H2A.Z localizes to promoters in embryonic stem cells and neural progenitor cells. (a) Heatmaps depict H2A.Z, H3K4me3, H3K27me3, TFIID and RNAPII ChIP-Seq and RNA-Seq signals at regions spanning all transcription start sites (±5 kb) in mES cells organized according to their chromatin status: H3K4me3 (green), H3K27me3 (red), bivalent (green and red), and no-mark (white). Active K4me3-only (green only) promoters show strong signals for H2A.Z, transcriptional machinery (TFIID, RNAP II) and mRNA, while bivalent promoters (green and red) are primarily enriched for H2A.Z. (b) Analogous heatmap for H2A.Z in human embryonic stem (hES) cells. H2A.Z occupancy at active and bivalent promoters is conserved between mES and hES cells. (c) Analogous heatmap for H2A.Z in mouse neural progenitor (mNP) cells. H2A.Z signal is depleted from monovalent K27me3-only promoters (red, in the absence of green). (d) ChIP-Seq tracks show H2A.Z localization to K4me3-only (Pol2rd) and bivalent promoters (St8sia4 and Ihh) in mES and hES cells. (e) ChIP-Seq tracks show H2A.Z localizes to K4me3-only (Pol2rd) and bivalent promoters (Jph1) in mNP cells, but not monovalent H3K27me3-only (Pou2af1) promoters. ChIP-Seq: chromatin immunoprecipitation coupled with high-throughput sequencing; hES: human embryonic stem; H3: histone H3 K: lysine; kb: kilobase; me1: monomethylation; me2: dimethylation; me3: trimethylation; mES: mouse embryonic stem; mNP: mouse neural progenitor; RNAPII: RNA polymerase II; TFIID: transcription factor IID; mRNA: messenger RNA.