Context-dependent interplay of Swi-Snf and Tup1-Cyc8 influences chromatin and transcription at antagonistically regulated genes

The yeast Swi-Snf co-activator was the first chromatin remodelling complex discovered which can disrupt promoter nucleosomes to enable transcription. The Tup1-Cyc8 complex was the first global co-repressor identified which can position nucleosomes across promoters to block transcription. However, the global extent of their antagonistic regulation of gene transcription in yeast is unknown. We have identified the genes repressed by Tup1-Cyc8 and activated by Swi-Snf in glucose-grown cells which include inactive and actively transcribed genes. We show that Swi-Snf and Tup1-Cyc8 are present at both active and inactive gene promoters, where SNF2 is required for full Tup1-Cyc8 occupancy. The influence of Swi-Snf and Tup1-Cyc8 upon nucleosome positioning is specific to each co-regulated gene and extends over the available upstream intergenic region. We propose Tup1-Cyc8 and Swi-Snf are constitutively present at co-regulated gene promoters where their interplay influences the entire intergenic upstream chromatin environment of target genes and transcription. Swi-Snf and Tup1-Cyc8 are archetypal regulators of transcription responsible for switching genes on and off. Here the authors show that both complexes are constitutively present at antagonistically regulated gene promoters where they influence the upstream chromatin environment and transcription.