Pcgf1 regulates genes of the HoxA cluster. (A-B) Expression analyses of lineage-depleted BM cells from 4 different Runx1^Δ/Δ mice isolated and transduced with Pcgf1 (shPcgf1) or control (shCtrl) shRNA are presented. (A) Normalized gene expression in samples with a Pcgf1 knockdown versus control samples in log2 scale is plotted against its P value (−log10). Blue dots display significant differentially regulated genes. Red circles mark selected HoxA cluster genes and Pcgf1. (B) Hierarchical cluster analysis of the 4 mice (experiments 1-4) revealed the up-regulation of several Hox genes on Pcgf1 knockdown (blue indicates down-regulation; red, up-regulation). (C) qRT-PCR analysis of selected HoxA genes in cells transduced with Pcgf1 shRNA compared with control shRNA-transduced cells. After transduction, cells were selected for puromycin resistance for 48 hours, and then total mRNA was isolated and Hox gene expression was analyzed with specific primers. RNA levels of indicated genes were normalized against β-actin. Mean values from 3 independent experiments and the corresponding SDs are shown. Significance of changes in shPcgf1 versus control transduced samples was determined using the Student t test. *P < .05; **P < .01.