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. Author manuscript; available in PMC: 2012 May 27.
Published in final edited form as: Cell. 2011 May 19;145(5):692–706. doi: 10.1016/j.cell.2011.03.053

Figure 6. Bivalent BPTF binding is important for localization of the BPTF PHD-bromodomain and full NURF complex.

Figure 6

(A) Native ChIP comparison of H3K4me3, H4K12ac, and H4K16ac marks. Four primer sets were employed to interrogate the HOXA9 locus (P1–P3, dark and light grey bars represent HOXA9 exons, and an untranslated region, respectively) and a distal intergenic site [(−) control region]. An average of three real-time PCR replicates of a representative experiment is displayed as a function of % input signal, with error bars reflecting PCR product threshold error amongst the replicates. For simplicity of HOXA9 display, the gene structure annotation represents the Crick strand sense of the genome in this as well as panels B and C. Data are represented as mean ± SD. (B) xChIP of HA-tagged BPTF from HEK293 cell lines that exhibit commensurate expression levels of the ectopic tagged constructs at the HOXA9 locus (with primer sets P2–P4). ChIP signal of tagged WT protein expressing cell lines is compared to discrete cell lines bearing the tagged mutant proteins corresponding to mutations depicted in Figure 4. Data are represented as mean ± SD. (C) ChIP-seq data for the HOXA9 locus, with the three histone modification tracks derived from nChIP-sequencing rendered in yellow, green and red as labelled with input tag counts overlayed in grey on the same scale. On the same abscissal scale and register, the xChIP sequencing counts from the 3xFLAG-tagged BPTF PHD-bromodomain are depicted in blue, with attendant input superimposed in grey. All tag counts are normalized by the factor (2×107/total mapped tags per track) and are unique. Below the continuous tag count graph, MACS peak-called regions relative to input for each sequencing track are depicted in rectangles of the same color. (C) Another example of histone modification patterns and PHD-bromodomain binding, displayed as in the previous panel. (E) Plot of average profile of the PHD-bromodomain at peak regions in the other datasets or intersects thereof. The average PHD signal is contoured on the regions that have MACS called peaks for each individual modification (colored as in 6C); or at loci with called peaks within the same 150 bp window for both H3K4me3 and H4K12ac datasets (purple); or H3K4me3 and H4K12ac datasets (blue). See also Figure S6.

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