Fig. 1

Hi-C analyses identify that small chromosomes (chr16–22) in the MCF10A genome show preferential associations with each other. Genome-wide all-by-all 1-Mb Hi-C interaction heatmap of MCF-10A (a) and MCF-7 (b) cells. The chromosomes in all-by-all heatmaps are stacked from top left to bottom right in order (chr1, chr2…chr22 and chrX). The gray regions indicate repetitive regions (such as centromeres) in which the sequencing reads could not be mapped. Intra-chromosomal interactions were much more frequent than inter-chromosomal interactions. The blocks of enriched inter-chromosomal interactions represent the translocated regions. In the lower panels, enlargements of the cis- and trans-interactions for chr16 through chr22 are shown. c Genome-wide heatmap of significant differential interactions between MCF-10A and MCF-7. Each dot denotes a genomic region of 6.5 Mb. Chromosomes are stacked from top left to bottom right from chr1 through chr22 and chrX. The red color indicates MCF-7-enriched interactions and the blue color indicates MCF-10A-enriched interactions. The white regions denote interacting regions that are not significantly changed between the cell lines. In the lower panel, significant interactions within and between chr16–22 are shown. d Boxplot showing the MCF-10A/MCF-7 inter-chromosomal interaction frequency differences between chr16 through chr22 and all the other chromosomes (grey) or between chr16 through chr22 (blue). The p value was determined using Wilcoxon rank-sum test. e First principal component of chr18, representing the open A-type (black) and closed B-type (grey) compartmentalization. Highlighted bars represent examples of regions with either stable or differential compartmentalization. The differential compartments are defined as genomic regions in which one type of compartmentalization is observed in one cell line and the other compartment type in the second cell line. f Pie chart showing the genomic compartment changes between MCF-10A and MCF-7 genomes. “A” and “B” denote the open and closed compartments, respectively. “A → A” represents compartments that are open in both cell lines, “B → B” represents compartments that are closed in both cell lines, “A → B” denotes compartments that are open in MCF-10A but closed in MCF-7, and “B → A” denotes compartments that are closed in MCF-10A and open in MCF-7. g Bar graph showing the percentage of compartments that have switched (A → B or B → A) or remained similar (A → A or B → B) between MCF-10A and MCF-7 genomes for chr16 through chr22 (blue) and the rest of the genome (grey). Chr16–22 display a higher percentage of B → A compartment switching, and a lower percentage of A → B compartment switching between MCF-10A and MCF-7, suggesting a more open compartmentalization in MCF-7. **P value < 0.001: Chi-square with Yates’ correction