title: Differences and similarities in DNA-binding preferences of MyoD and E2A protein complexes revealed by binding site selection.
abstract: A technique was developed for studying protein-DNA recognition that can be applied to any purified protein, partially purified protein, or cloned gene. From oligonucleotides in which particular positions are of random sequence, that subset to which a given protein binds is amplified by the polymerase chain reaction and sequenced as a pool. These selected and amplified binding site (SAAB) "imprints" provide a characteristic set of preferred sequences for protein binding. With this technique, it was shown that homo- and heterooligomers of the helix-loop-helix proteins MyoD and E2A recognize a common consensus sequence, CA--TG, but otherwise bind to flanking and internal positions with different sequence preferences that suggest half-site recognition. These findings suggest that different combinations of dimeric proteins can have different binding sequence preferences.
authors.affiliation: Department of Genetics, Fred Hutchinson Cancer Research Center, Seattle, WA.
authors.forename: T K
authors.initials: TK
authors.lastname: Blackwell
authors.forename: H
authors.initials: H
authors.lastname: Weintraub
mesh_terms: D001483:Base Sequence; D001665:Binding Sites; D004247:DNA / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000378:metabolism*; D005982:Glutathione Transferase; D046911:Macromolecular Substances; D008969:Molecular Sequence Data; D009124:Muscle Proteins / Q000378:metabolism*; D017570:MyoD Protein; D009841:Oligonucleotides / Q000378:metabolism; D016133:Polymerase Chain Reaction; D011487:Protein Conformation; D011993:Recombinant Fusion Proteins / Q000378:metabolism; D012091:Repetitive Sequences, Nucleic Acid; D051820:TCF Transcription Factors; D013698:Templates, Genetic; D058125:Transcription Factor 7-Like 1 Protein; D014157:Transcription Factors
chemical_list: D004268:DNA-Binding Proteins; D046911:Macromolecular Substances; D009124:Muscle Proteins; D017570:MyoD Protein; D009841:Oligonucleotides; D011993:Recombinant Fusion Proteins; D051820:TCF Transcription Factors; D058125:Transcription Factor 7-Like 1 Protein; D014157:Transcription Factors; D004247:DNA; D005982:Glutathione Transferase