Preferred Distances between Transcription Factor Binding Sites

I. V. Kulakovskiya,b, A. S. Kasianova, A. A. Belostotskyb,
I. A. Eliseeva
c, and V. J. Makeevb

aEngelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991 Russia

bResearch Institute for Genetics and Selection of Industrial Microorganisms, Moscow, 117545 Russia

cInstitute for Protein Research, Russian Academy of Sciences, Pushchino, 142290 Russia


Received July 6, 2010

Abstract—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 con-
sisting 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 reg-
ulatory regions while being significantly longer than the typical binding site length. We speculate that this phe-
nomenon can provide a key to decipher the structure of DNA regulatory regions in higher eukaryotes.

Keywords: transcription factor, binding sites, co-localization, hypoxia, Homo sapiens

DOI: 10.1134/S0006350911010155

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