Supplementary Figure 1: Characterization and validation of the catalog of bona fide bivalent genes.

a, Agarose gel image of n = 3 independent cell culture chromatin samples obtained from sonicating Mll2^WT ESC lysates for reChIP-seq. Samples were prepared following the manufacturer’s instructions (Methods). b, ChIP-seq profiles of the indicated histone modifications around the TSS of the 3,868 bona fide bivalent genes (left) and a group of 9,948 non-bivalent genes (right). Non-bivalent genes correspond to genes marked by H3K4me3 alone. c, GO term analysis of the 3,868 bona fide bivalent genes showing enrichment in categories corresponding to morphogenesis and differentiation. d, reChIP–qPCR validations at six bivalent gene promoters in wild-type mESCs. ReChIP-seq experiments using H3K4me3–IgG or H3K27me3–IgG were used as background controls. Values represent the mean and error bars correspond to the s.e.m. of n = 3 independent cell cultures. e, Venn diagram showing that about 76% of the bona fide bivalent genes are also MLL2 targets by ChIP-seq. f, Distribution of 524 non-TSS peaks (peaks outside the regions ±2.5 kb around the TSS), which are mostly located at intergenic and intragenic regions of the genome. Peaks were identified by overlapping individual H3K4me3, H3K27me3, and MLL2 ChIP-seq with H3K4me3–H3K27me3 and H3K27me3–H3K4me3 reChIP-seq experiments.