Correlated evolution of transcription factors and their binding sites

Shu Yang, Hari Krishna Yalamanchili, Xinran Li, Kwok Ming Yao, Pak Chung Sham, Michael Q. Zhang, Junwen Wang

Research output: Contribution to journalArticle

17 Scopus citations

Abstract

Motivation: The interaction between transcription factor (TF) and transcription factor binding site (TFBS) is essential for gene regulation. Mutation in either the TF or the TFBS may weaken their interaction and thus result in abnormalities. To maintain such vital interaction, a mutation in one of the interacting partners might be compensated by a corresponding mutation in its binding partner during the course of evolution. Confirming this co-evolutionary relationship will guide us in designing protein sequences to target a specific DNA sequence or in predicting TFBS for poorly studied proteins, or even correcting and rescuing disease mutations in clinical applications. Results: Based on six, publicly available, experimentally validated TF-TFBS binding datasets for the basic Helix-Loop-Helix (bHLH) family, Homeo family, High-Mobility Group (HMG) family and Transient Receptor Potential channels (TRP) family, we showed that the evolutions of the TFs and their TFBSs are significantly correlated across eukaryotes. We further developed a mutual information-based method to identify co-evolved protein residues and DNA bases. This research sheds light on the dynamic relationship between TF and TFBS during their evolution. The same principle and strategy can be applied to co-evolutionary studies on protein-DNA interactions in other protein families.

Original languageEnglish (US)
Article numberbtr503
Pages (from-to)2972-2978
Number of pages7
JournalBioinformatics
Volume27
Issue number21
DOIs
StatePublished - Nov 1 2011

ASJC Scopus subject areas

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

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    Yang, S., Yalamanchili, H. K., Li, X., Yao, K. M., Sham, P. C., Zhang, M. Q., & Wang, J. (2011). Correlated evolution of transcription factors and their binding sites. Bioinformatics, 27(21), 2972-2978. [btr503]. https://doi.org/10.1093/bioinformatics/btr503