Identification of PRDM11 target genes. (A) Pie plot of the overall distribution of PRDM11 binding sites in U2932 cells into TSS, promoter, exon, intron, and intergenic regions. (B) Mean distribution of tags across gene bodies for both PRDM11 antibodies, IgG, input, and total RNA polymerase II (RNAPII). (C) Histogram showing the distribution according to RNA polymerase II status of all genes and PRDM11 target genes (P < .01, Fisher’s exact test). (D) Graph illustrating the rank of genes according to RNA polymerase II stalling index (SI) (x-axis) plotted against the log₂ SI (y-axis). Vertical black bars on the x-axis mark the positions of PRDM11 targets, which correlate with stalled genes (P = 5.1E-62, Wilcoxon rank sum test). (E) Examples of ChIP-qRT-PCR results in control (shScr) or PRDM11-depleted (shPRDM11) U2932 cells. Percent of enrichment was calculated and normalized to the IgG control of each cell line. Mean ± SD of technical triplicates is shown. (F) Venn diagram showing the overlap between PRDM11 target genes bound by Ab1 and annotated genes upregulated or downregulated by PRDM11 shRNA in U2932 cells (log₂FC0.5, false discovery rate ≤0.05). (G) qRT-PCR validation of selected genes from the overlap between ChIP-seq and RNA-seq analysis of PRDM11-depleted U2932 cells (red) vs control cells (blue). Each messenger RNA was normalized to the average of the housekeeping genes β-actin, Ubiquitin, 36B4, and GAPDH and is shown relative to shScramble-1. Mean ± SD of technical triplicates is shown. FOS, P = .015; JUN, P = .003; and VAV3, P = .0005 (unpaired, two-tailed Student t test).