Analysis of Mef2c complexes in GM12878-transformed peripheral B cells and murine pre-B cells. (A) Regulatory regions of putative Mef2c/d target genes occupied by Mef2c and the indicated TFs (light blue) are shown. ChIP-seq data sets were generated from ENCODE⁴⁰  and visualized using the UCSC Genome Browser, showing conservation (100 species), exon-intron structures of genes, and a scale bar in kilobases. Transcript direction is indicated by an arrow. (B) The frequency of Irf4, Egr1, Ebf1, Pax5, and E2a peaks within the indicated distance from Mef2c summits in GM12878 B cells is depicted. (C) Hierarchical clustering of Mef2c-binding sites with coincident binding with Irf4, Egr1, Ebf1, Pax5, or E2a sites generated using GENE-E.⁴¹  For each peak (y-axis), green indicates overlapping bound regions (minimum of 2 bp). Peak regions for individual TFs were set at a standard width of 300 bp. (D) Interaction of Mef2c with Irf4 and Egr1 in Blnk-deficient pre-B cells. Mef2c was precipitated using specific antibody and protein G Sepharose beads. Irf4 or Egr1 were visualized using specific antibodies. Gapdh served as a control. Results shown are representative of 2 independent experiments performed. Protein molecular weights are given (kilodalton). (E) Gene expression profiles of Mef2c/d and other pre-B-cell regulatory genes during murine B-cell differentiation were collected from the Gene Expression Commons²²  and are represented in a heat map. CLP, common lymphoid progenitor; pro-B cell (Hardy Fraction [Fr.] B); large pre-B cell (Fr.C′); small pre-B cell (Fr.D); immature B cell (Fr.E).