Figure 2: BPTF silencing interferes with c-MYC recruitment to its target genes.

(a) Box plot showing the intensity of c-MYC ChIP-Seq signal (reads per peak) at MYC-enriched regions in control and BPTF-silenced HFF MYC-ER cells. MYC-enriched regions were defined in 4-OHT-treated control cells. c-MYC-binding intensity was measured as number of reads per peak. ***P<0.001 (Wilcoxon test). (b) Representative snapshots of c-MYC-bound genomic regions in control and BPTF-silenced HFF MYC-ER cells after stimulation with 4-OHT. (c) ChIP analysis of c-MYC enrichment at the promoters of ‘target’ and ‘non-target’ genes in control and BPTF-silenced HFF MYC-ER cells in the presence (white) or absence of 4-OHT (black). ChIP values are expressed as average±s.e.m. of % input chromatin. An isotype-matched IgG antibody was used as control (Supplementary Fig. 3f) and ≥3 independent experiments were analysed per promoter region. (d) Fold change in % of input following 4-OHT addition, averaged for the two different promoter populations in control and BPTF-silenced cells. ***P<0.001 (unpaired t-test). (e) Groups A and B are defined as in f. High-affinity MYC targets are significantly enriched among the genes for which MYC recruitment is less affected by BPTF knockdown. *P<0.05 (unpaired t-test). (f) c-MYC target genes ranked according to the change in c-MYC binding at their promoters after BPTF silencing. BPTF dependency of c-MYC recruitment to DNA is calculated as the Log₂ (reads shBPTF/reads shNt; left y axis). For the same collection of ranked genes, the transcriptional response to 4-OHT is shown (scatter plot right y axis). BPTF dependency of 4-OHT-dependent mRNA induction is calculated as the Log₂ (F.c. shBPTF/F.c. shNt). Four data points are outside the right y axis limits.