Skip to main content
RNA logoLink to RNA
. 2002 Jun;8(6):762–771. doi: 10.1017/s1355838202021507

Autoimmune epitopes in messenger RNA.

Barbara D Lipes 1, Jack D Keene 1
PMCID: PMC1370295  PMID: 12088149

Abstract

Patients with systemic autoimmune disorders produce autoantibodies against sequence-specific conformational RNA epitopes on U1 snRNA, 28S rRNA, and transfer RNAs. The molecular basis for immunological reactivity with these highly abundant and stable RNAs is not understood. Here, we report the existence of discrete RNA epitopes in messenger RNAs that are generally less abundant and less stable than snRNAs and tRNAs. An iterative selection and amplification procedure using pooled autoimmune patient sera identified immunoreactive mRNA species. Following deconvolution of the pools to identify the reactive sera, several mRNAs recognized by these autoantibodies were cloned and sequenced. Detailed analysis using one particular serum indicated reactivity against the messages encoding alternative splicing factor (ASF/SF2) and calmodulin. Deletion and site-directed mutagenesis determined that an epitope recognized by this serum is located in a 17-base stem-loop structure common to both messages. This serum was then used to immunoprecipitate native mRNAs encoding ASF/SF2 and calmodulin from total HeLa cell RNA. Our results demonstrate that despite its low abundance and instability, messenger RNA is capable of reacting with autoantibodies generated during an autoimmune response. These data are consistent with direct presentation as a model to explain the generation of RNA conformation-specific autoantibodies.

Full Text

The Full Text of this article is available as a PDF (250.7 KB).

Selected References

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

  1. Bunn C. C., Mathews M. B. Autoreactive epitope defined as the anticodon region of alanine transfer RNA. Science. 1987 Nov 20;238(4830):1116–1119. doi: 10.1126/science.2446387. [DOI] [PubMed] [Google Scholar]
  2. Chu J. L., Brot N., Weissbach H., Elkon K. Lupus antiribosomal P antisera contain antibodies to a small fragment of 28S rRNA located in the proposed ribosomal GTPase center. J Exp Med. 1991 Sep 1;174(3):507–514. doi: 10.1084/jem.174.3.507. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Conrad R. C., Baskerville S., Ellington A. D. In vitro selection methodologies to probe RNA function and structure. Mol Divers. 1995 Sep;1(1):69–78. doi: 10.1007/BF01715810. [DOI] [PubMed] [Google Scholar]
  4. Davis S., Watson J. C. In vitro activation of the interferon-induced, double-stranded RNA-dependent protein kinase PKR by RNA from the 3' untranslated regions of human alpha-tropomyosin. Proc Natl Acad Sci U S A. 1996 Jan 9;93(1):508–513. doi: 10.1073/pnas.93.1.508. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Deutscher S. L., Keene J. D. A sequence-specific conformational epitope on U1 RNA is recognized by a unique autoantibody. Proc Natl Acad Sci U S A. 1988 May;85(10):3299–3303. doi: 10.1073/pnas.85.10.3299. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Doudna J. A., Cech T. R., Sullenger B. A. Selection of an RNA molecule that mimics a major autoantigenic epitope of human insulin receptor. Proc Natl Acad Sci U S A. 1995 Mar 14;92(6):2355–2359. doi: 10.1073/pnas.92.6.2355. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Gao F. B., Carson C. C., Levine T., Keene J. D. Selection of a subset of mRNAs from combinatorial 3' untranslated region libraries using neuronal RNA-binding protein Hel-N1. Proc Natl Acad Sci U S A. 1994 Nov 8;91(23):11207–11211. doi: 10.1073/pnas.91.23.11207. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Hamm J. Characterisation of antibody-binding RNAs selected from structurally constrained libraries. Nucleic Acids Res. 1996 Jun 15;24(12):2220–2227. doi: 10.1093/nar/24.12.2220. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Hardin J. A. The lupus autoantigens and the pathogenesis of systemic lupus erythematosus. Arthritis Rheum. 1986 Apr;29(4):457–460. doi: 10.1002/art.1780290401. [DOI] [PubMed] [Google Scholar]
  10. Keene J. D. RNA recognition by autoantigens and autoantibodies. Mol Biol Rep. 1996;23(3-4):173–181. doi: 10.1007/BF00351166. [DOI] [PubMed] [Google Scholar]
  11. Keene J. D. RNA surfaces as functional mimetics of proteins. Chem Biol. 1996 Jul;3(7):505–513. doi: 10.1016/s1074-5521(96)90139-8. [DOI] [PubMed] [Google Scholar]
  12. Keene J. D. Randomization and selection of RNA to identify targets for RRM RNA-binding proteins and antibodies. Methods Enzymol. 1996;267:367–383. doi: 10.1016/s0076-6879(96)67023-2. [DOI] [PubMed] [Google Scholar]
  13. Lerner M. R., Steitz J. A. Antibodies to small nuclear RNAs complexed with proteins are produced by patients with systemic lupus erythematosus. Proc Natl Acad Sci U S A. 1979 Nov;76(11):5495–5499. doi: 10.1073/pnas.76.11.5495. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Nissen P., Kjeldgaard M., Nyborg J. Macromolecular mimicry. EMBO J. 2000 Feb 15;19(4):489–495. doi: 10.1093/emboj/19.4.489. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Nissen P., Kjeldgaard M., Thirup S., Polekhina G., Reshetnikova L., Clark B. F., Nyborg J. Crystal structure of the ternary complex of Phe-tRNAPhe, EF-Tu, and a GTP analog. Science. 1995 Dec 1;270(5241):1464–1472. doi: 10.1126/science.270.5241.1464. [DOI] [PubMed] [Google Scholar]
  16. Pisetsky D. S. The influence of base sequence on the immunostimulatory properties of DNA. Immunol Res. 1999;19(1):35–46. doi: 10.1007/BF02786475. [DOI] [PubMed] [Google Scholar]
  17. Rastinejad F., Blau H. M. Genetic complementation reveals a novel regulatory role for 3' untranslated regions in growth and differentiation. Cell. 1993 Mar 26;72(6):903–917. doi: 10.1016/0092-8674(93)90579-f. [DOI] [PubMed] [Google Scholar]
  18. Rastinejad F., Conboy M. J., Rando T. A., Blau H. M. Tumor suppression by RNA from the 3' untranslated region of alpha-tropomyosin. Cell. 1993 Dec 17;75(6):1107–1117. doi: 10.1016/0092-8674(93)90320-p. [DOI] [PubMed] [Google Scholar]
  19. Rinke J., Steitz J. A. Precursor molecules of both human 5S ribosomal RNA and transfer RNAs are bound by a cellular protein reactive with anti-La lupus antibodies. Cell. 1982 May;29(1):149–159. doi: 10.1016/0092-8674(82)90099-x. [DOI] [PubMed] [Google Scholar]
  20. Saitta M. R., Keene J. D. Molecular biology of nuclear autoantigens. Rheum Dis Clin North Am. 1992 May;18(2):283–310. [PubMed] [Google Scholar]
  21. Sri-Widada J., Graafland H., Dietz R., Brunel C., Cathala G., Jeanteur P. A human auto-immune antibody specifically recognizing initiator methionine tRNA from yeast and higher eucaryotes. Biochem Biophys Res Commun. 1986 Aug 29;139(1):275–280. doi: 10.1016/s0006-291x(86)80109-7. [DOI] [PubMed] [Google Scholar]
  22. Stollar B. D. Molecular analysis of anti-DNA antibodies. FASEB J. 1994 Mar 1;8(3):337–342. doi: 10.1096/fasebj.8.3.7511550. [DOI] [PubMed] [Google Scholar]
  23. Tan E. M. Autoantibodies in pathology and cell biology. Cell. 1991 Nov 29;67(5):841–842. doi: 10.1016/0092-8674(91)90356-4. [DOI] [PubMed] [Google Scholar]
  24. Tenenbaum S. A., Carson C. C., Lager P. J., Keene J. D. Identifying mRNA subsets in messenger ribonucleoprotein complexes by using cDNA arrays. Proc Natl Acad Sci U S A. 2000 Dec 19;97(26):14085–14090. doi: 10.1073/pnas.97.26.14085. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Tsai D. E., Kenan D. J., Keene J. D. In vitro selection of an RNA epitope immunologically cross-reactive with a peptide. Proc Natl Acad Sci U S A. 1992 Oct 1;89(19):8864–8868. doi: 10.1073/pnas.89.19.8864. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Uchiumi T., Traut R. R., Elkon K., Kominami R. A human autoantibody specific for a unique conserved region of 28 S ribosomal RNA inhibits the interaction of elongation factors 1 alpha and 2 with ribosomes. J Biol Chem. 1991 Feb 5;266(4):2054–2062. [PubMed] [Google Scholar]
  27. Van Venrooij W. J., Sillekens P. T. Small nuclear RNA associated proteins: autoantigens in connective tissue diseases. Clin Exp Rheumatol. 1989 Nov-Dec;7(6):635–645. [PubMed] [Google Scholar]
  28. Wilusz J., Keene J. D. Autoantibodies specific for U1 RNA and initiator methionine tRNA. J Biol Chem. 1986 Apr 25;261(12):5467–5472. [PubMed] [Google Scholar]
  29. van Venrooij W. J., Hoet R., Castrop J., Hageman B., Mattaj I. W., van de Putte L. B. Anti-(U1) small nuclear RNA antibodies in anti-small nuclear ribonucleoprotein sera from patients with connective tissue diseases. J Clin Invest. 1990 Dec;86(6):2154–2160. doi: 10.1172/JCI114954. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from RNA are provided here courtesy of The RNA Society

RESOURCES