A split binding site for transcription factor tau on the tRNA3Glu gene

Yeast transcription factor tau forms a stable complex with tRNA genes. Using this property, the factor could be highly purified on a specific tDNA column. The purified factor was found by DNA footprinting to protect the whole yeast tRNA3Glu gene from position -8 to +81. A DNase-sensitive site was retained in the middle of the gene on both strands. The 3' border of the complex was mapped by exonuclease digestion at +88, just downstream of the termination signal. The 5' limit of the complex was found at position -11. However, upon prolonged incubation with exonuclease, the -11 blockage disappeared and the DNA molecules were digested to position +30 to 38 in the middle of the gene. Contact points at guanine residues were identified by dimethyl sulphate protection experiments. Reduced methylation of G residues in the presence of factor was found solely within the A block and in the B block region. All six invariant GC pairs (i.e., G10, G18, G19 and G53, C56 and C61) were found to have strong contacts with the factor. These results show that tau factor interacts with both the 5' and 3' half of the tRNA3Glu gene, with the B block region being the predominant binding site. The presence of this dual binding site suggests a model in which the factor would bind alternately at the A and B block regions to allow transcription of the internal promoter by RNA polymerase C.