Binding site analysis of c-Myb: Screening of potential binding sites by using the mutation matrix derived from systematic binding affinity measurements

The c-Myb oncoprotein is known to bind to multiple sites in the promoters of target genes. We have developed a protocol to screen the binding site of c-Myb by using the systematic binding data derived from measurements of binding affinity for oligonucleotide containing a known Myb-binding site and its complete single mutants. We first applied the method to predict the binding affinity for the known binding sites and compared with available experimental data. The predicted binding sites agree with many putative binding sites of known target promoters. However, there are some binding sites not predicted by the analysis. These sequences deviate from the consensus sequence derived from the binding analyses. In the light of the structure of Myb-DNA complex, these results indicate that different DNA-binding modes may be used by c-Myb to recognize different classes of binding sites, We also screened the sequence database for potential Myb-binding sites, and found sequences of several promoters that have not been identified experimentally but could be the target for c-Myb.