Chromosome organization by one-sided and two-sided loop extrusion.

Edward J Banigan, Aafke A van den Berg, Hugo B Brandão, John F Marko, Leonid A Mirny

eLife 2020 Apr 06

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SMC complexes, such as condensin or cohesin, organize chromatin throughout the cell cycle by a process known as loop extrusion. SMC complexes reel in DNA, extruding and progressively growing DNA loops. Modeling assuming two-sided loop extrusion reproduces key features of chromatin organization across different organisms. In vitro single-molecule experiments confirmed that yeast condensins extrude loops, however, they remain anchored to their loading sites and extrude loops in a 'one-sided' manner. We therefore simulate one-sided loop extrusion to investigate whether 'one-sided' complexes can compact mitotic chromosomes, organize interphase domains, and juxtapose bacterial chromosomal arms, as can be done by 'two-sided' loop extruders. While one-sided loop extrusion cannot reproduce these phenomena, variants can recapitulate in vivo observations. We predict that SMC complexes in vivo constitute effectively two-sided motors or exhibit biased loading and propose relevant experiments. Our work suggests that loop extrusion is a viable general mechanism of chromatin organization. © 2020, Banigan et al.

Citation

Edward J Banigan, Aafke A van den Berg, Hugo B Brandão, John F Marko, Leonid A Mirny. Chromosome organization by one-sided and two-sided loop extrusion. eLife. 2020 Apr 06;9