Dr. Robert Waterland discusses how 3′ CpG island methylation may function as a key developmental activator of gene expression. This interview was shot at the Keystone Symposia’s meeting on Nutrition, Epigenetics and Human Disease, 2013 held in Santa Fe, New Mexico
3′ CpG Island Methylation in Gene Activation
Another really interesting project thatI’ve been involved with is in a collaboration with Lanlan Shen at Baylor College of Medicine. And we’ve been working on addressing some fundamental questions of the role of DNA methylation during development. And in this project, that was done mostly in her lab.
We did in vitro induced differentiation. So in human embryonic stem cells, we differentiated these– random differentiation in vitro and looked for methylation changes. And so we did a genome-wide screen looking for CpG islands that change methylation.
And we identified, of course, several 5-prime CpG islands that were changing methylation, but a large group of 3-primeCpG islands that underwent methylation– increases in methylation– that coincided with differentiation. And likewise, in induced dedifferentiation, the methylation status of these regions was decreased. And in each case, the methylation at these 3′ regions actually correlated with increased expression of these genes.
“…we’ve identified this whole class of genes that are transcriptionally activated by 3′ CpG island methylation.”
And moreover, we did some work with looking at– so basically looking at using luciferase reporter assays to try tounderstand the specific mechanism by which the 3-prime CpG island methylation is leading to actual activation of expression. And in at least two examples that we looked at found very strong evidence for basically an enhancer blocker activity of these 3′ CpG islands, which is mediated by CTCF binding.
So this is really, of course, reminiscent of what’s occurring at imprinted genes–like H19, IGF2, this sort of thing. But our data, which are now in press in molecular and cellular biology, now give kind of a new insight that 3′ CpG island methylation may generally serve as a developmental mode of gene regulation.
And very importantly, to activate expression of genes rather than to– and we’ve already heard in this meeting a couple times this morning about people making the statement that all DNA methylation is generally a repressive mark. But actually, it’s obviously much more complicated than that. And so we’ve identified this whole class of genes that are transcriptionally activated by 3′ CpG island methylation.