title: The DNA binding of insect Fork head factors is strongly influenced by the negative cooperation of neighbouring bases.
abstract: The Drosophila melanogaster Fork head and Bombyx mori SGF1/Fork head proteins are key regulators of tissue specific gene expression in the modified larval labial glands. Here we use the competitive electrophoretic mobility shift assay to create a detailed Fork head binding matrix and we investigate some unusual features of the Fork head interaction with DNA. We found that the Fork head-DNA interaction is context dependent--the binding specificity of the protein is partly determined by specific combinations of neighbouring bases. Although the total number of the sub-optimal dinucleotide steps is not high, the negative cooperation of neighbouring bases significantly contributes to the overall binding site specificity. Our results allow efficient recognition of insect Fork head binding sites and we show that the putative Fork head cognate elements preferentially accumulate in the near upstream region of genes abundantly expressed in the labial gland.
authors.affiliation: Center for Advanced Science and Technology, and Division of Bioscience, Graduate School of Environmental Earth Science, Hokkaido University, Kita-ku, Sapporo 060-0810, Japan.
authors.forename: Shigeharu
authors.initials: S
authors.lastname: Takiya
authors.forename: Michal
authors.initials: M
authors.lastname: Gazi
authors.forename: Václav
authors.initials: V
authors.lastname: Mach
mesh_terms: D000818:Animals; D001483:Base Sequence; D001665:Binding Sites; D012831:Bombyx / Q000235:genetics / Q000378:metabolism; D004247:DNA / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000235:genetics / Q000378:metabolism*; D018900:Dinucleotide Repeats; D004331:Drosophila melanogaster / Q000235:genetics / Q000378:metabolism; D024202:Electrophoretic Mobility Shift Assay / Q000379:methods; D051858:Forkhead Transcription Factors; D019476:Insect Proteins / Q000235:genetics / Q000378:metabolism*; D009687:Nuclear Proteins / Q000235:genetics / Q000378:metabolism*; D011401:Promoter Regions, Genetic; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism*
chemical_list: D004268:DNA-Binding Proteins; D051858:Forkhead Transcription Factors; D019476:Insect Proteins; D009687:Nuclear Proteins; D014157:Transcription Factors; D004247:DNA