darker green leaves were reported for Arabidopsis thaliana hac1 mutants, defective in a gene encoding a histone acetyltransferase in the CREB-binding protein family. Here, we show that two Arabidopsis hac1 alleles display delayed age-related developmental senescence, but have normal dark-induced senescence. Using a combination of ChIP-seq for H3K9ac and RNA-seq for gene expression, we identified 44 potential HAC1 targets during age-related developmental senescence. Genetic analysis demonstrated that one of these potential targets, ERF022, is a positive regulator of leaf senescence. ERF022 is regulated additively by HAC1 and MED25, suggesting MED25 may recruit HAC1 to the ERF022 promoter to increase its expression in older leaves.
2019-07-12 | GSE134176 | GEO
Project description:Leaf senescence is governed by a complex regulatory network involving dynamic reprogramming of gene expression. Recent evidence indicates that trimethylation of histone H3 at lysine 4 (H3K4me3) alters gene expression during leaf senescence. However, it is largely unknown how histone modification is regulated in an age-dependent manner. We found that JMJ16, an Arabidopsis JmjC-domain containing protein, is a specific H3K4 demethylase that negatively regulates leaf senescence. The histone demethylase activity and the JmjN, JmjC, and FYR domains of JMJ16, but not the zf-C5HC2 domain, are essential for JMJ16 function in the regulation of leaf senescence. Genome-wide analysis revealed a widespread coordinated up-regulation of H3K4me3 and gene expression associated with leaf senescence in the loss-of-function jmj16 mutant compared with the wild type. Genetic analysis indicated that JMJ16 negatively regulates leaf senescence at least partly through repressing the expression of WRKY53 and SAG201, two known positive regulators of leaf senescence. Further analyses demonstrated that JMJ16 associates with WRKY53 and SAG201, and represses precocious expression of WRKY53 and SAG201 in mature leaves by reducing H3K4me3 levels at these loci. Moreover, association of JMJ16 on WRKY53 and SAG201 loci increased at mature stage but decreased at later stage, suggesting that the age-dependent dynamic chromatin association of JMJ16 is required for precise transcriptional activation of SAGs during leaf senescence. Thus, JMJ16 is an important regulator of leaf senescence that demethylates H3K4 at senescence-associated genes in an age-dependent manner.
2019-04-17 | GSE115362 | GEO