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. 1988 Sep 26;16(18):8803–8815. doi: 10.1093/nar/16.18.8803

Oocyte and somatic 5S ribosomal RNA and 5S RNA encoding genes in Xenopus tropicalis.

W Nietfeld 1, M Digweed 1, H Mentzel 1, W Meyerhof 1, M Köster 1, W Knöchel 1, V A Erdmann 1, T Pieler 1
PMCID: PMC338636  PMID: 3174434

Abstract

We have investigated the structure of oocyte and somatic 5S ribosomal RNA and of 5S RNA encoding genes in Xenopus tropicalis. The sequences of the two 5S RNA families differ in four positions, but only one of these substitutions, a C to U transition in position 79 within the internal control region of the corresponding 5S RNA encoding genes, is a distinguishing characteristic of all Xenopus somatic and oocyte 5S RNAs characterized to date, including those from Xenopus laevis and Xenopus borealis. 5S RNA genes in Xenopus tropicalis are organized in clusters of multiple repeats of a 264 base pair unit; the structural and functional organization of the Xenopus tropicalis oocyte 5S gene is similar to the somatic but distinct from the oocyte 5S DNA in Xenopus laevis and Xenopus borealis. A comparative sequence analysis reveals the presence of a strictly conserved pentamer motif AAAGT in the 5'-flanking region of Xenopus 5S genes which we demonstrate in a separate communication to serve as a binding signal for an upstream stimulatory factor.

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Selected References

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

  1. Birkenmeier E. H., Brown D. D., Jordan E. A nuclear extract of Xenopus laevis oocytes that accurately transcribes 5S RNA genes. Cell. 1978 Nov;15(3):1077–1086. doi: 10.1016/0092-8674(78)90291-x. [DOI] [PubMed] [Google Scholar]
  2. Bisbee C. A., Baker M. A., Wilson A. C., Haji-Azimi I., Fischberg M. Albumin phylogeny for clawed frogs (Xenopus). Science. 1977 Feb 25;195(4280):785–787. doi: 10.1126/science.65013. [DOI] [PubMed] [Google Scholar]
  3. Bogenhagen D. F., Brown D. D. Nucleotide sequences in Xenopus 5S DNA required for transcription termination. Cell. 1981 Apr;24(1):261–270. doi: 10.1016/0092-8674(81)90522-5. [DOI] [PubMed] [Google Scholar]
  4. Denis H., Wegnez M. Evolution of the 5 S RNA genes in vertebrates. J Mol Evol. 1978 Oct 27;12(1):11–15. doi: 10.1007/BF01732542. [DOI] [PubMed] [Google Scholar]
  5. Digweed M., Pieler T., Kluwe D., Schuster L., Walker R., Erdmann V. A. Improved procedure for the isolation of a double-strand-specific ribonuclease and its application to structural analysis of various 5S rRNAs and tRNAs. Eur J Biochem. 1986 Jan 2;154(1):31–39. doi: 10.1111/j.1432-1033.1986.tb09355.x. [DOI] [PubMed] [Google Scholar]
  6. Donis-Keller H., Maxam A. M., Gilbert W. Mapping adenines, guanines, and pyrimidines in RNA. Nucleic Acids Res. 1977 Aug;4(8):2527–2538. doi: 10.1093/nar/4.8.2527. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Fedoroff N. V., Brown D. D. The nucleotide sequence of the repeating unit in the oocyte 5S ribosomal DNA of Xenopus laevis. Cold Spring Harb Symp Quant Biol. 1978;42(Pt 2):1195–1200. doi: 10.1101/sqb.1978.042.01.120. [DOI] [PubMed] [Google Scholar]
  8. Ford P. J., Southern E. M. Different sequences for 5S RNA in kidney cells and ovaries of Xenopus laevis. Nat New Biol. 1973 Jan 3;241(105):7–12. doi: 10.1038/newbio241007a0. [DOI] [PubMed] [Google Scholar]
  9. Henikoff S. Unidirectional digestion with exonuclease III creates targeted breakpoints for DNA sequencing. Gene. 1984 Jun;28(3):351–359. doi: 10.1016/0378-1119(84)90153-7. [DOI] [PubMed] [Google Scholar]
  10. Knöchel W., Korge E., Basner A., Meyerhof W. Globin evolution in the genus Xenopus: comparative analysis of cDNAs coding for adult globin polypeptides of Xenopus borealis and Xenopus tropicalis. J Mol Evol. 1986;23(3):211–223. doi: 10.1007/BF02115578. [DOI] [PubMed] [Google Scholar]
  11. Komiya H., Hasegawa M., Takemura S. Differentiation of oocyte- and somatic-type 5S rRNAs in animals. J Biochem. 1986 Aug;100(2):369–374. doi: 10.1093/oxfordjournals.jbchem.a121723. [DOI] [PubMed] [Google Scholar]
  12. Korn L. J., Brown D. D. Nucleotide sequence of Xenopus borealis oocyte 5S DNA: comparison of sequences that flank several related eucaryotic genes. Cell. 1978 Dec;15(4):1145–1156. doi: 10.1016/0092-8674(78)90042-9. [DOI] [PubMed] [Google Scholar]
  13. Ladiges W. C., Raff R. F., Brown S., Deeg H. J., Storb R. The canine major histocompatibility complex. Supertypic specificities defined by the primed lymphocyte test (PLT). Immunogenetics. 1984;19(4):359–365. doi: 10.1007/BF00345410. [DOI] [PubMed] [Google Scholar]
  14. McConkey G. A., Bogenhagen D. F. TFIIIA binds with equal affinity to somatic and major oocyte 5S RNA genes. Genes Dev. 1988 Feb;2(2):205–214. doi: 10.1101/gad.2.2.205. [DOI] [PubMed] [Google Scholar]
  15. Miller J. R., Brownlee G. G. Is there a correction mechanism in the 5S multigene system? Nature. 1978 Oct 12;275(5680):556–558. doi: 10.1038/275556a0. [DOI] [PubMed] [Google Scholar]
  16. Peattie D. A. Direct chemical method for sequencing RNA. Proc Natl Acad Sci U S A. 1979 Apr;76(4):1760–1764. doi: 10.1073/pnas.76.4.1760. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Peterson R. C., Doering J. L., Brown D. D. Characterization of two xenopus somatic 5S DNAs and one minor oocyte-specific 5S DNA. Cell. 1980 May;20(1):131–141. doi: 10.1016/0092-8674(80)90241-x. [DOI] [PubMed] [Google Scholar]
  18. Pieler T., Hamm J., Roeder R. G. The 5S gene internal control region is composed of three distinct sequence elements, organized as two functional domains with variable spacing. Cell. 1987 Jan 16;48(1):91–100. doi: 10.1016/0092-8674(87)90359-x. [DOI] [PubMed] [Google Scholar]
  19. Romaniuk P. J., de Stevenson I. L., Ehresmann C., Romby P., Ehresmann B. A comparison of the solution structures and conformational properties of the somatic and oocyte 5S rRNAs of Xenopus laevis. Nucleic Acids Res. 1988 Mar 25;16(5):2295–2312. doi: 10.1093/nar/16.5.2295. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Sakonju S., Brown D. D. Contact points between a positive transcription factor and the Xenopus 5S RNA gene. Cell. 1982 Dec;31(2 Pt 1):395–405. doi: 10.1016/0092-8674(82)90133-7. [DOI] [PubMed] [Google Scholar]
  21. Sanger F., Nicklen S., Coulson A. R. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463–5467. doi: 10.1073/pnas.74.12.5463. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Sharp S. J., Garcia A. D. Transcription of the Drosophila melanogaster 5S RNA gene requires an upstream promoter and four intragenic sequence elements. Mol Cell Biol. 1988 Mar;8(3):1266–1274. doi: 10.1128/mcb.8.3.1266. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Thiébaud C. H., Fischberg M. DNA content in the genus Xenopus. Chromosoma. 1977 Feb 3;59(3):253–257. doi: 10.1007/BF00292781. [DOI] [PubMed] [Google Scholar]
  24. Wegnez M., Monier R., Denis H. Sequence heterogeneity of 5 S RNA in Xenopus laevis. FEBS Lett. 1972 Sep 1;25(1):13–20. doi: 10.1016/0014-5793(72)80443-5. [DOI] [PubMed] [Google Scholar]
  25. Wormington W. M., Brown D. D. Onset of 5 S RNA gene regulation during Xenopus embryogenesis. Dev Biol. 1983 Sep;99(1):248–257. doi: 10.1016/0012-1606(83)90273-7. [DOI] [PubMed] [Google Scholar]

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