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. 1997 Nov 15;25(22):4513–4522. doi: 10.1093/nar/25.22.4513

Characterization of multiple alternative RNAs resulting from antisense transcription of the PR264/SC35 splicing factor gene.

A Sureau 1, J Soret 1, C Guyon 1, C Gaillard 1, S Dumon 1, M Keller 1, P Crisanti 1, B Perbal 1
PMCID: PMC147067  PMID: 9358160

Abstract

The PR264/SC35 splicing factor belongs to the family of SR proteins which function as essential and alternative splicing factors. Here, we report that the human PR264/SC35 locus is bidirectionally transcribed. Double in situ hybridization experiments have allowed simultaneous detection of sense and antisense RNA in human CCRF-CEM cells, suggesting that expression of the corresponding genes is not mutually exclusive. We have characterized three main classes of ET RNAs encoded by the opposite strand of the PR264/SC35 gene and containing PR264/SC35-overlapping sequences, PR264/SC35-non overlapping sequences or a combination of both. We show that their expression results from the use of alternative promoters, exons and polyadenylation signals. PR264/SC35-non overlapping ET mRNA species potentially encode two protein isoforms (449 and 397 amino acids) and are expressed from the PR264/SC35 promoting region. Northern blots and RNase protection analyses indicate that ET polyadenylated RNAs are differentially expressed in several human cell lines. Similar studies performed in the mouse have revealed that the bidirectional transcription of the PR264/SC35 locus is a conserved mechanism and that the open reading frame identified in a subset of human ET mRNAs is highly conserved (93% homology). Northern blot analyses performed with several murine tissues confirmed the differential expression of the ET gene and revealed that it is predominantly expressed in the testis.

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Selected References

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  1. Bass B. L., Weintraub H. An unwinding activity that covalently modifies its double-stranded RNA substrate. Cell. 1988 Dec 23;55(6):1089–1098. doi: 10.1016/0092-8674(88)90253-x. [DOI] [PubMed] [Google Scholar]
  2. Cáceres J. F., Stamm S., Helfman D. M., Krainer A. R. Regulation of alternative splicing in vivo by overexpression of antagonistic splicing factors. Science. 1994 Sep 16;265(5179):1706–1709. doi: 10.1126/science.8085156. [DOI] [PubMed] [Google Scholar]
  3. Dessen P., Fondrat C., Valencien C., Mugnier C. BISANCE: a French service for access to biomolecular sequence databases. Comput Appl Biosci. 1990 Oct;6(4):355–356. doi: 10.1093/bioinformatics/6.4.355. [DOI] [PubMed] [Google Scholar]
  4. Dolnick B. J. Cloning and characterization of a naturally occurring antisense RNA to human thymidylate synthase mRNA. Nucleic Acids Res. 1993 Apr 25;21(8):1747–1752. doi: 10.1093/nar/21.8.1747. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Farnham P. J., Abrams J. M., Schimke R. T. Opposite-strand RNAs from the 5' flanking region of the mouse dihydrofolate reductase gene. Proc Natl Acad Sci U S A. 1985 Jun;82(12):3978–3982. doi: 10.1073/pnas.82.12.3978. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Fromont-Racine M., Bertrand E., Pictet R., Grange T. A highly sensitive method for mapping the 5' termini of mRNAs. Nucleic Acids Res. 1993 Apr 11;21(7):1683–1684. doi: 10.1093/nar/21.7.1683. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Fu X. D., Maniatis T. The 35-kDa mammalian splicing factor SC35 mediates specific interactions between U1 and U2 small nuclear ribonucleoprotein particles at the 3' splice site. Proc Natl Acad Sci U S A. 1992 Mar 1;89(5):1725–1729. doi: 10.1073/pnas.89.5.1725. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Fu X. D., Mayeda A., Maniatis T., Krainer A. R. General splicing factors SF2 and SC35 have equivalent activities in vitro, and both affect alternative 5' and 3' splice site selection. Proc Natl Acad Sci U S A. 1992 Dec 1;89(23):11224–11228. doi: 10.1073/pnas.89.23.11224. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Fu X. D. The superfamily of arginine/serine-rich splicing factors. RNA. 1995 Sep;1(7):663–680. [PMC free article] [PubMed] [Google Scholar]
  10. Gallego M. E., Gattoni R., Stévenin J., Marie J., Expert-Bezançon A. The SR splicing factors ASF/SF2 and SC35 have antagonistic effects on intronic enhancer-dependent splicing of the beta-tropomyosin alternative exon 6A. EMBO J. 1997 Apr 1;16(7):1772–1784. doi: 10.1093/emboj/16.7.1772. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Heikkilä P., Soininen R., Tryggvason K. Directional regulatory activity of cis-acting elements in the bidirectional alpha 1(IV) and alpha 2(IV) collagen gene promoter. J Biol Chem. 1993 Nov 25;268(33):24677–24682. [PubMed] [Google Scholar]
  12. Hildebrandt M., Nellen W. Differential antisense transcription from the Dictyostelium EB4 gene locus: implications on antisense-mediated regulation of mRNA stability. Cell. 1992 Apr 3;69(1):197–204. doi: 10.1016/0092-8674(92)90130-5. [DOI] [PubMed] [Google Scholar]
  13. Inouye M. Antisense RNA: its functions and applications in gene regulation--a review. Gene. 1988 Dec 10;72(1-2):25–34. doi: 10.1016/0378-1119(88)90124-2. [DOI] [PubMed] [Google Scholar]
  14. Jannini E. A., Mitsuhashi T., Nikodem V. M. Developmental expression of mRNAs from a rat C-erbA genomic locus. Biochem Biophys Res Commun. 1992 Apr 30;184(2):739–745. doi: 10.1016/0006-291x(92)90652-2. [DOI] [PubMed] [Google Scholar]
  15. Johnson P., Friedmann T. Limited bidirectional activity of two housekeeping gene promoters: human HPRT and PGK. Gene. 1990 Apr 16;88(2):207–213. doi: 10.1016/0378-1119(90)90033-n. [DOI] [PubMed] [Google Scholar]
  16. Khochbin S., Lawrence J. J. An antisense RNA involved in p53 mRNA maturation in murine erythroleukemia cells induced to differentiate. EMBO J. 1989 Dec 20;8(13):4107–4114. doi: 10.1002/j.1460-2075.1989.tb08595.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Kimelman D., Kirschner M. W. An antisense mRNA directs the covalent modification of the transcript encoding fibroblast growth factor in Xenopus oocytes. Cell. 1989 Nov 17;59(4):687–696. doi: 10.1016/0092-8674(89)90015-9. [DOI] [PubMed] [Google Scholar]
  18. Kraus M. E., Lis J. T. The concentration of B52, an essential splicing factor and regulator of splice site choice in vitro, is critical for Drosophila development. Mol Cell Biol. 1994 Aug;14(8):5360–5370. doi: 10.1128/mcb.14.8.5360. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Krystal G. W., Armstrong B. C., Battey J. F. N-myc mRNA forms an RNA-RNA duplex with endogenous antisense transcripts. Mol Cell Biol. 1990 Aug;10(8):4180–4191. doi: 10.1128/mcb.10.8.4180. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Laabi Y., Gras M. P., Brouet J. C., Berger R., Larsen C. J., Tsapis A. The BCMA gene, preferentially expressed during B lymphoid maturation, is bidirectionally transcribed. Nucleic Acids Res. 1994 Apr 11;22(7):1147–1154. doi: 10.1093/nar/22.7.1147. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Lavia P., Macleod D., Bird A. Coincident start sites for divergent transcripts at a randomly selected CpG-rich island of mouse. EMBO J. 1987 Sep;6(9):2773–2779. doi: 10.1002/j.1460-2075.1987.tb02572.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Lazar M. A., Hodin R. A., Darling D. S., Chin W. W. A novel member of the thyroid/steroid hormone receptor family is encoded by the opposite strand of the rat c-erbA alpha transcriptional unit. Mol Cell Biol. 1989 Mar;9(3):1128–1136. doi: 10.1128/mcb.9.3.1128. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Lennard A. C., Fried M. The bidirectional promoter of the divergently transcribed mouse Surf-1 and Surf-2 genes. Mol Cell Biol. 1991 Mar;11(3):1281–1294. doi: 10.1128/mcb.11.3.1281. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Li A. W., Too C. K., Murphy P. R. The basic fibroblast growth factor (FGF-2) antisense RNA (GFG) is translated into a MutT-related protein in vivo. Biochem Biophys Res Commun. 1996 Jun 5;223(1):19–23. doi: 10.1006/bbrc.1996.0839. [DOI] [PubMed] [Google Scholar]
  25. Liu X., Gorovsky M. A. Mapping the 5' and 3' ends of Tetrahymena thermophila mRNAs using RNA ligase mediated amplification of cDNA ends (RLM-RACE). Nucleic Acids Res. 1993 Oct 25;21(21):4954–4960. doi: 10.1093/nar/21.21.4954. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Malik K. T., Wallace J. I., Ivins S. M., Brown K. W. Identification of an antisense WT1 promoter in intron 1: implications for WT1 gene regulation. Oncogene. 1995 Oct 19;11(8):1589–1595. [PubMed] [Google Scholar]
  27. Manley J. L., Tacke R. SR proteins and splicing control. Genes Dev. 1996 Jul 1;10(13):1569–1579. doi: 10.1101/gad.10.13.1569. [DOI] [PubMed] [Google Scholar]
  28. Melton D. W. Strategies and mechanisms for the control of transcriptional initiation of mammalian protein-coding genes. J Cell Sci. 1987 Oct;88(Pt 3):267–270. doi: 10.1242/jcs.88.3.267. [DOI] [PubMed] [Google Scholar]
  29. Miyajima N., Horiuchi R., Shibuya Y., Fukushige S., Matsubara K., Toyoshima K., Yamamoto T. Two erbA homologs encoding proteins with different T3 binding capacities are transcribed from opposite DNA strands of the same genetic locus. Cell. 1989 Apr 7;57(1):31–39. doi: 10.1016/0092-8674(89)90169-4. [DOI] [PubMed] [Google Scholar]
  30. Munroe S. H., Lazar M. A. Inhibition of c-erbA mRNA splicing by a naturally occurring antisense RNA. J Biol Chem. 1991 Nov 25;266(33):22083–22086. [PubMed] [Google Scholar]
  31. O'Hanlon T. P., Raben N., Miller F. W. A novel gene oriented in a head-to-head configuration with the human histidyl-tRNA synthetase (HRS) gene encodes an mRNA that predicts a polypeptide homologous to HRS. Biochem Biophys Res Commun. 1995 May 16;210(2):556–566. doi: 10.1006/bbrc.1995.1696. [DOI] [PubMed] [Google Scholar]
  32. Ring H. Z., Lis J. T. The SR protein B52/SRp55 is essential for Drosophila development. Mol Cell Biol. 1994 Nov;14(11):7499–7506. doi: 10.1128/mcb.14.11.7499. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Smale S. T., Baltimore D. The "initiator" as a transcription control element. Cell. 1989 Apr 7;57(1):103–113. doi: 10.1016/0092-8674(89)90176-1. [DOI] [PubMed] [Google Scholar]
  34. Spicer D. B., Sonenshein G. E. An antisense promoter of the murine c-myc gene is localized within intron 2. Mol Cell Biol. 1992 Mar;12(3):1324–1329. doi: 10.1128/mcb.12.3.1324. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Sureau A., Perbal B. Intermolecular recombination of human c-myb proto-oncogene coding sequences. C R Acad Sci III. 1991;312(7):323–328. [PubMed] [Google Scholar]
  36. Sureau A., Perbal B. Several mRNAs with variable 3' untranslated regions and different stability encode the human PR264/SC35 splicing factor. Proc Natl Acad Sci U S A. 1994 Feb 1;91(3):932–936. doi: 10.1073/pnas.91.3.932. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Sureau A., Soret J., Vellard M., Crochet J., Perbal B. The PR264/c-myb connection: expression of a splicing factor modulated by a nuclear protooncogene. Proc Natl Acad Sci U S A. 1992 Dec 15;89(24):11683–11687. doi: 10.1073/pnas.89.24.11683. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Vellard M., Soret J., Viegas-Pequignot E., Galibert F., Nguyen V. C., Dutrillaux B., Perbal B. C-myb proto-oncogene: evidence for intermolecular recombination of coding sequences. Oncogene. 1991 Apr;6(4):505–514. [PubMed] [Google Scholar]
  39. Volk R., Köster M., Pöting A., Hartmann L., Knöchel W. An antisense transcript from the Xenopus laevis bFGF gene coding for an evolutionarily conserved 24 kd protein. EMBO J. 1989 Oct;8(10):2983–2988. doi: 10.1002/j.1460-2075.1989.tb08448.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Wagner R. W., Smith J. E., Cooperman B. S., Nishikura K. A double-stranded RNA unwinding activity introduces structural alterations by means of adenosine to inosine conversions in mammalian cells and Xenopus eggs. Proc Natl Acad Sci U S A. 1989 Apr;86(8):2647–2651. doi: 10.1073/pnas.86.8.2647. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Wang J., Takagaki Y., Manley J. L. Targeted disruption of an essential vertebrate gene: ASF/SF2 is required for cell viability. Genes Dev. 1996 Oct 15;10(20):2588–2599. doi: 10.1101/gad.10.20.2588. [DOI] [PubMed] [Google Scholar]
  42. Zhang W. J., Wu J. Y. Functional properties of p54, a novel SR protein active in constitutive and alternative splicing. Mol Cell Biol. 1996 Oct;16(10):5400–5408. doi: 10.1128/mcb.16.10.5400. [DOI] [PMC free article] [PubMed] [Google Scholar]

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