Figure 2. Genome-Wide Mapping of H3K4me3 and H3K27me3 Profiles in qHF-SCs.
(A) Global in vivo H3K4me3 and H3K27me3 patterns in qHF-SC chromatin, compared with published in vitro data on chromatin from cultured murine ESCs, MEFs and NPCs (Mikkelson et al., 2007). In contrast to ESCs and MEFs, very few bivalent genes (yellow) were detected in qHF-SCs or NPCs. (B) Genes that in ESCs displayed one of four H3 methylation patterns (horizontal axis) and how this changes in qHF-SC chromatin. Each bar is normalized to 100% (n=number of ESC genes with each mark). Color-coding is for the qHF-SC genes and denotes the % of total genes within the ESC gene set that has either the same or a different mark in qHF-SCs. Green, H3K4me3; yellow, bivalent/dual marked with H3K4me3 and H3K27me3; red, H3K27me3; gray, neither mark. Note that most genes that were bivalent in ESCs are either H3K4me3 (primed/active) or H3K27me3 (repressed) in qHF-SCs. (C) Gene ontologies of bivalent ESC genes that display only H3K27me3 in qHF-SCs. Ontology terms are shown on the y axis; numbers of genes which fall into each category based upon functional studies are graphed along the x axis. (D) Except for Tcf3, ESC pluripotency genes are not transcribed in qHF-SCs. Shown are ChIP-seq signal tracks across indicated genes. Exon-intron structures and coding strand direction are depicted beneath. All tracks are set to the same scale (0–50); IGV browser. RT-PCR: pluripotency mRNAs from qHF-SCs and ESCs. Negative (-RT) and positive (Gapdh) controls. (E) Despite the silencing of pluripotency genes in qHF-SCs, ~80% of Sox2/Oct4/Nanog direct targets that are H3K4me3+ in ESCs (Boyer et al., 2006; Cole et al., 2008) are also H3K4me3+ in qHF-SCs. Examples of these genes are listed in the table. See also Table S2, S3.