Base preferences for DNA binding by the bHLH-Zip protein USF: effects of MgCl2on specificity and comparison with binding of Myc family members

Studies of the DNA binding specificity of transcription factors belonging to the basic helix-loop-helix (bHLH) family have identified the so-called E-box, CACGTG, as being a high affinity specific binding sequence for this class of DNA binding proteins. Binding sequences for HeLa USF were selected from an initially random population of 20 bp sequences, defining the optimum USF binding sequence as R-5Y-4C-3A-2C-1G+1T+2G+3R+4Y+5. The significance of the flanking bases was further demonstrated by showing that USF and the related proteins c-Myc and Max discriminate between CACGTG-type E-boxes and that the primary means of discrimination appears to be the identity of the nucleotide at +/- 4, the presence of a T at -4 being inhibitory to binding by Myc but not by USF or Max. This suggests one mechanism by which bHLH factors are partitioned between multiple potential binding sequences in the promoters and enhancers of viral and cellular genes. It was also demonstrated that MgCl2 has a significant influence on USF DNA binding specificity. A broader range of USF binding sites was selected in the absence of MgCl2, conforming to the altered half-site consensus gTGaY. Binding studies with specific oligonucleotides demonstrated significantly improved tolerance to sequence variation at positions 1, 4, and to a lesser extent 5, of the GTGRY consensus in the absence of MgCl2. The results indicate that Mg2+ ions have an integral role in the formation of the USF-DNA complex.