DNA-loop-extruding SMC complexes can traverse one another in vivo.

Hugo B Brandão,Xindan Wang,Leonid A Mirny,Xheni Karaboja,Zhongqing Ren

doi:10.1038/s41594-021-00626-1

Abstract

Chromosome organization mediated by structural maintenance of chromosomes (SMC) complexes is vital in many organisms. SMC complexes act as motors that extrude DNA loops, but it remains unclear what happens when multiple complexes encounter one another on the same DNA in living cells and how these interactions may help to organize an active genome. We therefore created a crash-course track system to study SMC complex encounters in vivo by engineering defined SMC loading sites in the Bacillus subtilis chromosome. Chromosome conformation capture (Hi-C) analyses of over 20 engineered strains show an amazing variety of chromosome folding patterns. Through three-dimensional polymer simulations and theory, we determine that these patterns require SMC complexes to bypass each other in vivo, as recently seen in an in vitro study. We posit that the bypassing activity enables SMC complexes to avoid traffic jams while spatially organizing the genome.

Highlights

Chromosomes from all kingdoms of life are actively maintained and spatially organized to ensure cell viability
structural maintenance of chromosomes (SMC) complexes play a key role in spatially organizing chromosomes and function in many processes like chromatin compaction, sister-chromatid cohesion, DNA break repair, and regulation of the interphase genome [1,2]
Recent single molecule experiments and chromosome conformation capture (Hi-C) studies have shown that the condensin and cohesin SMC complexes can translocate on DNA and extrude DNA loops at rates of ~1 kb/s 3–11

Summary

Main text

Chromosomes from all kingdoms of life are actively maintained and spatially organized to ensure cell viability. We observed this trend experimentally in a strain with two parS sites (Fig. S15): at the 60 min mark, we saw the traces typical of 90 min in the absence of condensin overexpression This confirms the role of condensin abundance in tuning chromosome spatial organization and the changing shapes of the Hi-C interaction patterns. Our study demonstrates that by harnessing the condensin-ParB-parS system, we can create complex chromosome folding patterns not seen before in natural systems, which helped understand what is happening in the wild-type cells These structures could be predicted by a quantitative model of condensin dynamics, which was central to identifying the bypassing mechanism as a key feature of B. subtilis condensin loop extrusion. H.B.B., L.A.M and X.W. interpreted results and wrote the article with input from all authors

Materials and Methods

Methods