Ikaros binds to the Cebpa and Hes1 genes, and loss of Ik results in altered histone modifications. (A) RVista/MultiTF analysis of consensus Ikzf1 (Ik), Stat5a- and Gata-binding sites (tick marks) in the flanking regions (transcriptional start site and 3′ CNS regions [II-IV]) of the Cebpa gene and upstream region of the Hes1 gene (promoter [Hes1p]). BLUE peaks and boxes denote exons and YELLOW, PINK and RED peaks designate intergenic or flanking regions exhibiting interspecies homology. (B) ChIP assays detect Ikaros-binding to the Cebpa and Hes1 genes in wild-type bone marrow derived mast cells. Primers flanking indicated regions (green boxes) were used. Data are expressed as percent of total input DNA. Negative controls (n.c.) include quantitative RT-PCR amplification with primers for a sequence distant from any known Ikaros-binding site. (C) H3K4me3 histone modifications at consensus Ikaros-binding sites, assessed by ChIP. Data are expressed as percent of total input DNA after subtraction of IgG control values. Results shown in panels B-C are representative of 4 experiments using 2 independent bone marrow cultures derived from wild-type and Ik^−/− mice.