title: The RNA polymerase I transactivator upstream binding factor requires its dimerization domain and high-mobility-group (HMG) box 1 to bend, wrap, and positively supercoil enhancer DNA.
abstract: Upstream binding factor (UBF) is an important transactivator of RNA polymerase I and is a member of a family of proteins that contain nucleic acid binding domains named high-mobility-group (HMG) boxes because of their similarity to HMG chromosomal proteins. UBF is a highly sequence-tolerant DNA-binding protein for which no binding consensus sequence has been identified. Therefore, it has been suggested that UBF may recognize preformed structural features of DNA, a hypothesis supported by UBF's ability to bind synthetic DNA cruciforms, four-way junctions, and even tRNA. We show here that full-length UBF can also bend linear DNA to mediate circularization of probes as small as 102 bp in the presence of DNA ligase. Longer probes in the presence of UBF become positively supercoiled when ligated, suggesting that UBF wraps the DNA in a right-handed direction, opposite the direction of DNA wrapping around a nucleosome. The dimerization domain and HMG box 1 are necessary and sufficient to circularize short probes and supercoil longer probes in the presence of DNA ligase. UBF's sequence tolerance coupled with its ability to bend and wrap DNA makes UBF an unusual eukaryotic transcription factor. However, UBF's ability to bend DNA might explain how upstream and downstream rRNA gene promoter domains interact. UBF-induced DNA wrapping could also be a mechanism by which UBF counteracts histone-mediated gene repression.
authors.affiliation: Biology Department, Washington University, St. Louis, Missouri 63130.
authors.forename: C D
authors.initials: CD
authors.lastname: Putnam
authors.forename: G P
authors.initials: GP
authors.lastname: Copenhaver
authors.forename: M L
authors.initials: ML
authors.lastname: Denton
authors.forename: C S
authors.initials: CS
authors.lastname: Pikaard
mesh_terms: D000818:Animals; D001483:Base Sequence; D011088:DNA Ligases / Q000378:metabolism; D015342:DNA Probes / Q000378:metabolism; D004278:DNA, Superhelical / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000235:genetics / Q000378:metabolism*; D003850:Deoxyribonuclease I / Q000378:metabolism; D004742:Enhancer Elements, Genetic; D006609:High Mobility Group Proteins / Q000235:genetics; D008954:Models, Biological; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D035463:Pol1 Transcription Initiation Complex Proteins; D011485:Protein Binding; D011487:Protein Conformation; D012318:RNA Polymerase I / Q000235:genetics*; D013329:Structure-Activity Relationship; D015534:Trans-Activators / Q000378:metabolism*; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism*; D014982:Xenopus laevis
chemical_list: D015342:DNA Probes; D004278:DNA, Superhelical; D004268:DNA-Binding Proteins; D006609:High Mobility Group Proteins; D035463:Pol1 Transcription Initiation Complex Proteins; D015534:Trans-Activators; D014157:Transcription Factors; C063844:transcription factor UBF; D012318:RNA Polymerase I; D003850:Deoxyribonuclease I; D011088:DNA Ligases