Abstract
To investigate the role of DNA topoisomerases in transcription, we have studied global gene expression in Saccharomyces cerevisiae cells deficient for topoisomerases I and II and performed single-gene analyses to support our findings. The genome-wide studies show a general transcriptional down-regulation upon lack of the enzymes, which correlates with gene activity but not gene length. Furthermore, our data reveal a distinct subclass of genes with a strong requirement for topoisomerases. These genes are characterized by high transcriptional plasticity, chromatin regulation, TATA box presence, and enrichment of a nucleosome at a critical position in the promoter region, in line with a repressible/inducible mode of regulation. Single-gene studies with a range of genes belonging to this group demonstrate that topoisomerases play an important role during activation of these genes. Subsequent in-depth analysis of the inducible PHO5 gene reveals that topoisomerases are essential for binding of the Pho4p transcription factor to the PHO5 promoter, which is required for promoter nucleosome removal during activation. In contrast, topoisomerases are dispensable for constitutive transcription initiation and elongation of PHO5, as well as the nuclear entrance of Pho4p. Finally, we provide evidence that topoisomerases are required to maintain the PHO5 promoter in a superhelical state, which is competent for proper activation. In conclusion, our results reveal a hitherto unknown function of topoisomerases during transcriptional activation of genes with a repressible/inducible mode of regulation.
Highlights
Studies of transcription have demonstrated that DNA topoisomerases are important in the transcription process [1]
Topological changes are constantly generated by DNA tracking processes and may influence gene expression if not constantly removed by DNA topoisomerases
Our findings show that topoisomerases play a profound role during transcriptional activation of genes with a repressible/inducible mode of regulation
Summary
Studies of transcription have demonstrated that DNA topoisomerases are important in the transcription process [1]. In Saccharomyces cerevisiae, DNA superhelicity is influenced by topoisomerases I and II (Top1p and Top2p), encoded by the TOP1 and TOP2 genes, respectively [3] Both enzymes are able to relax supercoiled DNA, they show different substrate preferences, with Top2p being much faster than Top1p, when nucleosomal DNA is relaxed, whereas the opposite is the case during relaxation of naked DNA [4]. Despite these differences, early studies in yeast have demonstrated that transcription is more or less unaffected in yeast cells lacking either Top1p or Top2p, indicating that the two enzymes are redundant in the transcription process. Top1Dtop2ts mutants grown under restrictive conditions display a decreased rate of both rRNA and mRNA synthesis [1]
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