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Fig. 3 | Genome Biology

Fig. 3

From: Chrom3D: three-dimensional genome modeling from Hi-C and nuclear lamin-genome contacts

Fig. 3

Chrom3D genome structures recapitulate features of genome organization estimated from single-cell analyses. a Percentage of LMNA-associated or LMNB1-associated TADs at a given distance from the NP across 400 structures; data are shown for TAD placement using LMNA or LMNB1 as radial constraint. P value for difference between the two curves is 9.53 × 10–7 (Wilcoxon rank sum test). Inset: percentages of LMNA-associated or LMNB1-associated TADs positioned at 0.7 μm from the nucleus edge shown for comparison with FISH data for LADs (see [41]); P < 2.2 × 10–16 (Mann–Whitney U test). b Heatmaps of radial stability of LMNA-associated or LMNB1-associated TADs in all chromosomes across 400 structures. “Blue” TADs are more stably placed in the nucleus center than “red” TADs, which are more stably placed at the NP. c Correlation analysis of lamin-associated TAD placement at the NP across 400 structures modeled with LMNA or LMNB1 constraints. d Comparison of TAD placement TADs modeled by Chrom3D with LMNB1 association frequency from the LMNB1 DamID in single cells [44]. Left, proportions of center, intermediate, and peripheral TADs in our structures associated with LMNB1 in the single-cell dataset; *P < 2.2 × 10–16 (Mann–Whitney U tests). Right, same as above, for TADs whose placement was modeled without lamin constraints; *P < 2.2 × 10–16; ns P = 0.755 (Mann–Whitney U tests). Comparisons between LMNB1 and no lamin constraint data: **P = 4.34 × 10–5, ***P = 6.20 × 10–5, ****P < 2.2 × 10–16, Mann–Whitney U tests. e Size distribution of LMNB1 LADs [44] in the structures; *P = 1.17 × 10–3; **P = 1.23 × 10–6; § P = 6.32 × 10–3 (Mann–Whitney U tests)

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