With many political parties fighting it out for influence in the UK general election last week, it is nice to see the spirit of cooperation alive and well in embryonic stem cells. In their latest study, Raul Mostoslavsky and colleagues show that two giants of epigenetic regulation, histone acetylation and DNA hydroxymethylation, team up to control the formation of neuroectoderm in differentiating stem cells.
The epigenetic landscape of embryonic stem cells (ESCs) is very different from that of differentiated cells. Low levels of DNA methylation (5mC) and histone hyperacetylation keep the genome globally uncondensed, ready to take on any state. High levels of 5-hydroxymethylation (5hmC), which is created when TET enzymes oxidize 5mC, are also important for pluripotency in ESCs. Although most of the actors of epigenetic regulation have been identified, we still don’t know how they all come together to regulate gene expression programs during differentiation.
Mostoslavsky’s team focused on the histone deacetylase SIRT6, which targets H3K56 acetylation in mouse ESCs. Curiously, during differentiation, SIRT6 knockout (KO) ESCs preferred to form neuroectoderm and continued to express high levels of the pluripotency factors Oct4, Sox2 and Nanog. In wild-type cells, SIRT6 bound to the promoter of these factors and in SIRT6 KO cells, high levels of H3K56 and H3K9 acetylation persisted at these regions after differentiation.
Suspecting interplay with other epigenetic mechanisms, the team examined how loss of SIRT6 affects the expression of Tet1 and Tet2, which are regulated by pluripotency factors.
- Levels of Tet1 and Tet2, as well as those of 5hmC, were high in SIRT6 KO cells.
- Loss of SIRT6 reduced the binding of Oct4 and Sox2 at the Tet1 and Tet2 promoters.
- Knockdown of either Tet1 or Tet2 rescued the SIRT6 KO phenotype in vitro, but also in in vivo in teratoma assays.
A sweep of the genome by 5hmC immunoprecipitation showed that in differentiating SIRT6 KO ESCs, 5hmC is enriched within exons encoding neuronal differentiation genes. These regions were also enriched in H3K4 dimethylation, turning this TET-à-TET between 5hmC and SIRT6 into a ménage à trois. Thus, SIRT6 controls differentiation in ESCs by repressing Oct4 and Sox2, which in turn leads to the down-regulation of Tet1 and Tet2 affecting levels of 5hmC at neuroectoderm genes. Moreover, this scenario seems to be conserved in human ESCs.
Check out this fine example of teamwork at Nature Cell Biology, May 2015.