Fig. 2

Interchromosomal translocations involving chromosome 4 (GGA4) in the HD3 cell line. a, e, i—Assemblies of HD3 Hi-C heatmaps indicating translocations of different regions of GGA4 to other chromosomes. Enrichment of interchromosomal contacts is detected between GGA4p, GGA5 and a part of GGA7p (a), centromere proximal region of GGA4q, GGA6 and GGA19 (e), centromere distal region of GGA4q with GGA17 (i). Blue squares on the heatmaps represent intrachromosomal contacts (chromosome territories). The relative positions of breakpoint regions are shown as red lines on the schematic depictions of chromosomes. Arrows point to the approximate positions of BAC probes. b, c, d—FISH verification of GGA4p translocations. Loss of GGA4p from one homologue of GGA4 was confirmed by using a GGA4 centromere-specific probe and a GGA4p paint probe (b). Fusion of translocated GGA4p with GGA5 (c) and a part of GGA7p (d) is confirmed by corresponding BAC-based probes. f, g—FISH verification of GGA4q breakage and translocation. Loss of the centromere-distal part of GGA4q from one homologue of GGA4 and its translocation to a microchromosome was confirmed by using a GGA4 centromere-specific probe and GGA4q paint probe (f). Fusion of GGA4 with GGA6 is confirmed by the corresponding BAC-based probes (g). Note the change in the centromere index of derivative chromosome 4 (metacentric) and unstained material in derivative chromosome 4q ter, indicating translocation from another chromosome, presumably GGA19; h, j, k—FISH localization of clusters of chicken tandem repeats CNM (h), PO41 (j) and telomere repeat (Tel) (k) in the HD3 chromosomes. Note the presence of centromeric and terminal clusters of CNM and PO41 repeats and an additional centromeric cluster of telomere repeat in derivative chromosome 4 compared to the normal homologue (h, j, k correspondingly, enlarged images); l—schematic depiction of possible derivative chromosomes containing GGA4 material. Chromosomes were counterstained with DAPI