Skip to main content
PMC home page
The EMBO Journal logoLink to The EMBO Journal
. 1993 Apr;12(4):1487–1497. doi: 10.1002/j.1460-2075.1993.tb05792.x

Generation of processed pseudogenes in murine cells.

T Tchénio 1, E Segal-Bendirdjian 1, T Heidmann 1
PMCID: PMC413361  PMID: 8385606

Abstract

Using as a reporter gene a non-coding proviral structure marked with an intron-containing indicator, we demonstrate the de novo formation, via a retrotransposition pathway, of canonical processed pseudogenes in cultured mammalian cells. Their structural features include endings corresponding to the start and termination of the RNA intermediate, intron loss, acquisition of a 3' poly(A) tail, and target site duplications of variable length. The absence of extracellular intermediates for these processes, and the elimination during retrotransposition of sequences in the reporter gene essential in cis for a retroviral cycle, further suggest that endogenous retroviruses or related elements are not involved. Pseudogene formation frequency is markedly increased (up to 10-fold) by several treatments including treatment with 5-azacytidine or tetradecanoyl phorbol acetate, or serum starvation, which do not act at the reporter gene transcription level, but rather on endogenous genes--including the LINE elements--necessarily involved in trans-complementation for retrotransposition.

Full text

PDF
1495

Images in this article

1488Image
on p.1488
1490Image
on p.1490
1492Image
on p.1492
1493Image
on p.1493
1494Image
on p.1494

Selected References

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

  1. Baltimore D. Retroviruses and retrotransposons: the role of reverse transcription in shaping the eukaryotic genome. Cell. 1985 Mar;40(3):481–482. doi: 10.1016/0092-8674(85)90190-4. [DOI] [PubMed] [Google Scholar]
  2. Boeke J. D., Corces V. G. Transcription and reverse transcription of retrotransposons. Annu Rev Microbiol. 1989;43:403–434. doi: 10.1146/annurev.mi.43.100189.002155. [DOI] [PubMed] [Google Scholar]
  3. Boeke J. D., Garfinkel D. J., Styles C. A., Fink G. R. Ty elements transpose through an RNA intermediate. Cell. 1985 Mar;40(3):491–500. doi: 10.1016/0092-8674(85)90197-7. [DOI] [PubMed] [Google Scholar]
  4. Bonnerot C., Rocancourt D., Briand P., Grimber G., Nicolas J. F. A beta-galactosidase hybrid protein targeted to nuclei as a marker for developmental studies. Proc Natl Acad Sci U S A. 1987 Oct;84(19):6795–6799. doi: 10.1073/pnas.84.19.6795. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Cedar H. DNA methylation and gene activity. Cell. 1988 Apr 8;53(1):3–4. doi: 10.1016/0092-8674(88)90479-5. [DOI] [PubMed] [Google Scholar]
  6. Chattopadhyay S. K., Cloyd M. W., Linemeyer D. L., Lander M. R., Rands E., Lowy D. R. Cellular origin and role of mink cell focus-forming viruses in murine thymic lymphomas. Nature. 1982 Jan 7;295(5844):25–31. doi: 10.1038/295025a0. [DOI] [PubMed] [Google Scholar]
  7. Deragon J. M., Sinnett D., Labuda D. Reverse transcriptase activity from human embryonal carcinoma cells NTera2D1. EMBO J. 1990 Oct;9(10):3363–3368. doi: 10.1002/j.1460-2075.1990.tb07537.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Derr L. K., Strathern J. N., Garfinkel D. J. RNA-mediated recombination in S. cerevisiae. Cell. 1991 Oct 18;67(2):355–364. doi: 10.1016/0092-8674(91)90187-4. [DOI] [PubMed] [Google Scholar]
  9. Dornburg R., Temin H. M. Presence of a retroviral encapsidation sequence in nonretroviral RNA increases the efficiency of formation of cDNA genes. J Virol. 1990 Feb;64(2):886–889. doi: 10.1128/jvi.64.2.886-889.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Dornburg R., Temin H. M. Retroviral vector system for the study of cDNA gene formation. Mol Cell Biol. 1988 Jun;8(6):2328–2334. doi: 10.1128/mcb.8.6.2328. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Dornburg R., Temin H. M. cDNA genes formed after infection with retroviral vector particles lack the hallmarks of natural processed pseudogenes. Mol Cell Biol. 1990 Jan;10(1):68–74. doi: 10.1128/mcb.10.1.68. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Fanning T. G., Singer M. F. LINE-1: a mammalian transposable element. Biochim Biophys Acta. 1987 Dec 8;910(3):203–212. doi: 10.1016/0167-4781(87)90112-6. [DOI] [PubMed] [Google Scholar]
  13. Grandgenett D. P., Mumm S. R. Unraveling retrovirus integration. Cell. 1990 Jan 12;60(1):3–4. doi: 10.1016/0092-8674(90)90707-l. [DOI] [PubMed] [Google Scholar]
  14. Heidmann O., Heidmann T. Retrotransposition of a mouse IAP sequence tagged with an indicator gene. Cell. 1991 Jan 11;64(1):159–170. doi: 10.1016/0092-8674(91)90217-m. [DOI] [PubMed] [Google Scholar]
  15. Heidmann T., Heidmann O., Nicolas J. F. An indicator gene to demonstrate intracellular transposition of defective retroviruses. Proc Natl Acad Sci U S A. 1988 Apr;85(7):2219–2223. doi: 10.1073/pnas.85.7.2219. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Ivanov V. A., Melnikov A. A., Siunov A. V., Fodor I. I., Ilyin Y. V. Authentic reverse transcriptase is coded by jockey, a mobile Drosophila element related to mammalian LINEs. EMBO J. 1991 Sep;10(9):2489–2495. doi: 10.1002/j.1460-2075.1991.tb07788.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Jensen S., Heidmann T. An indicator gene for detection of germline retrotransposition in transgenic Drosophila demonstrates RNA-mediated transposition of the LINE I element. EMBO J. 1991 Jul;10(7):1927–1937. doi: 10.1002/j.1460-2075.1991.tb07719.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Kazazian H. H., Jr, Wong C., Youssoufian H., Scott A. F., Phillips D. G., Antonarakis S. E. Haemophilia A resulting from de novo insertion of L1 sequences represents a novel mechanism for mutation in man. Nature. 1988 Mar 10;332(6160):164–166. doi: 10.1038/332164a0. [DOI] [PubMed] [Google Scholar]
  19. Leibold D. M., Swergold G. D., Singer M. F., Thayer R. E., Dombroski B. A., Fanning T. G. Translation of LINE-1 DNA elements in vitro and in human cells. Proc Natl Acad Sci U S A. 1990 Sep;87(18):6990–6994. doi: 10.1073/pnas.87.18.6990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Levine K. L., Steiner B., Johnson K., Aronoff R., Quinton T. J., Linial M. L. Unusual features of integrated cDNAs generated by infection with genome-free retroviruses. Mol Cell Biol. 1990 May;10(5):1891–1900. doi: 10.1128/mcb.10.5.1891. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Linial M. Creation of a processed pseudogene by retroviral infection. Cell. 1987 Apr 10;49(1):93–102. doi: 10.1016/0092-8674(87)90759-8. [DOI] [PubMed] [Google Scholar]
  22. Luria S. E., Delbrück M. Mutations of Bacteria from Virus Sensitivity to Virus Resistance. Genetics. 1943 Nov;28(6):491–511. doi: 10.1093/genetics/28.6.491. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Martin S. L. LINEs. Curr Opin Genet Dev. 1991 Dec;1(4):505–508. doi: 10.1016/s0959-437x(05)80199-6. [DOI] [PubMed] [Google Scholar]
  24. Martin S. L. Ribonucleoprotein particles with LINE-1 RNA in mouse embryonal carcinoma cells. Mol Cell Biol. 1991 Sep;11(9):4804–4807. doi: 10.1128/mcb.11.9.4804. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Mathias S. L., Scott A. F., Kazazian H. H., Jr, Boeke J. D., Gabriel A. Reverse transcriptase encoded by a human transposable element. Science. 1991 Dec 20;254(5039):1808–1810. doi: 10.1126/science.1722352. [DOI] [PubMed] [Google Scholar]
  26. Miki Y., Nishisho I., Horii A., Miyoshi Y., Utsunomiya J., Kinzler K. W., Vogelstein B., Nakamura Y. Disruption of the APC gene by a retrotransposal insertion of L1 sequence in a colon cancer. Cancer Res. 1992 Feb 1;52(3):643–645. [PubMed] [Google Scholar]
  27. Morse B., Rotherg P. G., South V. J., Spandorfer J. M., Astrin S. M. Insertional mutagenesis of the myc locus by a LINE-1 sequence in a human breast carcinoma. Nature. 1988 May 5;333(6168):87–90. doi: 10.1038/333087a0. [DOI] [PubMed] [Google Scholar]
  28. Mulligan R. C., Berg P. Selection for animal cells that express the Escherichia coli gene coding for xanthine-guanine phosphoribosyltransferase. Proc Natl Acad Sci U S A. 1981 Apr;78(4):2072–2076. doi: 10.1073/pnas.78.4.2072. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Panganiban A. T., Fiore D. Ordered interstrand and intrastrand DNA transfer during reverse transcription. Science. 1988 Aug 26;241(4869):1064–1069. doi: 10.1126/science.2457948. [DOI] [PubMed] [Google Scholar]
  30. Prats A. C., Roy C., Wang P. A., Erard M., Housset V., Gabus C., Paoletti C., Darlix J. L. cis elements and trans-acting factors involved in dimer formation of murine leukemia virus RNA. J Virol. 1990 Feb;64(2):774–783. doi: 10.1128/jvi.64.2.774-783.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Pélisson A., Finnegan D. J., Bucheton A. Evidence for retrotransposition of the I factor, a LINE element of Drosophila melanogaster. Proc Natl Acad Sci U S A. 1991 Jun 1;88(11):4907–4910. doi: 10.1073/pnas.88.11.4907. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Rogers J. H. The origin and evolution of retroposons. Int Rev Cytol. 1985;93:187–279. doi: 10.1016/s0074-7696(08)61375-3. [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. Swain A., Coffin J. M. Mechanism of transduction by retroviruses. Science. 1992 Feb 14;255(5046):841–845. doi: 10.1126/science.1371365. [DOI] [PubMed] [Google Scholar]
  35. Tchenio T., Heidmann T. Defective retroviruses can disperse in the human genome by intracellular transposition. J Virol. 1991 Apr;65(4):2113–2118. doi: 10.1128/jvi.65.4.2113-2118.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Tchenio T., Heidmann T. High-frequency intracellular transposition of a defective mammalian provirus detected by an in situ colorimetric assay. J Virol. 1992 Mar;66(3):1571–1578. doi: 10.1128/jvi.66.3.1571-1578.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Temin H. M. Reverse transcription in the eukaryotic genome: retroviruses, pararetroviruses, retrotransposons, and retrotranscripts. Mol Biol Evol. 1985 Nov;2(6):455–468. doi: 10.1093/oxfordjournals.molbev.a040365. [DOI] [PubMed] [Google Scholar]
  38. Vanin E. F. Processed pseudogenes: characteristics and evolution. Annu Rev Genet. 1985;19:253–272. doi: 10.1146/annurev.ge.19.120185.001345. [DOI] [PubMed] [Google Scholar]
  39. Weiner A. M., Deininger P. L., Efstratiadis A. Nonviral retroposons: genes, pseudogenes, and transposable elements generated by the reverse flow of genetic information. Annu Rev Biochem. 1986;55:631–661. doi: 10.1146/annurev.bi.55.070186.003215. [DOI] [PubMed] [Google Scholar]
  40. Wilde C. D. Pseudogenes. CRC Crit Rev Biochem. 1986;19(4):323–352. [PubMed] [Google Scholar]

Articles from The EMBO Journal are provided here courtesy of Nature Publishing Group

RESOURCES