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E-GEOD-111290

ABSTRACT: Gene expression profiling of the Arabidopsis Mediator MED5 mutants ref4-1 and ref4-3, CDK8 mutant cdk8-1 and ref4-3 cdk8-1

PROVIDER: E-GEOD-111290 | ExpressionAtlas | 2020-04-15

REPOSITORIES: ExpressionAtlas

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			Action	DRS
	E-GEOD-111290-analysis-methods.tsv	Tabular
	E-GEOD-111290-analytics.tsv	Tabular
	E-GEOD-111290-atlasExperimentSummary.Rdata	Rdata
	E-GEOD-111290-configuration.xml	Xml
	E-GEOD-111290-g5_g1-mvaPlot.png	Other

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E-GEOD-95574

Project description:Gene expression profiling of the Arabidopsis Mediator MED5 mutant ref4-3 and suppressors thereof

2020-04-15 | E-GEOD-95574 | ExpressionAtlas

Gene expression profiling of the Arabidopsis Mediator MED5 mutants ref4-1 and ref4-3, CDK8 mutant cdk8-1 and ref4-3 cdk8-1

Project description:Gene expression profiling of the Arabidopsis Mediator MED5 mutants ref4-1 and ref4-3, CDK8 mutant cdk8-1 and ref4-3 cdk8-1

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Gene expression profiling of the Arabidopsis Mediator MED5 mutants ref4-1 and ref4-3, CDK8 mutant cdk8-1 and ref4-3 cdk8-1

Project description:Purpose: To identify changes in gene expression in ref4-3 mutant that contribute to the mutant’s altered growth and metabolite accumulation by comparing differential gene expression in ref4-3 and ref4-3 cdk8-1. Methods: Gene expression profiles were generated from 20-day-old, pooled Arabidopsis rosettes in biological triplicate, by paried-end sequencing of 100 bp fragments using Illumina HiSeq 2500. The sequence reads that passed quality filters were aligned to the TAIR10 reference genome using TopHat. Gene counts were determined using HTseq-count. Differential expression analysis was performed using edgeR. Results: We identified 7,355 genes that were differentially expressed in ref4-3 compared to wild type, part of which were significantly rescued by loss of CDK8 (FDR <0.05).

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Project description:Gene expression profiling of the Arabidopsis Mediator MED5 mutant ref4-3 and suppressors thereof

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A semidominant point mutation of Mediator tail subunit MED5b in Arabidopsis leads to altered enrichment of H3K27me3 and reduced expression of targets of MYC2 [RNA-seq]

Project description:The Mediator complex coordinates regulatory input for transcription driven by RNA Polymerase II in eukaryotes. reduced epidermal fluorescence4-3 (ref4-3) is a semidominant mutation that results in a single amino acid substitution in the Mediator tail subunit Med5b. Previous characterization of ref4-3 revealed altered expression of a variety of loci in Arabidopsis, including those contributing to phenylpropanoid biosynthesis. Examination of existing RNA-seq data indicated that loci enriched for the transcriptionally repressive chromatin modification H3K27me3 are overrepresented among genes that are misregulated in ref4-3. We used ChIP-seq and RNA-seq to examine the possibility that perturbation of H3K27me3 homeostasis in ref4-3 plants contributed to altered transcript levels. We observed that ref4-3 results in a modest global reduction of H3K27me3 at enriched loci and that this reduction is not dependent on gene expression; however, altered H3K27me3 was not strongly predictive of altered expression in ref4-3 plants. Instead, our analyses revealed a substantial enrichment of targets of the MYC2 transcriptional regulator among genes that exhibit decreased expression in ref4-3. Consistent with previous characterization of ref4-3, we observed that ref4-3-dependent decreased expression of MYC2 targets can be suppressed by loss of another Mediator tail subunit, MED25. This observation is consistent with previous biochemical characterization of MYC2. Our data highlight the diverse and distinct impacts that a single amino acid change in the tail subunit of Mediator can have on transcriptional circuits and raise the prospect that Mediator directly contributes to H3K27me3 homeostasis in plants.

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A semidominant point mutation of Mediator tail subunit MED5b in Arabidopsis leads to altered enrichment of H3K27me3 and reduced expression of targets of MYC2 [ChIP-seq]

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Project description:Gene expression profiling by RNA-seq of wild-type, fpa mutant, bdr1 mutant, bdr2 mutant, bdr3 mutant and bdrs triple mutant Arabidopsis thaliana seedlings

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Project description:Transcription profiling by high throughput sequencing of Arabidopsis brat1 mutant, nrpe1 mutant and brat1, nrpe1 double mutants

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