Summary Protein-DNA binding is mediated by the recognition of the chemical signatures of the DNA bases and the 3D shape of the DNA molecule. Because DNA shape is a consequence of sequence, it is difficult to dissociate these modes of recognition. Here, we tease them apart in the context of Hox-DNA binding by mutating residues that, in a co-crystal structure, only recognize DNA shape. Complexes made with these mutants lose the preference to bind sequences with specific DNA shape features. Introducing shape-recognizing residues from one Hox protein to another swapped binding specificities in vitro and gene regulation in vivo. Statistical machine learning revealed that the accuracy of binding specificity predictions improves by adding shape features to a model that only depends on sequence, and feature selection identified shape features important for recognition. Thus, shape readout is a direct and independent component of binding site selection by Hox proteins.
Bibliographical noteFunding Information:
We thank Barry Honig, David Stern, and members of the R.R., H.J.B., and R.S.M. laboratories for feedback and comments on this project, and Vince FitzPatrick, Gabriella Martini, Todd Riley, and Roumen Voutev for technical assistance. This work was supported by the NIH (grants R01GM058575 to R.S.M., F32GM099160 to N.A., R01GM106056 and U01GM103804 to R.R., and R01HG003008 to H.J.B. and R.R.), the USC-Technion Visiting Fellows Program, and an Alfred P. Sloan Research Fellowship (to R.R.).
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