I don´t overeat! I’m not lazy! I’m not eating the agar plates when I´m working in the lab late, honest!
Psychologists consider denial as one of our most primitive defense mechanisms and recent studies of epigenetic defense mechanisms in embryonic stem cells (ESCs) by the labs of Olivier Elemento (Weill Cornell Medical College) and Danwei Huangfu (Sloan Kettering Institute, New York) have further strengthened this association.
This new study initially sought to discover any direct connections between the Ten-eleven translocation (TET) protein family-mediated DNA demethylation and transcriptional output at specific loci, as previous studies tended to be more global in their approach. Now, after some more targeted analysis, Verma and colleagues have established that TET proteins defend the lineage-specific differentiation of ESCs by denying DNA methylation at primed chromatin states known as bivalent domains, thus permitting ESCs to express differentiation-associated genes only when required. The TET enzymes themselves normally catalyze the first step of active DNA demethylation.
So what are the details of this new ESC-based study?
- The team first created TET1, TET2, and TET3 triple-knockout (TKO) ESCs
- TET knockout increased de novo DNA methylation at bivalent domains, but this did not alter gene expression
- However, TET knockout increased DNA methylation elsewhere in the genome, prompting a general decrease in gene expression under self-renewing conditions
- Focusing in on the PAX6 locus, a neural differentiation-associated factor, the authors observed increased DNA (cytosine-5)-methyltransferase 3B (DNMT3B) binding upon TET knockout
- The study observed no alterations to PAX6 expression under self-renewing conditions
- Following neural priming, DNMT3B-directed de novo DNA methylation of the PAX6 bivalent domain led to the repression of PAX6 gene expression and inhibited neural differentiation of TKO-ESCs
- Epigenetic editing of the PAX6-associated bivalent domain by dCas9 fused to the catalytic domain of TET1 prompted DNA demethylation and improved neural differentiation
There’s no denying it; these findings firmly establish the requirement for DNA demethylation by the TET enzymes at bivalent domains to defend the expression of differentiation-associated genes in ESCs. The authors hope that future studies will delineate the various factors that influence methylation status at bivalent domains and apply this combined knowledge to predict cell-type-specific gene transcription patterns during differentiation.
Don´t deny yourself a quick glance at this new study, head to Nature Genetics, December 2017 now!