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. 1991 Dec 11;19(23):6633–6637. doi: 10.1093/nar/19.23.6633

Identification of a sequence-specific protein binding the 5'-transcribed spacer of rat ribosomal genes.

A E Bogomolova 1, L G Nikolaev 1
PMCID: PMC329234  PMID: 1754399

Abstract

A novel 85-kD protein factor which interacts specifically with the 5'-transcribed spacer of rat ribosomal genes was identified using the gel mobility shift, DNase I protection and UV-crosslinking techniques. The binding site of the factor is located inside the 36 bp Alul-HindIII fragment of transcribed spacer, most probably in the region +94 to +115 with respect to the transcription initiation site. Factors giving very similar gel mobility shift patterns were also found in mouse and human cell extracts. Sequences resembling the binding site of this factor were revealed in corresponding regions of mouse and human ribosomal genes. The biological function of FTS remains to be elucidated.

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Selected References

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

  1. Bach R., Grummt I., Allet B. The nucleotide sequence of the initiation region of the ribosomal transcription unit from mouse. Nucleic Acids Res. 1981 Apr 10;9(7):1559–1569. doi: 10.1093/nar/9.7.1559. [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. Cassidy B. G., Yang-Yen H. F., Rothblum L. I. Additional RNA polymerase I initiation site within the nontranscribed spacer region of the rat rRNA gene. Mol Cell Biol. 1987 Jul;7(7):2388–2396. doi: 10.1128/mcb.7.7.2388. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Cassidy B., Haglund R., Rothblum L. I. Regions upstream from the core promoter of the rat ribosomal gene are required for the formation of a stable transcription initiation complex by RNA polymerase I in vitro. Biochim Biophys Acta. 1987 Jul 14;909(2):133–144. doi: 10.1016/0167-4781(87)90035-2. [DOI] [PubMed] [Google Scholar]
  7. Financsek I., Mizumoto K., Mishima Y., Muramatsu M. Human ribosomal RNA gene: nucleotide sequence of the transcription initiation region and comparison of three mammalian genes. Proc Natl Acad Sci U S A. 1982 May;79(10):3092–3096. doi: 10.1073/pnas.79.10.3092. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Financsek I., Mizumoto K., Muramatsu M. Nucleotide sequence of the transcription initiation region of a rat ribosomal RNA gene. Gene. 1982 May;18(2):115–122. doi: 10.1016/0378-1119(82)90109-3. [DOI] [PubMed] [Google Scholar]
  9. Fried M., Crothers D. M. Equilibria and kinetics of lac repressor-operator interactions by polyacrylamide gel electrophoresis. Nucleic Acids Res. 1981 Dec 11;9(23):6505–6525. doi: 10.1093/nar/9.23.6505. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Galas D. J., Schmitz A. DNAse footprinting: a simple method for the detection of protein-DNA binding specificity. Nucleic Acids Res. 1978 Sep;5(9):3157–3170. doi: 10.1093/nar/5.9.3157. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Grummt I., Kuhn A., Bartsch I., Rosenbauer H. A transcription terminator located upstream of the mouse rDNA initiation site affects rRNA synthesis. Cell. 1986 Dec 26;47(6):901–911. doi: 10.1016/0092-8674(86)90805-6. [DOI] [PubMed] [Google Scholar]
  12. Grummt I. Nucleotide sequence requirements for specific initiation of transcription by RNA polymerase I. Proc Natl Acad Sci U S A. 1982 Nov;79(22):6908–6911. doi: 10.1073/pnas.79.22.6908. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Haltiner M. M., Smale S. T., Tjian R. Two distinct promoter elements in the human rRNA gene identified by linker scanning mutagenesis. Mol Cell Biol. 1986 Jan;6(1):227–235. doi: 10.1128/mcb.6.1.227. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Harrington C. A., Chikaraishi D. M. Transcription of spacer sequences flanking the rat 45S ribosomal DNA gene. Mol Cell Biol. 1987 Jan;7(1):314–325. doi: 10.1128/mcb.7.1.314. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Henderson S. L., Sollner-Webb B. The mouse ribosomal DNA promoter has more stringent requirements in vivo than in vitro. Mol Cell Biol. 1990 Sep;10(9):4970–4973. doi: 10.1128/mcb.10.9.4970. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Henderson S., Sollner-Webb B. A transcriptional terminator is a novel element of the promoter of the mouse ribosomal RNA gene. Cell. 1986 Dec 26;47(6):891–900. doi: 10.1016/0092-8674(86)90804-4. [DOI] [PubMed] [Google Scholar]
  17. 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]
  18. Kuhn A., Grummt I. A novel promoter in the mouse rDNA spacer is active in vivo and in vitro. EMBO J. 1987 Nov;6(11):3487–3492. doi: 10.1002/j.1460-2075.1987.tb02673.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Laemmli U. K., Johnson R. A. Maturation of the head of bacteriophage T4. II. Head-related, aberrant tau-particles. J Mol Biol. 1973 Nov 15;80(4):601–611. doi: 10.1016/0022-2836(73)90199-x. [DOI] [PubMed] [Google Scholar]
  20. 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]
  21. Mahajan P. B., Thompson E. A. Hormonal regulation of transcription of rDNA. Purification and characterization of the hormone-regulated transcription factor IC. J Biol Chem. 1990 Sep 25;265(27):16225–16233. [PubMed] [Google Scholar]
  22. Maxam A. M., Gilbert W. Sequencing end-labeled DNA with base-specific chemical cleavages. Methods Enzymol. 1980;65(1):499–560. doi: 10.1016/s0076-6879(80)65059-9. [DOI] [PubMed] [Google Scholar]
  23. Miesfeld R., Arnheim N. Identification of the in vivo and in vitro origin of transcription in human rDNA. Nucleic Acids Res. 1982 Jul 10;10(13):3933–3949. doi: 10.1093/nar/10.13.3933. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Nagamine M., Kishimoto T., Aono J., Kato H., Kominami R., Muramatsu M. Sequestration analysis for RNA polymerase I transcription factors with various deletion and point mutations reveals different functional regions of the mouse rRNA gene promoter. Mol Cell Biol. 1987 Apr;7(4):1486–1495. doi: 10.1128/mcb.7.4.1486. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Nikolaev L. G., Glotov B. O., Belyavsky A. V., Grachev S. A., Levin A. V. Identification of sequence-specific DNA-binding factors by label transfer: application to the adenovirus-2 major late promoter. Nucleic Acids Res. 1988 Jan 25;16(2):519–535. doi: 10.1093/nar/16.2.519. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. 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]
  27. 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]
  28. 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]
  29. Reeder R. H. rRNA synthesis in the nucleolus. Trends Genet. 1990 Dec;6(12):390–395. doi: 10.1016/0168-9525(90)90298-k. [DOI] [PubMed] [Google Scholar]
  30. Safrany G., Tanaka N., Kishimoto T., Ishikawa Y., Kato H., Kominami R., Muramatsu M. Structural determinant of the species-specific transcription of the mouse rRNA gene promoter. Mol Cell Biol. 1989 Jan;9(1):349–353. doi: 10.1128/mcb.9.1.349. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. 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]
  32. Smale S. T., Tjian R. Transcription of herpes simplex virus tk sequences under the control of wild-type and mutant human RNA polymerase I promoters. Mol Cell Biol. 1985 Feb;5(2):352–362. doi: 10.1128/mcb.5.2.352. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. 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]
  34. Smith S. D., Oriahi E., Yang-Yen H. F., Xie W. Q., Chen C., Rothblum L. I. Interaction of RNA polymerase I transcription factors with a promoter in the nontranscribed spacer of rat ribosomal DNA. Nucleic Acids Res. 1990 Apr 11;18(7):1677–1685. doi: 10.1093/nar/18.7.1677. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Urano Y., Kominami R., Mishima Y., Muramatsu M. The nucleotide sequence of the putative transcription initiation site of a cloned ribosomal RNA gene of the mouse. Nucleic Acids Res. 1980 Dec 20;8(24):6043–6058. doi: 10.1093/nar/8.24.6043. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Wingender E. Compilation of transcription regulating proteins. Nucleic Acids Res. 1988 Mar 25;16(5):1879–1902. doi: 10.1093/nar/16.5.1879. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Yang-Yen H. F., Rothblum L. I. Purification and characterization of a high-mobility-group-like DNA-binding protein that stimulates rRNA synthesis in vitro. Mol Cell Biol. 1988 Aug;8(8):3406–3414. doi: 10.1128/mcb.8.8.3406. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Zenkova M. A., Karpova G. G., Levina A. S. Komplementarno adresovannoe alkilirovanie 16S rRNK Escherichia coli 2',3'-0-[4-N-(2-khlorétil)-N-metilamino]benzilidenovymi proizvodnymi oligodezoksiribonukleotidov. III. uchastki 16S rRNA, vzaimodeistvuiushchie s benzilidenovym proizvodnym d(pACCTTGTT)rA. Mol Biol (Mosk) 1989 Jul-Aug;23(4):1057–1066. [PubMed] [Google Scholar]

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