Identification of Specific Protein/E-Box-Containing DNA Complexes: Lessons from the Ubiquitously Expressed USF Transcription Factors of the b-HLH-LZ S

In order to determine how gene expression is regulated in response to environmental cues, it is necessary to identify the specific interaction between transcription factors and their cognate cis -regulatory DNA elements. Here we have out-lined electrophoretic mobility shift assay (EMSA) and chromatin immunoprecipitation (ChIP) protocols to define in vitro and in vivo USFs specific interacting sequences. The proposed procedures have been optimized for the USFs transcription factor family, allowing the identification of USF-specific targets.