I.V. Kulakovskiy, A.A. Belostotsky, A.S. Kasianov, N.G. Esipova, Y.A. Medvedeva, I.A Eliseeva, V.J. Makeev
Bioinformatics, 27(19), pp. 2621-2624, (2011)
experimental methods provide substantial information on protein-DNA
recognition. Studying arrangements of transcription factor binding sites
(TFBSs) of interacting transcription factors (TFs) advances
understanding of the transcription regulatory code.
constructed binding motifs for TFs forming a complex with HIF-1α at the
erythropoietin 3(')-enhancer. Corresponding TFBSs were predicted in the
segments around transcription start sites (TSSs) of all human genes.
Using the genome-wide set of regulatory regions, we observed several
strongly preferred distances between hypoxia-responsive element (HRE)
and binding sites of a particular cofactor protein. The set of preferred
distances was called as a preferred pair distance template (PPDT). PPDT
dramatically depended on the TF and orientation of its binding sites
relative to HRE. PPDT evaluated from the genome-wide set of regulatory
sequences was used to detect significant PPDT-consistent binding site
pairs in regulatory regions of hypoxia-responsive genes. We believe PPDT
can help to reveal the layout of eukaryotic regulatory segments.