Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences.

ABSTRACT: Most homeodomains are unique within a genome, yet many are highly conserved across vast evolutionary distances, implying strong selection on their precise DNA-binding specificities. We determined the binding preferences of the majority (168) of mouse homeodomains to all possible 8-base sequences, revealing rich and complex patterns of sequence specificity and showing that there are at least 65 distinct homeodomain DNA-binding activities. We developed a computational system that successfully predicts binding sites for homeodomain proteins as distant from mouse as Drosophila and C. elegans, and we infer full 8-mer binding profiles for the majority of known animal homeodomains. Our results provide an unprecedented level of resolution in the analysis of this simple domain structure and suggest

SUBMITTER: Berger MF 

PROVIDER: S-EPMC2531161 | biostudies-literature | 2008 Jun

REPOSITORIES: biostudies-literature