SELEX-seq: A method for characterizing the complete repertoire of binding site preferences for transcription factor complexes

Todd R. Riley, Matthew Slattery, Namiko Abe, Chaitanya Rastogi, Dahong Liu, Richard S. Mann, Harmen J. Bussemaker

Research output: Contribution to journalArticle

34 Scopus citations

Abstract

The closely related members of the Hox family of homeodomain transcription factors have similar DNA-binding preferences as monomers, yet carry out distinct functions in vivo. Transcription factors often bind DNA as multiprotein complexes, raising the possibility that complex formation might modify their DNA-binding specificities. To test this hypothesis we developed a new experimental and computational platform, termed SELEX-seq, to characterize DNA-binding specificities of Hox-based multiprotein complexes. We found that complex formation with the same cofactor reveals latent specificities that are not observed for monomeric Hox factors. The findings from this in vitro platform are consistent with in vivo data, and the “latent specificity” concept serves as a precedent for how the specificities of similar transcription factors might be distinguished in vivo. Importantly, the SELEX-seq platform is flexible and can be used to determine the relative affinities to any DNA sequence for any transcription factor or multiprotein complex.

Original languageEnglish (US)
Pages (from-to)255-278
Number of pages24
JournalMethods in Molecular Biology
Volume1196
DOIs
StatePublished - 2014

Keywords

  • Computational analysis
  • Extradenticle
  • Hox proteins
  • Next-generation sequencing
  • Pbx
  • SELEX
  • Transcription factor specificity

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