Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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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. 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.

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Reidunn Aalen

PROVIDER: E-GEOD-22990 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:We have implemented an integrated Systems Biology approach to analyze overall transcriptomic reprogramming and systems level defense responses in the model plant Arabidopsis thaliana during an insect (Brevicoryne brassicae) and a bacterial (Pseudomonas syringae pv. tomato strain DC3000) attack. The main aim of this study was to identify the attacker-specific and general defense response signatures in the model plant Arabidopsis thaliana while attacked by phloem feeding aphids or pathogenic bacteria. Defense responses and networks, unique and specific for aphid or Pseudomonas stresses were identified. Our analysis revealed a probable link between biotic stress and microRNAs in Arabidopsis and thus opened up a new direction to conduct large-scale targeted experiments to explore detailed regulatory links among them. The presented results provide a first comprehensive understanding of Arabidopsis - B. brassicae and Arabidopsis - P. syringae interactions at a systems biology level. Arabidopsis thaliana (ecotype Colombia-0) seeds were grown in 6-cm-diameter pots filled with a sterile soil mix (1.0 part soil and 0.5 part horticultural perlite), 3 plants per pot. Plants were kept in growth chambers VM-CM-6tsch VB 1514 (VM-CM-6tsch Industrietechnik GmbH, Germany) under the following conditions: a 8/16 h (light/dark) photoperiod at 22M-BM-0C/18M-BM-0C, 40%/70% relative humidity, and 70/0 M-NM-<mol m-2s-1 light intensity. After 32 days plants had 8 fully developed leaves. Each plant was infested with 32 wingless aphids [Brevicoryne Brassicae] (4 per leaf), which were transferred to leaves with a fine paintbrush. Infested plants and aphid-free controls were kept in plexiglass cylinders. Plants were harvested 72 h after infestation between the 6th and 8th hour of the light photoperiod. Four biological replicates were prepared from aphid infested and control plants, each sampled from 15 individual plants. Whole rosettes were cut at the hypocotyls and aphids were removed by washing with Milli-Q-filtered water. Differences in transcriptional responses were measured by comparing genes expression of aphid infested plants against non-infested control plants.

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

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