X-inactivation in female human embryonic stem cells is in a nonrandom pattern and prone to epigenetic alterations

Yin Shen*, Youko Matsuno†, Shaun D. Fouse*, Nagesh Rao‡, Sierra Root§, Renhe Xu§, Matteo Pellegrini¶, Arthur D. Riggs†_, and Guoping Fan*_

There is a need for a common set of quality control guidelines in the use of female human embryonic stem cells (hESCs). Suboptimal culture conditions can have an effect on X Chromosome Inactivation (XCI); an example of which is the irreversible, epigenetic silencing of XIST, a gene involved in XCI.

In females, x-inactivation is a required mechanism for dosage compensation. Dosage compensation is important as it means that females, who have two x-chromosomes, only express x-linked genes in the same dosage as males. It is important to make sure that x-inactivation in hESC lines is quality controlled as they are seen to be the most useful stem cells for regenerative medicine, and if they are not controlled, they cannot be used.

Yin Shen and associates have proven the need for common quality control guidelines when they showed us that x-inactivation in hESCs is in fact in a nonrandom pattern and prone to epigenetic alterations. They found that stress and suboptimal culture conditions can lead to the irreversible, epigenetic silencing of XIST. Shen et. al. also reports that when polymorphic x-linked genes (genes that have 2 different alleles) undergo x-inactivation, the genes are monoallelically expressed (the same allele is always expressed). This suggests that x-inactivation is in a nonrandom pattern. It was also found that in cells where XIST was no longer expressed there was 100% methylation of the XIST promoter suggesting that DNA hypermethylation is coupled with the loss of XIST expression. Shen et.al. also report that in 12.2% of x-linked genes can be reactivated in the absence of XIST. This means that dosage compensation in disrupted in the absence of XIST expression.

What does all of this mean? Human embryonic stem cells, the cells that are set to be the basis for human regenerative medicine, when cultured in a lab, are not stable. Standards need to be put in place to make sure that should any of these cells be used in regenerative medicine, they will not have undergone irreversible epigenetic silencing of the XIST gene, DNA hypermethylation of the XIST promoter has not occurred, and x-linked genes haven’t been reactivated and disrupted dosage compensation.

XCI markers need to be monitored in established cell lines of hESC’s.

Steph Grehan

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Article taken from PNAS, March 12, 2008, vol 105, no. 12