Ever taken one of those online personality tests, such as those that tell you if you’ve got a passive or active personality? Well researchers at Stanford set out to perform such a test, not on themselves, but to uncover the ‘personality’ of demethylation during development. DNA can be demethylated actively through the TET enzyme family, or passively during DNA replication, where the marks aren’t maintained as new DNA is synthesized, and thus there is an (asymmetric) hemi-methylated, pattern at a CpG where this is occurring.
The test that the research team from Stanford, along with researchers in the UK and Germany, used was deep hairpin bisulphate sequencing (DHBS). This technique, previously developed by the same researchers, lets you examine whether DNA methylation is symmetric across complementary strands at CpGs, therefore allowing for some detailed stem cell division methylation dynamics.
To offer up this fantastic epigenomic resolution, the technique can only be utilized at repetitive elements. The team chose to investigate LINE1 and major satellite receptive elements, since they are known to undergo demethylation during development, as well as IAP elements, which are known to be resistant to developmental demethylation.
By examining repetitive elements in the developing zygote, early embryo, and primordial germ cells (PGCs), which will go on to create the next generation, the researchers showed that in early mouse development:
- DNA methylation patterns change differently in maternal and paternal pronuclei, with both exhibiting passive demethylation.
- Interestingly, there was no overall change in the methylation levels of maternal DNA, but there was an increased level of dispersion of the hemi-methylated dyads throughout development, indicating some passive demethylation.
- DNA is continuously and progressively demethylated across cell divisions in replicating PGCs, whereas in the embryo the patterns change drastically after the first cell division and remain unchanged over the next three divisions.
Overall, the group concludes that the main driver of DNA demethylation in germ cells is the impairment of the maintenance of symmetric CpG sites. While providing some detailed dynamics on passive demethylation, the group also reminds us not to forget about the role of active demethylation, which teams up with the passive demethylation to counteract de novo methylation and achieve the patterns required to drive development.
Go and passively discover over in Epigenetics & Chromatin, January 2015