A systematic characterization of factors that regulate Drosophila segmentation via a bacterial one-hybrid system

Nucleic Acids Res. 2008 May;36(8):2547-60. doi: 10.1093/nar/gkn048. Epub 2008 Mar 10.

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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Bacteria / genetics
  • Base Sequence
  • Binding Sites
  • Body Patterning / genetics*
  • Computational Biology
  • Conserved Sequence
  • Drosophila Proteins / metabolism*
  • Drosophila melanogaster / embryology
  • Drosophila melanogaster / genetics*
  • Genomics
  • Regulatory Elements, Transcriptional*
  • Software
  • Transcription Factors / metabolism*
  • Two-Hybrid System Techniques*

Substances

  • Drosophila Proteins
  • Transcription Factors