title: DNA binding sites for the transcriptional activator/repressor YY1.
abstract: YY1 is ubiquitously expressed zinc finger DNA binding protein. It can act as a transcriptional repressor or activator and, when binding at the initiator element, as a component of the basal transcription complex. Binding sites for YY1 have been reported in a wide variety of promoters and they exhibit substantial diversity in their sequence. To better understand how YY1 interacts with DNA and to be able to predict the presence of YY1 sites in a more comprehensive fashion, we have selected YY1 binding sites from a random pool of oligonucleotides. The sites display considerable heterogeneity, but contain a conserved 5'-CAT-3' core flanked by variable regions, generating the consensus 5'-(C/g/a)(G/t)(C/t/a)CATN(T/a)(T/g/c)-3', where the upper case letters represent the preferred base. This high degree of flexibility in DNA recognition can be predicted by modeling the interaction of the four YY1 zinc fingers with DNA and a detailed model for this interaction is presented and discussed.
authors.affiliation: Howard Hughes Medical Institute, Department of Molecular Biology, Princeton University, NJ 08544-1014, USA.
authors.forename: R P
authors.initials: RP
authors.lastname: Hyde-DeRuyscher
authors.forename: E
authors.initials: E
authors.lastname: Jennings
authors.forename: T
authors.initials: T
authors.lastname: Shenk
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D001665:Binding Sites; D003001:Cloning, Molecular; D016384:Consensus Sequence; D004247:DNA / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000378:metabolism*; D016208:Databases, Factual; D050981:Erythroid-Specific DNA-Binding Factors; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009838:Oligodeoxyribonucleotides / Q000378:metabolism*; D011485:Protein Binding; D011993:Recombinant Fusion Proteins / Q000378:metabolism; D012097:Repressor Proteins / Q000235:genetics / Q000378:metabolism*; D012641:Selection, Genetic; D012689:Sequence Homology, Nucleic Acid; D013329:Structure-Activity Relationship; D014157:Transcription Factors / Q000378:metabolism*; D050986:YY1 Transcription Factor; D016335:Zinc Fingers / Q000235:genetics / Q000502:physiology*
chemical_list: D004268:DNA-Binding Proteins; D050981:Erythroid-Specific DNA-Binding Factors; D009838:Oligodeoxyribonucleotides; D011993:Recombinant Fusion Proteins; D012097:Repressor Proteins; D014157:Transcription Factors; D050986:YY1 Transcription Factor; D004247:DNA