Investigating chromatin remodelling by the Swi-Snf and Tup1-Cyc8 complexes

Abstract

Swi-Snf is an ATP-dependent chromatin remodelling complex which generally acts as a co-activator of gene transcription via its removal of promoter nucleosomes. Conversely, Tup1-Cyc8 (Ssn6) is a co-repressor complex which acts to repress transcription by positioning nucleosomes at gene promoters. The antagonistic activity of these two complexes has been investigated at only a handful of genes, including the FLO1 and SUC2 genes. We have identified all of the genes in Saccharomyces cerevisiae which are subject to co-regulation by these two complexes and have mapped the Snf2 and Tup1 proteins across the genome to identify genes directly under the control of Swi-Snf and Tup1-Cyc8. The impact upon chromatin structure of target genes by Tup1-Cyc8 and Swi-Snf has also been shown. The co-regulated genes are enriched for stress-response genes, and 30% of these genes reside in subtelomeric regions. Furthermore, the co-regulated subtelomeric genes are the most robustly regulated genes under the control of these two complexes. The data has revealed two potential models for the chromatin remodelling activities by Swi-Snf and Tup1-Cyc8 at co-regulated genes. In one model, Swi-Snf is recruited to Tup1-Cyc8 repressed genes in the absence of the co-repressor to activate transcription. In the second model, Snf2 and Tup1 both occupy the repressed gene, whilst gene activation correlates with an enrichment of Snf2 at target genes in the absence of Tup1. Thus, this study has identified (i) which genes are under control of the Swi-Snf activator and the Tup1-Cyc8 co-repressor, (ii) where Snf2 and Tup1 are located across the genome, and (iii) how these complexes remodel the chromatin at target genes.