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. 1984 Feb 10;12(3):1463–1471. doi: 10.1093/nar/12.3.1463

Pseudogenes for human U2 small nuclear RNA do not have a fixed site of 3' truncation.

S W Van Arsdell, A M Weiner
PMCID: PMC318589  PMID: 6199740

Abstract

We present the sequences of five additional human U2 pseudogenes which are very similar to the U2.13 pseudogene reported previously [Van Arsdell et al. (1981) Cell 26, 11-17]. All six U2 pseudogenes preserve the 5' end of the mature U2 snRNA sequence, and all six are flanked by nearly perfect direct repeats that differ in sequence and range in length from 16 to 21 base pairs. The 3' ends of the six U2 pseudogenes are truncated at five different sites between position 33 and 82, and in two cases the 3' end of the pseudogene overlaps the downstream direct repeat by 5 or 6 base pairs. The structure of these six U2 pseudogenes contrasts with that of four human U3 pseudogenes [Bernstein et al. (1983) Cell 32, 461-472] all of which are identically truncated at position 69 or 70, and appear to be derived from a self-primed 74 base reverse transcript of U3 snRNA. Comparison of the U2 and U3 pseudogenes suggests a model for their generation in which the 3' end of the pseudogene is always truncated relative to the initial cDNA template.

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Selected References

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

  1. Battey J., Max E. E., McBride W. O., Swan D., Leder P. A processed human immunoglobulin epsilon gene has moved to chromosome 9. Proc Natl Acad Sci U S A. 1982 Oct;79(19):5956–5960. doi: 10.1073/pnas.79.19.5956. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Been M. D., Champoux J. J. DNA breakage and closure by rat liver type 1 topoisomerase: separation of the half-reactions by using a single-stranded DNA substrate. Proc Natl Acad Sci U S A. 1981 May;78(5):2883–2887. doi: 10.1073/pnas.78.5.2883. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Bernstein L. B., Mount S. M., Weiner A. M. Pseudogenes for human small nuclear RNA U3 appear to arise by integration of self-primed reverse transcripts of the RNA into new chromosomal sites. Cell. 1983 Feb;32(2):461–472. doi: 10.1016/0092-8674(83)90466-x. [DOI] [PubMed] [Google Scholar]
  4. Denison R. A., Van Arsdell S. W., Bernstein L. B., Weiner A. M. Abundant pseudogenes for small nuclear RNAs are dispersed in the human genome. Proc Natl Acad Sci U S A. 1981 Feb;78(2):810–814. doi: 10.1073/pnas.78.2.810. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Denison R. A., Weiner A. M. Human U1 RNA pseudogenes may be generated by both DNA- and RNA-mediated mechanisms. Mol Cell Biol. 1982 Jul;2(7):815–828. doi: 10.1128/mcb.2.7.815. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Gellert M. DNA topoisomerases. Annu Rev Biochem. 1981;50:879–910. doi: 10.1146/annurev.bi.50.070181.004311. [DOI] [PubMed] [Google Scholar]
  7. Grimaldi G., Singer M. F. A monkey Alu sequence is flanked by 13-base pair direct repeats by an interrupted alpha-satellite DNA sequence. Proc Natl Acad Sci U S A. 1982 Mar;79(5):1497–1500. doi: 10.1073/pnas.79.5.1497. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Halligan B. D., Davis J. L., Edwards K. A., Liu L. F. Intra- and intermolecular strand transfer by HeLa DNA topoisomerase I. J Biol Chem. 1982 Apr 10;257(7):3995–4000. [PubMed] [Google Scholar]
  9. Hammarström K., Westin G., Pettersson U. A pseudogene for human U4 RNA with a remarkable structure. EMBO J. 1982;1(6):737–739. doi: 10.1002/j.1460-2075.1982.tb01239.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Hayashi K. Organization of sequences related to U6 RNA in the human genome. Nucleic Acids Res. 1981 Jul 24;9(14):3379–3388. doi: 10.1093/nar/9.14.3379. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Hollis G. F., Hieter P. A., McBride O. W., Swan D., Leder P. Processed genes: a dispersed human immunoglobulin gene bearing evidence of RNA-type processing. Nature. 1982 Mar 25;296(5855):321–325. doi: 10.1038/296321a0. [DOI] [PubMed] [Google Scholar]
  12. Jagadeeswaran P., Forget B. G., Weissman S. M. Short interspersed repetitive DNA elements in eucaryotes: transposable DNA elements generated by reverse transcription of RNA pol III transcripts? Cell. 1981 Oct;26(2 Pt 2):141–142. doi: 10.1016/0092-8674(81)90296-8. [DOI] [PubMed] [Google Scholar]
  13. Karin M., Richards R. I. Human metallothionein genes--primary structure of the metallothionein-II gene and a related processed gene. Nature. 1982 Oct 28;299(5886):797–802. doi: 10.1038/299797a0. [DOI] [PubMed] [Google Scholar]
  14. Lee M. G., Lewis S. A., Wilde C. D., Cowan N. J. Evolutionary history of a multigene family: an expressed human beta-tubulin gene and three processed pseudogenes. Cell. 1983 Jun;33(2):477–487. doi: 10.1016/0092-8674(83)90429-4. [DOI] [PubMed] [Google Scholar]
  15. Lemischka I., Sharp P. A. The sequences of an expressed rat alpha-tubulin gene and a pseudogene with an inserted repetitive element. Nature. 1982 Nov 25;300(5890):330–335. doi: 10.1038/300330a0. [DOI] [PubMed] [Google Scholar]
  16. Messing J., Vieira J. A new pair of M13 vectors for selecting either DNA strand of double-digest restriction fragments. Gene. 1982 Oct;19(3):269–276. doi: 10.1016/0378-1119(82)90016-6. [DOI] [PubMed] [Google Scholar]
  17. Piechaczyk M., Lelay-Taha M. N., Sri-Widada J., Brunel C., Liautard J. P., Jeanteur P. Mouse DNA sequences complementary to small nuclear RNA U1. Nucleic Acids Res. 1982 Aug 11;10(15):4627–4640. doi: 10.1093/nar/10.15.4627. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Reed R. R., Grindley N. D. Transposon-mediated site-specific recombination in vitro: DNA cleavage and protein-DNA linkage at the recombination site. Cell. 1981 Sep;25(3):721–728. doi: 10.1016/0092-8674(81)90179-3. [DOI] [PubMed] [Google Scholar]
  19. Sanger F., Nicklen S., Coulson A. R. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463–5467. doi: 10.1073/pnas.74.12.5463. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Schmid C. W., Jelinek W. R. The Alu family of dispersed repetitive sequences. Science. 1982 Jun 4;216(4550):1065–1070. doi: 10.1126/science.6281889. [DOI] [PubMed] [Google Scholar]
  21. Temin H. M. Origin of retroviruses from cellular moveable genetic elements. Cell. 1980 Oct;21(3):599–600. doi: 10.1016/0092-8674(80)90420-1. [DOI] [PubMed] [Google Scholar]
  22. Ueda S., Nakai S., Nishida Y., Hisajima H., Honjo T. Long terminal repeat-like elements flank a human immunoglobulin epsilon pseudogene that lacks introns. EMBO J. 1982;1(12):1539–1544. doi: 10.1002/j.1460-2075.1982.tb01352.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Van Arsdell S. W., Denison R. A., Bernstein L. B., Weiner A. M., Manser T., Gesteland R. F. Direct repeats flank three small nuclear RNA pseudogenes in the human genome. Cell. 1981 Oct;26(1 Pt 1):11–17. doi: 10.1016/0092-8674(81)90028-3. [DOI] [PubMed] [Google Scholar]

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