The XIST-coated X-chromosome silent compartment is severely disrupted in breast cancer cell lines. (A) Z-projections of sequential 3D RNA/DNA FISH show examples of XIST RNA coating (red) and X-chromosome territories (white or outlined) in normal (WI-38 and HMEC) and breast cancer cell lines (ZR-75-1, SK-BR-3, and MDA-MB-436). Scale bar, 5 µm. (B) Human SNP Array 6.0 (Affymetrix) genomic analysis (Popova et al. 2009) shows the copy number and allelic imbalance of X-chromosome fragments in breast cancer cell lines. The XIC locus is indicated with a green dotted line. (C) Immuno-RNA FISH using anti-RNA Pol II antibody, XIST/Cot-1 RNA FISH, and DAPI staining show the level of exclusion of RNA Pol II and Cot-1 RNA, as well as the level of chromatin compaction (i.e., Barr body) on XIST RNA domains (arrowheads) in normal and breast cancer cell lines. On the right, line scans (white arrows) show the relative levels of Cot-1 RNA (green), RNA Pol II (black), and DNA density (blue) at the XIST domain (black bar). Scale bar, 5 µm.
