KAP1 binding sites and chromatin modifications in B cells. Chromatin from wild-type and KAP1-deficient B splenocytes was immunoprecipitated with a KAP1- or H3K9me3-specific Ab and captured DNA was sequenced. (A) KAP1 binding sites identified in wild-type (left) and KAP1-deficient (KO; right) B splenocytes. Overlapping: number of wild-type (left) or KO (right) sites overlapping with at least 1 site identified in the KO (left) or wild-type (right) sample. The window set for the overlapping was ± 1 kb. (B) Stratification of the indicated features around KAP1 binding sites (set at 0), P values and correlation coefficient (R) are by Spearman test. (C) UCSC genes were sorted on the basis of expression as assessed in the microarray wild-type FO samples (supplemental Table 1) and distance to the nearest KAP1 H3K9me3 peak was evaluated. Absent indicates genes with expression signal < 30; Low-Mid, signal between 31 and 1000; and Hi, signal between 1001 and 45 000. Boxplots of boot-strapped values are shown. P values by Kruskal-Wallis test. Dunn posttest by pairs are: absent versus low-mid, P < .05; absent versus high, P < .05; and low-mid versus high, P > .05. Also see supplemental Figure 4.