Human condensin I and II drive extensive ATP–dependent compaction of nucleosome–bound DNA

Kong, Muwen; Cutts, Erin E.; Pan, Dongqing; Beuron, Fabienne; Kaliyappan, Thangavelu; Xue, Chuang; Morris, Edward P.; Musacchio, Andrea; Vannini, Alessandro; Greene, Eric C.

doi:10.1101/683540

Cited by 30 publications

(67 citation statements)

References 53 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…2D). Thus, our analysis demonstrates that loop extrusion in metaphase is preferentially one-sided, with extrusion speeds and stall forces similar to those measured in vitro 24,27,28 .…”

supporting

confidence: 74%

Cohesin and condensin extrude loops in a cell-cycle dependent manner

Golfier

Quail

Kimurâ

et al. 2019

Preprint

View full text Add to dashboard Cite

Chromatin undergoes a dramatic reorganization during the cell cycle 1-3 . In interphase, chromatin is organized into compartments and topological-associating domains (TADs) that are cell-type specific 4-7 , whereas in metaphase, chromosomes undergo large-scale compaction, leading to the loss of specific boundaries and the shutdown of transcription [8][9][10][11][12] . Loop extrusion by structural maintenance of chromosomes complexes (SMCs) has been proposed as a mechanism to organize chromatin in interphase and metaphase [13][14][15][16][17][18][19] . However, the requirements for chromatin organization in these cell phases are very different, and it is unknown whether loop extrusion dynamics and the complexes that extrude them also differ. Here, we used Xenopus egg extracts to reconstitute and image loop extrusion of single DNA molecules during the cell cycle. We show that loops form in both metaphase and interphase, but with distinct dynamic properties. Condensin extrudes asymmetric loops in metaphase, whereas cohesin extrudes symmetric loops in interphase. Our data show that loop extrusion is a general mechanism for the organization of DNA, with dynamic and structural properties that are molecularly regulated during the cell cycle. Main text:To visualize loop formation in Xenopus laevis egg extracts, we attached lambdaphage DNA to a cover slip using biotin-streptavidin linkers 20 in a custom-built microfluidic chamber (Fig. 1A). Addition of either metaphase-arrested or interphase Xenopus egg extracts into the chamber triggered the formation of small DNA enrichments, consistent with nucleosomal deposition 21,22 , that rapidly reduced any slack in the DNA molecules ( Fig. S1A and Movies 1-2). To allow enough slack for the formation of loops, we abolished nucleosomal assembly along the strand by depleting ~90-95% of soluble H3-H4 heterodimers in the extract 23 (Fig. S1B). This led to the formation of compacted DNA clusters that grew in size over time both in metaphase and interphase extracts ( Fig. 1B and Movies 3-8). To investigate whether these clusters exhibit a topology consistent with DNA loops, we applied hydrodynamic forces to the DNA strand by introducing a flow in the perpendicular direction to the strand. This procedure revealed DNA clusters with a characteristic loop topology similar to loop extrusion by yeast condensin in vitro 24 (Fig. 1C, Fig. S1C and Movie 9-12). In mock-depleted extracts, loops also formed but at a much lower frequency ( Fig. S1D and Movie 13) and seemed to compete with nucleosomes for free DNA. These results show that single DNA loop extrusion can be reconstituted in Xenopus egg extracts in metaphase and interphase.Current theoretical models propose that SMCs organize chromatin by extruding symmetric DNA loops 14,16,18 . However, recent experimental studies have shown that yeast condensin can extrude loops asymmetrically in vitro 24 . Although this supports the loop-extrusion hypothesis, it is inconsistent with the symmetric extrusion predicted by theory 25,26 . One reason for ...

show abstract

“…2D). Thus, our analysis demonstrates that loop extrusion in metaphase is preferentially one-sided, with extrusion speeds and stall forces similar to those measured in vitro 24,27,28 .…”

supporting

confidence: 74%

Cohesin and condensin extrude loops in a cell-cycle dependent manner

Golfier

Quail

Kimurâ

et al. 2019

Preprint

View full text Add to dashboard Cite

show abstract

“…We find that semi-diffusive LEFs can compact chromatin to a greater extent than pure one-sided LEFs in some scenarios, but are unable to achieve 1000-fold linear compaction for a plausible values of λ/d ( i.e. , λ/d <1000, which is expected from experimental measurements (Fukui and Uchiyama, 2007;Ganji et al, 2018;Gerlich et al, / 2006a;Kong et al, 2019;Takemoto et al, 2004;Terakawa et al, 2017;Walther et al, 2018) ( Figure 2 d (i) ). The enhanced compaction by semi-diffusive one-sided LEFs arises from their ability to close some unlooped gaps ( Figure 2 d (ii) ).…”

Section: Semi-diffusive One-sided Extrusion Does Not Efficiently Compmentioning

confidence: 61%

“…Therefore, biophysical capabilities beyond those observed for yeast condensins should be present for other organisms. Indeed, recent experimental evidence suggests that pairs of yeast condensins may be able to cooperatively grow loops bidirectionally , while human condensins can perform either one-or two-sided loop extrusion (Kong et al, 2019;Moevus, 2019) . Thus, we explored simple variations of the pure one-sided loop extrusion model and identified a class of one-sided extrusion models that can reproduce in vivo experimental observations ( Table 1 ).…”

Section: Discussionmentioning

confidence: 99%

“…One-sided extrusion alone, however, can reproduce dots when undergoing frequent stochastic switches in translocation direction, turning one-sided into effectively two-sided extrusion. Other mechanisms to generate two-sided or effectively two-sided extrusion have also been proposed Kong et al, 2019;Moevus, 2019) , and gap closure may be achieved by several other mechanisms, as we discuss below in the subsection "Molecular evidence and plausibility of different modes of loop extrusion." Another strategy to eliminate gaps between boundaries and generate dots is to have strongly (>100-fold) biased loading of LEFs at barriers.…”

Section: Unlooped Chromatin From One-sided Extrusion Hinders Eukaryotmentioning

confidence: 94%

“…Recent in vitro single-molecule experiments have imaged loop extrusion of DNA by individual SMC condensin complexes, demonstrating that yeast and human condensin complexes extrude DNA loops in an ATP-dependent, directed manner at speeds of order 1 kb/s. Strikingly, however, yeast condensins (Ganji et al, 2018) and a significant fraction of human condensins (Kong et al, 2019) reel in DNA from only one side, while the other side remains anchored to its DNA loading site. This contrasts with prior observations in bacteria demonstrating the direct involvement of SMC complexes in two-sided loop extrusion in vivo (Tran et al, 2017; .…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

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

Banigan

Berg

Brandão

et al. 2019

Preprint

View full text Add to dashboard Cite

AbstractSMC 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.Impact statementWe reconcile seemingly contradictory findings of single-molecule and in vivo experiments on a major mechanism of chromosome organization by computationally investigating mechanisms of loop extrusion that are consistent with both.

show abstract

Loop extrusion driven volume phase transition of entangled chromosomes

Yamamoto

Schiessel

2022

Biophysical Journal

View full text Add to dashboard Cite

Human condensin I and II drive extensive ATP–dependent compaction of nucleosome–bound DNA

Cited by 30 publications

References 53 publications

Cohesin and condensin extrude loops in a cell-cycle dependent manner

Cohesin and condensin extrude loops in a cell-cycle dependent manner

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

Loop extrusion driven volume phase transition of entangled chromosomes

Contact Info

Product

Resources

About