Chromatin immunoprecipitation was performed as previously described (Hatzis et al, 2008; Mokry et al, 2010). In brief, cells were cross-linked with 1% formaldehyde for 20 min at room temperature. For β-catenin ChIP-seq, cells were crosslinked for 40 min using ethylene glycol-bis(succinimidyl succinate) (Thermo Scientific, Waltham, MA, USA) at 12.5 mM final concentration, with the addition of formaldehyde (1% final concentration) after 20 min of incubation. The reaction was quenched with glycine and the cells were successively washed with phosphate-buffered saline, buffer B [0.25% Triton-X 100, 10 mM EDTA, 0.5 mM EGTA, 20 mM HEPES (pH 7.6)] and buffer C [0.15 M NaCl, 1 mM EDTA, 0.5 mM EGTA, 20 mM HEPES (pH 7.6)]. The cells were then resuspended in shearing buffer [0.3% SDS, 1% Triton-X 100, 0.15 M NaCl, 1 mM EDTA, 0.5 mM EGTA, 20 mM HEPES (pH 7.6)] and sheared using Covaris S2 (Covaris, Woburn, MA, USA) for 8 min with the following settings: duty cycle: max, intensity: max, cycles/burst: max, mode: Power Tracking. The sonicated chromatin was diluted to 0.15 SDS, incubated for 12 h at 4°C with 25 μl of the anti-TCF4 (N20) antibody (Santa Cruz), 5 μl of the anti-FLAG (M2) antibody (Sigma-Aldrich), 50 μl of the anti-β-catenin (H102) antibody (Santa Cruz Biotechnology Inc, Santa Cruz, CA, USA), 40ul of the HNF4α antibody (Santa Cruz SC8987), 40ul of the TCF1 antibody (Santa Cruz SC 8589) or 15ul of the LEF1 antibody (Millipore CS200635, Billerica, MA, USA) per IP with 100 ml of protein G beads (Upstate). The beads were successively washed two times with buffer 1 [0.1% SDS, 0.1% deoxycholate, 1% Triton X-100, 0.15 M NaCl, 1 mM EDTA, 0.5 mM EGTA, 20 mM HEPES (pH 7.6)], one time with buffer 2 [0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100, 0.5 M NaCl, 1 mM EDTA, 0.5 mM EGTA, 20 mM HEPES (pH 7.6)], one time with buffer 3 (0.25 M LiCl, 0.5% sodium deoxycholate, 0.5% NP-40, 1 mM EDTA, 0.5 mM EGTA, 20 mM HEPES (pH 7.6)], and two times with buffer 4 (1 mM EDTA, 0.5 mM EGTA, 20 mM HEPES (pH 7.6)] for 5 min each at 4°C. Chromatin was eluted by incubation of the beads with elution buffer (1% SDS, 0.1 M NaHCO3) After washing and elution, the immunoprecipitated chromatin was de-crosslinked by incubation at 65°C for 5 h in the presence of 200 mM NaCl, extracted with phenol-chloroform, and ethanol precipitated. Immunoprecipitated chromatin was used as input material for qPCR analysis with the primers listed in supplementary Table S4, or it was additionally sheared, end-repaired, sequencing adaptors were ligated and the library was amplified by LMPCR. After LMPCR, the library was purified and checked for the proper size range and for the absence of adaptor dimers on a 2% agarose gel and sequenced on SOLiD/ AB sequencer to produce 50-bp long reads. Sequencing reads were mapped against the reference genome (mm9 or hg19 assembly) using MAQ or BWA package. Cisgenome software package (Ji et al, 2008) was used for peak-calling with 0.1 FDR (supplementary Table S5).