Optimization of mESC ChIP-re-ChIP workflow

Epigenetics helps define current cell states, yet also shapes how cells respond to external cues such as differentiation or stress. The epigenetic plasticity of a cell describes how flexible this regulation is. Bivalent chromatin is an exemplar of epigenetic plasticity. This co-occurrence of the active-associated H3K4me3 and inactive-associated H3K27me3 histone modifications on opposite tails of the same nucleosome was first described in mouse embryonic stem cells where it is found at promoters of key developmental genes. It has been postulated that bivalent chromatin poises these promoters, keeping them free from repressive DNAmethylation, enabling them to be transcriptionally upregulated upon differentiation. Bivalent chromatin has also been reported in other cell types including somatic cells and cancer cells, however we know little of the dynamics, resolution and regulation of this chromatin state. This is partly due to the technical challenges distinguishing bone-fide bivalent chromatin, where both marks are on the same nucleosome, from sample heterogeneity where some alleles have H3K4me3 and others H3K27me3. We developed a robust and sensitive reChIP method to accurately profile bivalent chromatin in as little as 2 million mouse embryonic stem cells. We validated the sensitivity of our method to detect changes in bivalent chromatin by profiling mouse ESCs lacking the epigenetic priming factors Dppa2 and Dppa4. Sequential ChIPreChIP was performed on two biological replicates of E14 mouse embryonic stem cells, and two wild-type (WT) and two Dppa2/4 double knockout (DKO) clones to measure distribution of bivalent chromatin. For each sample corresponding to 2 million cells we generated in-line total H3K4me3, total H3K27me3, sequential reChIP in both orientations (H3K4me3 followed by H3K27me3 and vice versa) and IgG-IgG negative controls (one per experimental set).