ChIP-qPCR Assay for Gli Binding

ChIP was performed as described earlier.^{57 (link), 58 (link)} Immunoprecipitated DNA from HEK293T with Gli1 (H300) (cat.#sc-20687; Santa Cruz Biotechnology) or Maml1 (D3E9) or IgG (normal rabbit IgG) antibodies was eluted and analyzed by semiquantitative PCR, using a primer set encompassing two predicted binding sites for Gli zinc finger family (V$GLIF Matrix Family) (from −538 to −521; from −461 to −445, corresponding to dark circles in Figure 1f, low panel), on human Patched1 promoter (GXP_227868, from −891 to −87 relative to start codon). Human Patched1 promoter was identified using MatInspector (Software GmbH, Munich, Germany). The primer set used to specifically amplify Gli binding sites is the following: 5′-GAACCCAGCAGCCAGAGC-3′ and 5′-CGACCCCTTCACTGCAGAA-3′.