Extended Data Fig. 4: Single cells show consistent LAD patterning within the same developmental stages but parental genomes display distinct features. | Nature

Extended Data Fig. 4: Single cells show consistent LAD patterning within the same developmental stages but parental genomes display distinct features.

From: Genome–lamina interactions are established de novo in the early mouse embryo

Extended Data Fig. 4

a, Chromosome profiles of population average (n = 3) and single-cell average Dam–lamin B1 signals. Black boxes represent LAD domains called by HMM. b, Genomic location of example DNA FISH probes projected on Dam–lamin B1 chromosome profiles. c, Quantification of 3D preserved DNA FISH spot distances to the nuclear periphery in 2-cell and 8-cell embryos of probes in regions that change LAD status between 2-cell and 8-cell stages according to DamID. Box plots show the 25th and 75th percentiles (box), median (solid lines), the smallest and largest values within 1.5 × IQR of the hinge (whiskers) and outliers (grey circles). n = number of DNA FISH spots from at least three biologically independent samples. Wilcoxon rank-sum test P values shown (two-sided). **P ≤ 0.01, ****P ≤ 0.0001. d, Images of 3D DNA FISH in zygote pronuclei. Quantification shows distance to the nuclear periphery. Scale bars, 10 μm. Box plots show the 25th and 75th percentiles (box), median (solid lines), the smallest and largest values within 1.5 × IQR of the hinge (whiskers) and outliers (grey circles). n = number of DNA FISH spots from at least three biologically independent samples. e, Distance quantification of DNA FISH probes in maternal and paternal specific LADs in zygotes. Box plots show the 25th and 75th percentiles (box), median (solid lines), the smallest and largest values within 1.5 × IQR of the hinge (whiskers) and outliers (grey circles). n = number of DNA FISH spots from at least three biologically independent samples. Wilcoxon rank-sum test P values shown (two-sided). *P ≤ 0.05, **P ≤ 0.01, ***P ≤ 0.001,**** P ≤ 0.0001. f, t-SNE representation of the triplicate allelic Dam–lamin B1 population samples, including 2-cell embryos from reciprocal crosses. n = 3 biologically independent samples. g, Scatter plot comparison between average Dam–lamin B1 signals obtained from pronucleus separated and hybrid zygote DamID. n = biologically independent samples. Maternal pronucleus (n = 10), paternal pronucleus (n = 15) and hybrid zygote (n = 3). r = Spearman’s rho. h, Average CpG density, AT content and DHS sites over LAD boundaries ± 1.5 Mb defined specifically for maternal and paternal alleles in zygotes. i, Allelic correlation matrix (Pearson) of OE scores form Dam–lamin B1 embryos. j, Jaccard indexes calculated over HMM-called LAD domains.

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