Fig. 3.

PLA analysis and EMSA of tentative HNF-4α-binding sequences. (A) Three sequences identified by ChIP-chip analysis were analyzed by PLA for interactions with HNF-4α in HepG2 nuclear extracts together with a negative control (a p53 consensus oligonucleotide). The nuclear extract was diluted as indicated along the x axis to investigate the lowest dilution with detectable amounts of binding protein. S/N values are shown on the y axis. (B) EMSAs of sequences identified by ChIP-chip (Pos) along with negative control sequences (Neg), competitor oligonucleotides having the same (Self Comp) or an unrelated sequence (Unr.comp), and supershift reactions with HNF-4α antibodies (α-HNF-4α and with irrelevant AP2α antibodies (α-AP2α.