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

J Biol Chem. 2001 Mar 2;276(9):6675-88. doi: 10.1074/jbc.M001748200. Epub 2000 Oct 26.


STAT transcription factors are expressed in many cell types and bind to similar sequences. However, different STAT gene knock-outs show very distinct phenotypes. To determine whether differences between the binding specificities of STAT proteins account for these effects, we compared the sequences bound by STAT1, STAT5A, STAT5B, and STAT6. One sequence set was selected from random oligonucleotides by recombinant STAT1, STAT5A, or STAT6. For another set including many weak binding sites, we quantified the relative affinities to STAT1, STAT5A, STAT5B, and STAT6. We compared the results to the binding sites in natural STAT target genes identified by others. The experiments 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 preference of STAT6 for sites in which the half-palindromes (TTC) are separated by four nucleotides (N(4)) was confirmed, but analysis of weak binding sites showed that STAT6 binds fairly well to N(3) sites. As previously reported, STAT1 and STAT5 prefer N(3) sites; however, STAT5A, but not STAT1, weakly binds N(4) sites. None of the STATs bound to half-palindromes. There were no specificity differences between STAT5A and STAT5B.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • Binding Sites
  • DNA / metabolism
  • DNA-Binding Proteins / chemistry
  • DNA-Binding Proteins / metabolism*
  • Humans
  • Milk Proteins*
  • Molecular Sequence Data
  • Response Elements
  • STAT1 Transcription Factor
  • STAT5 Transcription Factor
  • STAT6 Transcription Factor
  • Trans-Activators / chemistry
  • Trans-Activators / metabolism*
  • Tumor Suppressor Proteins


  • DNA-Binding Proteins
  • Milk Proteins
  • STAT1 Transcription Factor
  • STAT1 protein, human
  • STAT5 Transcription Factor
  • STAT5A protein, human
  • STAT5B protein, human
  • STAT6 Transcription Factor
  • STAT6 protein, human
  • Trans-Activators
  • Tumor Suppressor Proteins
  • DNA