Skip to main content
PMC home page
The EMBO Journal logoLink to The EMBO Journal
. 1985 Jul;4(7):1827–1837. doi: 10.1002/j.1460-2075.1985.tb03857.x

Formation of the 3' end of U1 snRNA is directed by a conserved sequence located downstream of the coding region.

N Hernandez
PMCID: PMC554424  PMID: 2411548

Abstract

U1 is a small non-polyadenylated nuclear RNA that is transcribed by RNA polymerase II and is known to play a role in mRNA splicing. The mature 3' end of U1 snRNA is formed in at least two steps. The first step generates precursors of U1 RNA with a few extra nucleotides at the 3' end; in the second step, these precursors are shortened to mature U1 RNA. Here, I have determined the sequences required for the first step. Human U1 genes with various deletions and substitutions near the 3' end of the coding region were constructed and introduced into HeLa cells by DNA transfection. The structure of the RNA synthesized during transient expression of the exogenous U1 gene was analyzed by S1 mapping. The results show that a 13 nucleotide sequence located downstream from the U1 coding region and conserved among U1, U2 and U3 genes of different species is the only sequence required to direct the first step in the formation of the 3' end of U1 snRNA.

Full text

PDF

Images in this article

1828Fig. 2.
on p.1828
1829Fig. 3.
on p.1829
1829Fig. 4.
on p.1829
1830Fig. 5.
on p.1830
1832Fig. 6.
on p.1832
1833Fig. 7.
on p.1833
1834Fig. 8.
on p.1834

Selected References

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

  1. Acheson N. H. Polyoma virus giant RNAs contain tandem repeats of the nucleotide sequence of the entire viral genome. Proc Natl Acad Sci U S A. 1978 Oct;75(10):4754–4758. doi: 10.1073/pnas.75.10.4754. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Alonso A., Beck E., Jorcano J. L., Hovemann B. Divergence of U2 snRNA sequences in the genome of D. melanogaster. Nucleic Acids Res. 1984 Dec 21;12(24):9543–9550. doi: 10.1093/nar/12.24.9543. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Alonso A., Jorcano J. L., Beck E., Hovemann B., Schmidt T. Drosophila melanogaster U1 snRNA genes. J Mol Biol. 1984 Dec 25;180(4):825–836. doi: 10.1016/0022-2836(84)90259-6. [DOI] [PubMed] [Google Scholar]
  4. Amara S. G., Evans R. M., Rosenfeld M. G. Calcitonin/calcitonin gene-related peptide transcription unit: tissue-specific expression involves selective use of alternative polyadenylation sites. Mol Cell Biol. 1984 Oct;4(10):2151–2160. doi: 10.1128/mcb.4.10.2151. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Berget S. M. Are U4 small nuclear ribonucleoproteins involved in polyadenylation? Nature. 1984 May 10;309(5964):179–182. doi: 10.1038/309179a0. [DOI] [PubMed] [Google Scholar]
  6. Berk A. J., Lee F., Harrison T., Williams J., Sharp P. A. Pre-early adenovirus 5 gene product regulates synthesis of early viral messenger RNAs. Cell. 1979 Aug;17(4):935–944. doi: 10.1016/0092-8674(79)90333-7. [DOI] [PubMed] [Google Scholar]
  7. Birchmeier C., Folk W., Birnstiel M. L. The terminal RNA stem-loop structure and 80 bp of spacer DNA are required for the formation of 3' termini of sea urchin H2A mRNA. Cell. 1983 Dec;35(2 Pt 1):433–440. doi: 10.1016/0092-8674(83)90176-9. [DOI] [PubMed] [Google Scholar]
  8. Birchmeier C., Grosschedl R., Birnstiel M. L. Generation of authentic 3' termini of an H2A mRNA in vivo is dependent on a short inverted DNA repeat and on spacer sequences. Cell. 1982 Apr;28(4):739–745. doi: 10.1016/0092-8674(82)90053-8. [DOI] [PubMed] [Google Scholar]
  9. Birchmeier C., Schümperli D., Sconzo G., Birnstiel M. L. 3' editing of mRNAs: sequence requirements and involvement of a 60-nucleotide RNA in maturation of histone mRNA precursors. Proc Natl Acad Sci U S A. 1984 Feb;81(4):1057–1061. doi: 10.1073/pnas.81.4.1057. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Bringmann P., Appel B., Rinke J., Reuter R., Theissen H., Lührmann R. Evidence for the existence of snRNAs U4 and U6 in a single ribonucleoprotein complex and for their association by intermolecular base pairing. EMBO J. 1984 Jun;3(6):1357–1363. doi: 10.1002/j.1460-2075.1984.tb01977.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. 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]
  12. Chandrasekharappa S. C., Smith J. H., Eliceiri G. L. Biosynthesis of small nuclear RNAs in human cells. J Cell Physiol. 1983 Nov;117(2):169–174. doi: 10.1002/jcp.1041170206. [DOI] [PubMed] [Google Scholar]
  13. Eliceiri G. L. Formation of low molecular weight RNA species in HeLa cells. J Cell Physiol. 1980 Feb;102(2):199–207. doi: 10.1002/jcp.1041020211. [DOI] [PubMed] [Google Scholar]
  14. Eliceiri G. L., Sayavedra M. S. Small RNAs in the nucleus and cytoplasm of HeLa cells. Biochem Biophys Res Commun. 1976 Sep 20;72(2):507–512. doi: 10.1016/s0006-291x(76)80070-8. [DOI] [PubMed] [Google Scholar]
  15. Eliceiri G. L. Short-lived, small RNAs in the cytoplasm of HeLa cells. Cell. 1974 Sep;3(1):11–14. doi: 10.1016/0092-8674(74)90031-2. [DOI] [PubMed] [Google Scholar]
  16. Fitzgerald M., Shenk T. The sequence 5'-AAUAAA-3'forms parts of the recognition site for polyadenylation of late SV40 mRNAs. Cell. 1981 Apr;24(1):251–260. doi: 10.1016/0092-8674(81)90521-3. [DOI] [PubMed] [Google Scholar]
  17. Ford J. P., Hsu M. T. Transcription pattern of in vivo-labeled late simian virus 40 RNA: equimolar transcription beyond the mRNA 3' terminus. J Virol. 1978 Dec;28(3):795–801. doi: 10.1128/jvi.28.3.795-801.1978. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Frayne E. G., Leys E. J., Crouse G. F., Hook A. G., Kellems R. E. Transcription of the mouse dihydrofolate reductase gene proceeds unabated through seven polyadenylation sites and terminates near a region of repeated DNA. Mol Cell Biol. 1984 Dec;4(12):2921–2924. doi: 10.1128/mcb.4.12.2921. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Frederiksen S., Hellung-Larsen P., Gram Jensen E. The differential inhibitory effect of alpha-amanitin on the synthesis of low molecular weight RNA components in BHK cells. FEBS Lett. 1978 Mar 15;87(2):227–231. doi: 10.1016/0014-5793(78)80338-x. [DOI] [PubMed] [Google Scholar]
  20. Georgiev O., Birnstiel M. L. The conserved CAAGAAAGA spacer sequence is an essential element for the formation of 3' termini of the sea urchin H3 histone mRNA by RNA processing. EMBO J. 1985 Feb;4(2):481–489. doi: 10.1002/j.1460-2075.1985.tb03654.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Gil A., Proudfoot N. J. A sequence downstream of AAUAAA is required for rabbit beta-globin mRNA 3'-end formation. 1984 Nov 29-Dec 5Nature. 312(5993):473–474. doi: 10.1038/312473a0. [DOI] [PubMed] [Google Scholar]
  22. Hagenbüchle O., Wellauer P. K., Cribbs D. L., Schibler U. Termination of transcription in the mouse alpha-amylase gene Amy-2a occurs at multiple sites downstream of the polyadenylation site. Cell. 1984 Oct;38(3):737–744. doi: 10.1016/0092-8674(84)90269-1. [DOI] [PubMed] [Google Scholar]
  23. Hashimoto C., Steitz J. A. U4 and U6 RNAs coexist in a single small nuclear ribonucleoprotein particle. Nucleic Acids Res. 1984 Apr 11;12(7):3283–3293. doi: 10.1093/nar/12.7.3283. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Hentschel C. C., Birnstiel M. L. The organization and expression of histone gene families. Cell. 1981 Aug;25(2):301–313. doi: 10.1016/0092-8674(81)90048-9. [DOI] [PubMed] [Google Scholar]
  25. Hernandez N., Keller W. Splicing of in vitro synthesized messenger RNA precursors in HeLa cell extracts. Cell. 1983 Nov;35(1):89–99. doi: 10.1016/0092-8674(83)90211-8. [DOI] [PubMed] [Google Scholar]
  26. Higgs D. R., Goodbourn S. E., Lamb J., Clegg J. B., Weatherall D. J., Proudfoot N. J. Alpha-thalassaemia caused by a polyadenylation signal mutation. Nature. 1983 Nov 24;306(5941):398–400. doi: 10.1038/306398a0. [DOI] [PubMed] [Google Scholar]
  27. Hofer E., Darnell J. E., Jr The primary transcription unit of the mouse beta-major globin gene. Cell. 1981 Feb;23(2):585–593. doi: 10.1016/0092-8674(81)90154-9. [DOI] [PubMed] [Google Scholar]
  28. Krieg P. A., Melton D. A. Formation of the 3' end of histone mRNA by post-transcriptional processing. Nature. 1984 Mar 8;308(5955):203–206. doi: 10.1038/308203a0. [DOI] [PubMed] [Google Scholar]
  29. 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]
  30. 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]
  31. 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]
  32. 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]
  33. 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]
  34. Mather E. L., Nelson K. J., Haimovich J., Perry R. P. Mode of regulation of immunoglobulin mu- and delta-chain expression varies during B-lymphocyte maturation. Cell. 1984 Feb;36(2):329–338. doi: 10.1016/0092-8674(84)90226-5. [DOI] [PubMed] [Google Scholar]
  35. 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]
  36. Maxam A. M., Gilbert W. A new method for sequencing DNA. Proc Natl Acad Sci U S A. 1977 Feb;74(2):560–564. doi: 10.1073/pnas.74.2.560. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. McDevitt M. A., Imperiale M. J., Ali H., Nevins J. R. Requirement of a downstream sequence for generation of a poly(A) addition site. Cell. 1984 Jul;37(3):993–999. doi: 10.1016/0092-8674(84)90433-1. [DOI] [PubMed] [Google Scholar]
  38. McLauchlan J., Gaffney D., Whitton J. L., Clements J. B. The consensus sequence YGTGTTYY located downstream from the AATAAA signal is required for efficient formation of mRNA 3' termini. Nucleic Acids Res. 1985 Feb 25;13(4):1347–1368. doi: 10.1093/nar/13.4.1347. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Montell C., Fisher E. F., Caruthers M. H., Berk A. J. Inhibition of RNA cleavage but not polyadenylation by a point mutation in mRNA 3' consensus sequence AAUAAA. Nature. 1983 Oct 13;305(5935):600–605. doi: 10.1038/305600a0. [DOI] [PubMed] [Google Scholar]
  40. 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]
  41. 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]
  42. Nevins J. R., Blanchard J. M., Darnell J. E., Jr Transcription units of adenovirus type 2. Termination of transcription beyond the poly(A) addition site in early regions 2 and 4. J Mol Biol. 1980 Dec 15;144(3):377–386. doi: 10.1016/0022-2836(80)90096-0. [DOI] [PubMed] [Google Scholar]
  43. Nevins J. R., Darnell J. E., Jr Steps in the processing of Ad2 mRNA: poly(A)+ nuclear sequences are conserved and poly(A) addition precedes splicing. Cell. 1978 Dec;15(4):1477–1493. doi: 10.1016/0092-8674(78)90071-5. [DOI] [PubMed] [Google Scholar]
  44. 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]
  45. Price D. H., Parker C. S. The 3' end of drosophila histone H3 mRNA is produced by a processing activity in vitro. Cell. 1984 Sep;38(2):423–429. doi: 10.1016/0092-8674(84)90497-5. [DOI] [PubMed] [Google Scholar]
  46. 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]
  47. Sheffery M., Marks P. A., Rifkind R. A. Gene expression in murine erythroleukemia cells. Transcriptional control and chromatin structure of the alpha 1-globin gene. J Mol Biol. 1984 Feb 5;172(4):417–436. doi: 10.1016/s0022-2836(84)80015-7. [DOI] [PubMed] [Google Scholar]
  48. Simonsen C. C., Levinson A. D. Analysis of processing and polyadenylation signals of the hepatitis B virus surface antigen gene by using simian virus 40-hepatitis B virus chimeric plasmids. Mol Cell Biol. 1983 Dec;3(12):2250–2258. doi: 10.1128/mcb.3.12.2250. [DOI] [PMC free article] [PubMed] [Google Scholar]
  49. 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]
  50. Strub K., Galli G., Busslinger M., Birnstiel M. L. The cDNA sequences of the sea urchin U7 small nuclear RNA suggest specific contacts between histone mRNA precursor and U7 RNA during RNA processing. EMBO J. 1984 Dec 1;3(12):2801–2807. doi: 10.1002/j.1460-2075.1984.tb02212.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  51. Stunnenberg H. G., Birnstiel M. L. Bioassay for components regulating eukaryotic gene expression: a chromosomal factor involved in the generation of histone mRNA 3' termini. Proc Natl Acad Sci U S A. 1982 Oct;79(20):6201–6204. doi: 10.1073/pnas.79.20.6201. [DOI] [PMC free article] [PubMed] [Google Scholar]
  52. 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]
  53. 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]
  54. Weinberg R., Penman S. Metabolism of small molecular weight monodisperse nuclear RNA. Biochim Biophys Acta. 1969 Sep 17;190(1):10–29. doi: 10.1016/0005-2787(69)90150-6. [DOI] [PubMed] [Google Scholar]
  55. Westin G., Lund E., Murphy J. T., Pettersson U., Dahlberg J. E. Human U2 and U1 RNA genes use similar transcription signals. EMBO J. 1984 Dec 20;3(13):3295–3301. doi: 10.1002/j.1460-2075.1984.tb02293.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  56. Wickens M., Stephenson P. Role of the conserved AAUAAA sequence: four AAUAAA point mutants prevent messenger RNA 3' end formation. Science. 1984 Nov 30;226(4678):1045–1051. doi: 10.1126/science.6208611. [DOI] [PubMed] [Google Scholar]
  57. Wigler M., Pellicer A., Silverstein S., Axel R. Biochemical transfer of single-copy eucaryotic genes using total cellular DNA as donor. Cell. 1978 Jul;14(3):725–731. doi: 10.1016/0092-8674(78)90254-4. [DOI] [PubMed] [Google Scholar]
  58. Zhong R., Roeder R. G., Heintz N. The primary structure and expression of four cloned human histone genes. Nucleic Acids Res. 1983 Nov 11;11(21):7409–7425. doi: 10.1093/nar/11.21.7409. [DOI] [PMC free article] [PubMed] [Google Scholar]
  59. Zieve G., Benecke B. J., Penman S. Synthesis of two classes of small RNA species in vivo and in vitro. Biochemistry. 1977 Oct 4;16(20):4520–4525. doi: 10.1021/bi00639a029. [DOI] [PubMed] [Google Scholar]
  60. 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