Skip to main content
NCBI home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1996 Nov 1;24(21):4165–4170. doi: 10.1093/nar/24.21.4165

Monomeric scAlu and nascent dimeric Alu RNAs induced by adenovirus are assembled into SRP9/14-containing RNPs in HeLa cells.

D Y Chang 1, K Hsu 1, R J Maraia 1
PMCID: PMC146241  PMID: 8932367

Abstract

Nearly 1 000 000 copies of Alu interspersed elements comprise approximately 5% of human DNA. Alu elements cause gene disruptions by a process known as retrotransposition, in which dimeric Alu RNA is a presumed intermediate. Dimeric Alu transcripts are labile, giving rise to stable left monomeric scAlu RNAs whose levels are tightly regulated. Induction of Alu RNA by viral infection or cell stress leads to a dramatic increase in dimeric Alu transcripts, while scAlu RNA increases modestly. Each monomer of the dimeric Alu element shares sequence homology with the 7SL RNA component of the signal recognition particle (SRP). The SRP protein known as SRP9/14 is also found in a discrete complex with scAlu RNA, although whether dimeric Alu RNA is associated with SRP9/14 had been unknown. Here we show that antiserum to human SRP9 immunoprecipitates both scAlu RNA and dimeric Alu RNAs and that these RNPs accumulate after adenovirus infection, while levels of SRP9, SRP14, SRP54 and 7SL SRP RNA are unaffected. Dimeric Alu RNAs are also associated with the La protein, indicating that these are indeed nascent RNA polymerase III transcripts. This report documents that induced Alu transcripts are assembled into SRP9/14-containing RNPs in vivo while SRP levels are unchanged. Implications for Alu RNA metabolism and evolution are discussed.

Full Text

The Full Text of this article is available as a PDF (89.0 KB).

Selected References

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

  1. Andreazzoli M., Gerbi S. A. Changes in 7SL RNA conformation during the signal recognition particle cycle. EMBO J. 1991 Apr;10(4):767–777. doi: 10.1002/j.1460-2075.1991.tb08008.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Bovia F., Fornallaz M., Leffers H., Strub K. The SRP9/14 subunit of the signal recognition particle (SRP) is present in more than 20-fold excess over SRP in primate cells and exists primarily free but also in complex with small cytoplasmic Alu RNAs. Mol Biol Cell. 1995 Apr;6(4):471–484. doi: 10.1091/mbc.6.4.471. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Chang D. Y., Maraia R. J. A cellular protein binds B1 and Alu small cytoplasmic RNAs in vitro. J Biol Chem. 1993 Mar 25;268(9):6423–6428. [PubMed] [Google Scholar]
  4. Chang D. Y., Nelson B., Bilyeu T., Hsu K., Darlington G. J., Maraia R. J. A human Alu RNA-binding protein whose expression is associated with accumulation of small cytoplasmic Alu RNA. Mol Cell Biol. 1994 Jun;14(6):3949–3959. doi: 10.1128/mcb.14.6.3949. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Chang D. Y., Sasaki-Tozawa N., Green L. K., Maraia R. J. A trinucleotide repeat-associated increase in the level of Alu RNA-binding protein occurred during the same period as the major Alu amplification that accompanied anthropoid evolution. Mol Cell Biol. 1995 Apr;15(4):2109–2116. doi: 10.1128/mcb.15.4.2109. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Chu W. M., Liu W. M., Schmid C. W. RNA polymerase III promoter and terminator elements affect Alu RNA expression. Nucleic Acids Res. 1995 May 25;23(10):1750–1757. doi: 10.1093/nar/23.10.1750. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Dignam J. D., Lebovitz R. M., Roeder R. G. Accurate transcription initiation by RNA polymerase II in a soluble extract from isolated mammalian nuclei. Nucleic Acids Res. 1983 Mar 11;11(5):1475–1489. doi: 10.1093/nar/11.5.1475. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Gottlieb E., Steitz J. A. Function of the mammalian La protein: evidence for its action in transcription termination by RNA polymerase III. EMBO J. 1989 Mar;8(3):851–861. doi: 10.1002/j.1460-2075.1989.tb03446.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Gundelfinger E. D., Di Carlo M., Zopf D., Melli M. Structure and evolution of the 7SL RNA component of the signal recognition particle. EMBO J. 1984 Oct;3(10):2325–2332. doi: 10.1002/j.1460-2075.1984.tb02134.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Hsu K., Chang D. Y., Maraia R. J. Human signal recognition particle (SRP) Alu-associated protein also binds Alu interspersed repeat sequence RNAs. Characterization of human SRP9. J Biol Chem. 1995 Apr 28;270(17):10179–10186. doi: 10.1074/jbc.270.17.10179. [DOI] [PubMed] [Google Scholar]
  11. Jelinek W. R., Schmid C. W. Repetitive sequences in eukaryotic DNA and their expression. Annu Rev Biochem. 1982;51:813–844. doi: 10.1146/annurev.bi.51.070182.004121. [DOI] [PubMed] [Google Scholar]
  12. Jurka J., Zuckerkandl E. Free left arms as precursor molecules in the evolution of Alu sequences. J Mol Evol. 1991 Jul;33(1):49–56. doi: 10.1007/BF02100195. [DOI] [PubMed] [Google Scholar]
  13. Katze M. G., DeCorato D., Krug R. M. Cellular mRNA translation is blocked at both initiation and elongation after infection by influenza virus or adenovirus. J Virol. 1986 Dec;60(3):1027–1039. doi: 10.1128/jvi.60.3.1027-1039.1986. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Katze M. G., Lara J., Wambach M. Nontranslated cellular mRNAs are associated with the cytoskeletal framework in influenza virus or adenovirus infected cells. Virology. 1989 Apr;169(2):312–322. doi: 10.1016/0042-6822(89)90156-6. [DOI] [PubMed] [Google Scholar]
  15. Liu W. M., Chu W. M., Choudary P. V., Schmid C. W. Cell stress and translational inhibitors transiently increase the abundance of mammalian SINE transcripts. Nucleic Acids Res. 1995 May 25;23(10):1758–1765. doi: 10.1093/nar/23.10.1758. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Liu W. M., Leeflang E. P., Schmid C. W. Unusual sequences of two old, inactive human Alu repeats. Biochim Biophys Acta. 1992 Oct 20;1132(3):306–308. doi: 10.1016/0167-4781(92)90165-v. [DOI] [PubMed] [Google Scholar]
  17. Liu W. M., Maraia R. J., Rubin C. M., Schmid C. W. Alu transcripts: cytoplasmic localisation and regulation by DNA methylation. Nucleic Acids Res. 1994 Mar 25;22(6):1087–1095. doi: 10.1093/nar/22.6.1087. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Maraia R. J., Driscoll C. T., Bilyeu T., Hsu K., Darlington G. J. Multiple dispersed loci produce small cytoplasmic Alu RNA. Mol Cell Biol. 1993 Jul;13(7):4233–4241. doi: 10.1128/mcb.13.7.4233. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Maraia R. J., Kenan D. J., Keene J. D. Eukaryotic transcription termination factor La mediates transcript release and facilitates reinitiation by RNA polymerase III. Mol Cell Biol. 1994 Mar;14(3):2147–2158. doi: 10.1128/mcb.14.3.2147. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Maraia R. J. The subset of mouse B1 (Alu-equivalent) sequences expressed as small processed cytoplasmic transcripts. Nucleic Acids Res. 1991 Oct 25;19(20):5695–5702. doi: 10.1093/nar/19.20.5695. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Matera A. G., Hellmann U., Schmid C. W. A transpositionally and transcriptionally competent Alu subfamily. Mol Cell Biol. 1990 Oct;10(10):5424–5432. doi: 10.1128/mcb.10.10.5424. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Panning B., Smiley J. R. Activation of RNA polymerase III transcription of human Alu elements by herpes simplex virus. Virology. 1994 Jul;202(1):408–417. doi: 10.1006/viro.1994.1357. [DOI] [PubMed] [Google Scholar]
  23. Panning B., Smiley J. R. Activation of RNA polymerase III transcription of human Alu repetitive elements by adenovirus type 5: requirement for the E1b 58-kilodalton protein and the products of E4 open reading frames 3 and 6. Mol Cell Biol. 1993 Jun;13(6):3231–3244. doi: 10.1128/mcb.13.6.3231. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Panning B., Smiley J. R. Activation of expression of multiple subfamilies of human Alu elements by adenovirus type 5 and herpes simplex virus type 1. J Mol Biol. 1995 May 5;248(3):513–524. doi: 10.1006/jmbi.1995.0239. [DOI] [PubMed] [Google Scholar]
  25. Quentin Y. Origin of the Alu family: a family of Alu-like monomers gave birth to the left and the right arms of the Alu elements. Nucleic Acids Res. 1992 Jul 11;20(13):3397–3401. doi: 10.1093/nar/20.13.3397. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Reeves W. H., Nigam S. K., Blobel G. Human autoantibodies reactive with the signal-recognition particle. Proc Natl Acad Sci U S A. 1986 Dec;83(24):9507–9511. doi: 10.1073/pnas.83.24.9507. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. 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]
  28. Russanova V. R., Driscoll C. T., Howard B. H. Adenovirus type 2 preferentially stimulates polymerase III transcription of Alu elements by relieving repression: a potential role for chromatin. Mol Cell Biol. 1995 Aug;15(8):4282–4290. doi: 10.1128/mcb.15.8.4282. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Schmid C., Maraia R. Transcriptional regulation and transpositional selection of active SINE sequences. Curr Opin Genet Dev. 1992 Dec;2(6):874–882. doi: 10.1016/s0959-437x(05)80110-8. [DOI] [PubMed] [Google Scholar]
  30. Siegel V., Walter P. Each of the activities of signal recognition particle (SRP) is contained within a distinct domain: analysis of biochemical mutants of SRP. Cell. 1988 Jan 15;52(1):39–49. doi: 10.1016/0092-8674(88)90529-6. [DOI] [PubMed] [Google Scholar]
  31. Siegel V., Walter P. Removal of the Alu structural domain from signal recognition particle leaves its protein translocation activity intact. Nature. 1986 Mar 6;320(6057):81–84. doi: 10.1038/320081a0. [DOI] [PubMed] [Google Scholar]
  32. Singer M. F. SINEs and LINEs: highly repeated short and long interspersed sequences in mammalian genomes. Cell. 1982 Mar;28(3):433–434. doi: 10.1016/0092-8674(82)90194-5. [DOI] [PubMed] [Google Scholar]
  33. Sinnett D., Richer C., Deragon J. M., Labuda D. Alu RNA transcripts in human embryonal carcinoma cells. Model of post-transcriptional selection of master sequences. J Mol Biol. 1992 Aug 5;226(3):689–706. doi: 10.1016/0022-2836(92)90626-u. [DOI] [PubMed] [Google Scholar]
  34. Stefano J. E. Purified lupus antigen La recognizes an oligouridylate stretch common to the 3' termini of RNA polymerase III transcripts. Cell. 1984 Jan;36(1):145–154. doi: 10.1016/0092-8674(84)90083-7. [DOI] [PubMed] [Google Scholar]
  35. Steitz J. A. Immunoprecipitation of ribonucleoproteins using autoantibodies. Methods Enzymol. 1989;180:468–481. doi: 10.1016/0076-6879(89)80118-1. [DOI] [PubMed] [Google Scholar]
  36. Strub K., Walter P. Assembly of the Alu domain of the signal recognition particle (SRP): dimerization of the two protein components is required for efficient binding to SRP RNA. Mol Cell Biol. 1990 Feb;10(2):777–784. doi: 10.1128/mcb.10.2.777. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Targoff I. N., Johnson A. E., Miller F. W. Antibody to signal recognition particle in polymyositis. Arthritis Rheum. 1990 Sep;33(9):1361–1370. doi: 10.1002/art.1780330908. [DOI] [PubMed] [Google Scholar]
  38. Ullu E., Murphy S., Melli M. Human 7SL RNA consists of a 140 nucleotide middle-repetitive sequence inserted in an alu sequence. Cell. 1982 May;29(1):195–202. doi: 10.1016/0092-8674(82)90103-9. [DOI] [PubMed] [Google Scholar]
  39. Wallace M. R., Andersen L. B., Saulino A. M., Gregory P. E., Glover T. W., Collins F. S. A de novo Alu insertion results in neurofibromatosis type 1. Nature. 1991 Oct 31;353(6347):864–866. doi: 10.1038/353864a0. [DOI] [PubMed] [Google Scholar]
  40. Walter P., Blobel G. Signal recognition particle contains a 7S RNA essential for protein translocation across the endoplasmic reticulum. Nature. 1982 Oct 21;299(5885):691–698. doi: 10.1038/299691a0. [DOI] [PubMed] [Google Scholar]
  41. Weiner A. M. An abundant cytoplasmic 7S RNA is complementary to the dominant interspersed middle repetitive DNA sequence family in the human genome. Cell. 1980 Nov;22(1 Pt 1):209–218. doi: 10.1016/0092-8674(80)90169-5. [DOI] [PubMed] [Google Scholar]

Articles from Nucleic Acids Research are provided here courtesy of Oxford University Press

RESOURCES