Abstract
Recent studies have revealed that the DNA cross-inversion mechanism of topoisomerase II (topo II) not only removes DNA supercoils and DNA replication intertwines, but also produces small amounts of DNA knots within the clusters of nucleosomes that conform to eukaryotic chromatin. Here, we examine how transcriptional supercoiling of intracellular DNA affects the occurrence of these knots. We show that although (−) supercoiling does not change the basal DNA knotting probability, (+) supercoiling of DNA generated in front of the transcribing complexes increases DNA knot formation over 25-fold. The increase of topo II-mediated DNA knotting occurs both upon accumulation of (+) supercoiling in topoisomerase-deficient cells and during normal transcriptional supercoiling of DNA in TOP1 TOP2 cells. We also show that the high knotting probability (Pkn ≥ 0.5) of (+) supercoiled DNA reflects a 5-fold volume compaction of the nucleosomal fibers in vivo. Our findings indicate that topo II-mediated DNA knotting could be inherent to transcriptional supercoiling of DNA and other chromatin condensation processes and establish, therefore, a new crucial role of topoisomerase II in resetting the knotting–unknotting homeostasis of DNA during chromatin dynamics.
Highlights
During DNA transcription, rotation of the duplex relative to the RNA polymerase produces positive supercoiling of DNA ((+)S) in front of the transcribing complex and negative supercoiling ((−)S) behind it [1,2]
Our findings show that DNA knotting concurs normally with transcriptional supercoiling and other chromatin condensation processes, and establish a new crucial role of topoisomerase II (topo II) in resetting the DNA knotting–unknotting balance during the conformational transitions of intracellular chromatin
To discard the possibility that the increase of DNA knotting could be a product of the exogenous TopA activity, we examined knot formation in TOP1 TOP2 TopA+ cells sampled at 26◦C and following 120 min at 37◦C (Figure 3A)
Summary
During DNA transcription, rotation of the duplex relative to the RNA polymerase produces positive supercoiling of DNA ((+)S) in front of the transcribing complex and negative supercoiling ((−)S) behind it [1,2]. Topo II produces transient DNA double-strand breaks and passes across them another segment of DNA [6]. This DNA cross-inversion mechanism allows the relaxation of (+)S and (−)S, as well as the elimination of the DNA intertwines that arise during chromosome replication [3,4] (Figure 1A). Topo I is recruited in adjoining DNA-transcribing complexes, where nucleosomes are transiently disrupted and spinning of the duplex is fast [10], whereas topo II is recruited mainly in intergenic regions, away from open reading frames [11,12] (Figure 1A)
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