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Cell. 2011 Dec 9;147(6):1270-82. doi: 10.1016/j.cell.2011.10.053.

Cofactor binding evokes latent differences in DNA binding specificity between Hox proteins.

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  • 1Department of Biochemistry and Molecular Biophysics, Columbia University, 701 West 168(th) Street, HHSC 1104, New York, NY 10032, USA.

Abstract

Members of transcription factor families typically have similar DNA binding specificities yet execute unique 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 an experimental and computational platform, SELEX-seq, that can be used to determine the relative affinities to any DNA sequence for any transcription factor complex. Applying this method to all eight Drosophila Hox proteins, we show that they obtain novel recognition properties when they bind DNA with the dimeric cofactor Extradenticle-Homothorax (Exd). Exd-Hox specificities group into three main classes that obey Hox gene collinearity rules and DNA structure predictions suggest that anterior and posterior Hox proteins prefer DNA sequences with distinct minor groove topographies. Together, these data suggest that emergent DNA recognition properties revealed by interactions with cofactors contribute to transcription factor specificities in vivo.

Copyright © 2011 Elsevier Inc. All rights reserved.

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PMID:
22153072
[PubMed - indexed for MEDLINE]
PMCID:
PMC3319069
Free PMC Article

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