Transcription of Endogenous and Exogenous R2 Elements in the rRNA Gene Locus of Drosophila melanogaster

REFERENCES

• Burke, W. D., H. S. Malik, W. C. Lathe, and T. H. Eickbush. 1998. Are retrotransposons long term hitchhikers? Nature 239: 141–142.
   Google Scholar
• Burke, W. D., H. S. Malik, J. P. Jones, and T. H. Eickbush. 1999. The domain structure and retrotransposition mechanism of R2 elements are conserved throughout arthropods. Mol. Biol. Evol. 16: 502–511.
   PubMed Web of Science ®Google Scholar
• Burke, W. D., F. Müller, and T. H. Eickbush. 1995. R4, a non-LTR retrotransposon specific to the large subunit rRNA gene of nematodes. Nucleic Acids Res. 23: 4628–4634.
   PubMedGoogle Scholar
• Chooi, W. Y. 1979. The occurrence of long transcription units among the X and Y ribosomal genes of Drosophila melanogaster: transcription of insertion sequences. Chromosoma 74: 57–74.
   PubMedGoogle Scholar
• Clark, A. G., F. M. Szumski, and E. S. M. Lyckegaard. 1990. Population genetics of the Y chromosome of Drosophila melanogaster: rDNA variation and phenotypic correlates. Genet. Res. 58: 7–13.
   Google Scholar
• Cluster, P. D., D. Marinkovic, R. W. Allard, and F. J. Ayala. 1987. Correlations between developmental rates, enzyme activities, ribosomal DNA spacer-length phenotypes, and adaptation in Drosophila melanogaster. Proc. Natl. Acad. Sci. USA 84: 610–614.
   PubMedGoogle Scholar
• Conconi, A., J. M. Sogo, and C. A. Ryan. 1992. Ribosomal gene clusters are uniquely proportioned between open and closed chromatin structures in both tomato leaf cells and exponentially growing suspension cultures. Proc. Natl. Acad. Sci. USA 89: 5256–5260.
   PubMedGoogle Scholar
• Conconi, A., R. M. Widmer, T. Koller, and J. M. Sogo. 1989. Two different chromatin structures coexist in ribosomal RNA genes throughout the cell cycle. Cell 57: 753–761.
   PubMed Web of Science ®Google Scholar
• Dammann, R., R. Lucchini, T. Koller, and J. M. Sogo. 1995. Transcription in the yeast rRNA gene locus: distribution of the active gene copies and chromatin structure of their flanking regulatory sequences. Mol. Cell. Biol. 15: 5294–5303.
   PubMedGoogle Scholar
• Durica, D. S., and H. M. Krider. 1977. Studies on the ribosomal RNA cistrons in interspecific Drosophila hybrids. Dev. Biol. 59: 62–74.
   PubMed Web of Science ®Google Scholar
• Eickbush, D. G., and T. H. Eickbush. 1995. Vertical transmission of the retrotransposable elements R1 and R2 during the evolution of the Drosophila melanogaster species subgroup. Genetics 139: 671–684.
   PubMed Web of Science ®Google Scholar
• Eickbush, D. G., D. D. Luan, and T. H. Eickbush. 2000. Integration of Bombyx mori R2 sequences into the 28S ribosomal RNA genes of Drosophila melanogaster. Mol. Cell. Biol. 20: 213–223.
   PubMedGoogle Scholar
• Eickbush, T. H. 2002. R2 and related site-specific non-long terminal repeat retrotransposons, p. 813–835. In N. L. Craig, R. Craigie, M. Gellart, and A. M. Lambowitz (ed.), Mobile DNA II. American Society for Microbiology, Washington, D.C.
   Google Scholar
• Feng, Q., J. V. Moran, H. H. Kazazian, and J. D. Boeke. 1996. Human L1 retrotransposon encodes a conserved endonuclease required for retrotransposition. Cell 87: 905–916.
   PubMed Web of Science ®Google Scholar
• Frankham, R., D. A. Briscoe, and R. K. Nurthen. 1980. Unequal crossing over at the rDNA tandon as a source of quantitative genetic variation in Drosophila. Genetics 95: 727–742.
   PubMedGoogle Scholar
• Gentile, K. L., W. D. Burke, and T. H. Eickbush. 2001. Multiple lineages of R1 retrotransposable elements can coexist in the rDNA loci of Drosophila. Mol. Biol. Evol. 18: 235–245.
   PubMedGoogle Scholar
• George, J. A., W. D. Burke, and T. H. Eickbush. 1996. Analysis of the 5′ junctions of R2 insertions with the 28S gene: implications for non-LTR retrotransposition. Genetics 142: 853–863.
   PubMedGoogle Scholar
• Jakubczak, J. L., Y. Xiong, and T. H. Eickbush. 1990. Type I (R1) and type II (R2) ribosomal DNA insertions of Drosophila melanogaster are retrotransposable elements closely related to those of Bombyx mori. J. Mol. Biol. 212: 37–52.
   PubMedGoogle Scholar
• Jakubczak, J. L., M. K. Zenni, R. C. Woodruff, and T. H. Eickbush. 1992. Turnover of R1 (type I) and R2 (type II) retrotransposable elements in the ribosomal DNA of Drosophila melanogaster. Genetics 131: 129–142.
   PubMedGoogle Scholar
• Jamrich, M., and O. L. Miller, Jr. 1984. The rare transcripts of interrupted rRNA genes in Drosophila melanogaster are processed or degraded during synthesis. EMBO J. 3: 1541–1545.
   PubMed Web of Science ®Google Scholar
• Jolly, D. J., and C. A. Thomas. 1980. Nuclear RNA transcripts from Drosophila melanogaster ribosomal RNA genes containing introns. Nucleic Acids Res. 8: 67–84.
   PubMedGoogle Scholar
• Kerrebrock, A. W., R. Srivastava, and S. A. Gerbi. 1989. Isolation and characterization of ribosomal DNA variants from Sciara coprophila. J. Mol. Biol. 210: 1–13.
   PubMedGoogle Scholar
• Kidd, S. J., and D. M. Glover. 1981. Drosophila melanogaster ribosomal DNA containing type II insertions is variably transcribed in different strains and tissues. J. Mol. Biol. 151: 645–662.
   PubMedGoogle Scholar
• Lathe, W. C., III, and T. H. Eickbush. 1997. A single lineage of R2 retrotransposable elements is an active, evolutionarily stable component of the Drosophila rDNA locus. Mol. Biol. Evol. 14: 1232–1241.
   PubMedGoogle Scholar
• Long, E. O., M. Collins, B. I. Kiefer, and I. B. Dawid. 1981. Expression of the ribosomal DNA insertions in bobbed mutants of Drosophila melanogaster. Mol. Gen. Genet. 182: 377–384.
   PubMedGoogle Scholar
• Long, E. O., and I. B. Dawid. 1979. Expression of ribosomal DNA insertions in Drosophila melanogaster. Cell 18: 1185–1196.
   PubMed Web of Science ®Google Scholar
• Long, E. O., M. L. Rebbert, and I. B. Dawid. 1980. Structure and expression of ribosomal RNA genes of Drosophila melanogaster interrupted by type 2 insertions. Cold Spring Harbor Symp. Quant. Biol. 45: 667–672.
   Google Scholar
• Luan, D. D., and T. H. Eickbush. 1995. RNA template requirements for target DNA-primed reverse transcription by the R2 retrotransposable element. Mol. Cell. Biol. 15: 3882–3891.
   PubMedGoogle Scholar
• Luan, D. D., and T. H. Eickbush. 1996. Downstream 28S gene sequences on the RNA template affect the choice of primer and the accuracy of initiation by the R2 reverse transcriptase. Mol. Cell. Biol. 16: 4726–4734.
   PubMedGoogle Scholar
• Luan, D. D., M. H. Korman, J. L. Jakubczak, and T. H. Eickbush. 1993. Reverse transcription of R2Bm RNA is primed by a nick at the chromosomal target site: a mechanism for non-LTR retrotransposition. Cell 72: 595–605.
   PubMed Web of Science ®Google Scholar
• Makni, M., M. Marrakchi, and N. Prud'homme. 1989. The occurrence of long ribosomal transcripts homologous to type I insertions in bobbed mutants of Drosophila melanogaster. Genet. Res. 54: 127–135.
   PubMedGoogle Scholar
• McKnight, S. L., and O. L. Miller, Jr. 1976. Ultrastructural patterns of RNA synthesis during early embryogenesis of Drosophila melanogaster. Cell 8: 305–319.
   PubMed Web of Science ®Google Scholar
• Meyer, G. F., and W. Henning. 1974. The nucleolus in primary spermatocytes of Drosophila hydei. Chromosoma 46: 121–144.
   PubMedGoogle Scholar
• Penton, E. H., B. W. Sullender, and T. J. Crease. 2002. Pokey, a new DNA transposon in Daphnia (Cladocera: Crustacea). J. Mol. Evol. 55: 664–673.
   PubMedGoogle Scholar
• Perez-Gonzalez, C. E., and T. H. Eickbush. 2001. Dynamics of R1 and R2 elements in the rDNA locus of Drosophila simulans. Genetics 158: 1557–1567.
   PubMedGoogle Scholar
• Perez-Gonzalez, C. E., and T. H. Eickbush. 2002. Rates of R1 and R2 retrotransposition and elimination from the rDNA locus of Drosophila melanogaster. Genetics 162: 799–811.
   PubMed Web of Science ®Google Scholar
• Polanco, C., A. I. González, á. de la Fuente, and G. A. Dover. 1998. Multigene family of ribosomal DNA in Drosophila melanogaster reveals contrasting patterns of homogenization for IGS and ITS spacer regions: a possible mechanism to resolve this paradox. Genetics 149: 243–256.
   PubMed Web of Science ®Google Scholar
• Robinett, C. C., A. O'Connor, and M. Dunaway. 1997. The repeat organizer, a specialized insulator element within the intergenic spacer of the Xenopus rRNA genes. Mol. Cell. Biol. 17: 2866–2875.
   PubMedGoogle Scholar
• Stancheva, I., R. Lucchini, T. Koller, and J. M. Sogo. 1997. Chromatin structure and methylation of rat rRNA genes studied by formaldehyde fixation and psoralen cross-linking. Nucleic Acids Res. 25: 1727–1735.
   PubMedGoogle Scholar
• Terracol, R. 1986. Transcription of rDNA insertions in bobbed mutants of Drosophila melanogaster. Genet. Res. 48: 167–174.
   PubMedGoogle Scholar
• Wayne, R. L., Z. D. Sharp, and J. D. Procunier. 1985. Preferential DNase I sensitivity of insert-free ribosomal RNA of Drosophila melanogaster. Nucleic Acids Res. 13: 2869–2879.
   PubMedGoogle Scholar
• Williams, S. M., G. R. Furnier, E. Fuog, and C. Strobeck. 1987. Evolution of the ribosomal DNA spacers of Drosophila melanogaster: different patterns of variation on the X and Y chromosomes. Genetics 116: 225–232.
   PubMedGoogle Scholar
• Yang, J., H. S. Malik, and T. H. Eickbush. 1999. Identification of the endonuclease domain encoded by R2 and other site-specific, non-long terminal repeat retrotransposable elements. Proc. Natl. Acad. Sci. USA 96: 7847–7852.
   PubMed Web of Science ®Google Scholar
• Yang, Q., L. M. Angerer, and R. C. Angerer. 1989. Structure and tissue-specific developmental expression of a sea urchin arylsulfatase gene. Dev. Biol. 135: 53–65.
   PubMedGoogle Scholar