title: A systematic characterization of factors that regulate Drosophila segmentation via a bacterial one-hybrid system.
abstract: Specificity data for groups of transcription factors (TFs) in a common regulatory network can be used to computationally identify the location of cis-regulatory modules in a genome. The primary limitation for this type of analysis is the paucity of specificity data that is available for the majority of TFs. We describe an omega-based bacterial one-hybrid system that provides a rapid method for characterizing DNA-binding specificities on a genome-wide scale. Using this system, 35 members of the Drosophila melanogaster segmentation network have been characterized, including representative members of all of the major classes of DNA-binding domains. A suite of web-based tools was created that uses this binding site dataset and phylogenetic comparisons to identify cis-regulatory modules throughout the fly genome. These tools allow specificities for any combination of factors to be used to perform rapid local or genome-wide searches for cis-regulatory modules. The utility of these factor specificities and tools is demonstrated on the well-characterized segmentation network. By incorporating specificity data on an additional 66 factors that we have characterized, our tools utilize approximately 14% of the predicted factors within the fly genome and provide an important new community resource for the identification of cis-regulatory modules.
authors.affiliation: Program in Gene Function and Expression, Department of Biochemistry and Molecular Pharmacology, Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA.
authors.forename: Marcus B
authors.initials: MB
authors.lastname: Noyes
authors.forename: Xiangdong
authors.initials: X
authors.lastname: Meng
authors.forename: Atsuya
authors.initials: A
authors.lastname: Wakabayashi
authors.forename: Saurabh
authors.initials: S
authors.lastname: Sinha
authors.forename: Michael H
authors.initials: MH
authors.lastname: Brodsky
authors.forename: Scot A
authors.initials: SA
authors.lastname: Wolfe
mesh_terms: D000818:Animals; D001419:Bacteria / Q000235:genetics; D001483:Base Sequence; D001665:Binding Sites; D019521:Body Patterning / Q000235:genetics*; D019295:Computational Biology; D017124:Conserved Sequence; D029721:Drosophila Proteins / Q000378:metabolism*; D004331:Drosophila melanogaster / Q000196:embryology / Q000235:genetics*; D023281:Genomics; D050436:Regulatory Elements, Transcriptional; D012984:Software; D014157:Transcription Factors / Q000378:metabolism*; D020798:Two-Hybrid System Techniques
chemical_list: D029721:Drosophila Proteins; D014157:Transcription Factors