van de Peppel et al. demonstrate novel applications for microarray expression profiling. They compared the expression array data from yeast in which each nonessential subunit of the RNA polymerase II coregulator Mediator was independently (one gene) or doubly (two genes) deleted. From this analysis, structure-function relations among the subunits were revealed or validated. For example, expression profiles were identical for med20Δ and med18Δ, which confirmed that loss of one of these two components resulted in loss of the other. In addition, they used the expression profiles as phenotypes for genetic epistasis analysis. Using this type of analysis, the authors modeled the inhibitory effects of the Cdk8 subunit as occurring by its actions on subunits of the tail domain (Med2 subunit) and head domain (Med18) of the Mediator complex. Med2 is known to be phosphorylated in vitro by Cdk8. Comparison of expression profiles of a nonphosphorylatable mutant of Med2 to those of the cdk8Δ showed 12 genes that were increased in both cases, and 10 of these had a conserved motif for interaction with the transcription factor Rsc1, which is involved in activation of genes required under low iron conditions. Thus, this analysis resulted in identification of the specific effects of the Cdk8 kinase on Mediator to inhibit genes required for growth in low iron conditions. These experiments expand the application of expression profiling for analysis of regulatory cascades, as well as provide evidence that posttranslational modification of Mediator is a mechanism for gene repression.
J. van de Peppel, N. Kettelarij, H. van Bakel, T. T. J. P. Kockelkorn, D. van Leenen, F. C. P. Holstege, Mediator expression profiling epistasis reveals a signal transduction pathway with antagonistic submodules and highly specific downstream targets. Mol. Cell 19, 511-522 (2005). [Online Journal]