The characterization of Mediator12 and 13 as conditional positive gene regulators in Arabidopsis [RNA-seq]

Mediator is a multi-protein complex which facilitates the initial steps of gene transcription. Mediator 12 (MED12) and MED13 are components of a module that reversibly associates with the core Mediator complex, and both positively and negatively regulates gene expression. Here, in an Arabidopsis mutant screen for factors required for morc1 de-repressed gene expression, we identified MED12 and MED13 as positive gene regulators, both of which contribute broadly to morc1 de-repressed gene expression. Both MED12 and MED13 are preferentially required for the expression of genes lacking active chromatin marks, a chromatin signature shared with morc1 re-activated loci. We further discovered that MED12 tends to interact with genes that are responsive to environmental stimuli, including light and radiation. We demonstrate that the light-induced transient gene expression depends on MED12, and is accompanied by a concomitant increase in MED12 enrichment during induction. In contrast, the steady-state expression level of these genes showed little dependence on MED12, suggesting that MED12 is primarily required to aid the expression of genes in transition from non-active to active states. Overall design: The dataset contain 50 RNAseq samples, and 51 ChIPseq samples. Plants are of different genetic backgrounds, which include col-0, morc1 mutant, ddc mutant, med12 mutant, med13 mutant, med12/morc1 mutant, med13/morc1 mutant, med13/ddc mutant, and MED12-complementing line. Each sample has 3-4 biological replicates.