Arabidopsis thaliana
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA265379 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR1635390_1.fastq.gz | Fastqsanger.gz | |||
| SRR1635390_2.fastq.gz | Fastqsanger.gz | |||
| SRR1635490_1.fastq.gz | Fastqsanger.gz | |||
| SRR1635490_2.fastq.gz | Fastqsanger.gz | |||
| SRR1635840_1.fastq.gz | Fastqsanger.gz |
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Project description:Histone methylation modulates gene expression in response to external and internal cues. We uncovered a non-redundant role for the Arabidopsis histone methyltransferase, SDG8, which provides a unique opportunity to study the global function of a specific histone methyltransferase within in a multicellular organism. We previously used a promoter responsive to light and carbon in a positive genetic screen to identify an Arabidopsis carbon and light insensitive mutant cli186. In this study, we characterize the mutant cli186 as a complete deletion of a histone methyltransferase gene SDG8 (now renamed sdg8-5). To assess the global role of SDG8, we compared the global histone methylation patterns and the transcriptome of sdg8-5 to wild type (WT) in the context of a transient carbon and light treatment. We showed that the complete deletion of SDG8 in sdg8-5 is associated with a dramatic reduction of H3K36me3 towards the 3’ of the gene body, which correlates with significant reduction in gene expression. We uncovered 1,084 “high confidence” functional targets of SDG8 – affected in both H3K36me3 marks and gene expression – that are associated with specific biological processes including defense, photosynthesis, nutrient metabolism and energy metabolism. Importantly, 71% of these functional targets are responsive to carbon and/or light. Our model suggests that SDG8 functions to mark specific sets of genes with H3K36me3 in the gene body for active transcription, to tune genes involved in primary metabolism that are responsive to the energy level in the environment.
2015-03-01 | GSE62435 | GEO
Project description:Mutation of the ASHH2 gene has pleiotropic developmental effects. The aim of the study was to identify changes in gene expression in seedlings of the ashh2-1/sdg8-1 mutant (SALK_065480, insertion in the gene At1g77300, SDG8/EFS/ASHH2) and look for correlation wth changes in methylation marks on histone tails. Wild type Arabidopsis thaliana (ecotype Colombia) seedlings were used as reference. For low-expresssed tissue-specific genes there was a correlation between reduced H3K36me3 levels and reduction in expression. Although some highly expressed genes with low tissue-specificity show reduced H3K36me3 levels in the mutant, expression levels were, however, not affeccted.
2011-03-31 | GSE22990 | GEO
Project description:Histone methylation modulates gene expression in response to external and internal cues. We uncovered a non-redundant role for the Arabidopsis histone methyltransferase, SDG8, which provides a unique opportunity to study the global function of a specific histone methyltransferase within in a multicellular organism. We previously used a promoter responsive to light and carbon in a positive genetic screen to identify an Arabidopsis carbon and light insensitive mutant cli186. In this study, we characterize the mutant cli186 as a complete deletion of a histone methyltransferase gene SDG8 (now renamed sdg8-5). To assess the global role of SDG8, we compared the global histone methylation patterns and the transcriptome of sdg8-5 to wild type (WT) in the context of a transient carbon and light treatment. We showed that the complete deletion of SDG8 in sdg8-5 is associated with a dramatic reduction of H3K36me3 towards the 3’ of the gene body, which correlates with significant reduction in gene expression. We uncovered 1,084 “high confidence” functional targets of SDG8 – affected in both H3K36me3 marks and gene expression – that are associated with specific biological processes including defense, photosynthesis, nutrient metabolism and energy metabolism. Importantly, 71% of these functional targets are responsive to carbon and/or light. Our model suggests that SDG8 functions to mark specific sets of genes with H3K36me3 in the gene body for active transcription, to tune genes involved in primary metabolism that are responsive to the energy level in the environment. Wild type Arabidopisis and sdg8-5 plants were grown in hydroponics system for three weeks, then starved for carbonhydrate and light for 24 h. They were then treated with carbon and/or light or remained untreated as controls.Three biological replicates were collected, resulting in 24 samples (2 genotypes X 2 carbonhydrate treatmens X 2 light treatments X3 biological replicates).
2015-03-01 | E-GEOD-62435 | biostudies-arrayexpress
Project description:Mutation of the ASHH2 gene has pleiotropic developmental effects. The aim of the study was to identify changes in gene expression in seedlings of the ashh2-1/sdg8-1 mutant (SALK_065480, insertion in the gene At1g77300, SDG8/EFS/ASHH2) and look for correlation wth changes in methylation marks on histone tails. Wild type Arabidopsis thaliana (ecotype Colombia) seedlings were used as reference. For low-expresssed tissue-specific genes there was a correlation between reduced H3K36me3 levels and reduction in expression. Although some highly expressed genes with low tissue-specificity show reduced H3K36me3 levels in the mutant, expression levels were, however, not affeccted. Six biological replicates with 12 plants each both of Arabidopsis thaliana wild type (ecotype Colombia-0) and ashh2-1/sgd8-1 mutant (SALK_065480, insertion in the gene At1g77300, SDG8/EFS/ASHH2) were sown out on soil and grown under the following conditions; 22oC day and 18oC night, 16 hr day length with 30 min adjustment of light to on and off, and 85 μmol/m2/sek in light intensity. The inflorescences of each biological replikate were harvested in bulk from 30-36 days old plants at same time of the day (between 12:45 and 13:45) and at the same developmental stage in bulk.
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Project description:SDG7 and SDG8 ChIP in Arabidopsis thaliana
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Project description:Identification of changes in gene expression in seedlings of the ashh2/sdg8 Arabidopsis mutant
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Project description:Global gene expression analysis of Arabidopsis ppi2-1 mutant
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Project description:h3k36me3-Establishing a reference epigenome in arabidopsis seedlings
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Project description:Investigation of genome-wide expression in the mutant of histone H3K9 methyltransferase KRYPTONITE (KYP) or DNA methyltransferase CHROMOMETHYLASE3 (CMT3) in Arabidopsis. These mutants showed decrease in H3K9 methylation and DNA methylation levels, and transcriptional activation at transposons and repeats. Using NimbleGen DNA microarray, global pattern of expression of genes and transposons were examined in these mutants.
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