Extended Data Fig. 7: Transcription factors co-regulate convergent promoters.
(a-c) Heatmaps of transcription factor binding signals (left panels) and log2FC (Nutlin-3a vs DMSO control) at CAGE-seq peaks harboring TSSs (right panels) displayed for convergent promoters bound by (a) p53, (b) E2F4, and (c) RFX7. The convergent promoters are sorted by the occurrence of transcription factor peaks near the upstream (TSS#2) or downstream promoter (TSS#3). Complementary to Fig. 3a-c. (d) The PTP4A1 gene locus harbors PTP4A1 on the +strand and its downstream antisense RNA (daPTP4A1) on the -strand (upper panel). CRISPR/Cas9 has cut the p53RE located in the downstream promoter in RPE-1 cells. RT-qPCR data from parental RPE-1 cells, a wild-type clone, and two homozygous p53RE knock-out (KO) clones treated with Nutlin-3a or DMSO control (bottom panels). Expression has been normalized to GAPDH and DMSO control-treated parental cells. MDM2 expression served as positive control. Mean and standard deviation are displayed. Statistical significance was obtained through a two-sided t-test; n = 3 biological replicates. (e-g) Summary profiles (top panels) and heatmaps with individual convergent promoter regions (bottom panels) display epigenetic signals at MCF-7 convergent promoters. Convergent promoters are length-sorted in descending order. (e) H3K36me3, (f) H3K79me2, and (g) H4K20me1 signal p-values (-log10) at scale-adjusted convergent promoter regions. Negative decadic logarithms of signal p-values computed using a Poisson model-based statistical test were directly obtained from ENCODE data files.
