Figure 2.

The Hoxa1 promoter is preloaded with Pol II and recruits SEC after RA treatment in ES cells. (A) Bivalent marks, paused Pol II, and SEC recruitment to the Hoxa cluster. In ES cells, the whole Hoxa cluster is highly enriched for H3K27me3, and also contains H3K4me3 at the promoters of a subset of genes, including Hoxa1, Hoxa3, Hoxa4, and Hoxa7. These regions are preloaded with Pol II (bars indicate regions that have both a bivalent mark and Pol II). (B) Bivalent marks and paused Pol II are both largely absent from the Hoxb genes, which do not recruit SEC after 6 h of RA treatment. While H3K27me3 marks the whole cluster of Hoxb genes, only Hoxb4, Hoxb7, and Hoxb9 contain H3K4me3 at their promoters and can be considered bivalent. There is no significant Pol II detected on the promoters of the Hoxb genes in ES cells. The bar marks a peak of significant Pol II that does not correspond to a known gene feature. Before RA treatment, there is no detectable AFF4 and ELL2 signal on the Hoxa or Hoxb cluster genes. Both AFF4 and ELL2 are recruited to the Hoxa1, but not the Hoxb1, gene promoter after exposure to RA for 6 h. Blue boxes highlight the Hoxa1 and Hoxb1 genes. Expanded views of the Hoxa1 and Hoxb1 regions are shown in Supplemental Figure S4.