DNA binding specificity of different STAT proteins - Comparison of in vitro specificity with natural target sites

STAT transcription factors are expressed in many cell types and bind to sim ilar sequences. However, different STAT gene knock-outs show very distinct phenotypes. To determine whether differences between the binding specificit ies of STAT proteins account for these effects, we compared the sequences b ound by STAT1, STAT5A, STAT5B, and STAT6. One sequence set was selected fro m random oligonucleotides by recombinant STAT1, STAT5A, or STAT6. For anoth er set including many weak binding sites, we quantified the relative affini ties to STAT1, STAT5A, STAT5B, and STAT6. We compared the results to the bi nding sites in natural STAT target genes identified by others. The experime nts confirmed the similar specificity of different STAT proteins. Detailed analysis indicated that STAT5A specificity is more similar to that of STAT6 than that of STAT1, as expected from the evolutionary relationships. The p reference of STAT6 for sites in which the half-palindromes (TTC) are separa ted by four nucleotides (N-4) was confirmed, but analysis of weak binding s ites showed that STAT6 binds fairly well to N-3 sites. As previously report ed, STAT1 and STAT5 prefer N-3 sites; however, STAT5A, but not STAT1, weakl y binds N-4 sites. None of the STATs bound to half-palindromes. There were no specificity differences between STAT5A and STAT5B.