Chromatin regulates DNA torsional energy via topoisomerase II-mediated relaxation of positive supercoils

Eukaryotic topoisomerases I (topo I) and II (topo II) relax the positive (+) and negative (−) DNA torsional stress (TS) generated ahead and behind the transcription machinery. It is unknown how this DNA relaxation activity is regulated and whether (+) and (−)TS are reduced at similar rates. Here, we used yeast circular minichromosomes to conduct the first comparative analysis of topo I and topo II activities in relaxing chromatin under (+) and (−)TS. We observed that, while topo I relaxed (+) and (−)TS with similar efficiency, topo II was more proficient and relaxed (+)TS more quickly than (−)TS. Accordingly, we found that the relaxation rate of (+)TS by endogenous topoisomerases largely surpassed that of (−)TS. We propose a model of how distinct conformations of chromatin under (+) and (−)TS may produce this unbalanced relaxation of DNA. We postulate that, while quick relaxation of (+)TS may facilitate the progression of RNA and DNA polymerases, slow relaxation of (−)TS may serve to favor DNA unwinding and other structural transitions at specific regions often required for genomic transactions. Synopsis Comparative in vivo analyses show that twin domains of positive (+) and negative (−) DNA torsional stress, which simultaneously arise during DNA transcription, are not relaxed at the same rate in vivo . These findings suggest that the overall negative supercoiling status of native chromatin stems from differential relaxation activities of topoisomerases I and II. Chromatin delays the relaxation of both positive and negative DNA torsional stress by topoisomerase I. Chromatin favors quick relaxation of positive DNA supercoils by topoisomerase II. Unbalanced relaxation of positive supercoils may facilitate DNA unwinding in eukaryotic chromatin. Graphical Abstract Differential (+) and (−) torsional stress relaxation by topoisomerases I and II contributes to the overall negative supercoiling status of native chromatin, which may facilitate transactions such as DNA unwinding.