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Three-dimensional genome structures of single diploid human cells

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Science  31 Aug 2018:
Vol. 361, Issue 6405, pp. 924-928
DOI: 10.1126/science.aat5641
  • Fig. 1 Single-cell chromatin conformation capture and haplotype imputation by Dip-C.

    (A) Schematics of the chromatin conformation capture protocol. The 3D information of chromatin structure was encoded in the linear genome through proximity ligation of chromatin fragments, as in 3C (4) and Hi-C (5, 19). The ligation product was then amplified by META (15) and sequenced. Colors represent genomic coordinates. Note that ligation products may be linear (illustrated here) or circular (not shown). (B) Imputation of the two chromosome haplotypes linked by each chromatin “contact” (red dots) in a representative single cell.

  • Fig. 2 3D genome structures of single diploid human cells.

    (A) 3D genome structure of a representative GM12878 cell. Each particle represents 20 kb of chromatin, or a radius of ~100 nm. (B) Peculiar nuclear morphology in a cell that recently exited mitosis (top) and in a cell with multiple nuclear lobes (bottom). (C) Serial cross sections of a single cell showing compartmentalization of euchromatin (green) and heterochromatin (magenta), visualized by CpG frequency as a proxy (21). (D) Radial preferences across the human genome, as measured by average distances to the nuclear center of mass. Our results (black dots, smoothed by 1-Mb windows) agree well with published DNA FISH data (gray lines) on whole chromosomes (22) (shifted and rescaled) and provide fine-scale information. Lower and upper axis limits were 20 and 50 particle radii, respectively, for the black dots. GM12878 cell 4 (extensive chromosomal aberrations) and cell 16 (M/G1 phase) were excluded. (E) Example radial preferences of two chromosomes. The gene-rich chromosome 19 preferred the nuclear interior (left), whereas the gene-poor chromosome 18 almost always resided on the nuclear surface (right). (F) Stochastic fractal organization of chromatin was quantified by a matrix of radii of gyration of all possible subchains of each chromosome (heat maps). We identified a hierarchy of single-cell domains across genomic scales (black trees). A subtree was simplified as a black triangle if either of its two subtrees was below a certain size (from left to right: 10 Mb, 2 Mb, 500 kb, 100 kb). In each panel, the region from the previous panel is shown in transparent gray. In the rightmost panel, thick sticks (top) and circles (bottom) highlight the formation of a known CTCF loop (19). Spheres with arrows (top) indicate the positions and orientations of the two converging CTCF sites. Genomic coordinates are for the human genome assembly hg19.

  • Fig. 3 Distinct 3D structures of the maternal and paternal alleles.

    (A) Structural difference between the two alleles of the imprinted H19/IGF2 locus. Despite cell-to-cell heterogeneity, the maternal allele more frequently separated IGF2 from both H19 and the nearby HIDAD site and disrupted the IGF2-HIDAD CTCF loop (white and red circles). Spheres highlight three CTCF sites from bulk Hi-C. Heat maps show the root-mean-square average pairwise distances between all 20-kb particles. Haplotype-resolved bulk Hi-C (black heat map with 25-kb bins) is adapted from figure 7C of (19). (B) Active (red) and inactive (blue) X chromosomes prefer extended and compact morphologies, respectively, as shown by cross sections of two representative cells. (C) Individual active and inactive X chromosomes can be distinguished by PCA of single-cell chromatin compartments, defined for each 20-kb particle as the average CpG frequency of nearby (within 3 particle radii) particles. (D) The inactive X chromosome tends to form the previously reported “superloops,” 27 very-long-range (5 to 74 Mb) chromatin loops identified by bulk Hi-C (19, 20, 29). Superloops are sorted by size. (E) Haplotype-resolved contact maps (red dots) and 3D structures of the two X chromosomes in an example cell. Black circles denote all superloops (19). White spheres denote four example superloop anchors (DXZ4, x75, ICCE, and FIRRE). GM12878 cells 4 and 16 are excluded from (C) and (D).

  • Fig. 4 Cell type–specific chromatin structures.

    (A) Quantification of the organization of centromeres and telomeres. The mESCs exhibit stronger Rabl configuration (horizontal axis; the length of summed centromere-to-telomere vectors normalized by the total particle number, which differs between human and mouse; axis limit = 0.005 particle radii), whereas the PBMCs tend to point centromeres outward relative to telomeres (vertical axis; the summed centromere-to-telomere difference in distance from the nuclear center of mass normalized by the total particle number; axis limit = 0.007 particle radii). Each marker represents a single cell and was inferred by V(D)J recombination in PBMCs (table S1 and fig. S3B). (B) Quantification of chromosome intermingling (vertical axis; the average fraction of nearby particles that are not from the same chromosome) and chromatin compartmentalization (horizontal axis; Spearman correlation between each particle’s own CpG frequency and the average of nearby particles). (C) Example cross sections of three cell types, colored according to chromosome (left) or by the multichromosome intermingle index (right). (D) Among the human cells, four cell type clusters (shaded)—B lymphoblastoid cells, presumable T lymphocytes, B lymphocytes, and presumable monocytes/neutrophils (PBMC cells 9, 14, and 18)—could be distinguished from the differential formation (defined as end-to-end distance ≤ 3 particle radii) of known cell type–specific promoter-enhancer loops from published bulk promoter capture Hi-C (35). (E) The same four clusters could also be distinguished by unsupervised clustering via PCA of single-cell chromatin compartments, without the need for bulk data. The two alleles of each locus were treated as two different loci. GM12878 cell 16 was excluded from (D) and (E). (F) An example region that was differentially compartmentalized between two cell types (black, B lymphoblastoid cells; red, presumable T lymphocytes). Right panels visualize the configuration of the ~0.5-Mb region (chr 13: 62.5 to 63 Mb, thick yellow sticks) with respect to the rest of the genome (transparent, colored by CpG frequencies) in two representative cells. Only the paternal alleles are shown. Bulk Hi-C (black heat map with 50-kb bins) is from (19, 41). GM12878 cell 4 was excluded.

Supplementary Materials

  • Three-dimensional genome structures of single diploid human cells

    Longzhi Tan, Dong Xing, Chi-Han Chang, Heng Li, X. Sunney Xie

    Materials/Methods, Supplementary Text, Tables, Figures, and/or References

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    • Materials and Methods
    • Figs. S1 to S20
    • Captions for table S1 and S2
    • References
    Table S1
    Information about each single cell.
    Table S2
    Information about each library.

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