Fig. 7: Spreading of NL contacts is partially mirrored by H3K9me3 and often linked to gene repression.
From: Interactions between the genome and the nuclear lamina are multivalent and cooperative
a–c, Changes in H3K9me3 caused by recombinations. Domainograms (top) and pA-DamID tracks (bottom) show CAST allele-specific H3K9me3 levels in control (blue) and recombined (d3 (a), d6 (b) and i7 (c); green) cells. Arrowheads, regions that gain both NL interactions and H3K9me3; arrows, regions that gain or lose NL interactions but show no change in H3K9me3. Bottom: tracks showing the change in NL interactions in the recombined clone compared to the control (ΔLmnB1, recombined minus control). Data were smoothed. Dashed vertical lines mark positions of the recombined loxP sites. In c, data are plotted using coordinates of the recombined genome. d–f, Changes in gene expression in recombinations d3, d6 and i7. Bar graphs show the allele-specific log2 fold change in gene expression between the control and one recombined clone from recombinations d3 (d), d6 (e) and i7 (f), for each gene around the recombined sequences (n = 2). Genes are ordered by their chromosomal coordinates. Vertical lines represent the location of loxP recombination sites. Significant differentially expressed genes are colored in blue (P value corrected for multiple testing < 0.05 and fold change > 2). Horizontal dashed lines mark log2(fold change) values of 1 and −1. Crosses, no detectable mRNA in the control cell line (with hopped but nonrecombined loxP). Heat maps under the bar graphs show, for each gene (from top to bottom), (i) the expression level in WT F1 hybrid mES cells; (ii) the change in NL interaction pA-DamID score after recombination (recombined minus control); and (iii) the change in H3K9me3 pA-DamID score after recombination (recombined minus control). g, Correlation between changes in gene expression and the change in H3K9me3 levels (left) or NL interactions (right). The aggregate plot shows the combined data of the CAST alleles of all genes depicted in d–f and Extended Data Fig. 10c. Each dot represents a gene in one tested recombination. Dots are colored on the basis of the gene expression level in WT F1 hybrid mES cells. h, Linear model of changes in gene expression as function of changes in both NL interactions and H3K9me3. The bar plot shows weights of the fitted linear model. ***P = 1.11 × 10−6 and **P = 0.00824.
