Background: Human embryonic stem cells (hESCs) are interesting models for the study of epigenetic mechanisms. Epigenetic stability in hESCs is critical to ensure the quality and safety of these cells in regenerative medicine. One of the first measurable epigenetic phenomena is X chromosome inactivation (XCI).
Methods: XCI status was analyzed by methylation-specific PCR of the human androgen receptor (HUMARA) gene in five diploid (including one translocation line) and one triploid hESC lines established in our laboratory. For XCI skewing, only the hESC lines with a HUMARA heterozygous locus were further analyzed.
Results: Irrespective of their karyotypes, all hESC lines examined had active and inactive X chromosomes in the undifferentiated stage at very early passages. One line exhibited a random XCI status, although the remaining four heterozygous lines showed an extremely skewed XCI pattern. This skewed XCI pattern remained stable until differentiation. In addition, the XCI pattern in a triploid hESC line with two active X chromosomes varied after long-term culture.
Conclusions: Two types of XCI pattern were found in the female hESCs used in this study. Most hESCs fell into one category where the XCI pattern is extremely skewed, although the other category includes hESCs with random XCI. The XCI pattern in a triploid hESC line varies gradually and eventually reaches an extremely skewed XCI pattern after long-term culture. Our study demonstrates that there is a large variability in terms of X inactivation among hESC lines, and even at different passages of the same line.