Book of Abstracts: Albany 2011

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Conversation 17
June 14-18 2011
©Adenine Press (2010)

Preferred Pair Distance Templates for Identification of Functional Binding Sites for Interacting Transcription Factors

We study a set of transcription factors (TFs) including the hypoxia-inducible factor 1 (HIF-1) involved in regulation of hypoxia response in human cells. We demonstrate that binding sites for a pair of interacting TFs can be found at distances that are dramatically nonrandom and depend both on selected TFs and a relative orientation of their binding sites. The set of characteristic intersite distances forms a preferred pair distance template (PPDT).

We started identification of high-quality binding motifs with the help of our original computational tool, ChIPMunk. ChiPMunk performs motif discovery integrating data from different experimental sources1 including ChIP-chip and ChIP-Seq experiments2. Both our own3 and independent4 benchmarks have shown that ChIPMunk can produce high-quality motifs in a reasonable time.

The motifs discovered were used to detect transcription factor binding sites in the 5’ regulatory regions of all human genes (according to the UCSC hg18 assembly). For TFs involved in the known protein-protein interaction with the HIF1α we have observed a surprisingly large fraction of binding sites found at specific distances from HIF1α binding sites (see Figure 1). For some TF pairs the corresponding PPDTs contained quite large distances, sometimes longer than 200bp.

Ivan V. Kulakovskiy1,2,*
Alexander A. Belostotsky3
Vsevolod J. Makeev2,3

1Laboratory of Bioinformatics and System Biology, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov str. 32, Moscow 119991, Russia
2Laboratory of Bioinformatics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkina str. 3, Moscow 119991, Russia
3Laboratory of Bioinformatics, Research Institute for Genetics and Selection of Industrial Microorganisms, 1st Dorozhny proezd 1, Moscow 117545, Russia

fx: +7 499 1351405 ph: +7 499 1356000 ivan.kulakovskiy@gmail.com

Figure 1. Distance distribution between HRE elements (corresponding to the HIF 1α:ARNT dimer binding) and Sp1 binding sites. Y axis shows the number of genes for which at least one pair of binding sites is found at the selected distance (shown at X-axis) within the 10kb upstream promoter region. Panels: orientation of HRE in the reference to Sp1; (top) direct; (bottom) reverse.

Thus, with a help of PPDTs we can correctly identify composite elements5 in regulatory segments. Moreover, PPDT can be used as a filter to remove false positive binding sites in human cis-regulatory modules. PPDT also can be used to assess functional interaction between a pair of DNA binding proteins solely by means of sequence analysis. Currently we explore how PPDT information can be used together with gene expression data to identify correct target responding to hypoxia conditions. This research is supported by Russian Fund of Basic Research grant 10-04-92663-Ind.


  1. I.V. Kulakovskiy, V.J. Makeev, Biophysics 54, 667-674 (2009).
  2. I.V. Kulakovskiy, V.J. Makeev, V.A. Boeva, V.J. Makeev, Bioinformatics 26, 2622-2623 (2010).
  3. http://line.imb.ac.ru/ChIPMunk/Supplementary_text.pdf
  4. http://cmotifs.tchlab.org/help.html
  5. V. Matys, O.V. Kel-Margoulis, E. Fricke, et al., Nucleic Acids Res 34, D108-10 (2006).