A meta-analysis reveals complex regulatory properties at Taf14-repressed genes.

BACKGROUND: Regulation of gene transcription in response to stress is central to a cell's ability to cope with environmental challenges. Taf14 is a YEATS domain protein in S.cerevisiae that physically associates with several transcriptionally relevant multisubunit complexes including the general transcription factors TFIID and TFIIF and the chromatin-modifying complexes SWI/SNF, INO80, RSC and NuA3. TAF14 deletion strains are sensitive to a variety of stresses suggesting that it plays a role in the transcriptional stress response. RESULTS: In this report we survey published genome-wide transcriptome and occupancy data to define regulatory properties associated with Taf14-dependent genes. Our transcriptome analysis reveals that stress related, TATA-containing and SAGA-dependent genes were much more affected by TAF14 deletion than were TFIID-dependent genes. Comparison of Taf14 and multiple transcription factor occupancy at promoters genome-wide identified a group of proteins whose occupancy correlates with that of Taf14 and whose proximity to Taf14 suggests functional interactions. We show that Taf14-repressed genes tend to be extensively regulated, positively by SAGA complex and the stress dependent activators, Msn2/4 and negatively by a wide number of repressors that act upon promoter chromatin and TBP. CONCLUSIONS: Taken together our analyses suggest a novel role for Taf14 in repression and derepression of stress induced genes, most probably as part of a regulatory network which includes Cyc8-Tup1, Srb10 and histone modifying enzymes.

Solvent-exposed serines in the Gal4 DNA-binding domain are required for promoter occupancy and transcriptional activation in vivo.

The yeast transcriptional activator Gal4 has long been the prototype for studies of eukaryotic transcription. Gal4 is phosphorylated in the DNA-binding domain (DBD); however, the molecular details and functional significance of this remain unknown. We mutagenized seven potential phosphoserines that lie on the solvent-exposed face of the DBD structure and assessed them for transcriptional activity and DNA binding in vivo. Serine to alanine mutants at positions 22, 47, and 85 show the greatest reduction in promoter occupancy and transcriptional activity at the MEL1 promoter containing a single UASGAL . Substitutions with the phosphomimetic aspartate restored DNA-binding and transcriptional activity at serines 22 and 85, suggesting that they are potential sites of Gal4 phosphorylation in vivo. In contrast, the serine to alanine mutants, except serine 22, were fully proficient for binding to the GAL1-10 promoter, containing multiple UASGAL sites, although they had a reduced ability to activate transcription. Collectively, these data show that at the GAL1-10 promoter, functions of the DBD in transcriptional activation can be uncoupled from roles in promoter binding. We suggest that the serines in the DBD mediate protein-protein contacts with the transcription machinery, leading to stabilization of Gal4 at promoters.

The two faces of Cdk8, a positive/negative regulator of transcription.

Three cyclin dependent kinases, Cdk7, Cdk8 and Cdk9 are intimately connected with the processes of RNA polymerase II dependent transcription initiation and elongation in eukaryotic cells. Each of these kinases is part of a larger multisubunit complex, TFIIH, Mediator and p-TEFb respectively. Of the three kinases, Cdk8 is the most complex given that it has been associated with both positive and negative effects on transcription via mechanisms that include regulation of transcription factor turnover, regulation of CTD phosphorylation and regulation of activator or repressor function. Furthermore, Cdk8 has emerged as a key regulator of multiple transcriptional programs linked to nutrient/growth factor sensing and differentiation control. As such Cdk8 represents a potentially interesting therapeutic drug target. In this review we summarize the current state of knowledge on Cdk8 function both in yeast and higher eukaryotes as well as discussing the effects of Cdk8 null mutations at the organismal level.