Abstract
Transcription of Xenopus ribosomal genes by RNA polymerase I is directed by a stable transcription complex that forms on the gene promoter. This complex is comprised of the HMG box factor UBF and the TBP-containing complex Rib1. Repeated sequence elements found upstream of the ribosomal gene promoter act as RNA polymerase I-specific trans-criptional enhancers. These enhancers function by increasing the probability of a stable transcription complex forming on the adjacent promoter. UBF is required for enhancer function. This role in enhancement is distinct from that at the promoter and does not involve translocation of UBF from enhancer repeats to the promoter. Here we utilize an in vitro system to demonstrate that a combination of the dimerization domain of UBF and HMG boxes 1-3 are sufficient to specify its role in enhancement. We also demonstrate that the acidic C-terminus of UBF is primarilyresponsible for its observed interaction with Rib1. Thus, we have uncoupled the Rib1 interaction and enhancer functions of UBF and can conclude that direct interaction with Rib1 is not a prerequisite for the enhancer function of UBF.
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Selected References
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- 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]
- Bazett-Jones D. P., Leblanc B., Herfort M., Moss T. Short-range DNA looping by the Xenopus HMG-box transcription factor, xUBF. Science. 1994 May 20;264(5162):1134–1137. doi: 10.1126/science.8178172. [DOI] [PubMed] [Google Scholar]
- Beckmann H., Chen J. L., O'Brien T., Tjian R. Coactivator and promoter-selective properties of RNA polymerase I TAFs. Science. 1995 Dec 1;270(5241):1506–1509. doi: 10.1126/science.270.5241.1506. [DOI] [PubMed] [Google Scholar]
- 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]
- Bodeker M., Cairns C., McStay B. Upstream binding factor stabilizes Rib 1, the TATA-binding-protein-containing Xenopus laevis RNA polymerase I transcription factor, by multiple protein interactions in a DNA-independent manner. Mol Cell Biol. 1996 Oct;16(10):5572–5578. doi: 10.1128/mcb.16.10.5572. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Busby S. J., Reeder R. H. Spacer sequences regulate transcription of ribosomal gene plasmids injected into Xenopus embryos. Cell. 1983 Oct;34(3):989–996. doi: 10.1016/0092-8674(83)90556-1. [DOI] [PubMed] [Google Scholar]
- Cairns C., McStay B. HMG box 4 is the principal determinant of species specificity in the RNA polymerase I transcription factor UBF. Nucleic Acids Res. 1995 Nov 25;23(22):4583–4590. doi: 10.1093/nar/23.22.4583. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Hempel W. M., Cavanaugh A. H., Hannan R. D., Taylor L., Rothblum L. I. The species-specific RNA polymerase I transcription factor SL-1 binds to upstream binding factor. Mol Cell Biol. 1996 Feb;16(2):557–563. doi: 10.1128/mcb.16.2.557. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Hu C. H., McStay B., Jeong S. W., Reeder R. H. xUBF, an RNA polymerase I transcription factor, binds crossover DNA with low sequence specificity. Mol Cell Biol. 1994 May;14(5):2871–2882. doi: 10.1128/mcb.14.5.2871. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 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]
- 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]
- Krebs J. E., Dunaway M. The scs and scs' insulator elements impart a cis requirement on enhancer-promoter interactions. Mol Cell. 1998 Jan;1(2):301–308. doi: 10.1016/s1097-2765(00)80030-1. [DOI] [PubMed] [Google Scholar]
- 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]
- 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]
- Labhart P., Reeder R. H. Characterization of three sites of RNA 3' end formation in the Xenopus ribosomal gene spacer. Cell. 1986 May 9;45(3):431–443. doi: 10.1016/0092-8674(86)90329-6. [DOI] [PubMed] [Google Scholar]
- Labhart P., Reeder R. H. Enhancer-like properties of the 60/81 bp elements in the ribosomal gene spacer of Xenopus laevis. Cell. 1984 May;37(1):285–289. doi: 10.1016/0092-8674(84)90324-6. [DOI] [PubMed] [Google Scholar]
- 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]
- 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]
- 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]
- McStay B., Sullivan G. J., Cairns C. The Xenopus RNA polymerase I transcription factor, UBF, has a role in transcriptional enhancement distinct from that at the promoter. EMBO J. 1997 Jan 15;16(2):396–405. doi: 10.1093/emboj/16.2.396. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 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]
- Moss T. A transcriptional function for the repetitive ribosomal spacer in Xenopus laevis. Nature. 1983 Mar 17;302(5905):223–228. doi: 10.1038/302223a0. [DOI] [PubMed] [Google Scholar]
- Mougey E. B., Pape L. K., Sollner-Webb B. Virtually the entire Xenopus laevis rDNA multikilobase intergenic spacer serves to stimulate polymerase I transcription. J Biol Chem. 1996 Oct 25;271(43):27138–27145. doi: 10.1074/jbc.271.43.27138. [DOI] [PubMed] [Google Scholar]
- O'Mahony D. J., Xie W. Q., Smith S. D., Singer H. A., Rothblum L. I. Differential phosphorylation and localization of the transcription factor UBF in vivo in response to serum deprivation. In vitro dephosphorylation of UBF reduces its transactivation properties. J Biol Chem. 1992 Jan 5;267(1):35–38. [PubMed] [Google Scholar]
- Osheim Y. N., Mougey E. B., Windle J., Anderson M., O'Reilly M., Miller O. L., Jr, Beyer A., Sollner-Webb B. Metazoan rDNA enhancer acts by making more genes transcriptionally active. J Cell Biol. 1996 Jun;133(5):943–954. doi: 10.1083/jcb.133.5.943. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 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]
- 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]
- 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]
- Pikaard C. S. Ribosomal gene promoter domains can function as artificial enhancers of RNA polymerase I transcription, supporting a promoter origin for natural enhancers in Xenopus. Proc Natl Acad Sci U S A. 1994 Jan 18;91(2):464–468. doi: 10.1073/pnas.91.2.464. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Putnam C. D., Copenhaver G. P., Denton M. L., Pikaard C. S. 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. Mol Cell Biol. 1994 Oct;14(10):6476–6488. doi: 10.1128/mcb.14.10.6476. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Reeder R. H., Roan J. G., Dunaway M. Spacer regulation of Xenopus ribosomal gene transcription: competition in oocytes. Cell. 1983 Dec;35(2 Pt 1):449–456. doi: 10.1016/0092-8674(83)90178-2. [DOI] [PubMed] [Google Scholar]
- Schnapp A., Clos J., Hädelt W., Schreck R., Cvekl A., Grummt I. Isolation and functional characterization of TIF-IB, a factor that confers promoter specificity to mouse RNA polymerase I. Nucleic Acids Res. 1990 Mar 25;18(6):1385–1393. doi: 10.1093/nar/18.6.1385. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 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]
- Stefanovsky V. Y., Bazett-Jones D. P., Pelletier G., Moss T. The DNA supercoiling architecture induced by the transcription factor xUBF requires three of its five HMG-boxes. Nucleic Acids Res. 1996 Aug 15;24(16):3208–3215. doi: 10.1093/nar/24.16.3208. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 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]
- Voit R., Kuhn A., Sander E. E., Grummt I. Activation of mammalian ribosomal gene transcription requires phosphorylation of the nucleolar transcription factor UBF. Nucleic Acids Res. 1995 Jul 25;23(14):2593–2599. doi: 10.1093/nar/23.14.2593. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Voit R., Schnapp A., Kuhn A., Rosenbauer H., Hirschmann P., Stunnenberg H. G., Grummt I. The nucleolar transcription factor mUBF is phosphorylated by casein kinase II in the C-terminal hyperacidic tail which is essential for transactivation. EMBO J. 1992 Jun;11(6):2211–2218. doi: 10.1002/j.1460-2075.1992.tb05280.x. [DOI] [PMC free article] [PubMed] [Google Scholar]