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. 1987 Dec;84(24):9094–9098. doi: 10.1073/pnas.84.24.9094

Nucleotide sequence of a bean (Phaseolus vulgaris) U1 small nuclear RNA gene: implications for plant pre-mRNA splicing.

V L van Santen 1, R A Spritz 1
PMCID: PMC299698  PMID: 3480532

Abstract

We have isolated a U1 small nuclear RNA (snRNA) gene from common bean (Phaseolus vulgaris). The haploid bean genome contains only one or a few copies of the U1 snRNA gene. The bean and human U1 snRNA genes are 65% homologous but share no significant similarity in the 5' or 3' flanking regions. The predicted secondary structure of bean U1 snRNA is identical to that of other U1 snRNAs, and the sequences of the single-stranded regions have been highly conserved. Thus, both the sequence of the single-stranded regions and the secondary structure of U1 snRNA appear to be important for its function. The role of U1 snRNA in pre-mRNA splicing is probably similar in plants and animals.

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Selected References

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

  1. Alonso A., Jorcano J. L., Beck E., Spiess E. Isolation and characterization of Drosophila melanogaster U2 small nuclear RNA genes. J Mol Biol. 1983 Sep 25;169(3):691–705. doi: 10.1016/s0022-2836(83)80165-x. [DOI] [PubMed] [Google Scholar]
  2. Ares M., Jr, Mangin M., Weiner A. M. Orientation-dependent transcriptional activator upstream of a human U2 snRNA gene. Mol Cell Biol. 1985 Jul;5(7):1560–1570. doi: 10.1128/mcb.5.7.1560. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Black D. L., Chabot B., Steitz J. A. U2 as well as U1 small nuclear ribonucleoproteins are involved in premessenger RNA splicing. Cell. 1985 Oct;42(3):737–750. doi: 10.1016/0092-8674(85)90270-3. [DOI] [PubMed] [Google Scholar]
  4. Branlant C., Krol A., Ebel J. P., Gallinaro H., Lazar E., Jacob M. The conformation of chicken, rat and human U1A RNAs in solution. Nucleic Acids Res. 1981 Feb 25;9(4):841–858. doi: 10.1093/nar/9.4.841. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. 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]
  6. Branlant C., Krol A., Ebel J. P., Lazar E., Haendler B., Jacob M. U2 RNA shares a structural domain with U1, U4, and U5 RNAs. EMBO J. 1982;1(10):1259–1265. doi: 10.1002/j.1460-2075.1982.tb00022.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Brown J. W. A catalogue of splice junction and putative branch point sequences from plant introns. Nucleic Acids Res. 1986 Dec 22;14(24):9549–9559. doi: 10.1093/nar/14.24.9549. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Brown J. W., Feix G., Frendewey D. Accurate in vitro splicing of two pre-mRNA plant introns in a HeLa cell nuclear extract. EMBO J. 1986 Nov;5(11):2749–2758. doi: 10.1002/j.1460-2075.1986.tb04563.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. 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]
  10. Ciliberto G., Buckland R., Cortese R., Philipson L. Transcription signals in embryonic Xenopus laevis U1 RNA genes. EMBO J. 1985 Jun;4(6):1537–1543. doi: 10.1002/j.1460-2075.1985.tb03814.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Dynan W. S., Tjian R. Control of eukaryotic messenger RNA synthesis by sequence-specific DNA-binding proteins. 1985 Aug 29-Sep 4Nature. 316(6031):774–778. doi: 10.1038/316774a0. [DOI] [PubMed] [Google Scholar]
  12. Ephrussi A., Church G. M., Tonegawa S., Gilbert W. B lineage--specific interactions of an immunoglobulin enhancer with cellular factors in vivo. Science. 1985 Jan 11;227(4683):134–140. doi: 10.1126/science.3917574. [DOI] [PubMed] [Google Scholar]
  13. Falkner F. G., Zachau H. G. Correct transcription of an immunoglobulin kappa gene requires an upstream fragment containing conserved sequence elements. Nature. 1984 Jul 5;310(5972):71–74. doi: 10.1038/310071a0. [DOI] [PubMed] [Google Scholar]
  14. Forbes D. J., Kirschner M. W., Caput D., Dahlberg J. E., Lund E. Differential expression of multiple U1 small nuclear RNAs in oocytes and embryos of Xenopus laevis. Cell. 1984 Oct;38(3):681–689. doi: 10.1016/0092-8674(84)90263-0. [DOI] [PubMed] [Google Scholar]
  15. Green M. R. Pre-mRNA splicing. Annu Rev Genet. 1986;20:671–708. doi: 10.1146/annurev.ge.20.120186.003323. [DOI] [PubMed] [Google Scholar]
  16. Gruss P., Dhar R., Khoury G. Simian virus 40 tandem repeated sequences as an element of the early promoter. Proc Natl Acad Sci U S A. 1981 Feb;78(2):943–947. doi: 10.1073/pnas.78.2.943. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Hernandez N. Formation of the 3' end of U1 snRNA is directed by a conserved sequence located downstream of the coding region. EMBO J. 1985 Jul;4(7):1827–1837. doi: 10.1002/j.1460-2075.1985.tb03857.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Kato N., Harada F. New U1 RNA species found in Friend SFFV (spleen focus forming virus)-transformed mouse cells. J Biol Chem. 1985 Jun 25;260(12):7775–7782. [PubMed] [Google Scholar]
  19. Keller E. B., Noon W. A. Intron splicing: a conserved internal signal in introns of Drosophila pre-mRNAs. Nucleic Acids Res. 1985 Jul 11;13(13):4971–4981. doi: 10.1093/nar/13.13.4971. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Kiss T., Antal M., Solymosy F. Plant small nuclear RNAs. III. The complete primary and secondary structure of broad bean U2 RNA: phylogenetic and functional implications. Nucleic Acids Res. 1987 Feb 11;15(3):1332–1332. doi: 10.1093/nar/15.3.1332. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Kiss T., Tóth M., Solymosy F. Plant small nuclear RNAs. Nucleolar U3 snRNA is present in plants: partial characterization. Eur J Biochem. 1985 Oct 15;152(2):259–266. doi: 10.1111/j.1432-1033.1985.tb09192.x. [DOI] [PubMed] [Google Scholar]
  22. Krol A., Ebel J. P., Rinke J., Luhrmann R. U1, U2 and U5 small nuclear RNAs are found in plants cells. Complete nucleotide sequence of the U5 RNA family from pea nuclei. Nucleic Acids Res. 1983 Dec 20;11(24):8583–8594. doi: 10.1093/nar/11.24.8583. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Krol A., Lund E., Dahlberg J. E. The two embryonic U1 RNA genes of Xenopus laevis have both common and gene-specific transcription signals. EMBO J. 1985 Jun;4(6):1529–1535. doi: 10.1002/j.1460-2075.1985.tb03813.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Lang K. M., Spritz R. A. RNA splice site selection: evidence for a 5' leads to 3' scanning model. Science. 1983 Jun 24;220(4604):1351–1355. doi: 10.1126/science.6304877. [DOI] [PubMed] [Google Scholar]
  25. 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]
  26. Liautard J. P., Sri-Widada J., Brunel C., Jeanteur P. Structural organization of ribonucleoproteins containing small nuclear RNAs from HeLa cells. Proteins interact closely with a similar structural domain of U1, U2, U4 and U5 small nuclear RNAs. J Mol Biol. 1982 Dec 15;162(3):623–643. doi: 10.1016/0022-2836(82)90392-8. [DOI] [PubMed] [Google Scholar]
  27. 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]
  28. Madore S. J., Wieben E. D., Pederson T. Intracellular site of U1 small nuclear RNA processing and ribonucleoprotein assembly. J Cell Biol. 1984 Jan;98(1):188–192. doi: 10.1083/jcb.98.1.188. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Mangin M., Ares M., Jr, Weiner A. M. Human U2 small nuclear RNA genes contain an upstream enhancer. EMBO J. 1986 May;5(5):987–995. doi: 10.1002/j.1460-2075.1986.tb04313.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Mattaj I. W., De Robertis E. M. Nuclear segregation of U2 snRNA requires binding of specific snRNP proteins. Cell. 1985 Jan;40(1):111–118. doi: 10.1016/0092-8674(85)90314-9. [DOI] [PubMed] [Google Scholar]
  31. Mattaj I. W., Lienhard S., Jiricny J., De Robertis E. M. An enhancer-like sequence within the Xenopus U2 gene promoter facilitates the formation of stable transcription complexes. Nature. 1985 Jul 11;316(6024):163–167. doi: 10.1038/316163a0. [DOI] [PubMed] [Google Scholar]
  32. 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]
  33. 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]
  34. Mount S. M. A catalogue of splice junction sequences. Nucleic Acids Res. 1982 Jan 22;10(2):459–472. doi: 10.1093/nar/10.2.459. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. 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]
  36. Nojima H., Kornberg R. D. Genes and pseudogenes for mouse U1 and U2 small nuclear RNAs. J Biol Chem. 1983 Jul 10;258(13):8151–8155. [PubMed] [Google Scholar]
  37. Norrander J., Kempe T., Messing J. Construction of improved M13 vectors using oligodeoxynucleotide-directed mutagenesis. Gene. 1983 Dec;26(1):101–106. doi: 10.1016/0378-1119(83)90040-9. [DOI] [PubMed] [Google Scholar]
  38. Padgett R. A., Grabowski P. J., Konarska M. M., Seiler S., Sharp P. A. Splicing of messenger RNA precursors. Annu Rev Biochem. 1986;55:1119–1150. doi: 10.1146/annurev.bi.55.070186.005351. [DOI] [PubMed] [Google Scholar]
  39. Reddy R., Henning D., Epstein P., Busch H. Primary and secondary structure of U2 snRNA. Nucleic Acids Res. 1981 Nov 11;9(21):5645–5658. doi: 10.1093/nar/9.21.5645. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. 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]
  41. Sharp P. A. Splicing of messenger RNA precursors. Science. 1987 Feb 13;235(4790):766–771. doi: 10.1126/science.3544217. [DOI] [PubMed] [Google Scholar]
  42. Skuzeski J. M., Lund E., Murphy J. T., Steinberg T. H., Burgess R. R., Dahlberg J. E. Synthesis of human U1 RNA. II. Identification of two regions of the promoter essential for transcription initiation at position +1. J Biol Chem. 1984 Jul 10;259(13):8345–8352. [PubMed] [Google Scholar]
  43. Smith H. O., Birnstiel M. L. A simple method for DNA restriction site mapping. Nucleic Acids Res. 1976 Sep;3(9):2387–2398. doi: 10.1093/nar/3.9.2387. [DOI] [PMC free article] [PubMed] [Google Scholar]
  44. 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]
  45. Tollervey D., Mattaj I. W. Fungal small nuclear ribonucleoproteins share properties with plant and vertebrate U-snRNPs. EMBO J. 1987 Feb;6(2):469–476. doi: 10.1002/j.1460-2075.1987.tb04777.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  46. Van Arsdell S. W., Weiner A. M. Human genes for U2 small nuclear RNA are tandemly repeated. Mol Cell Biol. 1984 Mar;4(3):492–499. doi: 10.1128/mcb.4.3.492. [DOI] [PMC free article] [PubMed] [Google Scholar]
  47. Yuo C. Y., Ares M., Jr, Weiner A. M. Sequences required for 3' end formation of human U2 small nuclear RNA. Cell. 1985 Aug;42(1):193–202. doi: 10.1016/s0092-8674(85)80115-x. [DOI] [PubMed] [Google Scholar]
  48. de Vegvar H. E., Lund E., Dahlberg J. E. 3' end formation of U1 snRNA precursors is coupled to transcription from snRNA promoters. Cell. 1986 Oct 24;47(2):259–266. doi: 10.1016/0092-8674(86)90448-4. [DOI] [PubMed] [Google Scholar]

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