PRC1, PRC2, and PhoRC control different gene sets in HSC/progenitors. (A-B) Log₂-fold changes for 7824 differentially expressed Illumina expression array probes in fetal liver LSK cells, comparing Bmi1^−/− and Bmi1^+/+ (PRC1 vs wild-type), Suz12^Plt8/+ and Suz12^+/+ (PRC2 vs wild-type), and Yy1^+/− and Yy1^+/+ (PhoRC vs wild-type). Probes (blue) in panel A are the same as probes (blue) in panel B, and similarly for those colors shown (red, yellow, or green). (C) Romer analysis of gene expression comparisons shown in panel A. Broad Institute gene sets that are enriched in particular comparisons are listed (in supplemental material for full analysis). (D) Image showing the multifaceted regulation of gene expression by PRCs. PRC1, and PRC2 may bind some targets cooperatively to repress expression; these genes are named blue genes shown in panel A. PRC2 and PRC1 may act independently at some loci, and other loci may be differentially sensitive to depletion of PRC1 (eg, Bmi1) or PRC2 (eg, Suz12).