Fig. 6

Chromatin compaction at subregion 2 of the 16p11.2 RER region in breast cancer cell lines, in normal breast tissue and in primary breast tumors. a Box plots comparing the distribution of normalized FISH interprobe distances (d ² /r ²) measured across subregion 2 of the 16p11.2 RER region in a normal breast cell line (HMLE) and in ER+ (MCF7, LY2, MDAMB361) and ER− (MDAMB231 and MDAMB468) breast cancer cell lines. n = 45–60 cells. The significance of differences between datasets was assessed by Wilcox test (Table S3 in Additional file 1). b Box plots showing the distribution of normalized FISH interprobe distances (d ² /r ²) measured across subregion 2 of the 16p11.2 RER region in normal breast tissue and in ER+ and ER− tumor tissues. n = 250–300 alleles. Distances in the ER+ tumor were significantly greater than in normal tissue (p < 0.0001) or in the ER− tumor (p = 0.004). Differences between normal and ER− tumor tissue were not significant (p = 0.24). c Example FISH images using probe pairs (red and green) that delineate subregion 2 in normal breast tissue and in ER+ and ER− tumor tissue. DNA is stained with DAPI (blue). Scale bar = 5 μm