Hox proteins are homeodomain transcription factors that help to define cellular and tissue identities, and thus diversify body patterning on the anterior-posterior axis (1). Understanding the DNA-binding specificities of Hox proteins will therefore provide insight into the regulation of Hox target genes and animal morphogenesis. Advanced by the SELEX-seq method, the complete repertoire of DNA sequences that bind to Drosophila Hox proteins with their cofactors Extradenticle (Exd) and Homothorax (Hth) has been obtained. A range of unique DNA-binding specificities has been observed among these Hox proteins, raising the question of how such diverse DNA-binding specificities are generated.

Using multiple sequence alignments of Hox proteins, we identified partially conserved residues that correlate with DNA-binding specificity. Possible functions of these residues were inferred by mapping them onto available 3D structures. In parallel, using Monte Carlo simulations (2), we predicted the width of DNA minor groove for different Hox binding sites identified by SELEX-seq. We find that DNA sequences preferred by Hox proteins that control posterior patterning have similar minor groove shape, and this shape is different than that of DNA sequences preferred by Hox proteins that define anterior morphology. In particular, within the Exd-Hox binding site, high-affinity DNA sequences for Hox protein Scr have two narrow regions while sequences preferred by Hox protein Ubx have only one. As revealed by previous studies (3,4), the additional narrow minor groove of Scr induces enhanced negative electrostatic potential, which attracts Arg3 of Scr. Our work leads to a new understanding of the structural basis of specific DNA-binding for Hox proteins in Drosophila, linking DNA binding site preferences to common DNA shapes.

References

1. R. S. Mann, K. M. Lelli and R. Joshi. Curr Top Dev Biol 88, 63-101 (2009).
2. R. Rohs, H. Sklenar and Z. Shakked. Structure 13, 1499-1509 (2005).
3. R. Joshi, J. M. Passner, R. Rohs, R. Jain, A. Sosinsky, M. A. Crickmore, V. Jacob, A. K. Aggarwal, B. Honig and R. S. Mann. Cell 131, 530-543 (2007).
4. R. Rohs, S. M. West, A. Sosinsky, P. Liu, R. S. Mann and B. Honig. Nature 461, 1248-1253 (2009).