The Set1 complex is dimeric and acts with Proof Only Jhd2 demethylation to convey symmetrical H3K4 trimethylation [Spike-in-ChIP-seq]

Epigenetic that deposit and/or propagate symmetry or asymmetry are not understood. Here we report that yeast Set1C/ COMPASS (complex of proteins associated with Set1) is dimeric and, consequently, symmetrically trimethylates histone 3 Lys4 (H3K4me3) on promoter nucleosomes. Mutation of the dimer interface to make Set1C monomeric abolished H3K4me3 on most promoters. The most active promoters, particularly those involved in the oxidative phase of the yeast metabolic cycle, displayed H3K4me2, which is normally excluded from active promoters, and a subset of these also displayed H3K4me3. In wild-type yeast, deletion of the sole H3K4 demethylase, Jhd2, has no effect. However, in monomeric Set1C yeast, Jhd2 deletion increased H3K4me3 levels on the H3K4me2 promoters. Notably, the association of Set1C with the elongating polymerase was not perturbed by monomerization. These results imply that symmetrical H3K4 methylation is an embedded consequence of Set1C dimerism and that Jhd2 demethylates asymmetric H3K4me3. Consequently, rather than methylation and demethylation acting in opposition as logic would suggest, a dimeric methyltransferase and monomeric demethylase cooperate to eliminate asymmetry and focus symmetrical H3K4me3 onto selected nucleosomes. This presents a new paradigm for the establishment of epigenetic detail. Quantitative examination of 3 different H3K4 modifications in Wt, three different sdc1 mutant, Jhd2 deletion, double mutantion of sdc1 point mutant along with Jhd2 deletion and set1 deletion mutant by ChIP sequencing. For quantifying changes in the methylation in different Saccharomyces cerevisiae cells we spiked in the ChIP with closely related Schizosaccharomyces pombe cells. The cells were mixed in a 2:1 ratio, respectively.