The RNA polymerase I transcription factor UBF is a sequence-tolerant HMG-box protein that can recognize structured nucleic acids.
Upstream Binding Factor (UBF) is important for activation of ribosomal RNA transcription and belongs to a family of proteins containing nucleic acid binding domains, termed HMG-boxes, with similarity to High Mobility Group (HMG) chromosomal proteins. Proteins in this family can be sequence-specific or highly sequence-tolerant binding proteins. We show that Xenopus UBF can be classified among the sequence-tolerant class. Methylation interference assays using enhancer DNA probes failed to reveal any critical nucleotides required for UBF binding. Selection by UBF of optimal binding sites among a population of enhancer oligonucleotides with randomized sequences also failed to reveal any consensus sequence. The minor groove specific drugs chromomycin A3, distamycin A and actinomycin D competed against UBF for enhancer binding, suggesting that UBF, like other HMG-box proteins, probably interacts with the minor groove. UBF also shares with other HMG box proteins the ability to bind synthetic cruciform DNA. However, UBF appears different from other HMG-box proteins in that it can bind both RNA (tRNA) and DNA. The sequence-tolerant nature of UBF-nucleic acid interactions may accommodate the rapid evolution of ribosomal RNA gene sequences.
Copenhaver
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GP
Biology Department, Washington University, St Louis, MO 63130.
Putnam
C D
CD
Denton
M L
ML
Pikaard
C S
CS
D000818:Animals; D001483:Base Sequence; D014128:Chromomycin A3 / Q000494:pharmacology; D004247:DNA / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000378:metabolism*; D003609:Dactinomycin / Q000494:pharmacology; D004214:Distamycins / Q000494:pharmacology; D004742:Enhancer Elements, Genetic; D006609:High Mobility Group Proteins / Q000378:metabolism*; D008745:Methylation; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D035463:Pol1 Transcription Initiation Complex Proteins; D012318:RNA Polymerase I / Q000378:metabolism*; D012343:RNA, Transfer / Q000378:metabolism*; D014157:Transcription Factors / Q000378:metabolism*; D014982:Xenopus laevis
D004268:DNA-Binding Proteins; D004214:Distamycins; D006609:High Mobility Group Proteins; D035463:Pol1 Transcription Initiation Complex Proteins; D014157:Transcription Factors; C063844:transcription factor UBF; D003609:Dactinomycin; C030000:stallimycin; D004247:DNA; D012343:RNA, Transfer; D014128:Chromomycin A3; D012318:RNA Polymerase I