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Noyes, M.B., Meng, X., Wakabayashi, A., Sinha, S., Brodsky, M.H., Wolfe, S.A. (2008). A systematic characterization of factors that regulate Drosophila segmentation via a bacterial one-hybrid system.  Nucleic Acids Res. 36(8): 2547--2560.
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Research paper

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.

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PMC2377422 (PMC) (EuropePMC)
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    Nucleic Acids Res.
    Nucleic Acids Research
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