In a paper in press at Cell Reports, we revisit promoter bivalency in naive mouse embryonic stem cells (mESC) using multiplexed quantitative MINUTE-ChIP. Transitioning between Serum-primed and naïve state, both H3K27me3 and H3K4me3 are subject to global alterations. These changes are uncoupled and, in fact, controlled by different external stimuli in the growth media.
The ultra-low technical background of our method allows us to quantify the true distribution of histone H3K27me3 above the technical background. Strikingly, naive mouse ESC have twice as much H3K27me3 methylated nucleosomes as ESC in Serum, and the gained H3K27me3 modifications distributes broadly across the genome while traditional Polycomb targets, such as bivalent domains retain approximately equal levels.
H3K27me3 is an abundant and extremely broad modification in the ground state of pluripotency. Essentially no new H3K27me3 peaks are formed upon transition to a primed state; instead the ambient H3K27me3 ‘background’ is more and more suppressed, ‘revealing’ existing H3K27m3 peaks at all cognate PcG. We further show that the ground state is characterized by particularly low levels of H3K4me3 (more than two-fold lower than Serum-primed), leading to a new model:
Bivalent domains start out in the ground state mainly covered by H3K27me3, and only upon priming, accumulate H3K4me3 levels comparable to those at active genes. We hypothesize that low H3K4me3 together with high H3K27me3 levels at bivalent promoters act to safeguard the ground state of pluripotency.