Fig. 4

TFAP2A binds directly to the Zeb2 promoter region. a Sketch of the region around the second exon of mouse Zeb2, showing the two transcription start sites found in SwissRegulon [44]. The blue filled box indicates the non-coding untranslated region (UTR) in exon 2, while the white filled box designates the start of the coding region (CDS). The predicted TFAP2A binding sites from SwissRegulon are marked with red arrows, and the probes that were used in (b) are indicated with green lines below the gene structure. Predicted transcription start sites (TSS) are also indicated. b Radiography of TFAP2A Electrophoretic Mobility Shift Assay (EMSA) with radiolabeled oligonucleotides, each spanning one of the predicted binding sites. The presence or absence of TFAP2A protein in the assay is indicated by a + or – sign, respectively. Cold competitors were used at 200-fold excess over the radiolabelled probes. Wt corresponds to unlabeled probe; M indicates a double-stranded oligonucleotide with a mutated TFAP2A binding site. Red arrows indicate the predicted TFAP2A binding probes that behave as expected from specific binding of TFAP2A. c TFAP2A ChIP was performed in NMuMG cells stably transduced with pCLX-TFAP2A (denoted as TFAP2A-OE (blue)) or with pCLX-GFP (denoted as TFAP2A-GFP (green)) viral vectors and further treated with 2 μg/mL doxycycline. Quantitative PCR data shows the enrichment of Zeb2 promoter relative to a non-transcribed genomic region in TFAP2A-ChIP normalized to IgG control (red). Two independent experiments were performed for each condition and shown are means and standard deviations. The one-tail paired t-test indicates that TFAP2A is significantly enriched at the Zeb2 (** for p < 0.01). d ChIP-seq libraries from TFAP2A ChIP or input chromatin were generated and the coverage of the genomic region spanning the second exon of Zeb2 by reads is shown in a mouse genome browser (www.clipz.unibas.ch and [45]). The results of two independent experiments are presented. The TFAP2A ChIP-seq the Zeb2 promoter region previously assessed by qPCR is enriched with respect to the input control sample. Mapping, annotation and visualization of deep-sequencing data was done with the ClipZ server [45]