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Hox Genes pp 255-278 | Cite as

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. MannEmail author
  • Harmen J. BussemakerEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1196)

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.

Key words

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

Notes

Acknowledgements

We thank the members of the Bussemaker and Mann labs for comments and feedback during the course of these studies. This work was supported by NIH grants R01GM054510, R01HG003008, U54CA121852, and P50GM071508; a John Simon Guggenheim Foundation Fellowship; and Columbia University’s RISE program.

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Copyright information

© Springer Science+Business Media New York 2014

Authors and Affiliations

  • Todd R. Riley
    • 1
    • 2
  • Matthew Slattery
    • 3
    • 4
  • Namiko Abe
    • 3
  • Chaitanya Rastogi
    • 1
    • 5
  • Dahong Liu
    • 1
  • Richard S. Mann
    • 3
    Email author
  • Harmen J. Bussemaker
    • 1
    Email author
  1. 1.Department of Biological SciencesColumbia UniversityNew YorkUSA
  2. 2.Department of BiologyUniversity of Massachusetts - BostonBostonUSA
  3. 3.Department of Biochemistry and Molecular BiophysicsColumbia University Medical CenterNew YorkUSA
  4. 4.Department of Biomedical SciencesUniversity of Minnesota Medical SchoolDuluthUSA
  5. 5.Department of Applied Physics and Applied MathematicsColumbia UniversityNew YorkUSA

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