PT  - JOURNAL ARTICLE
AU  - Ryota Takaki
AU  - Atreya Dey
AU  - Guang Shi
AU  - D. Thirumalai
TI  - On the theory of condensin mediated loop extrusion in genomes
AID  - 10.1101/2020.05.27.119578
DP  - 2020 Jan 01
TA  - bioRxiv
PG  - 2020.05.27.119578
4099  - http://biorxiv.org/content/early/2020/05/30/2020.05.27.119578.short
4100  - http://biorxiv.org/content/early/2020/05/30/2020.05.27.119578.full
AB  - The condensation of several mega base pair human chromosomes in a small cell volume is a spectacular phenomenon in biology. This process, involving the formation of loops in chromosomes, is facilitated by ATP consuming motors (condensin and cohesin), that interact with chromatin segments thereby actively extruding loops. Motivated by real time videos of loop extrusion (LE), we created an analytically solvable model, which yields the LE velocity as a function of external load acting on condensin. The theory fits the experimental data quantitatively, and suggests that condensin must undergo a large conformational change, triggered by ATP binding and hydrolysis, that brings distant parts of the motor to proximity. Simulations using a simple model confirm that a transition between an open and closed states is necessary for LE. Changes in the orientation of the motor domain are transmitted over ~ 50 nm, connecting the motor head and the hinge, thus providing a plausible mechanism for LE. The theory and simulations are applicable to loop extrusion in other structural maintenance complexes.Competing Interest StatementThe authors have declared no competing interest.