[Preferred distances between DNA binding sites for factors regulating transcription initiation]

Transcriptional regulation of gene expression in higher eukaryotes is driven by sophisticated protein complexes of transcription factors. On the DNA level, there are composite elements containing sites of different DNA-binding proteins. We use the hypoxia-response system to identify preferred localization distances for the 'hypoxia-induced factor-1 binding site-co-factor binding site" pairs in promoter DNA regions of the human genome. Such characteristic colocalization distances agree with the supposed scale of regulatory regions, while being significantly longer than the typical binding site length. We speculate that this phenomenon can provide a key to decipher the structure of DNA regulatory regions of higher eukaryotes.