A deeper look into transcription regulatory code by preferred pair distance templates for transcription factor binding sites

I.V. Kulakovskiy, A.A. Belostotsky, A.S. Kasianov, N.G. Esipova, Y.A. Medvedeva, I.A Eliseeva, V.J. Makeev
Bioinformatics, 27(19):2621-4, (2011)

A deeper look into transcription regulatory code by preferred pair distance templates for transcription factor binding sites

Keywords

Transcription factor binding sites

Abstract

MOTIVATION:

Modern 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.

RESULTS:

We 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.

Code

DOI: 10.1093/bioinformatics/btr453

Sources

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