A) H3.3, H3K4me1, and H3K36me3 are enriched in the gene body of the highly expressed pluripotency gene Esrrb in ES cells, and this enrichment is largely lost upon differentiation to NPCs.
B) The epidermal growth factor receptor gene Egfr is H3K4me3/H3K27me3 bivalent and transcriptionally repressed in ES cells. Upon differentiation to NPCs, H3.3, H3K4me1, and H3K36me3 are enriched in the Egfr gene body.
C) H3.3, H3K4me1, and H3K36me3 are enriched in the gene body of the housekeeping gene lactate dehydrogenase A Ldha in both ES cells and NPCs, and is not enriched in the neighboring Ldhc gene. The Y-axes in panels A-C are identical (indicated in the right side of panel C).
D–E) H3.3 is enriched genome-wide around ES cell TFBS. Crosslinking ChIP-seq genome-wide profiles of H3 variants as indicated around ES binding sites for Nanog, Oct4, Sox2, Smad1, and STAT3. TFBS in mouse ES cells were from a previous ChIP-seq study (), and classified as promoter (black), gene body (dark blue), or intergenic (light blue). Panel D represents data from ES cells, while panel E represents data from NPCs at identical regions. Y-axis represents number of tags per binding site per 200 bp per 1 million mapped reads. Data for H3 in ES cells is from (). In A–E, “(native)” indicates native H3.3-HA ChIP-seq, and “(replicate)” indicates biological replicate H3.3-HA ChIP-seq from F1 hybrid ES background.
F) H3.3 and H3K4me1 are enriched at an intergenic region bound by multiple transcription factors () specifically in ES cells.
G) H3.3 and H3K4me1 are enriched at an intergenic region specifically in NPCs. See also .