Skip to main content
PMC home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1992 Mar 25;20(6):1215–1221. doi: 10.1093/nar/20.6.1215

An additional long-range interaction in human U1 snRNA.

C Sturchler 1, P Carbon 1, A Krol 1
PMCID: PMC312161  PMID: 1532853

Abstract

We present evidence for the existence of an additional long-range interaction in vertebrate U1 snRNAs. By submitting human U1 snRNP, HeLa nuclear extracts, authentic human or X. laevis in vitro transcribed U1 snRNAs to RNase V1, a nuclease specific for double-stranded regions, cleavages occurred in the sequence psi psi ACC (positions 5-9) residing in the 5' terminal region of the RNA. The RNase V1 sensitive region is insensitive to single-stranded probes, something unexpected knowing that it was considered single-stranded in order to base-pair to pre-mRNA 5' splice site. We have identified the sequence GGUAG (positions 132-136) as the only possible 3' partner. Mutants, either abolishing or restoring the interaction between the partners, coupled to an RNase V1 assay, served to substantiate this base-pairing model. The presence of this additional helix, even detected in nuclear extracts under in vitro splicing conditions, implies that a conformational change must occur to release a free U1 snRNA 5' end.

Full text

PDF

Images in this article

1217Image
on p.1217
1218Image
on p.1218
1219Image
on p.1219

Selected References

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

  1. Bach M., Bringmann P., Lührmann R. Purification of small nuclear ribonucleoprotein particles with antibodies against modified nucleosides of small nuclear RNAs. Methods Enzymol. 1990;181:232–257. doi: 10.1016/0076-6879(90)81125-e. [DOI] [PubMed] [Google Scholar]
  2. Barabino S. M., Blencowe B. J., Ryder U., Sproat B. S., Lamond A. I. Targeted snRNP depletion reveals an additional role for mammalian U1 snRNP in spliceosome assembly. Cell. 1990 Oct 19;63(2):293–302. doi: 10.1016/0092-8674(90)90162-8. [DOI] [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. Brown D. T., Morris G. F., Chodchoy N., Sprecher C., Marzluff W. F. Structure of the sea urchin U1 RNA repeat. Nucleic Acids Res. 1985 Jan 25;13(2):537–556. doi: 10.1093/nar/13.2.537. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Datta B., Weiner A. M. Genetic evidence for base pairing between U2 and U6 snRNA in mammalian mRNA splicing. Nature. 1991 Aug 29;352(6338):821–824. doi: 10.1038/352821a0. [DOI] [PubMed] [Google Scholar]
  7. Dignam J. D., Lebovitz R. M., Roeder R. G. Accurate transcription initiation by RNA polymerase II in a soluble extract from isolated mammalian nuclei. Nucleic Acids Res. 1983 Mar 11;11(5):1475–1489. doi: 10.1093/nar/11.5.1475. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Guthrie C. Messenger RNA splicing in yeast: clues to why the spliceosome is a ribonucleoprotein. Science. 1991 Jul 12;253(5016):157–163. doi: 10.1126/science.1853200. [DOI] [PubMed] [Google Scholar]
  9. Guthrie C., Patterson B. Spliceosomal snRNAs. Annu Rev Genet. 1988;22:387–419. doi: 10.1146/annurev.ge.22.120188.002131. [DOI] [PubMed] [Google Scholar]
  10. Hamm J., Kazmaier M., Mattaj I. W. In vitro assembly of U1 snRNPs. EMBO J. 1987 Nov;6(11):3479–3485. doi: 10.1002/j.1460-2075.1987.tb02672.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Hanley B. A., Schuler M. A. cDNA cloning of U1, U2, U4 and U5 snRNA families expressed in pea nuclei. Nucleic Acids Res. 1991 Apr 25;19(8):1861–1869. doi: 10.1093/nar/19.8.1861. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Heinrichs V., Bach M., Winkelmann G., Lührmann R. U1-specific protein C needed for efficient complex formation of U1 snRNP with a 5' splice site. Science. 1990 Jan 5;247(4938):69–72. doi: 10.1126/science.2136774. [DOI] [PubMed] [Google Scholar]
  13. Krainer A. R., Maniatis T. Multiple factors including the small nuclear ribonucleoproteins U1 and U2 are necessary for pre-mRNA splicing in vitro. Cell. 1985 Oct;42(3):725–736. doi: 10.1016/0092-8674(85)90269-7. [DOI] [PubMed] [Google Scholar]
  14. Kretzner L., Krol A., Rosbash M. Saccharomyces cerevisiae U1 small nuclear RNA secondary structure contains both universal and yeast-specific domains. Proc Natl Acad Sci U S A. 1990 Jan;87(2):851–855. doi: 10.1073/pnas.87.2.851. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Krol A., Carbon P. A guide for probing native small nuclear RNA and ribonucleoprotein structures. Methods Enzymol. 1989;180:212–227. doi: 10.1016/0076-6879(89)80103-x. [DOI] [PubMed] [Google Scholar]
  16. Krol A., Westhof E., Bach M., Lührmann R., Ebel J. P., Carbon P. Solution structure of human U1 snRNA. Derivation of a possible three-dimensional model. Nucleic Acids Res. 1990 Jul 11;18(13):3803–3811. doi: 10.1093/nar/18.13.3803. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Krämer A., Keller W., Appel B., Lührmann R. The 5' terminus of the RNA moiety of U1 small nuclear ribonucleoprotein particles is required for the splicing of messenger RNA precursors. Cell. 1984 Aug;38(1):299–307. doi: 10.1016/0092-8674(84)90551-8. [DOI] [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. Lowman H. B., Draper D. E. On the recognition of helical RNA by cobra venom V1 nuclease. J Biol Chem. 1986 Apr 25;261(12):5396–5403. [PubMed] [Google Scholar]
  20. Lührmann R., Kastner B., Bach M. Structure of spliceosomal snRNPs and their role in pre-mRNA splicing. Biochim Biophys Acta. 1990 Nov 30;1087(3):265–292. doi: 10.1016/0167-4781(90)90001-i. [DOI] [PubMed] [Google Scholar]
  21. Mount S. M., Pettersson I., Hinterberger M., Karmas A., Steitz J. A. The U1 small nuclear RNA-protein complex selectively binds a 5' splice site in vitro. Cell. 1983 Jun;33(2):509–518. doi: 10.1016/0092-8674(83)90432-4. [DOI] [PubMed] [Google Scholar]
  22. 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]
  23. Murgo S., Krol A., Carbon P. Sequence, organization and transcriptional analysis of a gene encoding a U1 snRNA from the axolotl, Ambystoma mexicanum. Gene. 1991 Mar 15;99(2):163–170. doi: 10.1016/0378-1119(91)90123-s. [DOI] [PubMed] [Google Scholar]
  24. Myslinski E., Wilhelm F. X., Branlant C. A structural analysis of P. polycephalum U1 RNA at the RNA and gene levels. Are there differentially expressed U1 RNA genes in P. polycephalum? U1 RNA evolution. Nucleic Acids Res. 1989 Feb 11;17(3):1019–1034. doi: 10.1093/nar/17.3.1019. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Orum H., Nielsen H., Engberg J. Spliceosomal small nuclear RNAs of Tetrahymena thermophila and some possible snRNA-snRNA base-pairing interactions. J Mol Biol. 1991 Nov 20;222(2):219–232. doi: 10.1016/0022-2836(91)90208-n. [DOI] [PubMed] [Google Scholar]
  26. Porter G., Brennwald P., Wise J. A. U1 small nuclear RNA from Schizosaccharomyces pombe has unique and conserved features and is encoded by an essential single-copy gene. Mol Cell Biol. 1990 Jun;10(6):2874–2881. doi: 10.1128/mcb.10.6.2874. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Rinke J., Appel B., Blöcker H., Frank R., Lührmann R. The 5'-terminal sequence of U1 RNA complementary to the consensus 5' splice site of hnRNA is single-stranded in intact U1 snRNP particles. Nucleic Acids Res. 1984 May 25;12(10):4111–4126. doi: 10.1093/nar/12.10.4111. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Stolow D. T., Berget S. M. Identification of nuclear proteins that specifically bind to RNAs containing 5' splice sites. Proc Natl Acad Sci U S A. 1991 Jan 15;88(2):320–324. doi: 10.1073/pnas.88.2.320. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Thomas J., Lea K., Zucker-Aprison E., Blumenthal T. The spliceosomal snRNAs of Caenorhabditis elegans. Nucleic Acids Res. 1990 May 11;18(9):2633–2642. doi: 10.1093/nar/18.9.2633. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Wu J. A., Manley J. L. Base pairing between U2 and U6 snRNAs is necessary for splicing of a mammalian pre-mRNA. Nature. 1991 Aug 29;352(6338):818–821. doi: 10.1038/352818a0. [DOI] [PubMed] [Google Scholar]
  31. Zhuang Y., Weiner A. M. A compensatory base change in U1 snRNA suppresses a 5' splice site mutation. Cell. 1986 Sep 12;46(6):827–835. doi: 10.1016/0092-8674(86)90064-4. [DOI] [PubMed] [Google Scholar]

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

RESOURCES