Bivalent genes are highly enriched in mesenchymal cells. (A) Venn diagram of bivalent genes in human mammary epithelial (HMLE) vector cells and HMLE Twist- cells. (B) Landscape of H3K4me3 and H3K27me3 mark for the homeobox gene HOXA11. Note that HOXA11 is marked by H3K27me3 in both epithelial and mesenchymal cells. In HMLE Twist cells, HOXA11 gains H3K4me3 mark in addition to H3K27me3 mark. (C) Bar graph showing the number of bivalent genes in HMLE vector cells, and HMLE Twist cells in a monolayer (Twist-2D) and sphere culture (Twist-MS). (D) Changes in histone modifications among genes becoming bivalent in HMLE Twist cells (Twist-2D) as compared to HMLE vector cells. (E) Gene ontology of newly bivalent genes in HMLE Twist cells cultured in monolayer (Twist-2D). (F) Gene ontology of newly bivalent genes in HMLE Twist cells cultured in spheres (Twist-MS). 2D, monolayer; MS, mammosphere.