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. 1996 Nov 15;24(22):4525–4534. doi: 10.1093/nar/24.22.4525

Increasing the distance between the snRNA promoter and the 3' box decreases the efficiency of snRNA 3'-end formation.

L Ramamurthy 1, T C Ingledue 1, D R Pilch 1, B K Kay 1, W F Marzluff 1
PMCID: PMC146281  PMID: 8948645

Abstract

Chimeric genes which contained the mouse U1b snRNA promoter, portions of the histone H2a or globin coding regions and the U1b 3'-end followed by a histone 3'-end were constructed. The distance between the U1 promoter and the U1 3' box was varied between 146 and 670 nt. The chimeric genes were introduced into CHO cells by stable transfection or into Xenopus oocytes by microinjection. The efficiency of utilization of the U1 3' box, as measured by the relative amounts of transcripts that ended at the U1 3' box and the histone 3'-end, was dependent on the distance between the promoter and 3'-end box. U1 3'-ends were formed with >90% efficiency on transcripts shorter than 200 nt, with 50-70% efficiency on transcripts of 280-400 nt and with only 10-20% efficiency on transcripts >500 nt. Essentially identical results were obtained after stable transfection of CHO cells or after injecting the genes into Xenopus oocytes. The distance between the U1 promoter and the U1 3' box must be <280 nt for efficient transcription termination at the U1 3' box, regardless of the sequence transcribed.

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Selected References

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

  1. Ach R. A., Weiner A. M. The highly conserved U small nuclear RNA 3'-end formation signal is quite tolerant to mutation. Mol Cell Biol. 1987 Jun;7(6):2070–2079. doi: 10.1128/mcb.7.6.2070. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Bartlett J. S., Sethna M., Ramamurthy L., Gowen S. A., Samulski R. J., Marzluff W. F. Efficient expression of protein coding genes from the murine U1 small nuclear RNA promoters. Proc Natl Acad Sci U S A. 1996 Aug 20;93(17):8852–8857. doi: 10.1073/pnas.93.17.8852. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Bentley D. L., Groudine M. Sequence requirements for premature termination of transcription in the human c-myc gene. Cell. 1988 Apr 22;53(2):245–256. doi: 10.1016/0092-8674(88)90386-8. [DOI] [PubMed] [Google Scholar]
  4. Birnstiel M. L., Busslinger M., Strub K. Transcription termination and 3' processing: the end is in site! Cell. 1985 Jun;41(2):349–359. doi: 10.1016/s0092-8674(85)80007-6. [DOI] [PubMed] [Google Scholar]
  5. Chaney W. G., Howard D. R., Pollard J. W., Sallustio S., Stanley P. High-frequency transfection of CHO cells using polybrene. Somat Cell Mol Genet. 1986 May;12(3):237–244. doi: 10.1007/BF01570782. [DOI] [PubMed] [Google Scholar]
  6. Connelly S., Filipowicz W. Activity of chimeric U small nuclear RNA (snRNA)/mRNA genes in transfected protoplasts of Nicotiana plumbaginifolia: U snRNA 3'-end formation and transcription initiation can occur independently in plants. Mol Cell Biol. 1993 Oct;13(10):6403–6415. doi: 10.1128/mcb.13.10.6403. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Evans J. P., Kay B. K. Biochemical fractionation of oocytes. Methods Cell Biol. 1991;36:133–148. doi: 10.1016/s0091-679x(08)60275-7. [DOI] [PubMed] [Google Scholar]
  8. Graves R. A., Wellman S. E., Chiu I. M., Marzluff W. F. Differential expression of two clusters of mouse histone genes. J Mol Biol. 1985 May 25;183(2):179–194. doi: 10.1016/0022-2836(85)90211-6. [DOI] [PubMed] [Google Scholar]
  9. 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]
  10. Hernandez N., Lucito R. Elements required for transcription initiation of the human U2 snRNA gene coincide with elements required for snRNA 3' end formation. EMBO J. 1988 Oct;7(10):3125–3134. doi: 10.1002/j.1460-2075.1988.tb03179.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Hernandez N., Weiner A. M. Formation of the 3' end of U1 snRNA requires compatible snRNA promoter elements. Cell. 1986 Oct 24;47(2):249–258. doi: 10.1016/0092-8674(86)90447-2. [DOI] [PubMed] [Google Scholar]
  12. Hurt M. M., Chodchoy N., Marzluff W. F. The mouse histone H2a.2 gene from chromosome 3. Nucleic Acids Res. 1989 Nov 11;17(21):8876–8876. doi: 10.1093/nar/17.21.8876. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Kay B. K. Xenopus laevis: Practical uses in cell and molecular biology. Injections of oocytes and embryos. Methods Cell Biol. 1991;36:663–669. [PubMed] [Google Scholar]
  14. Kephart D. D., Marshall N. F., Price D. H. Stability of Drosophila RNA polymerase II elongation complexes in vitro. Mol Cell Biol. 1992 May;12(5):2067–2077. doi: 10.1128/mcb.12.5.2067. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Kleinschmidt A. M., Pederson T. Accurate and efficient 3' processing of U2 small nuclear RNA precursor in a fractionated cytoplasmic extract. Mol Cell Biol. 1987 Sep;7(9):3131–3137. doi: 10.1128/mcb.7.9.3131. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Levine B. J., Liu T. J., Marzluff W. F., Skoultchi A. I. Differential expression of individual members of the histone multigene family due to sequences in the 5' and 3' regions of the genes. Mol Cell Biol. 1988 May;8(5):1887–1895. doi: 10.1128/mcb.8.5.1887. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Liu T. J., Levine B. J., Skoultchi A. I., Marzluff W. F. The efficiency of 3'-end formation contributes to the relative levels of different histone mRNAs. Mol Cell Biol. 1989 Aug;9(8):3499–3508. doi: 10.1128/mcb.9.8.3499. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Lobo S. M., Marzluff W. F. Synthesis of U1 RNA in isolated mouse cell nuclei: initiation and 3'-end formation. Mol Cell Biol. 1987 Dec;7(12):4290–4296. doi: 10.1128/mcb.7.12.4290. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Lund E., Dahlberg J. E. In vitro synthesis of vertebrate U1 snRNA. EMBO J. 1989 Jan;8(1):287–292. doi: 10.1002/j.1460-2075.1989.tb03375.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Marshall N. F., Price D. H. Control of formation of two distinct classes of RNA polymerase II elongation complexes. Mol Cell Biol. 1992 May;12(5):2078–2090. doi: 10.1128/mcb.12.5.2078. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. 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]
  22. Middleton K. M., Morgan G. T. Premature termination of transcription can be induced on an injected alpha-tubulin gene in Xenopus oocytes. Mol Cell Biol. 1990 Feb;10(2):727–735. doi: 10.1128/mcb.10.2.727. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Moussa N. M., el-Din A. S., Lobo S. M., Marzluff W. F. A mouse Ulb-2 gene with extensive sequence similarity to a rat Ula gene for 670 nucleotides 5' to the gene. Nucleic Acids Res. 1987 Apr 24;15(8):3622–3622. doi: 10.1093/nar/15.8.3622. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. 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]
  25. Neuman de Vegvar H. E., Dahlberg J. E. Nucleocytoplasmic transport and processing of small nuclear RNA precursors. Mol Cell Biol. 1990 Jul;10(7):3365–3375. doi: 10.1128/mcb.10.7.3365. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Parry H. D., Tebb G., Mattaj I. W. The Xenopus U2 gene PSE is a single, compact, element required for transcription initiation and 3' end formation. Nucleic Acids Res. 1989 May 25;17(10):3633–3644. doi: 10.1093/nar/17.10.3633. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Patterson B., Guthrie C. An essential yeast snRNA with a U5-like domain is required for splicing in vivo. Cell. 1987 Jun 5;49(5):613–624. doi: 10.1016/0092-8674(87)90537-x. [DOI] [PubMed] [Google Scholar]
  28. Pilch D. R., Marzluff W. F. Expression of histone-U1 snRNA chimeric genes: U1 promoters are compatible with histone 3' end formation. Gene Expr. 1991 Apr;1(1):41–53. [PMC free article] [PubMed] [Google Scholar]
  29. Roiha H., Shuster E. O., Brow D. A., Guthrie C. Small nuclear RNAs from budding yeasts: phylogenetic comparisons reveal extensive size variation. Gene. 1989 Oct 15;82(1):137–144. doi: 10.1016/0378-1119(89)90038-3. [DOI] [PubMed] [Google Scholar]
  30. Spencer C. A., Groudine M. Transcription elongation and eukaryotic gene regulation. Oncogene. 1990 Jun;5(6):777–785. [PubMed] [Google Scholar]
  31. Sun J., Pilch D. R., Marzluff W. F. The histone mRNA 3' end is required for localization of histone mRNA to polyribosomes. Nucleic Acids Res. 1992 Nov 25;20(22):6057–6066. doi: 10.1093/nar/20.22.6057. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Wendelburg B. J., Marzluff W. F. Formation of the 3' end of sea urchin U1 small nuclear RNA occurs independently of the conserved 3' box and on transcripts initiated from a histone promoter. Mol Cell Biol. 1992 Sep;12(9):4132–4141. doi: 10.1128/mcb.12.9.4132. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Yang H., Moss M. L., Lund E., Dahlberg J. E. Nuclear processing of the 3'-terminal nucleotides of pre-U1 RNA in Xenopus laevis oocytes. Mol Cell Biol. 1992 Apr;12(4):1553–1560. doi: 10.1128/mcb.12.4.1553. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. 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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