SELEX-seq: A Method for Characterizing the Complete Repertoire of Binding Site Preferences for Transcription Factor Complexes
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 wordsHox proteins Transcription factor specificity Extradenticle Pbx SELEX Next-generation sequencing Computational analysis
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.
- 10.Slattery M, Riley T, Liu P, Abe N, Gomez-Alcala P, Dror I, Zhou T, Rohs R, Honig B, Bussemaker HJ, Mann RS (2011) Cofactor binding evokes latent differences in DNA binding specificity between Hox proteins. Cell 147(6):1270–1282. doi: 10.1016/j.cell.2011.10.053 PubMedCentralPubMedCrossRefGoogle Scholar
- 14.Jolma A, Yan J, Whitington T, Toivonen J, Nitta KR, Rastas P, Morgunova E, Enge M, Taipale M, Wei G, Palin K, Vaquerizas JM, Vincentelli R, Luscombe NM, Hughes TR, Lemaire P, Ukkonen E, Kivioja T, Taipale J (2013) DNA-binding specificities of human transcription factors. Cell 152(1–2):327–339. doi: 10.1016/j.cell.2012.12.009 PubMedCrossRefGoogle Scholar
- 18.Jolma A, Kivioja T, Toivonen J, Cheng L, Wei G, Enge M, Taipale M, Vaquerizas JM, Yan J, Sillanpaa MJ, Bonke M, Palin K, Talukder S, Hughes TR, Luscombe NM, Ukkonen E, Taipale J (2010) Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities. Genome Res 20(6):861–873. doi: 10.1101/gr.100552.109 PubMedCentralPubMedCrossRefGoogle Scholar