DNA loop extrusion - example simulation

A simulation of DNA loops and domains forming through loop extrusion. In the extrusion model, an extrusion complex (yellow) containing two subunits first attaches to DNA, forming a small loop. Next, the two subunits slide along the DNA in opposite directions, growing the loop.

The extrusion complex looks for a specific motif (purple triangles) which causes a protein called CTCF to bind to the DNA. If a subunit encounters a CTCF motif that is pointing at it, the subunit tends to stop. If the CTCF motif is pointing in the other direction, the motif won’t be recognized.

A schematic of the extrusion process is shown below the simulation. Two domains are formed, shown in red and blue.

For more information, see

"Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes." Sanborn and Rao et al., PNAS 2015.

Video by Najeeb Tarazi and Adrian Sanborn