Figure 5.

Pushing of cohesin handcuffs by supercoiling can also explain why the orientation of CTCF binding sites determines the stability of chromatin loops forming TADs. (A) Transcribing RNA polymerase in association with TOP1 induces formation of negative supercoils. Cohesin handcuffs load near a crossing caused by negative supercoiling. (B) The growing plectoneme pushes cohesin handcuffs irrespectively of the orientation of CTCF sites at TADs borders. (C) When CTCF binding sites are convergent, the C terminal parts of bound CTCF protein can contact cohesin rings and this interaction stabilizes cohesin handcuffs and formed chromatin loops. On contact maps, such TADs form triangles with strong tips. (D) When CTCF binding sites are divergent, the C terminal part of bound CTCF protein is unavailable for contacts with cohesin rings. Without these stabilizing interactions cohesin rings dissociate from chromatin and this permits rapid relaxation of accumulated torsional stress by TOP2B that is normally associated with the N terminal part of bound CTCF. On contact maps, such TADs form triangles without strong tips.