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. 1984 May;3(5):1075–1081. doi: 10.1002/j.1460-2075.1984.tb01931.x

Xenopus laevis U1 snRNA genes: characterisation of transcriptionally active genes reveals major and minor repeated gene families.

R Zeller, M T Carri, I W Mattaj, E M De Robertis
PMCID: PMC557475  PMID: 6203742

Abstract

Xenopus laevis U1 snRNA genes are found in several different genomic arrangements. The major family of genes is organised in tandem repeats of 1.8 kb. The minor U1-family is much less abundant and is present on 1.2-kb HinfI restriction fragments. In addition there are genomic arrangements present in one or very few copies, which could represent the ends of repeating units. There is no evidence for the presence of U1 pseudogenes in Xenopus. A cluster of U1 snRNA genes consisting of a member of the minor class of U1 snRNA genes and two of the 'rarely represented' genes was cloned. All three genes were expressed upon microinjection into frog oocytes. A fragment containing 149 bp of 5' flanking sequence, the RNA coding sequence, and 27 bp of 3' flanking sequence was shown to be accurately transcribed into U1 snRNA. These oocyte transcripts are assembled into specific U1 snRNPs. Sequence comparison of the regions flanking Xenopus U1 and U2 snRNA genes showed the presence of two blocks of homology, which are also conserved in many other U snRNA genes. One of these blocks is found at position -60 to -50 before the coding sequence, and we discuss its possible role in the correct initiation of transcription. The other is 3' to the coding sequence and may be involved in the accurate production of mature 3' ends in the RNA.

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Selected References

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

  1. 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]
  2. Bernstein L. B., Mount S. M., Weiner A. M. Pseudogenes for human small nuclear RNA U3 appear to arise by integration of self-primed reverse transcripts of the RNA into new chromosomal sites. Cell. 1983 Feb;32(2):461–472. doi: 10.1016/0092-8674(83)90466-x. [DOI] [PubMed] [Google Scholar]
  3. Branlant C., Krol A., Ebel J. P., Lazar E., Gallinaro H., Jacob M., Sri-Widada J., Jeanteur P. Nucleotide sequences of nuclear U1A RNAs from chicken, rat and man. Nucleic Acids Res. 1980 Sep 25;8(18):4143–4154. doi: 10.1093/nar/8.18.4143. [DOI] [PMC free article] [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. Card C. O., Morris G. F., Brown D. T., Marzluff W. F. Sea urchin small nuclear RNA genes are organized in distinct tandemly repeating units. Nucleic Acids Res. 1982 Dec 11;10(23):7677–7688. doi: 10.1093/nar/10.23.7677. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Corden J., Wasylyk B., Buchwalder A., Sassone-Corsi P., Kedinger C., Chambon P. Promoter sequences of eukaryotic protein-coding genes. Science. 1980 Sep 19;209(4463):1406–1414. doi: 10.1126/science.6251548. [DOI] [PubMed] [Google Scholar]
  7. Cortese R., Harland R., Melton D. Transcription of tRNA genes in vivo: single-stranded compared to double-stranded templates. Proc Natl Acad Sci U S A. 1980 Jul;77(7):4147–4151. doi: 10.1073/pnas.77.7.4147. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. De Robertis E. M., Lienhard S., Parisot R. F. Intracellular transport of microinjected 5S and small nuclear RNAs. Nature. 1982 Feb 18;295(5850):572–577. doi: 10.1038/295572a0. [DOI] [PubMed] [Google Scholar]
  9. De Robertis E. M. Nucleocytoplasmic segregation of proteins and RNAs. Cell. 1983 Apr;32(4):1021–1025. doi: 10.1016/0092-8674(83)90285-4. [DOI] [PubMed] [Google Scholar]
  10. 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]
  11. Galli G., Hofstetter H., Stunnenberg H. G., Birnstiel M. L. Biochemical complementation with RNA in the Xenopus oocyte: a small RNA is required for the generation of 3' histone mRNA termini. Cell. 1983 Oct;34(3):823–828. doi: 10.1016/0092-8674(83)90539-1. [DOI] [PubMed] [Google Scholar]
  12. Garber R. L., Kuroiwa A., Gehring W. J. Genomic and cDNA clones of the homeotic locus Antennapedia in Drosophila. EMBO J. 1983;2(11):2027–2036. doi: 10.1002/j.1460-2075.1983.tb01696.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Humphries P., Old R., Coggins L. W., McShane T., Watson C., Paul J. Recombinant plasmids containing Xenopus laevis globin structural genes derived from complementary DNA. Nucleic Acids Res. 1978 Mar;5(3):905–924. doi: 10.1093/nar/5.3.905. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Lerner E. A., Lerner M. R., Janeway C. A., Jr, Steitz J. A. Monoclonal antibodies to nucleic acid-containing cellular constituents: probes for molecular biology and autoimmune disease. Proc Natl Acad Sci U S A. 1981 May;78(5):2737–2741. doi: 10.1073/pnas.78.5.2737. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Lerner M. R., Boyle J. A., Mount S. M., Wolin S. L., Steitz J. A. Are snRNPs involved in splicing? Nature. 1980 Jan 10;283(5743):220–224. doi: 10.1038/283220a0. [DOI] [PubMed] [Google Scholar]
  16. Lerner M. R., Steitz J. A. Snurps and scyrps. Cell. 1981 Aug;25(2):298–300. doi: 10.1016/0092-8674(81)90047-7. [DOI] [PubMed] [Google Scholar]
  17. Lund E., Bostock C., Robertson M., Christie S., Mitchen J. L., Dahlberg J. E. U1 small nuclear RNA genes are located on human chromosome 1 and are expressed in mouse-human hybrid cells. Mol Cell Biol. 1983 Dec;3(12):2211–2220. doi: 10.1128/mcb.3.12.2211. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Lund E., Dahlberg J. E. True genes for human U1 small nuclear RNA. Copy number, polymorphism, and methylation. J Biol Chem. 1984 Feb 10;259(3):2013–2021. [PubMed] [Google Scholar]
  19. Manser T., Gesteland R. F. Human U1 loci: genes for human U1 RNA have dramatically similar genomic environments. Cell. 1982 May;29(1):257–264. doi: 10.1016/0092-8674(82)90110-6. [DOI] [PubMed] [Google Scholar]
  20. Marzluff W. F., Brown D. T., Lobo S., Wang S. S. Isolation and characterization of two linked mouse U1b small nuclear RNA genes. Nucleic Acids Res. 1983 Sep 24;11(18):6255–6270. doi: 10.1093/nar/11.18.6255. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Mattaj I. W., Zeller R. Xenopus laevis U2 snRNA genes: tandemly repeated transcription units sharing 5' and 3' flanking homology with other RNA polymerase II transcribed genes. EMBO J. 1983;2(11):1883–1891. doi: 10.1002/j.1460-2075.1983.tb01675.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Matter L., Schopfer K., Wilhelm J. A., Nyffenegger T., Parisot R. F., De Robertis E. M. Molecular characterization of ribonucleoprotein antigens bound by antinuclear antibodies. A diagnostic evaluation. Arthritis Rheum. 1982 Nov;25(11):1278–1283. doi: 10.1002/art.1780251102. [DOI] [PubMed] [Google Scholar]
  23. 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]
  24. Messing J., Vieira J. A new pair of M13 vectors for selecting either DNA strand of double-digest restriction fragments. Gene. 1982 Oct;19(3):269–276. doi: 10.1016/0378-1119(82)90016-6. [DOI] [PubMed] [Google Scholar]
  25. Monstein H. J., Westin G., Philipson L., Pettersson U. A candidate gene for human U1 RNA. EMBO J. 1982;1(1):133–137. doi: 10.1002/j.1460-2075.1982.tb01136.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Mount S. M., Steitz J. A. Sequence of U1 RNA from Drosophila melanogaster: implications for U1 secondary structure and possible involvement in splicing. Nucleic Acids Res. 1981 Dec 11;9(23):6351–6368. doi: 10.1093/nar/9.23.6351. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Murphy J. T., Burgess R. R., Dahlberg J. E., Lund E. Transcription of a gene for human U1 small nuclear RNA. Cell. 1982 May;29(1):265–274. doi: 10.1016/0092-8674(82)90111-8. [DOI] [PubMed] [Google Scholar]
  28. Newport J., Kirschner M. A major developmental transition in early Xenopus embryos: II. Control of the onset of transcription. Cell. 1982 Oct;30(3):687–696. doi: 10.1016/0092-8674(82)90273-2. [DOI] [PubMed] [Google Scholar]
  29. Nishikura K., Kurjan J., Hall B. D., De Robertis E. M. Genetic analysis of the processing of a spliced tRNA. EMBO J. 1982;1(2):263–268. doi: 10.1002/j.1460-2075.1982.tb01157.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Ohshima Y., Itoh M., Okada N., Miyata T. Novel models for RNA splicing that involve a small nuclear RNA. Proc Natl Acad Sci U S A. 1981 Jul;78(7):4471–4474. doi: 10.1073/pnas.78.7.4471. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Padgett R. A., Mount S. M., Steitz J. A., Sharp P. A. Splicing of messenger RNA precursors is inhibited by antisera to small nuclear ribonucleoprotein. Cell. 1983 Nov;35(1):101–107. doi: 10.1016/0092-8674(83)90212-x. [DOI] [PubMed] [Google Scholar]
  32. Rogers J., Wall R. A mechanism for RNA splicing. Proc Natl Acad Sci U S A. 1980 Apr;77(4):1877–1879. doi: 10.1073/pnas.77.4.1877. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Roop D. R., Kristo P., Stumph W. E., Tsai M. J., O'Malley B. W. Structure and expression of a chicken gene coding for U1 RNA. Cell. 1981 Mar;23(3):671–680. doi: 10.1016/0092-8674(81)90430-x. [DOI] [PubMed] [Google Scholar]
  34. 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]
  35. Southern E. M. Detection of specific sequences among DNA fragments separated by gel electrophoresis. J Mol Biol. 1975 Nov 5;98(3):503–517. doi: 10.1016/s0022-2836(75)80083-0. [DOI] [PubMed] [Google Scholar]
  36. Tani T., Watanabe-Nagasu N., Okada N., Ohshima Y. Molecular cloning and characterization of a gene for rat U2 small nuclear RNA. J Mol Biol. 1983 Aug 15;168(3):579–594. doi: 10.1016/s0022-2836(83)80303-9. [DOI] [PubMed] [Google Scholar]
  37. Wahli W., Dawid I. B. Isolation of two closely related vitellogenin genes, including their flanking regions, from a Xenopus laevis gene library. Proc Natl Acad Sci U S A. 1980 Mar;77(3):1437–1441. doi: 10.1073/pnas.77.3.1437. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Watanabe-Nagasu N., Itoh Y., Tani T., Okano K., Koga N., Okada N., Ohshima Y. Structural analysis of gene loci for rat U1 small nuclear RNA. Nucleic Acids Res. 1983 Mar 25;11(6):1791–1801. doi: 10.1093/nar/11.6.1791. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. 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]
  40. Yang V. W., Lerner M. R., Steitz J. A., Flint S. J. A small nuclear ribonucleoprotein is required for splicing of adenoviral early RNA sequences. Proc Natl Acad Sci U S A. 1981 Mar;78(3):1371–1375. doi: 10.1073/pnas.78.3.1371. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. 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]

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