Skip to main content
PMC home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1994 Jul 11;22(13):2651–2657. doi: 10.1093/nar/22.13.2651

The RNA polymerase I transcription factor UBF is a sequence-tolerant HMG-box protein that can recognize structured nucleic acids.

G P Copenhaver 1, C D Putnam 1, M L Denton 1, C S Pikaard 1
PMCID: PMC308223  PMID: 8041627

Abstract

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.

Full text

PDF

Images in this article

2653Image
on p.2653
2655Image
on p.2655
2655Image
on p.2655

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Bachvarov D., Moss T. The RNA polymerase I transcription factor xUBF contains 5 tandemly repeated HMG homology boxes. Nucleic Acids Res. 1991 May 11;19(9):2331–2335. doi: 10.1093/nar/19.9.2331. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Bell S. P., Jantzen H. M., Tjian R. Assembly of alternative multiprotein complexes directs rRNA promoter selectivity. Genes Dev. 1990 Jun;4(6):943–954. doi: 10.1101/gad.4.6.943. [DOI] [PubMed] [Google Scholar]
  3. Bell S. P., Learned R. M., Jantzen H. M., Tjian R. Functional cooperativity between transcription factors UBF1 and SL1 mediates human ribosomal RNA synthesis. Science. 1988 Sep 2;241(4870):1192–1197. doi: 10.1126/science.3413483. [DOI] [PubMed] [Google Scholar]
  4. Bell S. P., Pikaard C. S., Reeder R. H., Tjian R. Molecular mechanisms governing species-specific transcription of ribosomal RNA. Cell. 1989 Nov 3;59(3):489–497. doi: 10.1016/0092-8674(89)90032-9. [DOI] [PubMed] [Google Scholar]
  5. Bianchi M. E., Beltrame M., Paonessa G. Specific recognition of cruciform DNA by nuclear protein HMG1. Science. 1989 Feb 24;243(4894 Pt 1):1056–1059. doi: 10.1126/science.2922595. [DOI] [PubMed] [Google Scholar]
  6. Clos J., Buttgereit D., Grummt I. A purified transcription factor (TIF-IB) binds to essential sequences of the mouse rDNA promoter. Proc Natl Acad Sci U S A. 1986 Feb;83(3):604–608. doi: 10.1073/pnas.83.3.604. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Comai L., Tanese N., Tjian R. The TATA-binding protein and associated factors are integral components of the RNA polymerase I transcription factor, SL1. Cell. 1992 Mar 6;68(5):965–976. doi: 10.1016/0092-8674(92)90039-f. [DOI] [PubMed] [Google Scholar]
  8. Cormack B. P., Struhl K. The TATA-binding protein is required for transcription by all three nuclear RNA polymerases in yeast cells. Cell. 1992 May 15;69(4):685–696. doi: 10.1016/0092-8674(92)90232-2. [DOI] [PubMed] [Google Scholar]
  9. Culotta V. C., Wilkinson J. K., Sollner-Webb B. Mouse and frog violate the paradigm of species-specific transcription of ribosomal RNA genes. Proc Natl Acad Sci U S A. 1987 Nov;84(21):7498–7502. doi: 10.1073/pnas.84.21.7498. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Dunaway M. A transcription factor, TFIS, interacts with both the promoter and enhancer of the Xenopus rRNA genes. Genes Dev. 1989 Nov;3(11):1768–1778. doi: 10.1101/gad.3.11.1768. [DOI] [PubMed] [Google Scholar]
  11. Ferrari S., Harley V. R., Pontiggia A., Goodfellow P. N., Lovell-Badge R., Bianchi M. E. SRY, like HMG1, recognizes sharp angles in DNA. EMBO J. 1992 Dec;11(12):4497–4506. doi: 10.1002/j.1460-2075.1992.tb05551.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Fisher R. P., Parisi M. A., Clayton D. A. Flexible recognition of rapidly evolving promoter sequences by mitochondrial transcription factor 1. Genes Dev. 1989 Dec;3(12B):2202–2217. doi: 10.1101/gad.3.12b.2202. [DOI] [PubMed] [Google Scholar]
  13. Fox K. R., Howarth N. R. Investigations into the sequence-selective binding of mithramycin and related ligands to DNA. Nucleic Acids Res. 1985 Dec 20;13(24):8695–8714. doi: 10.1093/nar/13.24.8695. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Giese K., Amsterdam A., Grosschedl R. DNA-binding properties of the HMG domain of the lymphoid-specific transcriptional regulator LEF-1. Genes Dev. 1991 Dec;5(12B):2567–2578. doi: 10.1101/gad.5.12b.2567. [DOI] [PubMed] [Google Scholar]
  15. Griess E. A., Rensing S. A., Grasser K. D., Maier U. G., Feix G. Phylogenetic relationships of HMG box DNA-binding domains. J Mol Evol. 1993 Aug;37(2):204–210. doi: 10.1007/BF02407357. [DOI] [PubMed] [Google Scholar]
  16. Grummt I., Roth E., Paule M. R. Ribosomal RNA transcription in vitro is species specific. Nature. 1982 Mar 11;296(5853):173–174. doi: 10.1038/296173a0. [DOI] [PubMed] [Google Scholar]
  17. Hendrickson W., Schleif R. A dimer of AraC protein contacts three adjacent major groove regions of the araI DNA site. Proc Natl Acad Sci U S A. 1985 May;82(10):3129–3133. doi: 10.1073/pnas.82.10.3129. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Hisatake K., Nishimura T., Maeda Y., Hanada K., Song C. Z., Muramatsu M. Cloning and structural analysis of cDNA and the gene for mouse transcription factor UBF. Nucleic Acids Res. 1991 Sep 11;19(17):4631–4637. doi: 10.1093/nar/19.17.4631. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Hsu T., King D. L., LaBonne C., Kafatos F. C. A Drosophila single-strand DNA/RNA-binding factor contains a high-mobility-group box and is enriched in the nucleolus. Proc Natl Acad Sci U S A. 1993 Jul 15;90(14):6488–6492. doi: 10.1073/pnas.90.14.6488. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Jantzen H. M., Admon A., Bell S. P., Tjian R. Nucleolar transcription factor hUBF contains a DNA-binding motif with homology to HMG proteins. Nature. 1990 Apr 26;344(6269):830–836. doi: 10.1038/344830a0. [DOI] [PubMed] [Google Scholar]
  21. Jantzen H. M., Chow A. M., King D. S., Tjian R. Multiple domains of the RNA polymerase I activator hUBF interact with the TATA-binding protein complex hSL1 to mediate transcription. Genes Dev. 1992 Oct;6(10):1950–1963. doi: 10.1101/gad.6.10.1950. [DOI] [PubMed] [Google Scholar]
  22. Kuhn A., Deppert U., Grummt I. A 140-base-pair repetitive sequence element in the mouse rRNA gene spacer enhances transcription by RNA polymerase I in a cell-free system. Proc Natl Acad Sci U S A. 1990 Oct;87(19):7527–7531. doi: 10.1073/pnas.87.19.7527. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Kuhn A., Grummt I. Dual role of the nucleolar transcription factor UBF: trans-activator and antirepressor. Proc Natl Acad Sci U S A. 1992 Aug 15;89(16):7340–7344. doi: 10.1073/pnas.89.16.7340. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Kuhn A., Stefanovsky V., Grummt I. The nucleolar transcription activator UBF relieves Ku antigen-mediated repression of mouse ribosomal gene transcription. Nucleic Acids Res. 1993 May 11;21(9):2057–2063. doi: 10.1093/nar/21.9.2057. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Laudet V., Stehelin D., Clevers H. Ancestry and diversity of the HMG box superfamily. Nucleic Acids Res. 1993 May 25;21(10):2493–2501. doi: 10.1093/nar/21.10.2493. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Learned R. M., Cordes S., Tjian R. Purification and characterization of a transcription factor that confers promoter specificity to human RNA polymerase I. Mol Cell Biol. 1985 Jun;5(6):1358–1369. doi: 10.1128/mcb.5.6.1358. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Learned R. M., Learned T. K., Haltiner M. M., Tjian R. T. Human rRNA transcription is modulated by the coordinate binding of two factors to an upstream control element. Cell. 1986 Jun 20;45(6):847–857. doi: 10.1016/0092-8674(86)90559-3. [DOI] [PubMed] [Google Scholar]
  28. Leblanc B., Read C., Moss T. Recognition of the Xenopus ribosomal core promoter by the transcription factor xUBF involves multiple HMG box domains and leads to an xUBF interdomain interaction. EMBO J. 1993 Feb;12(2):513–525. doi: 10.1002/j.1460-2075.1993.tb05683.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Maeda Y., Hisatake K., Kondo T., Hanada K., Song C. Z., Nishimura T., Muramatsu M. Mouse rRNA gene transcription factor mUBF requires both HMG-box1 and an acidic tail for nucleolar accumulation: molecular analysis of the nucleolar targeting mechanism. EMBO J. 1992 Oct;11(10):3695–3704. doi: 10.1002/j.1460-2075.1992.tb05454.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Maxam A. M., Gilbert W. A new method for sequencing DNA. Proc Natl Acad Sci U S A. 1977 Feb;74(2):560–564. doi: 10.1073/pnas.74.2.560. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. McStay B., Frazier M. W., Reeder R. H. xUBF contains a novel dimerization domain essential for RNA polymerase I transcription. Genes Dev. 1991 Nov;5(11):1957–1968. doi: 10.1101/gad.5.11.1957. [DOI] [PubMed] [Google Scholar]
  32. McStay B., Hu C. H., Pikaard C. S., Reeder R. H. xUBF and Rib 1 are both required for formation of a stable polymerase I promoter complex in X. laevis. EMBO J. 1991 Aug;10(8):2297–2303. doi: 10.1002/j.1460-2075.1991.tb07766.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Miesfeld R., Arnheim N. Species-specific rDNA transcription is due to promoter-specific binding factors. Mol Cell Biol. 1984 Feb;4(2):221–227. doi: 10.1128/mcb.4.2.221. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Mishima Y., Financsek I., Kominami R., Muramatsu M. Fractionation and reconstitution of factors required for accurate transcription of mammalian ribosomal RNA genes: identification of a species-dependent initiation factor. Nucleic Acids Res. 1982 Nov 11;10(21):6659–6670. doi: 10.1093/nar/10.21.6659. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. O'Mahony D. J., Smith S. D., Xie W., Rothblum L. I. Analysis of the phosphorylation, DNA-binding and dimerization properties of the RNA polymerase I transcription factors UBF1 and UBF2. Nucleic Acids Res. 1992 Mar 25;20(6):1301–1308. doi: 10.1093/nar/20.6.1301. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Pape L. K., Windle J. J., Sollner-Webb B. Half helical turn spacing changes convert a frog into a mouse rDNA promoter: a distant upstream domain determines the helix face of the initiation site. Genes Dev. 1990 Jan;4(1):52–62. doi: 10.1101/gad.4.1.52. [DOI] [PubMed] [Google Scholar]
  37. Parisi M. A., Clayton D. A. Similarity of human mitochondrial transcription factor 1 to high mobility group proteins. Science. 1991 May 17;252(5008):965–969. doi: 10.1126/science.2035027. [DOI] [PubMed] [Google Scholar]
  38. Pikaard C. S., McStay B., Schultz M. C., Bell S. P., Reeder R. H. The Xenopus ribosomal gene enhancers bind an essential polymerase I transcription factor, xUBF. Genes Dev. 1989 Nov;3(11):1779–1788. doi: 10.1101/gad.3.11.1779. [DOI] [PubMed] [Google Scholar]
  39. Pikaard C. S., Pape L. K., Henderson S. L., Ryan K., Paalman M. H., Lopata M. A., Reeder R. H., Sollner-Webb B. Enhancers for RNA polymerase I in mouse ribosomal DNA. Mol Cell Biol. 1990 Sep;10(9):4816–4825. doi: 10.1128/mcb.10.9.4816. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Pikaard C. S., Reeder R. H. Sequence elements essential for function of the Xenopus laevis ribosomal DNA enhancers. Mol Cell Biol. 1988 Oct;8(10):4282–4288. doi: 10.1128/mcb.8.10.4282. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Pikaard C. S., Smith S. D., Reeder R. H., Rothblum L. rUBF, an RNA polymerase I transcription factor from rats, produces DNase I footprints identical to those produced by xUBF, its homolog from frogs. Mol Cell Biol. 1990 Jul;10(7):3810–3812. doi: 10.1128/mcb.10.7.3810. [DOI] [PMC free article] [PubMed] [Google Scholar]
  42. Putnam C. D., Pikaard C. S. Cooperative binding of the Xenopus RNA polymerase I transcription factor xUBF to repetitive ribosomal gene enhancers. Mol Cell Biol. 1992 Nov;12(11):4970–4980. doi: 10.1128/mcb.12.11.4970. [DOI] [PMC free article] [PubMed] [Google Scholar]
  43. Radebaugh C. A., Matthews J. L., Geiss G. K., Liu F., Wong J. M., Bateman E., Camier S., Sentenac A., Paule M. R. TATA box-binding protein (TBP) is a constituent of the polymerase I-specific transcription initiation factor TIF-IB (SL1) bound to the rRNA promoter and shows differential sensitivity to TBP-directed reagents in polymerase I, II, and III transcription factors. Mol Cell Biol. 1994 Jan;14(1):597–605. doi: 10.1128/mcb.14.1.597. [DOI] [PMC free article] [PubMed] [Google Scholar]
  44. Read C. M., Cary P. D., Crane-Robinson C., Driscoll P. C., Norman D. G. Solution structure of a DNA-binding domain from HMG1. Nucleic Acids Res. 1993 Jul 25;21(15):3427–3436. doi: 10.1093/nar/21.15.3427. [DOI] [PMC free article] [PubMed] [Google Scholar]
  45. Schnapp A., Grummt I. Transcription complex formation at the mouse rDNA promoter involves the stepwise association of four transcription factors and RNA polymerase I. J Biol Chem. 1991 Dec 25;266(36):24588–24595. [PubMed] [Google Scholar]
  46. Schultz M. C., Reeder R. H., Hahn S. Variants of the TATA-binding protein can distinguish subsets of RNA polymerase I, II, and III promoters. Cell. 1992 May 15;69(4):697–702. doi: 10.1016/0092-8674(92)90233-3. [DOI] [PubMed] [Google Scholar]
  47. Smith S. D., Oriahi E., Lowe D., Yang-Yen H. F., O'Mahony D., Rose K., Chen K., Rothblum L. I. Characterization of factors that direct transcription of rat ribosomal DNA. Mol Cell Biol. 1990 Jun;10(6):3105–3116. doi: 10.1128/mcb.10.6.3105. [DOI] [PMC free article] [PubMed] [Google Scholar]
  48. Tanaka N., Kato H., Ishikawa Y., Hisatake K., Tashiro K., Kominami R., Muramatsu M. Sequence-specific binding of a transcription factor TFID to the promoter region of mouse ribosomal RNA gene. J Biol Chem. 1990 Aug 15;265(23):13836–13842. [PubMed] [Google Scholar]
  49. Tower J., Culotta V. C., Sollner-Webb B. Factors and nucleotide sequences that direct ribosomal DNA transcription and their relationship to the stable transcription complex. Mol Cell Biol. 1986 Oct;6(10):3451–3462. doi: 10.1128/mcb.6.10.3451. [DOI] [PMC free article] [PubMed] [Google Scholar]
  50. Van Dyke M. W., Hertzberg R. P., Dervan P. B. Map of distamycin, netropsin, and actinomycin binding sites on heterogeneous DNA: DNA cleavage-inhibition patterns with methidiumpropyl-EDTA.Fe(II). Proc Natl Acad Sci U S A. 1982 Sep;79(18):5470–5474. doi: 10.1073/pnas.79.18.5470. [DOI] [PMC free article] [PubMed] [Google Scholar]
  51. Weir H. M., Kraulis P. J., Hill C. S., Raine A. R., Laue E. D., Thomas J. O. Structure of the HMG box motif in the B-domain of HMG1. EMBO J. 1993 Apr;12(4):1311–1319. doi: 10.1002/j.1460-2075.1993.tb05776.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  52. White R. J., Jackson S. P. The TATA-binding protein: a central role in transcription by RNA polymerases I, II and III. Trends Genet. 1992 Aug;8(8):284–288. doi: 10.1016/0168-9525(92)90255-3. [DOI] [PubMed] [Google Scholar]
  53. Wilkinson J. K., Sollner-Webb B. Transcription of Xenopus ribosomal RNA genes by RNA polymerase I in vitro. J Biol Chem. 1982 Dec 10;257(23):14375–14383. [PubMed] [Google Scholar]
  54. Wright J. M., Dixon G. H. Induction by torsional stress of an altered DNA conformation 5' upstream of the gene for a high mobility group protein from trout and specific binding to flanking sequences by the gene product HMG-T. Biochemistry. 1988 Jan 26;27(2):576–581. doi: 10.1021/bi00402a012. [DOI] [PubMed] [Google Scholar]
  55. van de Wetering M., Clevers H. Sequence-specific interaction of the HMG box proteins TCF-1 and SRY occurs within the minor groove of a Watson-Crick double helix. EMBO J. 1992 Aug;11(8):3039–3044. doi: 10.1002/j.1460-2075.1992.tb05374.x. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Nucleic Acids Research are provided here courtesy of Oxford University Press

RESOURCES