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

Abstract

<jats:title>Abstract</jats:title><jats:p>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. <jats:italic>In vitro</jats:italic> 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 <jats:italic>in vivo</jats:italic> observations. We predict that SMC complexes <jats:italic>in vivo</jats:italic> 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.</jats:p><jats:sec><jats:title>Impact statement</jats:title><jats:p>We reconcile seemingly contradictory findings of single-molecule and <jats:italic>in vivo</jats:italic> experiments on a major mechanism of chromosome organization by computationally investigating mechanisms of loop extrusion that are consistent with both.</jats:p></jats:sec>

Limits of Chromosome Compaction by Loop-Extruding Motors

“…Furthermore, 3D simulations indicate that without 3D interactions, polymers compacted by one-sided loop extrusion are isotropic random walks [65]. This result is expected from theoretical and computational studies of polymer "combs" [74][75][76][77][78], i.e., polymers with side chains (or here, loops) sparsely grafted to the main backbone.…”

“…This model could be induced by subunit exchange [53], ambient conditions (e.g., concentration or ionic composition) [42], or protein modifications [60,61] not present in the single-molecule experiments. Another possibility is that LEFs extrude asymmetrically with speeds v 1 > v 2 , in which case we would observe effectively two-sided extrusion if the slow side is fast enough to close gaps before disassociation (i.e., v 2 =k u ≫ d) [65]. Yet another possibility is that in vivo factors or conditions enable actual two-sided loop extrusion, as it is described by previous models [17,20,21,23] but not observed in vitro [42].…”

“…A stochastic, but steady, population of gaps (of mean size g ¼ d) remains in the steady state of dynamically exchanging LEFs, and gaps cannot be eliminated merely by increasing the number of bound LEFs. Moreover, these gaps cannot be reliably eliminated if the "safety belt" that anchors each one-sided LEF [42,60] is released to allow free diffusion along DNA; gaps would not be eliminated because loop growth would be inhibited by loop conformational entropy [65]. We emphasize that the failure of pure one-sided loop extrusion to compact chromosomes is not strictly due to the simplicity of the model; the similarly simple two-sided extrusion model can easily achieve 1000fold compaction [17,21].…”

CTCF as a boundary factor for cohesin-mediated loop extrusion: evidence for a multi-step mechanism

“…If CTCF dissociates first, it is not known if cohesin remains or continues to extrude ( Figure 2c ). Polymer simulations of the simple loop extrusion model with just cohesin and CTCF generate contact maps similar to experimental maps at the level of TADs and loop domains [ 17 , 18 , 38 , 44 , 77 ]. This is a simplified picture of loop extrusion and it is important to note that loop extrusion inside the cell is likely not this simple: the transcriptional machinery, for example, is likely to also serve as a partial boundary to cohesin-mediated loop extrusion [ 76 , 78 – 80 ].…”

Chromatin Compaction Multiscale Modeling: A Complex Synergy Between Theory, Simulation, and Experiment

“…Loop formation has also been studied with mesoscopic models, where it was observed to depend on linker histone presence, ion concentration, and linker DNA length (Bascom et al, 2016). In addition to the "one-sided" loop extrusion mechanism described above, recent research indicates that "two-sided" loop extrusion might prove to be more robust in explaining experimental data (Banigan et al, 2019).…”