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. 1994 Jan;14(1):77–86. doi: 10.1128/mcb.14.1.77

Exon size affects competition between splicing and cleavage-polyadenylation in the immunoglobulin mu gene.

M L Peterson 1, M B Bryman 1, M Peiter 1, C Cowan 1
PMCID: PMC358358  PMID: 7903422

Abstract

The alternative RNA processing of microseconds and microns mRNAs from a single primary transcript depends on competition between a cleavage-polyadenylation reaction to produce microseconds mRNA and a splicing reaction to produce microns mRNA. The ratio of microseconds to microns mRNA is regulated during B-cell maturation; relatively more spliced microns mRNA is made in B cells than in plasma cells. The balance between the efficiencies of splicing and cleavage-polyadenylation is critical to the regulation. The mu gene can be modified to either reduce or improve the efficiency of each reaction and thus alter the ratio of the two RNAs produced. However, as long as neither reaction is so strong that it totally dominates, expression of the modified mu genes is regulated in B cells and plasma cells. The current experiments reveal a relationship between the C mu 4 exon size and the microseconds/microns expression ratio. The shorter the distance between the C mu 4 5' splice site and the nearest upstream 3' splice site, the more spliced microns mRNA was produced. Conversely, when this exon was expanded, more microseconds mRNA was produced. Expression from these mu genes with altered exon sizes were regulated between B cells and plasma cells. Since RNA processing in the mu gene can be considered a competition between defining the C mu 4 exon as an internal exon (in microns mRNA) versus a terminal exon (in microseconds mRNA), exon size may affect the competition among factors interacting with this exon.

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Selected References

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

  1. Brewer G., Ross J. Messenger RNA turnover in cell-free extracts. Methods Enzymol. 1990;181:202–209. doi: 10.1016/0076-6879(90)81122-b. [DOI] [PubMed] [Google Scholar]
  2. Buchman A. R., Berg P. Comparison of intron-dependent and intron-independent gene expression. Mol Cell Biol. 1988 Oct;8(10):4395–4405. doi: 10.1128/mcb.8.10.4395. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Chang D. D., Sharp P. A. Messenger RNA transport and HIV rev regulation. Science. 1990 Aug 10;249(4969):614–615. doi: 10.1126/science.2143313. [DOI] [PubMed] [Google Scholar]
  4. Chiou H. C., Dabrowski C., Alwine J. C. Simian virus 40 late mRNA leader sequences involved in augmenting mRNA accumulation via multiple mechanisms, including increased polyadenylation efficiency. J Virol. 1991 Dec;65(12):6677–6685. doi: 10.1128/jvi.65.12.6677-6685.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Chung S., Perry R. P. Importance of introns for expression of mouse ribosomal protein gene rpL32. Mol Cell Biol. 1989 May;9(5):2075–2082. doi: 10.1128/mcb.9.5.2075. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Cooper T. A. In vitro splicing of cardiac troponin T precursors. Exon mutations disrupt splicing of the upstream intron. J Biol Chem. 1992 Mar 15;267(8):5330–5338. [PubMed] [Google Scholar]
  7. Dominski Z., Kole R. Cooperation of pre-mRNA sequence elements in splice site selection. Mol Cell Biol. 1992 May;12(5):2108–2114. doi: 10.1128/mcb.12.5.2108. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Dominski Z., Kole R. Selection of splice sites in pre-mRNAs with short internal exons. Mol Cell Biol. 1991 Dec;11(12):6075–6083. doi: 10.1128/mcb.11.12.6075. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Galli G., Guise J. W., McDevitt M. A., Tucker P. W., Nevins J. R. Relative position and strengths of poly(A) sites as well as transcription termination are critical to membrane versus secreted mu-chain expression during B-cell development. Genes Dev. 1987 Jul;1(5):471–481. doi: 10.1101/gad.1.5.471. [DOI] [PubMed] [Google Scholar]
  10. Galli G., Guise J., Tucker P. W., Nevins J. R. Poly(A) site choice rather than splice site choice governs the regulated production of IgM heavy-chain RNAs. Proc Natl Acad Sci U S A. 1988 Apr;85(8):2439–2443. doi: 10.1073/pnas.85.8.2439. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Grosschedl R., Baltimore D. Cell-type specificity of immunoglobulin gene expression is regulated by at least three DNA sequence elements. Cell. 1985 Jul;41(3):885–897. doi: 10.1016/s0092-8674(85)80069-6. [DOI] [PubMed] [Google Scholar]
  12. Hawkins J. D. A survey on intron and exon lengths. Nucleic Acids Res. 1988 Nov 11;16(21):9893–9908. doi: 10.1093/nar/16.21.9893. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Higgins C. F. Stability and degradation of mRNA. Curr Opin Cell Biol. 1991 Dec;3(6):1013–1018. doi: 10.1016/0955-0674(91)90122-f. [DOI] [PubMed] [Google Scholar]
  14. Hoffman B. E., Grabowski P. J. U1 snRNP targets an essential splicing factor, U2AF65, to the 3' splice site by a network of interactions spanning the exon. Genes Dev. 1992 Dec;6(12B):2554–2568. doi: 10.1101/gad.6.12b.2554. [DOI] [PubMed] [Google Scholar]
  15. Huang M. T., Gorman C. M. Intervening sequences increase efficiency of RNA 3' processing and accumulation of cytoplasmic RNA. Nucleic Acids Res. 1990 Feb 25;18(4):937–947. doi: 10.1093/nar/18.4.937. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Lassman C. R., Milcarek C. Regulated expression of the mouse gamma 2b Ig H chain gene is influenced by polyA site order and strength. J Immunol. 1992 Apr 15;148(8):2578–2585. [PubMed] [Google Scholar]
  17. Luo Y., Carmichael G. G. Splice site choice in a complex transcription unit containing multiple inefficient polyadenylation signals. Mol Cell Biol. 1991 Oct;11(10):5291–5300. doi: 10.1128/mcb.11.10.5291. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Luo Y., Carmichael G. G. Splice site skipping in polyomavirus late pre-mRNA processing. J Virol. 1991 Dec;65(12):6637–6644. doi: 10.1128/jvi.65.12.6637-6644.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Nesic D., Cheng J., Maquat L. E. Sequences within the last intron function in RNA 3'-end formation in cultured cells. Mol Cell Biol. 1993 Jun;13(6):3359–3369. doi: 10.1128/mcb.13.6.3359. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Nishikura K., Vuocolo G. A. Synthesis of two mRNAs by utilization of alternate polyadenylation sites: expression of SV40-mouse immunoglobulin mu chain gene recombinants in Cos monkey cells. EMBO J. 1984 Apr;3(4):689–699. doi: 10.1002/j.1460-2075.1984.tb01871.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Niwa M., Berget S. M. Mutation of the AAUAAA polyadenylation signal depresses in vitro splicing of proximal but not distal introns. Genes Dev. 1991 Nov;5(11):2086–2095. doi: 10.1101/gad.5.11.2086. [DOI] [PubMed] [Google Scholar]
  22. Niwa M., Berget S. M. Polyadenylation precedes splicing in vitro. Gene Expr. 1991 Apr;1(1):5–14. [PMC free article] [PubMed] [Google Scholar]
  23. Niwa M., MacDonald C. C., Berget S. M. Are vertebrate exons scanned during splice-site selection? Nature. 1992 Nov 19;360(6401):277–280. doi: 10.1038/360277a0. [DOI] [PubMed] [Google Scholar]
  24. Niwa M., Rose S. D., Berget S. M. In vitro polyadenylation is stimulated by the presence of an upstream intron. Genes Dev. 1990 Sep;4(9):1552–1559. doi: 10.1101/gad.4.9.1552. [DOI] [PubMed] [Google Scholar]
  25. Peterson M. L. Balanced efficiencies of splicing and cleavage-polyadenylation are required for mu-s and mu-m mRNA regulation. Gene Expr. 1992;2(4):319–327. [PMC free article] [PubMed] [Google Scholar]
  26. Peterson M. L., Gimmi E. R., Perry R. P. The developmentally regulated shift from membrane to secreted mu mRNA production is accompanied by an increase in cleavage-polyadenylation efficiency but no measurable change in splicing efficiency. Mol Cell Biol. 1991 Apr;11(4):2324–2327. doi: 10.1128/mcb.11.4.2324. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Peterson M. L., Perry R. P. Regulated production of mu m and mu s mRNA requires linkage of the poly(A) addition sites and is dependent on the length of the mu s-mu m intron. Proc Natl Acad Sci U S A. 1986 Dec;83(23):8883–8887. doi: 10.1073/pnas.83.23.8883. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Peterson M. L., Perry R. P. The regulated production of mu m and mu s mRNA is dependent on the relative efficiencies of mu s poly(A) site usage and the c mu 4-to-M1 splice. Mol Cell Biol. 1989 Feb;9(2):726–738. doi: 10.1128/mcb.9.2.726. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Reed R., Maniatis T. A role for exon sequences and splice-site proximity in splice-site selection. Cell. 1986 Aug 29;46(5):681–690. doi: 10.1016/0092-8674(86)90343-0. [DOI] [PubMed] [Google Scholar]
  30. Robberson B. L., Cote G. J., Berget S. M. Exon definition may facilitate splice site selection in RNAs with multiple exons. Mol Cell Biol. 1990 Jan;10(1):84–94. doi: 10.1128/mcb.10.1.84. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Ryu W. S., Mertz J. E. Simian virus 40 late transcripts lacking excisable intervening sequences are defective in both stability in the nucleus and transport to the cytoplasm. J Virol. 1989 Oct;63(10):4386–4394. doi: 10.1128/jvi.63.10.4386-4394.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Schibler U., Marcu K. B., Perry R. P. The synthesis and processing of the messenger RNAs specifying heavy and light chain immunoglobulins in MPC-11 cells. Cell. 1978 Dec;15(4):1495–1509. doi: 10.1016/0092-8674(78)90072-7. [DOI] [PubMed] [Google Scholar]
  33. Shapiro M. B., Senapathy P. RNA splice junctions of different classes of eukaryotes: sequence statistics and functional implications in gene expression. Nucleic Acids Res. 1987 Sep 11;15(17):7155–7174. doi: 10.1093/nar/15.17.7155. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Sterner D. A., Berget S. M. In vivo recognition of a vertebrate mini-exon as an exon-intron-exon unit. Mol Cell Biol. 1993 May;13(5):2677–2687. doi: 10.1128/mcb.13.5.2677. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Tsurushita N., Avdalovic N. M., Korn L. J. Regulation of differential processing of mouse immunoglobulin mu heavy-chain mRNA. Nucleic Acids Res. 1987 Jun 11;15(11):4603–4615. doi: 10.1093/nar/15.11.4603. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Wassarman K. M., Steitz J. A. Association with terminal exons in pre-mRNAs: a new role for the U1 snRNP? Genes Dev. 1993 Apr;7(4):647–659. doi: 10.1101/gad.7.4.647. [DOI] [PubMed] [Google Scholar]
  37. Watakabe A., Inoue K., Sakamoto H., Shimura Y. A secondary structure at the 3' splice site affects the in vitro splicing reaction of mouse immunoglobulin mu chain pre-mRNAs. Nucleic Acids Res. 1989 Oct 25;17(20):8159–8169. doi: 10.1093/nar/17.20.8159. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Watakabe A., Sakamoto H., Shimura Y. Repositioning of an alternative exon sequence of mouse IgM pre-mRNA activates splicing of the preceding intron. Gene Expr. 1991;1(3):175–184. [PMC free article] [PubMed] [Google Scholar]
  39. Watakabe A., Tanaka K., Shimura Y. The role of exon sequences in splice site selection. Genes Dev. 1993 Mar;7(3):407–418. doi: 10.1101/gad.7.3.407. [DOI] [PubMed] [Google Scholar]
  40. Xu R., Teng J., Cooper T. A. The cardiac troponin T alternative exon contains a novel purine-rich positive splicing element. Mol Cell Biol. 1993 Jun;13(6):3660–3674. doi: 10.1128/mcb.13.6.3660. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Yuan D., Dang T. Regulation of microM vs microS mRNA expression in an inducible B cell line. Mol Immunol. 1989 Nov;26(11):1059–1067. doi: 10.1016/0161-5890(89)90070-9. [DOI] [PubMed] [Google Scholar]

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