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Cited by 794Genomics and Chromatin DynamicsChromatin Remodeling and CancerChromosomal and Genetic Variations

Cell-cycle dynamics of chromosomal organization at single-cell resolution

Open access
Nagano, Takashi, Lubling, Yaniv, Várnai, Csilla, Dudley, Carmel, Leung, Wing, Baran, Yael, Mendelson Cohen, Netta, Wingett, Steven +2 more·2017·Nature
DOI 10.1038/nature23001PMC PMC5567812

Published version of a preprint

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Abstract

Chromosomes in proliferating metazoan cells undergo marked structural metamorphoses every cell cycle, alternating between highly condensed mitotic structures that facilitate chromosome segregation, and decondensed interphase structures that accommodate transcription, gene silencing and DNA replication. Here we use single-cell Hi-C (high-resolution chromosome conformation capture) analysis to study chromosome conformations in thousands of individual cells, and discover a continuum of cis-interaction profiles that finely position individual cells along the cell cycle. We show that chromosomal compartments, topological-associated domains (TADs), contact insulation and long-range loops, all defined by bulk Hi-C maps, are governed by distinct cell-cycle dynamics. In particular, DNA replication correlates with a build-up of compartments and a reduction in TAD insulation, while loops are generally stable from G1 to S and G2 phase. Whole-genome three-dimensional structural models reveal a radial architecture of chromosomal compartments with distinct epigenomic signatures. Our single-cell data therefore allow re-interpretation of chromosome conformation maps through the prism of the cell cycle.

AI snapshot

Written from the paper’s full text.

TL;DR

Single-cell Hi-C across thousands of mouse ESCs reveals a continuous cell-cycle trajectory of chromosome conformation, with TAD insulation, A/B compartments, loops, and 3D radial organization each showing distinct dynamics. The work provides an in-silico phasing framework and reinterprets bulk Hi-C maps through the cell cycle.

Key findings

  • From 2,924 single F1 hybrid 129 x Castaneus mouse ESCs, 1,992 cells (68.1%) passed QC, with median coverage of 393,506 restriction fragments and 127,233 distinct >1 kb contacting pairs per cell; median trans-chromosomal contacts were 5.87%.
  • Cell-cycle phasing ordered cells along a smooth trajectory from mitosis through G1, S, and G2; total contacts increased during S phase and peaked at G2 at almost 2-fold higher than G1, while trans-chromosomal contacts rose from ~3% in G2/mitosis to ~8% in early S phase.
  • TAD insulation and compartmentalization have distinct dynamics: insulation emerges in early G1, peaks in G1, declines during S phase, and remains low through G2; compartmentalization is weak in G1, increases in S phase, peaks in G2, and is lost approaching mitosis.
  • Loops are generally stable from G1 through S and G2, with only slight decreases during replication for early- or late-replicating loops; 2,036 top-scoring CTCF-associated loops were analyzed, and no phase-specific loops were detected.
  • Whole-genome 3D models from 126 high-quality G1 haploid cells showed A compartments expand more than B compartments during G1, B compartments occupy more peripheral nuclear positions, and pseudo-compartments form a radial epigenetic gradient.

Methods

  • Improved multiplexed single-cell Hi-C used a 4-cutter restriction enzyme, Tn5 tagmentation, flow cytometry sorting into 96-well plates, and partially automated library preparation; diploid and haploid mouse ESCs were processed, with 1,992 diploid and 1,247 haploid QC-positive maps analyzed.
  • In-silico cell-cycle phasing used contact-distance bins, mitotic-contact fraction, short-range contact fraction, and repli-score to assign cells to post-M, G1, early-S, late-S/G2, and pre-M regimes, then order cells within regimes; FACS with Geminin and DNA content validated phasing in 1,169 cells and 342 profiles.
  • Analyses included pooled and single-cell insulation, A/B compartment scores, CTCF loop enrichment, TAD condensation, pseudo-compartment interaction maps, and restraint-based 3D modeling with simulated annealing over >30,000 whole-genome models for 190 single-cell datasets.

Limitations

  • The paper states that assay resolution is not sufficient to detect individual loop turnover at single-cell resolution, leaving unresolved regimes for rapid loop dynamics.
  • The paper notes that potential involvement of trans sister chromatid contacts in increased mean contact distance cannot be determined unambiguously, though delayed compaction after replication argues sister chromatids cannot fully account for the dynamics.
  • The paper states that lack of loop contact enrichment in mitotic maps does not necessarily imply loops are disassembled, since mitotic condensation may increase local contact frequency and decrease Hi-C sensitivity; low-mappability regions also tend to be more flexible and uncertain in 3D models.

Model-written summary. Check it against the paper before relying on it.

Integrity signals

Registry

Crossref · 10.1038/nature23001

Cites

33 of 33 references verified0 citation errors · 0 not checkable

Statistics

Nothing to recompute.

Claims the paper makes

0 of 25 cited sources checked · 0 supported · 0 flagged

  • Findingown data

    Comparison of frequency of contacts in mitotic range to short-range contacts shows a circular pattern evocative of gradual chromosome remodelling as cells enter and exit mitosis.

    “Comparison of the frequency of contacts in the mitotic range to the frequency of contacts at shorter distances (short-range contacts < 2 Mb; Fig. 1e) shows a remarkable circular pattern evocative of a gradual chromosome remodelling process as cells enter and exit mitosis.”
    Quote in the paperSubstantial claim
  • Findingown data

    2924 single F1 hybrid 129 x Castaneus mouse ESCs were processed using 1.5 million reads per cell on average.

    “We processed a total of 2924 single F1 hybrid 129 x Castaneus mouse ESCs grown in 2i media using 1.5 million reads per cell on average”
    Quote in the paperSubstantial claim
  • Findingown data

    DNA replication correlates with reduction in TAD insulation.

    “DNA replication correlates with build-up of compartments and reduction in TAD insulation”
    Quote in the paperSubstantial claim
  • Findingown data

    Combining repli-score with circular pattern yields expected trajectory of low G1, increasing early S, peaking mid-S, declining late S, low G2/M.

    “Combining repli-score with the circular pattern exhibited by the frequencies of short-range and mitotic contacts yields exactly that expected trajectory”
    Quote in the paperSubstantial claim
  • Findingown data

    DNA replication correlates with build-up of compartments.

    “DNA replication correlates with build-up of compartments and reduction in TAD insulation”
    Quote in the paperSubstantial claim
  • May combine two claims. 51
  • Classified as probably not a substantial claim. 16

  • May combine two claims.

    Findingown data

    Whole-genome 3D structural models reveal a radial architecture of chromosomal compartments with distinct epigenomic signatures.

    “Whole-genome 3D structural models reveal a radial architecture of chromosomal compartments with distinct epigenomic signatures.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingnone given

    In all cases, insulation remains low post-replication, not re-emerging until next cell cycle.

    “In all cases, insulation remains low post-replication, not re-emerging until the next cell cycle.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Twenty high-resolution pseudo-compartments form a gradient generalising this observation, with strongest B-like pseudo-compartments most compact and strongest A-like most expanded.

    “Remarkably, the twenty high-resolution pseudo-compartments form a gradient that generalises this observation, with the strongest B-like pseudo-compartments most compact and the strongest A-like pseudo-compartments the most expanded”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    A-score variation decreases in early and late S-phase, consistent with overall increase in A/B compartment strength.

    “Further analysis (Fig. 4f) showed that A-score variation decreases in early and late S-phase, consistent with the overall increase in A/B compartment strength above.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Long-range cis-contacts are re-established very early in G1 phase, while trans compartmentalisation is not re-established until late G1.

    “show that long-range cis-contacts are re-established very early in G1 phase, while trans compartmentalisation is not re-established until late G1”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [18] Dileep, V. et al. Topologically associating domains and their long-range contacts are established during early G1 coincident with the establishment of the replication-timing program. Genome Res. 25, 1104–1113 (2015) source

      Not checked in the free run.

  • May combine two claims.

    Findingown data

    C1 has weakest G1 insulation, shows gradual and delayed loss of insulation, and is enriched for borders between late-replicating domains.

    “C1, which has the weakest G1 insulation, shows gradual and delayed loss of insulation, and is enriched for borders between late-replicating domains.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Insulation is not detectable in mitotic maps and emerges rapidly upon exit from mitosis in early G1.

    “Insulation is not detectable in mitotic maps (Extended Data Fig. 7d-e), and emerges rapidly upon exit from mitosis in early G1.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Loop enrichment increases after mitosis, is generally stable through G1, then decreases slightly in early S phase for early-replicating loops and in late S phase for later-replicating loops.

    “We found that loop enrichment increases after mitosis, is generally stable through G1, but then decreases slightly in early S phase for early-replicating loops and in late S phase for later-replicating loops.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    No loops specific to a certain cell-cycle phase were detected, suggesting loops are significantly observed even when decreased in average intensity during replication.

    “We do not detect loops that are specific to a certain cell-cycle phase (Extended Data Fig. 7i), suggesting that even when decreased in average intensity during replication, loops are significantly observed in the data.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Early-replicating TADs are further de-condensed in early S phase, before showing remarkable increase in condensation at mid-S, likely after their replication is complete.

    “Early-replicating TADs are further de-condensed in early S phase, before showing a remarkable increase in condensation at mid-S, likely after their replication is complete.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    A-scores are conserved between diploid and haploid cells and growth conditions, suggesting continuum of compartment affinities is robust property of chromosomal domains.

    “These scores are conserved between diploid and haploid cells and growth conditions (Extended Data Fig. 9a), suggesting that a continuum of compartment affinities is a robust property of chromosomal domains.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Mid-late and late-replicating TADs show constitutively high condensation in G1 and throughout S, with further marked increases for mid-late TADs in G2.

    “Mid-late and late-replicating TADs, on the other hand, show constitutively high condensation in G1 and throughout S, with further marked increases observed for mid-late TADs in G2.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    B compartments occupy more peripheral locations and A compartments tend toward nuclear interior for cells 9-16 and onward (P<0.001).

    “We observed B compartments occupying more peripheral locations and A compartments tending toward the nuclear interior for cells 9-16 and onward (P < 0.001, one-sided MW test”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    A-scores correlate with time of replication; high A-score TADs are early-replicating and low A-score TADs are late-replicating.

    “A-scores correlate with time of replication; high A-score TADs are early-replicating and low A-score TADs are late-replicating”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    A and B compartments are similarly compact upon mitotic exit (P>0.05), but as cells progress through G1, A compartments expand more rapidly and to larger extent than B compartments (P<0.005).

    “A and B compartments are similarly compact upon mitotic exit (P > 0.05, two-sided MW test), but as cells progress through G1, A compartments expands more rapidly and to a larger extent than B compartments (P < 0.005, one-sided MW test)”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Compartmentalisation is weak during G1, increases upon entering S, further increases in late S, reaches maximum in G2, then rapid complete loss approaching mitosis.

    “compartmentalisation is weak during G1 phase and increases upon entering S phase, with a further increase in late S phase, reaching a maximum in G2, just before a rapid and complete loss approaching mitosis”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Cells with less than 63% short-range contacts do not include replication group and likely represent a G1 regime.

    “we observed that cells with less than 63% short-range contacts do not include the replication group and likely represent a G1 regime (blue).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Borders in C3 show gradual increase in insulation well into S-phase, followed by abrupt loss in mid-S.

    “Borders in C3 show a gradual increase in insulation well into S-phase, followed by abrupt loss of insulation in mid-S.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Total number of contacts increases gradually during S-phase, peaking at G2 at almost 2-fold higher level than G1, before dropping sharply after mitosis.

    “The total number of contacts (Fig. 2e), which unlike the repli-score is a-priori independent of the inferred phasing, was shown to increase gradually during S-phase, peaking at G2 at almost a 2-fold higher level than G1, before dropping sharply after mitosis.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Compartment association polarises in late S/G2, with many TADs shifting from broadly spread association in G1 or early S to preferential contacts with TADs in narrower range of A-scores following replication.

    “The same analysis indicated that compartment association polarises in late S/G2, with many TADs shifting from broadly spread association in G1 or early S, to preferential contacts with TADs in a narrower range of A-scores following replication.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    TADs vary quantitatively in A-association, but no significant group shows bimodal compartment association distribution.

    “Both sorting TADs by their mean A-association scores (Fig. 4g) and grouping these distributions by unsupervised clustering (Extended Data Fig. 9b) showed that TADs vary quantitatively in their A-association, but no significant group of TADs shows a bimodal compartment association distribution.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Chromosome condensation occurs in preparation for mitosis, and rapid expansion in early G1, while extensive remodelling occurs during replication.

    “we show chromosome condensation in preparation for mitosis, and rapid expansion in early G1, while also finding extensive remodelling during replication”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [11] Naumova, N. et al. Organization of the mitotic chromosome. Science 342, 948–953 (2013) source

      Not checked in the free run.

  • May combine two claims.

    Findingown data

    Loops are still apparent in cells approaching mitosis despite fast chromosomal condensation, unlike cells after mitosis, which do not have any contact enrichment around loops.

    “Interestingly, loops are still apparent in cells approaching mitosis despite the fast chromosomal condensation – unlike cells after mitosis, which do not have any contact enrichment around loops”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Insulation increases to maximum during G1, declines when replication begins, plateaus at mid S-phase at lowest interphase level, and remains fixed through G2 until mitosis.

    “Insulation increases to its maximum during G1, but declines when replication begins, plateauing at mid S-phase at its lowest interphase level and remaining fixed through G2 until mitosis.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Locations of TAD borders are generally unchanged in G1, early-S, late-S/G2 sub-pools, but average intensity of borders is dynamic.

    “We found that the locations of TAD borders are generally unchanged in these pools, but that the average intensity of the borders is dynamic”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Repli-score is low during G1 and G2, increases gradually during early S, and decreases during late S.

    “validating that it was low during G1 and G2, showed consistent gradual increase during early S phase, and decreased during late S phase”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Standard deviation of A-association scores for individual TADs across entire haploid single-cell cohort was less than 0.06, suggesting limited variability of A-score between cells.

    “The standard deviation of A-association scores for individual TADs across the entire haploid single-cell cohort was less than 0.06 (Fig. 4e), suggesting limited variability of A-score between cells.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Borders demonstrate similar qualitative dynamics in all clusters, but each cluster varies in timing and intensity of deterioration in insulation during S-phase.

    “Borders demonstrate similar qualitative dynamics in all clusters. However, each cluster varies in timing and intensity of deterioration in insulation during S-phase”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Cluster C4 includes borders showing strongest G1 insulation and C2 borders show earliest loss of insulation in S.

    “Cluster C4 includes borders showing the strongest G1 insulation and C2 borders show the earliest loss of insulation in S.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingown data

    Unsupported contacts (median 1.06% of contacts) were removed from the sc-HiC libraries before 3D modelling.

    “These unsupported contacts (median 1.06% of contacts, Extended Data Fig. 10a) were removed from the sc-HiC libraries before 3D modelling.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Findingown data

    Although the nuclear lamina is not modelled by the force field, the models turn out to be near spherical (a ≈ b ≈ c) and roughly the same size.

    “We noted that although the nuclear lamina is not modelled by the force field, the models turn out to be near spherical (a ≈ b ≈ c) and roughly the same size (Extended Data Fig. 10g, nucleus a/c ratio).”
    Quote in the paperNot a substantial claim
    • The authors state this as an assumption: Chromatin can be modeled as a simple non-overlapping beads-on-a-string polymer subject to data-derived constraints.

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Findingown data

    Fine-tuning the initial cell-cycle phase assignment by k-means clustering and majority vote reassigned 5.7% of diploid cells and 8.2% of haploid cells, with almost all (>99.8%) reassignments involving adjacent groups.

    “This resulted in reassigning 5.7% and 8.2% of the cells in the diploid and haploid datasets, respectively, with almost all (>99.8%) re-assignments involving adjacent groups.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingown data

    Low mappability regions tend to be more flexible and uncertain in their position in the computed models.

    “We also noted that low mappability regions tend to be more flexible and uncertain in their position in the computed models, illustrated by the unconstrained region around chrX:30Mb (the white chromatin region looping out of the models in Extended Data Fig. 10e).”
    Quote in the paperNot a substantial claim
    • The authors state this as an assumption: Chromatin can be modeled as a simple non-overlapping beads-on-a-string polymer subject to data-derived constraints.

  • May combine two claims.

    Findingown data

    The distances of removed contacts are noticeably shorter in their corresponding model than in randomly selected other cell, indicating that the proximity of the chromosome pair is preserved.

    “The distances of these removed contacts are noticeably shorter in their corresponding model than they are in randomly selected other cell, indicating that the proximity of the chromosome pair is preserved.”
    Quote in the paperSubstantial claim
    • The authors state this as an assumption: Chromatin can be modeled as a simple non-overlapping beads-on-a-string polymer subject to data-derived constraints.

  • Classified as probably not a substantial claim. May combine two claims.

    Findingown data

    Contacts in distance bins 1-37 were noisy and were discarded, making bins 38-143 the valid bins.

    “Contacts in bins 1-37 were found to be noisy and were discarded, making bins 38-143 the valid bins.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Study design and conductown data

    Median coverage was 393,506 restriction fragments and 127,233 distinct >1kb contacting pairs per cell.

    “This provided median coverage of 393,506 restriction fragments, and 127,233 distinct >1kb contacting pairs per cell”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Mammalian mitotic chromosomes are rod-shaped.

    “Mammalian mitotic chromosomes are rod-shaped”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [11] Naumova, N. et al. Organization of the mitotic chromosome. Science 342, 948–953 (2013) source

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    Early- and late-replicating domains are defined by copy number dynamics during S phase and show distinct enrichment for active and inactive epigenetic marks respectively.

    “Early- and late-replicating domains are defined by their copy number dynamics during S phase, and show distinct enrichment for active and inactive epigenetic marks respectively14.”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [14] Pope, B. D. et al. Topologically associating domains are stable units of replication-timing regulation. Nature 515, 402–405 (2014) source

      Not checked in the free run.

  • Classified as probably not a substantial claim.

    Premisenone given

    Chromosomes in proliferating metazoan cells alternate between highly condensed mitotic structures facilitating chromosome segregation and decondensed interphase structures accommodating transcription, gene silencing and DNA replication.

    “Chromosomes in proliferating metazoan cells undergo dramatic structural metamorphoses every cell cycle, alternating between highly condensed mitotic structures facilitating chromosome segregation, and decondensed interphase structures accommodating transcription, gene silencing and DNA replication.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    In the previous version of the single-cell Hi-C protocol, molecules supported by a single read (singleton contacts) usually represented spurious ligations and were therefore discarded.

    “In our previous version of the single-cell Hi-C protocol12 we found that molecules supported by a single read (singleton contacts) usually represented spurious ligations and were therefore discarded.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [12] Nagano, T. et al. Single-cell Hi-C reveals cell-to-cell variability in chromosome structure. Nature 502, 59–64 (2013) source

      Not checked in the free run.

  • May combine two claims.

    Interpretationreasoning

    Effects of major transitions extend throughout entire cell cycle, such that genome is not stably folded at any point in interphase.

    “Importantly, the effects of these major transitions extend throughout the entire cell cycle, such that the genome is not stably folded at any point in interphase.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Interpretationown data

    Universality of these processes shows haploid ESCs are comparable to normal diploid cells and a good model for studying chromosome conformation and dynamics.

    “The universality of these processes shows that haploid ESCs are comparable to normal diploid cells, and a good model for studying chromosome conformation and dynamics”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Study design and conductown data

    Haploid ESC maps show comparable QC metrics to diploid cells, with less than half of contacts per cell and some specific patterns of chromosome loss filtered in-silico.

    “We confirmed haploid ESC maps show comparable QC metrics to diploid cells, with less than half of the contacts per cell and some specific patterns of chromosome loss that we filtered in-silico”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductnone given

    Potential involvement of trans sister chromatid contacts in driving observed increase in mean contact distance cannot be determined unambiguously.

    “We note that the potential involvement of trans sister chromatid contacts in driving the observed increase in mean contact distance cannot be determined unambiguously.”
    Quote in the paperNot a substantial claim

  • Classified as probably not a substantial claim.

    Interpretationown data

    Refined ordering within each coarse-grained stage likely represents cell-cycle progression at high resolution.

    “We further hypothesise that the refined ordering we impose within each coarse-grained stage is likely to represent cell-cycle progression at high resolution.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Study design and conductnone given

    Assay's resolution is not sufficient to allow detection of individual loop turnover at single-cell resolution, leaving unresolved regimes for rapid loop dynamics.

    “However, the assay’s resolution is not sufficient to allow detection of individual loop turnover at single-cell resolution, leaving unresolved regimes for rapid loop dynamics.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Interpretationown data

    Genome folding is highly heterogeneous at single-cell level, but variation is far from random, reflecting combination of deterministic dynamics and stochastic effects.

    “We confirmed that genome folding is highly heterogeneous at the single-cell level, but variation is far from random, reflecting a combination of deterministic dynamics and stochastic effects.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Interpretationown data

    Pseudo-compartments capture large-scale trans- and cis-chromosomal conformation at population and single-cell level, generalising binary A/B compartment scheme.

    “Together, these data suggest pseudo-compartments capture large-scale trans- and cis-chromosomal conformation at the population and single-cell level, generalising the binary A/B compartment scheme.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Study design and conductown data

    Using phasing strategy, distribution of genomic contact distances shows smooth cyclical transition, insensitive to batch effects and robust to subsampling or specific chromosomes.

    “we observed a smooth, cyclical transition of the distribution of genomic contact distances (Fig. 1f), which is insensitive to batch effects (Extended Data Fig. 6c-d) and robust to subsampling of the data or analysis of specific chromosomes”
    Quote in the paperSubstantial claim

  • Classified as probably not a substantial claim. May combine two claims.

    Study design and conductreasoning

    The resulting expected ensemble map has an identical number of contacts for each locus, and identical probability for a contact at a given genomic distance, as in the observed map.

    “The resulting expected ensemble map has an identical number of contacts for each locus, and identical probability for a contact at a given genomic distance, as in the observed map.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Premisereasoning

    In haploid G1 cells there is only one copy of the genome, so after removal of PCR duplicates each observed fragment end should be in contact with at most one other fragment end.

    “In haploid G1 cells there is only one copy of the genome, hence after removal of PCR-duplicates each observed fragment end should be in contact with at most one other fragment end.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Interpretationown data

    Larger a/c ratios together with b/c ≈ 1 in early G1 indicate rod-like structures that decondense into a more spherical structure as a/c decreases to a ≈ b ≈ c.

    “Larger a/c ratios together with b/c ≈ 1 in early G1 indicate rod-like structures that decondense into a more spherical structure as a/c decreases to a ≈ b ≈ c.”
    Quote in the paperSubstantial claim
    • The authors state this as an assumption: Chromatin can be modeled as a simple non-overlapping beads-on-a-string polymer subject to data-derived constraints.

  • May combine two claims.

    Interpretationown data

    Cluster 1 domains were assigned to the B/inactive compartment and cluster 2 domains to the A/active compartment.

    “Domains in each cluster exhibit distinct epigenetic and time of replication signatures (Extended Data Fig. 3d-e) pointing us to assign the 1221 domains in cluster 1 to the B-, inactive-compartment and 1673 domains in cluster 2 to the A-, active compartment (haploids had 1353 A- and 1296 B-domains).”
    Quote in the paperSubstantial claim

  • Classified as probably not a substantial claim. May combine two claims.

    Study design and conductown data

    Cells with strictly normal chromosomal coverage (max chromosomal coverage aberration between 0.82-1.23) were selected, ending up using 46% of the cells.

    “Therefore we selected cells with strictly normal chromosomal coverage (cells with max chromosomal coverage aberration between 0.82-1.23), ending up using 46% of the cells.”
    Quote in the paperSubstantial claim
    • Rests on an assumption: The generation of an ordered correlation matrix of normalized domain copy-number is very sensitive to chromosomal copy-number variations.

  • Classified as probably not a substantial claim.

    Premisecitation

    Chromosomes 11, 12, 15, 16, 18 and 19 are Nucleolar Organiser Region (NOR) chromosomes.

    “Chromosomes were divided into two groups, Nucleolar Organiser Region (NOR) chromosomes (chromosomes 11, 12, 15, 16, 18 and 19), and other chromosomes19.”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [19] Britton-Davidian, J., Cazaux, B. & Catalan, J. Chromosomal dynamics of nucleolar organizer regions (NORs) in the house mouse: micro-evolutionary insights. Heredity 108, 68–74 (2012) source

      Not checked in the free run.

  • Classified as probably not a substantial claim. May combine two claims.

    Study design and conductreasoning

    The shuffling preserves marginal coverage and contact distance distribution but does not retain compartment or TAD structure.

    “Briefly, we shuffled contacts using a Markov Chain Monte Carlo-like approach, first within each chromosome and then genome-wide, such that the primary factors that define contact distributions are preserved - the marginal coverage and contact distance distribution - but any compartment or TAD structure that may be present is not retained.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Premisecitation

    Repli-chip values are bimodal around zero, with early replicating loci having positive values and late replicating loci negative values.

    “Repli-chip values are bimodal around zero, with early replicating loci having positive values and late loci negative ones.”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [15] Mouse ENCODE Consortium et al. An encyclopedia of mouse DNA elements (Mouse ENCODE). Genome Biol. 13, 418 (2012) source

      Not checked in the free run.

  • Classified as probably not a substantial claim.

    Study design and conductown data

    126 ordered G1 cells with high-quality models were used for downstream analysis.

    “We further discarded one cell that had more than 10% of a chromosome missing, resulting in 126 ordered G1 cells with high-quality models for downstream analysis.”
    Quote in the paperSubstantial claim
    • The authors state this as an assumption: Chromatin can be modeled as a simple non-overlapping beads-on-a-string polymer subject to data-derived constraints.

  • May combine two claims.

    Study design and conductown data

    Results were robust to changes to the initial conditions, indicating the convergence of the simulations.

    “Results were robust to changes to the initial conditions, indicating the convergence of the simulations, which was measured by computing the distribution of the root-mean-square-distance (RMSD) between aligned models of the same cell compared to different cells (Extended Data Fig. 10e).”
    Quote in the paperSubstantial claim
    • The authors state this as an assumption: Chromatin can be modeled as a simple non-overlapping beads-on-a-string polymer subject to data-derived constraints.

  • May combine two claims.

    Study design and conductown data

    Phasing positions determined by two disjoint sets of chromosomes largely concur, with most differences concentrated at the interfaces between G1 and early S, or early S and late S/G2; only 38 of 1942 cells differ by more than 10%.

    “Phasing positions determined by both sets largely concur, with most of the differences concentrated on the interfaces between G1 and early S, or early S late S/G2 groups. The positions of only 38 out of the 1942 cells participated in both sets (<2) differ by more than 10%.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Interpretationreasoning

    The overall three-dimensional shape of the entire genome is purely determined by the filtered and supported chromosome contacts in the corresponding single-cell Hi-C library.

    “Note that no other physical parameter, e.g. the overall shape or size of the nuclear envelope, is constrained by our modelling approach, hence the overall three-dimensional shape of the entire genome is purely determined by the filtered and supported chromosome contacts in the corresponding single-cell Hi-C library.”
    Quote in the paperNot a substantial claim
    • The authors state this as an assumption: Chromatin can be modeled as a simple non-overlapping beads-on-a-string polymer subject to data-derived constraints.
61 of 61

  • The paper relies on this without support.

    The vast majority of ultra-close cis contacts (between fends less than 1 kb apart) originate from non-digested DNA.

    “The vast majority of these ultra-close cis contacts originate from non-digested DNA and therefore this metric quantifies the digestion efficiency of the experiment.”

  • The paper relies on this without support.

    The generation of an ordered correlation matrix of normalized domain copy-number is very sensitive to chromosomal copy-number variations.

    “The generation of ordered correlation matrix of normalized domain copy-number (Extended Data Fig. 4c) is very sensitive to chromosomal copy-number variations.”

  • The paper relies on this without support.

    Structural modelling is sensitive to low levels of noise.

    “Since structural modelling is sensitive to low levels of noise, haploid G1 cells were processed using stringent contact filtering to remove contacts that are more likely to be technical artefacts.”

  • The authors state this as an assumption.

    Chromatin can be modeled as a simple non-overlapping beads-on-a-string polymer subject to data-derived constraints.

    “We modeled chromatin as a simple non-overlapping beads-on-a-string polymer12 subject to data derived constraints.”
4 of 4

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • The major effect of the cell cycle on chromosome architecture is rarely accounted for in 3D genome mapping studies.

    “the major effect of the cell cycle on chromosome architecture (Nagano et al., 2017, Naumova et al., 2013) is rarely accounted for in 3D genome mapping studies.”

    From Multiscale 3D Genome Rewiring during Mouse Neural Development (2017) · cites this paper as Nagano et al., 2017

  • TADs and loops are absent in mitosis, but present in G1-phase.

    “What has been clear is that TADs and loops are absent in mitosis, but present in G1-phase.54,55”

    From Recent evidence that TADs and chromatin loops are dynamic structures (2018) · cites this paper as [55]

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

Each contradiction between two passages listed here was confirmed by an independent check.

  • A-score has two different definitions

    Minor

    The Results define a TAD's A-score as the fraction of its trans contacts made with the A-compartment. The Methods call that quantity the A-fraction and define the A-score instead as a contact-weighted mean of the A-fractions of the domains it contacts. These are not generally the same value.

1 of 1

Cites

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Related

Authors
Nagano, T., Lubling, Y., Várnai, C., Dudley, C., Leung, W., Baran, Y., Mendelson Cohen, N., Wingett, S., Fraser, P., & Tanay, A.
Affiliations
  • Babraham Institute (GB)
  • Weizmann Institute of Science (IL)
  • Florida State University (US)
Corresponding author
  • Várnai, Csilla
  • Fraser, Peter
  • Tanay, Amos
ORCID
Venue
Nature
Publisher
Springer Science and Business Media LLC
Published
2017-07
Volume
547
Issue
7661
Pages
61-67
ISSN
  • 0028-0836 (ISSN-L)
  • 1476-4687
DOI
10.1038/nature23001
PMC
PMC5567812
OpenAlex
W2731989040
Semantic Scholar
19b592cfb0f15630cc04ef820fda6f580885d40c
Cited by
794
References
33
Citations by year
2026: 46 · 2025: 80 · 2024: 79 · 2023: 67 · 2022: 92 · 2021: 112 · 2020: 104 · 2019: 86 · 2018: 86 · 2017: 39 · 2016: 1
FWCI
35.28
Type
journal article
Language
en
Open access
Licence
www.springer.com/tdm (tdm)
Locations
  • Nature (publishedVersion)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
  • PubMed (publishedVersion)
  • Europe PMC (PubMed Central) (acceptedVersion)
  • PubMed Central (acceptedVersion)
  • RePEc: Research Papers in Economics (submittedVersion)
  • University of Birmingham Research Portal (University of Birmingham) (submittedVersion)
Funders
National Heart, Lung, and Blood Institute (U01HL129971)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
Keywords
cell cycle, chromosome conformation, 3D genome organization, chromatin insulation, DNA replication, mouse embryonic stem cells, single-cell Hi-C, 3D structural model, epigenomic signatures
MeSH terms
Mouse Embryonic Stem Cells, Animals, Cell Compartmentation, Cell Cycle, Haploidy, Reproducibility of Results, Imaging, Three-Dimensional, Chromosomes, Mammalian, Epigenesis, Genetic, Mice, Single-Cell Analysis

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Claims read by deepseek-v4.1-flash under definition version 3 (extract-v3) on 2026-10-10.

Classified by jev-1.13-20260917 (gold-guideline-v0.2) on 2026-10-10.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

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