The Shores of CpG Islands Reveal Differences Between iPS and ES cells

November 5, 2009 With headquarters in Del Mar, CA, you don’t have to tell us that the shores are where the action is, so it makes sense that the shores of CpG islands are a hot spot for epigenetic movers and shakers like DNAm. In fact, researchers have found evidence in the shores of CpG islands that induced pluripotent stem (iPS) cells may not be all that they seem (sounds a little like LA to us).

The team compared iPS cells, embryonic stem (ES) cells, and fibroblasts using the comprehensive high-throughput array-based relative methylation (CHARM) analysis in two separate experiments. To hit most of the CpG islands and shores in the human genome, they used a custom-designed NimbleGen HD2 array.

 Here’s a little of what they found:

• Many of these R-DMRs (reprogrammed-cell DMRs) overlapped T-DMRs that previously were found to distinguish tissue types in normal development.

• The methylation patterns of iPS cells sometimes resembled that of ES cells, but—and here’s the kicker—at other times, iPS methylation didn’t look like either fibroblast or ES cell methylation. (Thus, iPS cells may be some weird Frankensteinian aberration.)

• The researchers also found that hypomethylated R-DMRs in iPS cells co-localized with hypermethylated Cancer-DMRs (C-DMRs) and bivalent chromatin marks WHILE hypermethylated R-DMRs localized with hypomethylated C-DMRs in areas with no bivalent chromatin marks, suggesting two parallel mechanisms of epigenetic reprogramming in iPS cells and cancer.