Identification of specific protein/E-box-containing DNA complexes: lessons from the ubiquitously expressed USF transcription factors of the b-HLH-LZ super family.
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.
Galibert
Marie-Dominique
MD
Genetic and Development Institute of Rennes, Transcriptional Regulation and Oncogenesis Team, Rennes University, Rennes, France. mgaliber@univ-rennes1.fr
Baron
Yorann
Y
D001483:Base Sequence; D001667:Binding, Competitive; D002460:Cell Line; D002467:Cell Nucleus / Q000378:metabolism; D047369:Chromatin Immunoprecipitation; D004247:DNA / Q000235:genetics* / Q000378:metabolism*; D024721:E-Box Elements / Q000235:genetics*; D024202:Electrophoretic Mobility Shift Assay; D005786:Gene Expression Regulation; D006801:Humans; D009154:Mutation; D011401:Promoter Regions, Genetic / Q000235:genetics; D011485:Protein Binding; D020133:Reverse Transcriptase Polymerase Chain Reaction; D013379:Substrate Specificity; D051720:Upstream Stimulatory Factors / Q000378:metabolism*
D051720:Upstream Stimulatory Factors; D004247:DNA