Preferred distances between transcription factor binding sites

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Transcriptional regulation of gene expression in higher eukaryotes is driven by elaborate protein complexes of transcription factors. At the DNA level, these complexes interact with composite elements consisting of specific binding sites for different proteins. We use the hypoxia-response system to identify preferred localization distances between “hypoxia-induced factor-1 — cofactor” binding site pairs in promoter DNA regions of the human genome. Such characteristic co-localization distances agree with a 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 in higher eukaryotes.