Fig. 3. Functions of topoisomerases in genome organization.

a–d | The loop extrusion model, with proposed roles for topoisomerase 1 (TOP1) and TOP2B.⁵⁷: cohesin holds two ends of a chromatin loop containing an enhancer, TOP1 preferentially removes positive DNA supercoiling induced by enhancer RNA (eRNA) synthesis, the resulting negative DNA supercoiling is proposed to pull the ends of DNA through the cohesin complex, and TOP2B bound to CCCTC-binding factor (CTCF) may allow this translocation by removing topological obstacles such as knots and supercoils (part a); as eRNA transcription continues, the extruded loop increases in size, and extrusion of one end (left) is arrested when cohesin encounters CTCF (part b); following further loop extrusion, the enhancer comes into contact with a promoter, and mRNA synthesis begins (part c); CTCF at the second end of the loop comes into contact with the cohesin complex and the chromatin loop is fully extruded, with TOP1 shown acting next to the promoter and TOP2 at DNA crossovers (part d). e–g | Proposed roles of cohesins, TOP1 and TOP2B in assembly of chromatin loops and topologically associating domains (TADs): cohesin and condensin complexes are loaded onto DNA during G1 phase of cell cycle, along with transcription resumption after mitosis (part e); transcription-driven negative DNA supercoiling is proposed to extrude chromatin loops (parts a–d) and form TADs, with TOP2B removing associated topological barriers such as DNA crossovers and catenanes (part f), resulting in TAD formation (part g). h | During mitosis, TOP2A is part of the chromosome scaffold comprising condensin complexes, whereas TOP1 is present in loop domains. i | Transversal axial view of chromatin scaffolded around TOP2A and condensins, with TOP1 in loop domains to remove supercoiling tension. Pol II, polymerase II. Sc, supercoiling.