Skip to main content
PMC home page
The EMBO Journal logoLink to The EMBO Journal
. 1982;1(10):1259–1265. doi: 10.1002/j.1460-2075.1982.tb00022.x

U2 RNA shares a structural domain with U1, U4, and U5 RNAs.

C Branlant, A Krol, J P Ebel, E Lazar, B Haendler, M Jacob
PMCID: PMC553198  PMID: 6202507

Abstract

We previously reported common structural features within the 3'-terminal regions of U1, U4, and U5 RNAs. To check whether these features also exist in U2 RNA, the primary and secondary structures of the 3'-terminal regions of chicken, pheasant, and rat U2 RNAs were examined. Whereas no difference was observed between pheasant and chicken, the chicken and rat sequences were only 82.5% homologous. Such divergence allowed us to propose a unique model of secondary structure based on maximum base-pairing and secondary structure conservation. The same model was obtained from the results of limited digestion of U2 RNA with various nucleases. Comparison of this structure with those of U1, U4, and U5 RNAs shows that the four RNAs share a common structure designated as domain A, and consisting of a free single-stranded region with the sequence Pu-A-(U)n-G-Pup flanked by two hairpins. The hairpin on the 3' side is very stable and has the sequence Py-N-Py-Gp in the loop. The presence of this common domain is discussed in connection with relationships among U RNAs and common protein binding sites.

Full text

PDF
1259

Images in this article

1261Fig. 2.
on p.1261

Selected References

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

  1. 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]
  2. 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]
  3. Branlant C., Krol A., Machatt M. A., Pouyet J., Ebel J. P., Edwards K., Kössel H. Primary and secondary structures of Escherichia coli MRE 600 23S ribosomal RNA. Comparison with models of secondary structure for maize chloroplast 23S rRNA and for large portions of mouse and human 16S mitochondrial rRNAs. Nucleic Acids Res. 1981 Sep 11;9(17):4303–4324. doi: 10.1093/nar/9.17.4303. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Calvet J. P., Pederson T. Base-pairing interactions between small nuclear RNAs and nuclear RNA precursors as revealed by psoralen cross-linking in vivo. Cell. 1981 Nov;26(3 Pt 1):363–370. doi: 10.1016/0092-8674(81)90205-1. [DOI] [PubMed] [Google Scholar]
  5. Deimel B., Louis C. H., Sekeris C. E. The presence of small molecular weight RNAs in nuclear ribonucleoprotein particles carrying HnRNA. FEBS Lett. 1977 Jan 15;73(1):80–84. [PubMed] [Google Scholar]
  6. Deininger P. L., Jolly D. J., Rubin C. M., Friedmann T., Schmid C. W. Base sequence studies of 300 nucleotide renatured repeated human DNA clones. J Mol Biol. 1981 Sep 5;151(1):17–33. doi: 10.1016/0022-2836(81)90219-9. [DOI] [PubMed] [Google Scholar]
  7. Denison R. A., Van Arsdell S. W., Bernstein L. B., Weiner A. M. Abundant pseudogenes for small nuclear RNAs are dispersed in the human genome. Proc Natl Acad Sci U S A. 1981 Feb;78(2):810–814. doi: 10.1073/pnas.78.2.810. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. 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]
  9. Epstein P., Reddy R., Busch H. Site-specific cleavage by T1 RNase of U-1 RNA in u-1 ribonucleoprotein particles. Proc Natl Acad Sci U S A. 1981 Mar;78(3):1562–1566. doi: 10.1073/pnas.78.3.1562. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Epstein P., Reddy R., Henning D., Busch H. The nucleotide sequence of nuclear U6 (4.7 S) RNA. J Biol Chem. 1980 Sep 25;255(18):8901–8906. [PubMed] [Google Scholar]
  11. Gallinaro H., Jacob M. An evaluation of small nuclear RNA in hnRNP. FEBS Lett. 1979 Aug 1;104(1):176–182. doi: 10.1016/0014-5793(79)81110-2. [DOI] [PubMed] [Google Scholar]
  12. Grimaldi G., Queen C., Singer M. F. Interspersed repeated sequences in the African green monkey genome that are homologous to the human Alu family. Nucleic Acids Res. 1981 Nov 11;9(21):5553–5568. doi: 10.1093/nar/9.21.5553. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Guimont-Ducamp C., Sri-Widada J., Jeanteur P. Occurrence of small molecular weight RNAs in Hela nuclear ribonucleoprotein particles containing HnRNA. Biochimie. 1977;59(8-9):755–758. doi: 10.1016/s0300-9084(77)80259-9. [DOI] [PubMed] [Google Scholar]
  14. Hayashi K. Organization of sequences related to U6 RNA in the human genome. Nucleic Acids Res. 1981 Jul 24;9(14):3379–3388. doi: 10.1093/nar/9.14.3379. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Krol A., Branlant C., Lazar E., Gallinaro H., Jacob M. Primary and secondary structures of chicken, rat and man nuclear U4 RNAs. Homologies with U1 and U5 RNAs. Nucleic Acids Res. 1981 Jun 25;9(12):2699–2716. doi: 10.1093/nar/9.12.2699. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Krol A., Gallinaro H., Lazar E., Jacob M., Branlant C. The nuclear 5S RNAs from chicken, rat and man. U5 RNAs are encoded by multiple genes. Nucleic Acids Res. 1981 Feb 25;9(4):769–787. doi: 10.1093/nar/9.4.769. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Krupp G., Gross H. J. Rapid RNA sequencing: nucleases from Staphylococcus aureus and Neurospora crassa discriminate between uridine and cytidine. Nucleic Acids Res. 1979 Aug 10;6(11):3481–3490. doi: 10.1093/nar/6.11.3481. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Lazar E., Jacob M., Krol A., Branlant C. Accessibility of U1 RNA to base pairing with a single-stranded DNA fragment mimicking the intron extremities at the splice junction. Nucleic Acids Res. 1982 Feb 25;10(4):1193–1201. doi: 10.1093/nar/10.4.1193. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. 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]
  20. Lerner M. R., Steitz J. A. Antibodies to small nuclear RNAs complexed with proteins are produced by patients with systemic lupus erythematosus. Proc Natl Acad Sci U S A. 1979 Nov;76(11):5495–5499. doi: 10.1073/pnas.76.11.5495. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Manser T., Gesteland R. F. Characterization of small nuclear RNA U1 gene candidates and pseudogenes from the human genome. J Mol Appl Genet. 1981;1(2):117–125. [PubMed] [Google Scholar]
  22. Miller T. E., Huang C. Y., Pogo A. O. Rat liver nuclear skeleton and small molecular weight RNA species. J Cell Biol. 1978 Mar;76(3):692–704. doi: 10.1083/jcb.76.3.692. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. 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]
  24. 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]
  25. Northemann W., Scheurlen M., Gross V., Heinrich P. C. Circular dichroism of ribonucleoprotein complexes from rat liver nuclei. Biochem Biophys Res Commun. 1977 Jun 20;76(4):1130–1137. doi: 10.1016/0006-291x(77)90973-1. [DOI] [PubMed] [Google Scholar]
  26. 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]
  27. Ohshima Y., Okada N., Tani T., Itoh Y., Itoh M. Nucleotide sequences of mouse genomic loci including a gene or pseudogene for U6 (4.8S) nuclear RNA. Nucleic Acids Res. 1981 Oct 10;9(19):5145–5158. doi: 10.1093/nar/9.19.5145. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. 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]
  29. Prestayko A. W., Tonato M., Lewis B. C., Busch H. Heterogeneity of nucleolar U3 ribonucleic acid of the Novikoff hepatoma. J Biol Chem. 1971 Jan 10;246(1):182–187. [PubMed] [Google Scholar]
  30. Raj N. B., Ro-Choi T. S., Busch H. Nuclear ribonucleoprotein complexes containing U1 and U2 RNA. Biochemistry. 1975 Oct 7;14(20):4380–4385. doi: 10.1021/bi00691a006. [DOI] [PubMed] [Google Scholar]
  31. 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]
  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. Sri-Widada J., Liautard J. P., Assens C., Brunel C. Primary structure identification of snRNAs present in highly purified snRNPs from HeLa cells. Mol Biol Rep. 1981 Nov 30;8(1):29–36. doi: 10.1007/BF00798382. [DOI] [PubMed] [Google Scholar]
  34. Stiegler P., Carbon P., Ebel J. P., Ehresmann C. A general secondary-structure model for procaryotic and eucaryotic RNAs from the small ribosomal subunits. Eur J Biochem. 1981 Dec;120(3):487–495. doi: 10.1111/j.1432-1033.1981.tb05727.x. [DOI] [PubMed] [Google Scholar]
  35. Van Arsdell S. W., Denison R. A., Bernstein L. B., Weiner A. M., Manser T., Gesteland R. F. Direct repeats flank three small nuclear RNA pseudogenes in the human genome. Cell. 1981 Oct;26(1 Pt 1):11–17. doi: 10.1016/0092-8674(81)90028-3. [DOI] [PubMed] [Google Scholar]
  36. Westin G., Monstein H. J., Zabielski J., Philipson L., Pettersson U. Human DNA sequences complementary to the small nuclear RNA U2. Nucleic Acids Res. 1981 Dec 11;9(23):6323–6338. doi: 10.1093/nar/9.23.6323. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Zaug A. J., Cech T. R. The intervening sequence excised from the ribosomal RNA precursor of Tetrahymena contains a 5-terminal guanosine residue not encoded by the DNA. Nucleic Acids Res. 1982 May 11;10(9):2823–2838. doi: 10.1093/nar/10.9.2823. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. 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 The EMBO Journal are provided here courtesy of Nature Publishing Group

RESOURCES