Analysis of the CDX2 promoter. A) The promoter region cloned in pGL4.10. The coordinates are relative to +1, the transcriptional start site. The arrows indicate primers used in the real-time qPCR. The possible HNF4α binding site and the mutated sequence is shown below. B) HNF4α ChIP-chip and AcHis3 ChIP-chip results for probes spanning the CDX2 promoter. Enrichments are shown as Log2 ratios between immunoprecipitated and input DNA. N = 3. C) Real-time qPCR with CDX2 and IgG intron primers using HNF4α ChIP, HA ChIP and input DNA. Enrichments are presented as percent of total input. N = 4. The CDX2 promoter enrichment is statistical significant (p-values < 0.05, Student T test). D) Gel shift analysis of the HNF4α site in the CDX2 promoter using Caco-2 nuclear extract (lane 1). Competition by unlabelled wt (lane 2), mut-HNF4α oligonucleotides (lane 3) and an unrelated oligonucleotide (lane 4) demonstrating a specific binding. One of the two protein/DNA bands can be supershifted with HNF4α antibody (lane 5). E) Promoter analysis of CDX2 promoter in Caco-2 (grey bars) and COS7 (white bars) cells with and without co-transfection of HNF4α expression plasmid. The binding site for HNF4α was mutated in order to analyze the functional importance of the HNF4α site (pGL4-CDX2 mutHNF4). The luciferase activity was corrected for transfection efficiency and normalized to the expression of pGL4-CDX2, N = 4.