Department of Biological Chemistry, David Geffen School of Medicine, and the Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA.
Proc Natl Acad Sci U S A. 2011 Aug 2;108(31):12693-8. doi: 10.1073/pnas.1106834108. Epub 2011 Jul 19.
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.
DNA 拓扑异构酶被认为可以通过去除延伸过程中产生的过多 DNA 超螺旋来促进转录。然而，在核小体背景下，真核生物中的拓扑异构酶如何被招募并在转录途径中发挥作用尚不清楚。为了解决这个问题，我们呈现了芽殖酵母酿酒酵母中主要的真核拓扑异构酶之一拓扑异构酶 II（Top2）和核小体的高分辨率全基因组图谱。我们的数据表明，在启动子处，Top2 主要与无核小体的 DNA 结合。然而，尽管核小体的丢失可以使 Top2 占据，但情况并非如此，Top2 的丢失对核小体密度几乎没有影响。我们还发现 Top2 参与转录。不仅 Top2 在高度转录的基因中富集，而且 Top2 与 Top1 冗余，以在其启动子处最佳招募 RNA 聚合酶 II。这些发现以及对候选激活基因的检查表明，在基因激活过程中核小体重塑因子诱导的核小体丢失使 Top2 结合，反过来与 Top1 冗余以增强 RNA 聚合酶 II 的募集。
