title: Identifying cis-acting DNA elements within a control region.
abstract: Computational methods can be used to identify DNA sequence motifs that have been conserved through evolution, as well as motifs that correspond to recognition sites for known DNA-binding proteins. These computational methods, when combined with chromatin immunoprecipitation and other basic experiments, can provide preliminary insight into the elements and factors that regulate a gene of interest. When pursuing a more complete understanding of a control region of interest, a comprehensive mutant analysis should generally be performed as a critical step toward more advanced functional studies. This article describes strategies for such a comprehensive analysis. It also summarizes the insights provided by a comprehensive mutant analysis versus a phylogenetic analysis.
authors.forename: Michael F
authors.initials: MF
authors.lastname: Carey
authors.forename: Craig L
authors.initials: CL
authors.lastname: Peterson
authors.forename: Stephen T
authors.initials: ST
authors.lastname: Smale
mesh_terms: D001665:Binding Sites; D047369:Chromatin Immunoprecipitation / Q000379:methods*; D019295:Computational Biology / Q000379:methods*; D004247:DNA / Q000235:genetics* / Q000378:metabolism*; D004252:DNA Mutational Analysis / Q000379:methods*; D004268:DNA-Binding Proteins / Q000378:metabolism; D050436:Regulatory Elements, Transcriptional; D014158:Transcription, Genetic
chemical_list: D004268:DNA-Binding Proteins; D004247:DNA