Supplementary Figure 2: Example and characteristics of Structural Variants in the balancer chromosomes.
From: Highly rearranged chromosomes reveal uncoupling between genome topology and gene expression
a, A 258 kb balancer-specific duplication in chr2L. Top to bottom: wild-type and balancer Hi-C contact maps, log2 fold change before normalization (balancer/wild-type, red/blue), gene models, and differential gene expression (balancer/wild-type, log2 fold change). Differentially expressed genes (DE-genes) in orange, non-differentially expressed (non-DE) genes in blue and non-tested genes (lowly expressed or lacking SNVs) in grey. Hi-C contacts (~two-fold increase in balancer) confirm the duplication, inserted in an inverted orientation shown in (b). Expressed genes have a ~2-fold increase in allelic expression, as expected. Dotted lines indicate TAD boundaries. b, Model of the duplication and associated changes in TAD structure. Arrows mark the duplicated fragment, gradient indicates newly created contacts. c, Number of DNase hypersensitive (DHS) peaks deleted by ≥ 5% of their length in the wild-type (top) and balancer (bottom), indicated by orange vertical line. Deletions generally overlap a DHS less frequently than expected from randomly shuffling deleted regions in the genome (blue, green bars, respectively), as anticipated due to purifying selection. d-e, A 17.5 kb balancer-specific deletion at the breakpoint of the inversion chr3R:20.32 Mb: Wild-type (d) and balancer (e) Hi-C contact maps, deleted region in balancer highlighted in grey (d). DHS, gene models, and differential gene expression (balancer/wild-type, log2 fold change) are shown underneath. DE-genes in orange, non-DE genes in blue and non-tested genes (lowly expressed or lacking SNVs) in grey. Dashed purple lines indicate the ___location of the inversion boundary.
