DNA methylation assay for X-chromosome inactivation in female human iPS cells.

Remarkable interest in the epigenetic status of human induced pluripotent stem (iPS) cells inspired numerous studies of their X-inactivation patterns. However, both the presence and the absence of X-inactivation have been described to date in undifferentiated iPS cells. The reasons for the discordant results between different studies are unclear, and further X-inactivation testing is warranted for all female human iPS cell lines. Some of the inconsistency in the current data most likely results from the use of different X-inactivation assays by different authors. We provide a detailed protocol for a simple, reliable and affordable X-inactivation assay based on promoter methylation and CAG-repeat polymorphism in the human androgen receptor (AR) gene at Xq11.2. This assay is commonly used in clinical genetic laboratories and we propose that it could be ideal for routine assessment and monitoring of the X-inactivation status in female human iPS cell lines.