During the past 12 months we have made significant progress on the data analysis of 141 paired (early passage-late passage) human embryonic stem cell lines (HESCs). The data in question was generated using a custom Illumina GoldenGate array of known Polycomb targets in HESCs, as described by Lee et al 2006. Briefly, we profiled the DNA methylation status of 1,536 loci on 282 specimens. This profiling was used to determine whether DNA methylation changes in HESCs arise as a result of time in culture at the examined loci. This determination was made by comparing the DNA methylation status of a sample of an early passage line with a late passage sample of the same line.
Interestingly, we found that DNA methylation in Polycomb target genes is highly affected by time in culture in a cell line-specific manner. That is, in some cell lines few DNA methylation changes were observed, while in the majority of them a large number of loci showed either an increase or decrease in DNA methylation. Via collaboration with the University of Sheffield, we were able to determine that DNA methylation instability seems to be independent of genetic instability. Furthermore, genetic instability seems to be a function of passage time in culture.