Topoisomerase II binds nucleosome-free DNA and acts redundantly with topoisomerase I to enhance recruitment of RNA Pol II in budding yeast

Abstract

DNA topoisomerases are believed to promote transcription by removing excessive DNA supercoils produced during elongation. However, it is unclear how topoisomerases in eukaryotes are recruited and function in the transcription pathway in the context of nucleosomes. To address this problem we present high-resolution genome-wide maps of one of the major eukaryotic topoisomerases, Topoisomerase II (Top2) and nucleosomes in the budding yeast, Saccharomyces cerevisiae. Our data indicate that at promoters Top2 binds primarily to DNA that is nucleosome-free. However, although nucleosome loss enables Top2 occupancy, the opposite is not the case and the loss of Top2 has little effect on nucleosome density. We also find that Top2 is involved in transcription. Not only is Top2 enriched at highly transcribed genes, but Top2 is required redundantly with Top1 for optimal recruitment of RNA polymerase II at their promoters. These findings and the examination of candidate-activated genes suggest that nucleosome loss induced by nucleosome remodeling factors during gene activation enables Top2 binding, which in turn acts redundantly with Top1 to enhance recruitment of RNA polymerase II.histone eviction | relaxase | gene regulation

Gene regulation and priming by topoisomerase IIα in embryonic stem cells

“…As we detect TOP2a at certain promoters in the absence of RNA Pol II, it is possible that TOP2a is recruited before actual transcriptional activation and may have a role in recruiting and promoting RNA Pol II function at transcriptionally active loci. These findings are in agreement with observation made in yeast 54,55 and provide fundamental insights into the mechanism how these enzymes may constitute an important layer of the gene regulatory network.…”

Genome-wide TOP2A DNA cleavage is biased toward translocated and highly transcribed loci

“…The discoveries of TOP2A in the Pol II complex and TOP2A requirement for chromatin dependent in vitro transcription (Mondal and Parvin 2001) are in concert with this conclusion, as are the enriched TOP2 binding in highly transcribed Saccharomyces cerevisiae genes (Sperling et al 2011) and the reduced expression of longer genes with yeast Top2 inhibition (Joshi et al 2012). Although murine ES cells display TOP2A binding at promoters (Thakurela et al 2013), we do not find TOP2A CCR enrichment at promoters.…”

Topoisomerase IIβ Deficiency Enhances Camptothecin-induced Apoptosis

“…Recent studies have suggested a possible overlapping function of Top1 and Top2 in transcription. It has been shown that both Top1 and Top2 can enhance RNA polymerase II recruitment to nucleosome-free DNA regions in yeast (6). It is thus possible that Top2 can functionally substitute Top1 during transcription and vice versa.…”

“…The increased CPT sensitivity in Top2␤-deficient cells may also be related to the function of both Top1 and Top2 in transcription. Chromatin immunoprecipitation (ChIP) analysis has revealed the binding of both Top1 and Top2 to chromosomal regions that maintain active transcription in yeasts and mammalian cells (6,17,18,63). The inactivation of both Top1 and Top2 in yeast reduces RNA polymerase I density, an indication of slowed transcription elongation, on rDNA (19).…”

“…Top2␤ has been proposed to participate in transcription regulation with binding sites located at both the promoter and transcribed regions (17,18). Recent studies have also indicated a potential overlapping function of both Top1 and Top2 in transcription (6,19) and thus suggest that Top2␤ may regulate transcription in collaboration with Top1 in nonproliferating cells.…”