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

Ivan V. Kulakovskiy, A. A. Belostotsky, Artem S. Kasianov, Natalia G. Esipova, Yulia Medvedeva, Irina A. Eliseeva, Vsevolod J. Makeev

Research output: Contribution to journalArticlepeer-review

5 Scopus citations

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. © The Author 2011. Published by Oxford University Press. All rights reserved.
Original languageEnglish (US)
Pages (from-to)2621-2624
Number of pages4
JournalBioinformatics
Volume27
Issue number19
DOIs
StatePublished - Aug 18 2011

ASJC Scopus subject areas

  • Biochemistry
  • Computational Theory and Mathematics
  • Computational Mathematics
  • Molecular Biology
  • Statistics and Probability
  • Computer Science Applications

Fingerprint Dive into the research topics of 'A deeper look into transcription regulatory code by preferred pair distance templates for transcription factor binding sites'. Together they form a unique fingerprint.

Cite this