Theory and simulations of condensin mediated loop extrusion in DNA

Ryota Takaki, Atreya Dey, Guang Shi and D. Thirumalai ()
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Ryota Takaki: The University of Texas at Austin
Atreya Dey: The University of Texas at Austin
Guang Shi: The University of Texas at Austin
D. Thirumalai: The University of Texas at Austin

Nature Communications, 2021, vol. 12, issue 1, 1-10

Abstract: Abstract Condensation of hundreds of mega-base-pair-long human chromosomes in a small nuclear volume is a spectacular biological phenomenon. This process is driven by the formation of chromosome loops. The ATP consuming motor, condensin, interacts with chromatin segments to actively extrude loops. Motivated by real-time imaging of loop extrusion (LE), we created an analytically solvable model, predicting the LE velocity and step size distribution as a function of external load. The theory fits the available experimental data quantitatively, and suggests that condensin must undergo a large conformational change, induced by ATP binding, bringing distant parts of the motor to proximity. Simulations using a simple model confirm that the motor transitions between an open and a closed state in order to extrude loops by a scrunching mechanism, similar to that proposed in DNA bubble formation during bacterial transcription. Changes in the orientation of the motor domains are transmitted over ~50 nm, connecting the motor head and the hinge, thus providing an allosteric basis for LE.

Date: 2021
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DOI: 10.1038/s41467-021-26167-1

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