ΔCDK-RB causes a reorganization of interactions between RB-bound loci within 19q13.42. (A and B) Interaction map of 19q13.42 from Wang et al. (2018) showing the four TADs and position of primers. (A) 3C was used to examine inter-TAD interactions between sites at TAD boundaries. Sites tested are indicated as green bars on the map, the origin is indicated by a brown bar, and these sites are listed in the table. Interactions between sites are shown in the right panel, with graph showing the fold-change (enrichment over TAD4-reg1 [origin] self-ligation product signal; see Materials and methods for details) detected in cells expressing either WT RB or ΔCDK-RB. (B) 3C was used to detect interactions between sites near to RB-bound loci. Green bars on map indicate position of the loci tested, and origin for 3C is indicated by red bar. These sites are listed in the table. Interactions (fold-change calculated as enrichment over KMT5C [origin] self-ligation product signal) were detected between the origin and multiple sites; of these, three showed significant differences (PRPF31, PTPRH, and UBE2S) between cells expressing WT RB or ΔCDK-RB. Graphs show mean fold-change of three independent biological replicates, set-up and performed on different days. Error bars are SEM. Nonparametric two-tailed multiple t tests (with correction for multiple comparisons) was used to calculate P values for PRPF31 (P = 0.0004), PTPRH (P = 0.15), and UBE2S (P = 0.008).