Skip to main content
PMC home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1992 Oct 25;20(20):5435–5442. doi: 10.1093/nar/20.20.5435

Genes for Xenopus laevis U3 small nuclear RNA.

R Savino 1, Y Hitti 1, S A Gerbi 1
PMCID: PMC334353  PMID: 1437561

Abstract

Genomic Southern blots showed there are only 14 to 20 copies of U3 snRNA genes per somatic genome in Xenopus laevis, unlike the highly repetitive, tandem arrangement of other snRNA genes in this organism. Sequencing of two U3 snRNA genes from lambda clones of a genomic library revealed striking similarity upstream, but much more divergence downstream. Consensus motifs common to other U snRNA genes were also found: a distal sequence element (DSE, octamer motif at -222 to -215), a proximal sequence element (PSE, at -62 to -52) and a 3' Box (15 or 16 bp downstream of the U3 genes). The DSE of mammals also has an inverted CCAAT motif specific for U3 snRNA genes, and we find this is conserved in the amphibian U3 snRNA genes. The Xenopus inverted CCAAT motif is exactly one helical turn further upstream of the octamer motif than its mammalian counterpart, suggesting interaction of putative transcription factors bound to these motifs. Mutation of the inverted CCAAT motif and part of an adjacent Sp1 site greatly depresses transcription of the mutant U3 snRNA gene in Xenopus oocytes, implying a role in transcriptional efficiency. Electrophoretic mobility shift assays implicate transcription factor binding to this region.

Full text

PDF
5435

Images in this article

5438Image
on p.5438
5438Image
on p.5438
5440Image
on p.5440
5441Image
on p.5441

Selected References

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

  1. Ach R. A., Weiner A. M. Cooperation between CCAAT and octamer motifs in the distal sequence element of the rat U3 small nucleolar RNA promoter. Nucleic Acids Res. 1991 Aug 11;19(15):4209–4218. doi: 10.1093/nar/19.15.4209. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Benton W. D., Davis R. W. Screening lambdagt recombinant clones by hybridization to single plaques in situ. Science. 1977 Apr 8;196(4286):180–182. doi: 10.1126/science.322279. [DOI] [PubMed] [Google Scholar]
  3. 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]
  4. Busch H., Reddy R., Rothblum L., Choi Y. C. SnRNAs, SnRNPs, and RNA processing. Annu Rev Biochem. 1982;51:617–654. doi: 10.1146/annurev.bi.51.070182.003153. [DOI] [PubMed] [Google Scholar]
  5. Dynan W. S., Tjian R. The promoter-specific transcription factor Sp1 binds to upstream sequences in the SV40 early promoter. Cell. 1983 Nov;35(1):79–87. doi: 10.1016/0092-8674(83)90210-6. [DOI] [PubMed] [Google Scholar]
  6. Forbes D. J., Kornberg T. B., Kirschner M. W. Small nuclear RNA transcription and ribonucleoprotein assembly in early Xenopus development. J Cell Biol. 1983 Jul;97(1):62–72. doi: 10.1083/jcb.97.1.62. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Frederiksen S., Pedersen I. R., Hellung-Larsen P., Engberg J. Metabolic studies of small molecular weight nuclear RNA components in BHK-21 cells. Biochim Biophys Acta. 1974 Feb 27;340(1):64–76. doi: 10.1016/0005-2787(74)90174-9. [DOI] [PubMed] [Google Scholar]
  8. Hamelin R., Larsen C. J., Tavitian A. Effects of actinomycin D, toyocamycin and cycloheximide on the synthesis of low-molecular-weight nuclear RNAs in HeLa cells. Eur J Biochem. 1973 Jun;35(2):350–356. doi: 10.1111/j.1432-1033.1973.tb02846.x. [DOI] [PubMed] [Google Scholar]
  9. Hughes J. M., Ares M., Jr Depletion of U3 small nucleolar RNA inhibits cleavage in the 5' external transcribed spacer of yeast pre-ribosomal RNA and impairs formation of 18S ribosomal RNA. EMBO J. 1991 Dec;10(13):4231–4239. doi: 10.1002/j.1460-2075.1991.tb05001.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Hughes J. M., Konings D. A., Cesareni G. The yeast homologue of U3 snRNA. EMBO J. 1987 Jul;6(7):2145–2155. doi: 10.1002/j.1460-2075.1987.tb02482.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Jeppesen C., Stebbins-Boaz B., Gerbi S. A. Nucleotide sequence determination and secondary structure of Xenopus U3 snRNA. Nucleic Acids Res. 1988 Mar 25;16(5):2127–2148. doi: 10.1093/nar/16.5.2127. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Kass S., Tyc K., Steitz J. A., Sollner-Webb B. The U3 small nucleolar ribonucleoprotein functions in the first step of preribosomal RNA processing. Cell. 1990 Mar 23;60(6):897–908. doi: 10.1016/0092-8674(90)90338-f. [DOI] [PubMed] [Google Scholar]
  13. Kiss T., Marshallsay C., Filipowicz W. Alteration of the RNA polymerase specificity of U3 snRNA genes during evolution and in vitro. Cell. 1991 May 3;65(3):517–526. doi: 10.1016/0092-8674(91)90469-f. [DOI] [PubMed] [Google Scholar]
  14. Liu J. K., Bergman Y., Zaret K. S. The mouse albumin promoter and a distal upstream site are simultaneously DNase I hypersensitive in liver chromatin and bind similar liver-abundant factors in vitro. Genes Dev. 1988 May;2(5):528–541. doi: 10.1101/gad.2.5.528. [DOI] [PubMed] [Google Scholar]
  15. Lund E., Bostock C. J., Dahlberg J. E. The transcription of Xenopus laevis embryonic U1 snRNA genes changes when oocytes mature into eggs. Genes Dev. 1987 Mar;1(1):47–56. doi: 10.1101/gad.1.1.47. [DOI] [PubMed] [Google Scholar]
  16. Mazan S., Bachellerie J. P. Structure and organization of mouse U3B RNA functional genes. J Biol Chem. 1988 Dec 25;263(36):19461–19467. [PubMed] [Google Scholar]
  17. Mazan S., Qu L. H., Sri-Widada J., Nicoloso M., Bachellerie J. P. Presence of a differentially expressed U3A RNA variant in mouse. Structure and evolutive implications. FEBS Lett. 1990 Jul 2;267(1):121–125. doi: 10.1016/0014-5793(90)80304-2. [DOI] [PubMed] [Google Scholar]
  18. Meyuhas O., Baldin V., Bouche G., Amalric F. Glucocorticoids repress ribosome biosynthesis in lymphosarcoma cells by affecting gene expression at the level of transcription, posttranscription and translation. Biochim Biophys Acta. 1990 May 24;1049(1):38–44. doi: 10.1016/0167-4781(90)90082-d. [DOI] [PubMed] [Google Scholar]
  19. Myslinski E., Ségault V., Branlant C. An intron in the genes for U3 small nucleolar RNAs of the yeast Saccharomyces cerevisiae. Science. 1990 Mar 9;247(4947):1213–1216. doi: 10.1126/science.1690452. [DOI] [PubMed] [Google Scholar]
  20. Porter G. L., Brennwald P. J., Holm K. A., Wise J. A. The sequence of U3 from Schizosaccharomyces pombe suggests structural divergence of this snRNA between metazoans and unicellular eukaryotes. Nucleic Acids Res. 1988 Nov 11;16(21):10131–10152. doi: 10.1093/nar/16.21.10131. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Prather R., Simerly C., Schatten G., Pilch D. R., Lobo S. M., Marzluff W. F., Dean W. L., Schultz G. A. U3 snRNPs and nucleolar development during oocyte maturation, fertilization and early embryogenesis in the mouse: U3 snRNA and snRNPs are not regulated coordinate with other snRNAs and snRNPs. Dev Biol. 1990 Apr;138(2):247–255. doi: 10.1016/0012-1606(90)90195-o. [DOI] [PubMed] [Google Scholar]
  22. Prestayko A. W., Tonato M., Busch H. Low molecular weight RNA associated with 28 s nucleolar RNA. J Mol Biol. 1970 Feb 14;47(3):505–515. doi: 10.1016/0022-2836(70)90318-9. [DOI] [PubMed] [Google Scholar]
  23. Queen C., Korn L. J. A comprehensive sequence analysis program for the IBM personal computer. Nucleic Acids Res. 1984 Jan 11;12(1 Pt 2):581–599. doi: 10.1093/nar/12.1part2.581. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Reddy R., Henning D., Busch H. Substitutions, insertions, and deletions in two highly conserved U3 RNA species. J Biol Chem. 1980 Jul 25;255(14):7029–7033. [PubMed] [Google Scholar]
  25. Ruberti I., Beccari E., Bianchi E., Carnevali F. Large scale isolation of nuclei from oocytes of Xenopus laevis. Anal Biochem. 1989 Jul;180(1):177–180. doi: 10.1016/0003-2697(89)90108-5. [DOI] [PubMed] [Google Scholar]
  26. Savino R., Gerbi S. A. In vivo disruption of Xenopus U3 snRNA affects ribosomal RNA processing. EMBO J. 1990 Jul;9(7):2299–2308. doi: 10.1002/j.1460-2075.1990.tb07401.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Stroke I. L., Weiner A. M. Genes and pseudogenes for rat U3A and U3B small nuclear RNA. J Mol Biol. 1985 Jul 20;184(2):183–193. doi: 10.1016/0022-2836(85)90372-9. [DOI] [PubMed] [Google Scholar]
  28. Suh D., Busch H., Reddy R. Isolation and characterization of a human U3 small nucleolar RNA gene. Biochem Biophys Res Commun. 1986 Jun 30;137(3):1133–1140. doi: 10.1016/0006-291x(86)90343-8. [DOI] [PubMed] [Google Scholar]
  29. Tyc K., Steitz J. A. U3, U8 and U13 comprise a new class of mammalian snRNPs localized in the cell nucleolus. EMBO J. 1989 Oct;8(10):3113–3119. doi: 10.1002/j.1460-2075.1989.tb08463.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Weinberg R. A., Penman S. Small molecular weight monodisperse nuclear RNA. J Mol Biol. 1968 Dec;38(3):289–304. doi: 10.1016/0022-2836(68)90387-2. [DOI] [PubMed] [Google Scholar]
  31. Wise J. A., Weiner A. M. Dictyostelium small nuclear RNA D2 is homologous to rat nucleolar RNA U3 and is encoded by a dispersed multigene family. Cell. 1980 Nov;22(1 Pt 1):109–118. doi: 10.1016/0092-8674(80)90159-2. [DOI] [PubMed] [Google Scholar]
  32. Yuan Y., Reddy R. Genes for human U3 small nucleolar RNA contain highly conserved flanking sequences. Biochim Biophys Acta. 1989 Jun 1;1008(1):14–22. doi: 10.1016/0167-4781(89)90164-4. [DOI] [PubMed] [Google Scholar]
  33. Zaret K. S., Liu J. K., DiPersio C. M. Site-directed mutagenesis reveals a liver transcription factor essential for the albumin transcriptional enhancer. Proc Natl Acad Sci U S A. 1990 Jul;87(14):5469–5473. doi: 10.1073/pnas.87.14.5469. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Zeller R., Nyffenegger T., De Robertis E. M. Nucleocytoplasmic distribution of snRNPs and stockpiled snRNA-binding proteins during oogenesis and early development in Xenopus laevis. Cell. 1983 Feb;32(2):425–434. doi: 10.1016/0092-8674(83)90462-2. [DOI] [PubMed] [Google Scholar]
  35. Zieve G., Penman S. Small RNA species of the HeLa cell: metabolism and subcellular localization. Cell. 1976 May;8(1):19–31. doi: 10.1016/0092-8674(76)90181-1. [DOI] [PubMed] [Google Scholar]

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

RESOURCES