Fig. 6
Active genes in each LAD class are localized in euchromatic environments of low lamin enrichment. a Mean expression z-score of DE genes in each LAD class, scaled across time points; data are also shown with gene names for all LAD classes in Additional file 1, Fig. S5. b H3K4me1, H3K4me3, and H3K27ac levels around the TSS of all expressed (active; n = 116) and non-expressed (inactive; n = 3702) genes in cLADs (mean ChIP-seq read counts normalized to library size and averaged across all 0–72-h time points). An expressed gene is a gene with a normalized read count ≥ 15 at at least one time point. c H3K9me3 enrichment and d LMNB1 enrichment in H3K4me1 regions and in non-H3K4me1 regions in cLADs, and across the entire cLADs; bar, median; cross, mean; box, 25–75% percentile; whiskers, min-max ****P < 10−4, ANOVA with Welch’s correction. An H3K4me1 region is a cLAD region containing at least one H3K4me1 peak at at least one time point in the 0–72-h time course. A non-H3K4me1 region never contains any H3K4me1 peak at any time point. e Genome browser views of reduced LMNB1 and H3K9me3 enrichment at DE genes in cLADs (boxed areas). Enrichments of H3K4me3, H3K4me1, and H3K27ac are shown; ranges of Log2(ChIP/input) ratios shown in brackets; mRNA levels shown with read count scales in brackets. f Zoom-in views of LMNB1 and H3K9me3 depletion at the PXDN, INSIG1, and TRNT1 start sites; H3K4me3 enrichments are also shown; ranges shown in brackets. g Numbers of repressed genes (concordant with the overall repressed status of LADs) and of DE genes (discordant with LAD status) in cLADs, all time points confounded