title: Analysis of homeodomain specificities allows the family-wide prediction of preferred recognition sites.
abstract: We describe the comprehensive characterization of homeodomain DNA-binding specificities from a metazoan genome. The analysis of all 84 independent homeodomains from D. melanogaster reveals the breadth of DNA sequences that can be specified by this recognition motif. The majority of these factors can be organized into 11 different specificity groups, where the preferred recognition sequence between these groups can differ at up to four of the six core recognition positions. Analysis of the recognition motifs within these groups led to a catalog of common specificity determinants that may cooperate or compete to define the binding site preference. With these recognition principles, a homeodomain can be reengineered to create factors where its specificity is altered at the majority of recognition positions. This resource also allows prediction of homeodomain specificities from other organisms, which is demonstrated by the prediction and analysis of human homeodomain specificities.
authors.affiliation: Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA.
authors.forename: Marcus B
authors.initials: MB
authors.lastname: Noyes
authors.forename: Ryan G
authors.initials: RG
authors.lastname: Christensen
authors.forename: Atsuya
authors.initials: A
authors.lastname: Wakabayashi
authors.forename: Gary D
authors.initials: GD
authors.lastname: Stormo
authors.forename: Michael H
authors.initials: MH
authors.lastname: Brodsky
authors.forename: Scot A
authors.initials: SA
authors.lastname: Wolfe
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001419:Bacteria / Q000737:chemistry / Q000235:genetics; D001483:Base Sequence; D004247:DNA / Q000737:chemistry / Q000378:metabolism*; D029721:Drosophila Proteins / Q000737:chemistry* / Q000235:genetics; D004331:Drosophila melanogaster / Q000737:chemistry* / Q000235:genetics; D049750:Genome, Insect; D018398:Homeodomain Proteins / Q000737:chemistry* / Q000235:genetics; D006801:Humans; D008958:Models, Molecular; D010802:Phylogeny; D015202:Protein Engineering; D017434:Protein Structure, Tertiary; D020798:Two-Hybrid System Techniques
chemical_list: D029721:Drosophila Proteins; D018398:Homeodomain Proteins; D004247:DNA