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Identification of changes in gene expression in seedlings of the ashh2/sdg8 Arabidopsis mutant

ABSTRACT: 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.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE22990 | GEO | 2011/03/31

SECONDARY ACCESSION(S): PRJNA127773

REPOSITORIES: GEO

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Identification of changes in gene expression in seedlings of the ashh2/sdg8 Arabidopsis mutant

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.

2011-03-31 | E-GEOD-22990 | biostudies-arrayexpress

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2016-10-01 | GSE71927 | GEO

Identification of changes in gene expression in inflorescences of the ashh2/sdg8 Arabidopsis mutant

Project description:Mutation of the ASHH2 gene has pleiotropic developmental effects. We have focused on the role of ASHH2 in plant reproduction.The aim of the study was to identify changes in gene expression in inflorescences of the ashh2-1/sdg8-1 mutant (SALK_065480, insertion in the gene At1g77300, SDG8/EFS/ASHH2) compared to wt Arabidopsis thaliana (ecotype Colombia) inflorescences. On the female side, close to 80% of mature ovules lack embryo sac. On the male side, anthers frequently develop without pollen sacs or with specific defects in the tapetum layer, resulting in reduction in the number of functional pollen per anther by up to ~90%. ashh2 mutations also result in homeotic changes in floral organ identity. Transcriptional profiling identified more than 300 up-regulated and 600 down-regulated genes in ashh2 mutant inflorescences, whereof the latter included genes involved in determination of floral organ identity, embryo sac and anther/pollen development. This was confirmed by real-time PCR. In the chromatin of such genes (AP1, AtDMC1 and MYB99) we observed a reduction of H3K36 trimethylation (me3), but not H3K4me3 or H3K36me2.

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Global Functional Targets of the Histone Methyltransferase SDG8 Uncover a Role for Histone Modification in Energy Metabolism

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).

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Global Functional Targets of the Histone Methyltransferase SDG8 Uncover a Role for Histone Modification in Energy Metabolism

2015-03-01 | GSE62435 | GEO

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2018-12-25 | GSE120418 | GEO

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2017-05-10 | GSE85280 | GEO

Arabidopsis thaliana

Project description:Global H3K36me3 pattern of Arabidopsis sdg8-5 mutant

| PRJNA265379 | ENA

H3K36ac is an evolutionary conserved histone modification that marks active genes in plants

Project description:In eukaryotic cells, DNA is tightly packed in the nucleus in chromatin which has histones as its main protein component. Histones are subject to a large number of distinct post-translational modifications, whose sequential or combinatorial action affects genome function. Here, we report the identification of acetylation at lysine 36 in histone H3 (H3K36ac) as a modification in Arabidopsis thaliana. H3K36ac was found to be an evolutionary conserved modification in seed plants. It is highly enriched in euchromatin and very low in heterochromatin. Genome-wide ChIP-seq experiments revealed that H3K36ac is generally found at the 5â?? end of genes. Independently of gene length, H3K36ac covers about 500 bp, about two to three nucleosomes, immediately downstream of the transcriptional start. H3K36ac overlaps with H3K4me3 and the H2A.Z histone variant. The histone acetyl transferase GCN5 and the histone deacetylase HDA19 are required for normal steady state levels of H3K36ac in plants. There is negative crosstalk between H3K36ac and H3K36me3, mediated by the histone methyl transferase SDG8 and GCN5. H3K36ac levels are associated with transcriptional activity but show no linear relation. Instead, H3K36ac is a binary indicator of transcription Characterization of the genome-wide distribution of H3K36ac using ChIP-seq. Analysis of the mechanistic crosstalk in the deposition of acetylation and methylation at H3K36 by ChIP-seq of H3K36ac and H3K36me3 in sdg8-2 and gcn5-1, respectively.

2016-04-05 | E-GEOD-74841 | biostudies-arrayexpress

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