Cofactor Binding Evokes Latent Differences in DNA Binding Specificity between Hox Proteins

SummaryMembers 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.

Graphical AbstractFigure optionsDownload full-size imageDownload high-quality image (290 K)Download as PowerPoint slideHighlights► Hox DNA binding specificities change when they bind with the cofactor Exd ► The binding specificities of Exd-Hox heterodimers group into three classes ► Preferred binding sites of anterior and posterior Hox proteins have distinct shapes ► Exd-Ubx binding sites are overrepresented in fragments bound by Ubx in vivo