A. Valdes, L. Coronel, B. Martinez-Garcia, J. Segura, S. Dyson, O. Diaz-Ingelmo, C. Micheletti and J. Roca
Transcriptional supercoiling boosts topoisomerase II-mediated knotting of intracellular DNA
Nucleic Acids Res., 2019, 47 , 6946-6955
Link to online article

Abstract
Recent studies have revealed that the DNA-cross inversion mechanism of topoisomerase II not only removes DNA supercoils and DNA replication intertwines, but produces also small amounts of DNA knots within the clusters of nucleosomes that conform eukaryotic chromatin. Here we examine how transcriptional supercoiling of intracellular DNA affects the occurrence of these knots. We show that, whereas (-) supercoiling does not change the basal DNA knotting probability, (+) supercoiling of DNA generated in front 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 show also that the high knotting probability (P_kn≥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 can 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.