The GLI gene encodes a nuclear protein which binds specific sequences in the human genome

The Gli gene is amplified in a subset of human tumors and encodes a protein product with five zinc finger DNA-binding motifs. In this study, we show that the Gli gene product has a predominantly nuclear localization and binds DNA in a sequence-specific fashion. Three Gli binding sites were identified by using a novel procedure in which total human DNA was bound to a Gli recombinant fusion protein, and the polymerase chain reaction was used to amplify and recover the bound sequences. The Gli protein protected a 23- to 24-base region within all three binding sites, and the protected region in each case included the 9-base-pair sequence 5'-GACCACCCA-3'. One of the binding sites was contained within a 63-base-pair repeat of the variable number of tandem repeat type, whereas the other two sites were represented once in the genome. The approach used here to identify Gli binding sites should be applicable to the characterization of other zinc finger proteins.