DNA Topoisomerases Maintain Promoters in a State Competent for Transcriptional Activation in Saccharomyces cerevisiae

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.

Ligand-Dependent Enhancer Activation Regulated by Topoisomerase-I Activity

“…One mechanism that resolves the undesirable effects of excessive supercoiling employs DNA topoisomerases, including topoisomerase I (TOP1). TOP1 can relax both negative and positive supercoils by transient single-strand breaks for the passage of individual DNA strands through one another, followed by the rejoining of the phosphodiester backbone of DNA (Pedersen et al, 2012; Pommier et al, 2006). …”

Physiological functions of programmed DNA breaks in signal-induced transcription

“…The enzymes regulate the expression of a range of inducible genes — in particular, those characterized by high transcriptional plasticity 18 . Interestingly, in human Burkitt’s lymphoma cells, the requirement for TOP1 and TOP2 to resolve dynamic supercoiling suggests a model in which the activity of promoters that support low levels of transcription are managed mainly by TOP1, distributed over a broad upstream region, whereas high transcription activity recruits TOP2 to the vicinity of transcription start sites (TSSs) 5 .…”

RNA Polymerase II Regulates Topoisomerase 1 Activity to Favor Efficient Transcription

“…TOP1 may assist nucleosome disassembly at promoters prior to transcription initiation (Durand-Dubief et al, 2010) and help orchestrate the program of induction or repression of gene expression (Pedersen et al, 2012). Together these studies suggest that TOP1 participates in early phases of transcription, but do not reveal its scope and mechanism in vivo.…”