Supplementary Figure 4: Extensive genome rearrangements within TADs have limited impact on gene expression.
From: Highly rearranged chromosomes reveal uncoupling between genome topology and gene expression
a, Insulation score profiles, calculated at 21,800 genomic bins, are highly correlated between wild-type and balancer haplotypes when comparing replicates (R1 and R2) for each allele, even when considering regions affected by nested inversion breakpoints (red). Pearson correlation coefficient (r) indicated. Average r between biological replicates (same haplotype) = 0.912, average r between haplotypes (i.e. between the wild-type and balancer) = 0.857. b-c, Zoomed-in versions of Fig. 3b, c. d, Location (promoter) and change in expression (balancer/wild-type, log2 fold change) of differentially expressed genes (DE-genes, orange, 23 genes), non-differentially expressed (non-DE, blue, 138 genes), lowly expressed (light-blue, 161), not testable due to lack of SNVs (grey, 121) genes within the 16 disrupted TADs. TADs (outlined in grey) are centered on the ___location of the inversion breakpoint, indicated by the vertical dashed line (purple). In the top six, the closest gene to the breakpoint is differentially expressed (orange), while the 10 TADs below the dashed line have one or more non-DE genes (blue, light blue) closer to the breakpoint. e, Expression levels of DE-genes and non-DE genes within disrupted TADs; FPKM, Fragments Per Kilobase of transcript per Million mapped reads.
