A chromosome folding intermediate at the condensin-to-cohesin transition during telophase

Abramo, Kristin; Valton, Anne‐Laure; Venev, Sergey V.; Özadam, Hakan; Fox, A. Nicole; Dekker, Job

doi:10.1038/s41556-019-0406-2

Cited by 176 publications

(227 citation statements)

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“…The different dynamic properties of loop formation we observe in interphase and metaphase suggest that different molecular activities may be responsible for loop formation during the cell cycle 15,29 . Recent work has suggested that cohesin could extrude loops in interphase, though this activity has not been directly visualized in cellular contexts [30][31][32] .…”

mentioning

confidence: 78%

“…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.…”

mentioning

confidence: 99%

“…Recent work has suggested that cohesin could extrude loops in interphase, though this activity has not been directly visualized in cellular contexts [30][31][32] . Thus, cell-cycle-dependent activities of condensin and cohesin could account for the transition between symmetric and non-symmetric loop extrusion 15 . To assess the role of cohesin and condensin during loop extrusion in interphase and metaphase, we selectively depleted these proteins in egg extract using antibodies ( Fig.…”

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

Golfier

Quail

Kimurâ

et al. 2019

Preprint

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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 ...

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confidence: 99%

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confidence: 99%

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

Golfier

Quail

Kimurâ

et al. 2019

Preprint

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“…To measure more precisely the spatial distributions of cohesin loops, we computed the loop spectrum on pairs of cohesin peaks (Fig 2d) using Hi-C data of Hela synchronized cells released from mitosis into G1 [17]. At the beginning of the kinetics, the spectrum is flat with no significant loop scores.…”

Section: Detection and Quantification In Mammalsmentioning

confidence: 99%

Computer vision for pattern detection in chromosome contact maps

Matthey-Doret

Baudry

Breuer

et al. 2020

Preprint

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Chromosomes of all species studied so far display a variety of higher-order organizational features such as domains, loops, or compartments. Many of these structures have been characterized from the genome-wide contact maps generated by chromosome conformation capture approaches (Hi-C, ChIA-PET,...). Indeed, DNA 3D structures translate as distinct patterns visible on these maps. We developed Chromosight, an algorithm based on computer vision approaches that automatically detect and quantify any type of pattern in contact data. Chromosight detects 3 times as many patterns as existing programs, while being faster and fit to any genome, including small, compact ones. Chromosight is user-friendly and can be extended to user-provided patterns. We validated the program by applying it to a variety of chromosomal structures found in mammals. Code and documentation: https://github.com/koszullab/chromosight

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“…C-Walks generated from Hi-C data C-walks were computationally generated from non-synchronous HeLa S3 pairwise Hi-C data. The Hi-C experiment was performed as described 48,49 . For each computationally generated walk, one 1 kb bin from chromosome 4 was selected at random.…”

Section: Virtually Digest Reads At Gatc Sitesmentioning

confidence: 99%

Multi-contact 3C data reveal that the human genome is largely unentangled

Tavares-Cadete

Norouzi

Dekker

et al. 2020

Preprint

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The genome is organized into chromosome territories that are themselves spatially segregated in A and B compartments. The extent to which interacting compartment domains and chromosomes are topologically entangled is not known. We show that detection of series of co-occurring chromatin interactions using multi-contact 3C (MC-3C) reveals insights into the topological entanglement of compartment domains and territories. We find that series of co-occurring interactions and their order represent interaction percolation paths through nuclear space in single cells where fragment 1 interacts with fragment 2, which in turn interacts with fragment 3 and so on. Analysis of paths that cross two chromosome territories revealed very little mixing of chromatin from the two chromosomes. Similarly, paths that cross compartment domains show that loci from interacting domains do not mix. Polymer simulations show that such paths are consistent with chromosomes and compartment domains behaving as topologically closed polymers that are not catenated with one another. Simulations show that even low levels of random strand passage, e.g. through topoisomerase II activity, would result in entanglements and mixing of loci of different chromosomes and compartment domains with concomitant changes in interaction paths inconsistent with MC-3C data.Our results show that cells maintain a largely unentangled state of chromosomes and compartment domains.3

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A chromosome folding intermediate at the condensin-to-cohesin transition during telophase

Abstract: A chromosome folding intermediate at the condensin-to-cohesin transition during telophase.

Cited by 176 publications

References 68 publications

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

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

Computer vision for pattern detection in chromosome contact maps

Multi-contact 3C data reveal that the human genome is largely unentangled

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