• We are sorry, but NCBI web applications do not support your browser and may not function properly. More information
Logo of geneticsGeneticsCurrent IssueInformation for AuthorsEditorial BoardSubscribeSubmit a Manuscript
Genetics. Mar 1996; 142(3): 853–863.
PMCID: PMC1207023

Analysis of the 5' Junctions of R2 Insertions with the 28s Gene: Implications for Non-Ltr Retrotransposition


R2 elements are non-long terminal repeat retrotransposable elements that insert into 28S rRNA genes of most insect species. The single open reading frame of R2 encodes a protein with both endonuclease activity, which cleaves the target site, and reverse transcriptase activity, which uses this cleavage to prime reverse transcription. This target-primed reverse transcription mechanism is also used by group II introns. Little is known of the mechanism by which the 5' end of R2 is integrated after reverse transcription. We have determined the 5' junction sequence of 94 R2 elements from 14 different species of Drosophila. Only 37% of the full-length elements contained precise 5' junctions; the remainder contained deletions of the 28S gene and/or insertions of additional sequences. Because the 5' junctions of truncated copies were similar to full-length elements, no sequences at the 5' end of R2 appear to be required for element integration. A model in which the R2 reverse transcriptase is capable of switching templates from the R2 RNA transcript to the upstream 28S gene can best explain the observed 5' junction sequences. This template jumping is analogous to the template switching of retroviral reverse transcriptases during formation of the double-stranded integration products.

Full Text

The Full Text of this article is available as a PDF (3.8M).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Bollag RJ, Waldman AS, Liskay RM. Homologous recombination in mammalian cells. Annu Rev Genet. 1989;23:199–225. [PubMed]
  • Bucheton A. I transposable elements and I-R hybrid dysgenesis in Drosophila. Trends Genet. 1990 Jan;6(1):16–21. [PubMed]
  • Burke WD, Calalang CC, Eickbush TH. The site-specific ribosomal insertion element type II of Bombyx mori (R2Bm) contains the coding sequence for a reverse transcriptase-like enzyme. Mol Cell Biol. 1987 Jun;7(6):2221–2230. [PMC free article] [PubMed]
  • Burke WD, Müller F, Eickbush TH. R4, a non-LTR retrotransposon specific to the large subunit rRNA genes of nematodes. Nucleic Acids Res. 1995 Nov 25;23(22):4628–4634. [PMC free article] [PubMed]
  • Dawid IB, Rebbert ML. Nucleotide sequences at the boundaries between gene and insertion regions in the rDNA of Drosophilia melanogaster. Nucleic Acids Res. 1981 Oct 10;9(19):5011–5020. [PMC free article] [PubMed]
  • DeStefano JJ, Bambara RA, Fay PJ. The mechanism of human immunodeficiency virus reverse transcriptase-catalyzed strand transfer from internal regions of heteropolymeric RNA templates. J Biol Chem. 1994 Jan 7;269(1):161–168. [PubMed]
  • Eickbush DG, Eickbush TH. Vertical transmission of the retrotransposable elements R1 and R2 during the evolution of the Drosophila melanogaster species subgroup. Genetics. 1995 Feb;139(2):671–684. [PMC free article] [PubMed]
  • Eickbush TH. Transposing without ends: the non-LTR retrotransposable elements. New Biol. 1992 May;4(5):430–440. [PubMed]
  • Evans JP, Palmiter RD. Retrotransposition of a mouse L1 element. Proc Natl Acad Sci U S A. 1991 Oct 1;88(19):8792–8795. [PMC free article] [PubMed]
  • Hu WS, Temin HM. Retroviral recombination and reverse transcription. Science. 1990 Nov 30;250(4985):1227–1233. [PubMed]
  • 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. [PMC free article] [PubMed]
  • Martin SL. LINEs. Curr Opin Genet Dev. 1991 Dec;1(4):505–508. [PubMed]
  • Long EO, Rebbert ML, Dawid IB. Structure and expression of ribosomal RNA genes of Drosophila melanogaster interrupted by type-2 insertions. Cold Spring Harb Symp Quant Biol. 1981;45(Pt 2):667–672. [PubMed]
  • Luan DD, Eickbush TH. RNA template requirements for target DNA-primed reverse transcription by the R2 retrotransposable element. Mol Cell Biol. 1995 Jul;15(7):3882–3891. [PMC free article] [PubMed]
  • Lukacsovich T, Yang D, Waldman AS. Repair of a specific double-strand break generated within a mammalian chromosome by yeast endonuclease I-SceI. Nucleic Acids Res. 1994 Dec 25;22(25):5649–5657. [PMC free article] [PubMed]
  • Martín F, Marañn C, Olivares M, Alonso C, López MC. Characterization of a non-long terminal repeat retrotransposon cDNA (L1Tc) from Trypanosoma cruzi: homology of the first ORF with the ape family of DNA repair enzymes. J Mol Biol. 1995 Mar 17;247(1):49–59. [PubMed]
  • Peacock WJ, Appels R, Endow S, Glover D. Chromosomal distribution of the major insert in Drosophila melanogaster 28S rRNA genes. Genet Res. 1981 Apr;37(2):209–214. [PubMed]
  • Pélisson A, Finnegan DJ, 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. [PMC free article] [PubMed]
  • Roiha H, Miller JR, Woods LC, Glover DM. Arrangements and rearrangements of sequences flanking the two types of rDNA insertion in D. melanogaster. Nature. 1981 Apr 30;290(5809):749–753. [PubMed]
  • Roth DB, Wilson JH. Nonhomologous recombination in mammalian cells: role for short sequence homologies in the joining reaction. Mol Cell Biol. 1986 Dec;6(12):4295–4304. [PMC free article] [PubMed]
  • Schwarz-Sommer Z, Leclercq L, Göbel E, Saedler H. Cin4, an insert altering the structure of the A1 gene in Zea mays, exhibits properties of nonviral retrotransposons. EMBO J. 1987 Dec 20;6(13):3873–3880. [PMC free article] [PubMed]
  • Szostak JW, Orr-Weaver TL, Rothstein RJ, Stahl FW. The double-strand-break repair model for recombination. Cell. 1983 May;33(1):25–35. [PubMed]
  • Thacker J, Chalk J, Ganesh A, North P. A mechanism for deletion formation in DNA by human cell extracts: the involvement of short sequence repeats. Nucleic Acids Res. 1992 Dec 11;20(23):6183–6188. [PMC free article] [PubMed]
  • Whitcomb JM, Hughes SH. Retroviral reverse transcription and integration: progress and problems. Annu Rev Cell Biol. 1992;8:275–306. [PubMed]
  • Wu W, Blumberg BM, Fay PJ, Bambara RA. Strand transfer mediated by human immunodeficiency virus reverse transcriptase in vitro is promoted by pausing and results in misincorporation. J Biol Chem. 1995 Jan 6;270(1):325–332. [PubMed]
  • Xiong Y, Eickbush TH. Similarity of reverse transcriptase-like sequences of viruses, transposable elements, and mitochondrial introns. Mol Biol Evol. 1988 Nov;5(6):675–690. [PubMed]
  • Xiong YE, Eickbush TH. Functional expression of a sequence-specific endonuclease encoded by the retrotransposon R2Bm. Cell. 1988 Oct 21;55(2):235–246. [PubMed]
  • Zhang J, Temin HM. Rate and mechanism of nonhomologous recombination during a single cycle of retroviral replication. Science. 1993 Jan 8;259(5092):234–238. [PubMed]
  • Zhang J, Temin HM. Retrovirus recombination depends on the length of sequence identity and is not error prone. J Virol. 1994 Apr;68(4):2409–2414. [PMC free article] [PubMed]

Articles from Genetics are provided here courtesy of Genetics Society of America


Related citations in PubMed

See reviews...See all...

Cited by other articles in PMC

See all...


Recent Activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...