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. 1981 Oct 10;9(19):5011–5020. doi: 10.1093/nar/9.19.5011

Nucleotide sequences at the boundaries between gene and insertion regions in the rDNA of Drosophila melanogaster

Igor B Dawid 1, Martha L Rebbert 1
PMCID: PMC327495  PMID: 6273792

Abstract

Ribosomal RNA genes interrupted by type 1 insertions of 1 kb and 0.5 kb have been sequenced through the insertion region and compared with an uninterrupted gene. The 0.5 kb insertion is flanked by a duplication of a 14 bp segment that is present once in the uninterrupted gene; the 1 kb insertion is flanked by a duplication of 11 of these 14 bp. Short insertions are identical in their entire length to downstream regions of long insertions. No internal repeats occur in the insertion. The presence of target site duplications suggests that type 1 insertions arose by the introduction of transposable elements into rDNA. Short sequence homologies between the upstream ends of the insertions and the 28S′ boundaries of the rRNA coding region suggest that short type 1 insertions may have arisen by recombination from longer insertions.

We have sequenced both boundaries of two molecules containing type 2 insertions and the upstream boundary of a third; the points of interruption at the upstream boundary (28S′ site) differ from each other in steps of 2 bp. Between the boundary in the 0.5 kb type 1 insertion and the type 2 boundaries there are distances of 74, 76, and 78 bp. At the downstream boundary (28S′′ site) the two sequenced type 2 insertions are identical. The rRNA coding region of one molecule extends across the insertion without deletion or duplication, but a 2 bp deletion in the RNA coding region is present in the second molecule. Stretches of 13 or 22 adenine residues occur at the downstream (28S′′) end of the two type 2 insertions.

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Selected References

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

  1. Botchan P., Reeder R. H., Dawid I. B. Restriction analysis of the nontranscribed spacers of Xenopus laevis ribosomal DNA. Cell. 1977 Jul;11(3):599–607. doi: 10.1016/0092-8674(77)90077-0. [DOI] [PubMed] [Google Scholar]
  2. Brown D. D., Sugimoto K. 5 S DNAs of Xenopus laevis and Xenopus mulleri: evolution of a gene family. J Mol Biol. 1973 Aug 15;78(3):397–415. doi: 10.1016/0022-2836(73)90464-6. [DOI] [PubMed] [Google Scholar]
  3. Brown D. D., Wensink P. C., Jordan E. A comparison of the ribosomal DNA's of Xenopus laevis and Xenopus mulleri: the evolution of tandem genes. J Mol Biol. 1972 Jan 14;63(1):57–73. doi: 10.1016/0022-2836(72)90521-9. [DOI] [PubMed] [Google Scholar]
  4. Calos M. P., Miller J. H. Transposable elements. Cell. 1980 Jul;20(3):579–595. doi: 10.1016/0092-8674(80)90305-0. [DOI] [PubMed] [Google Scholar]
  5. Cameron J. R., Loh E. Y., Davis R. W. Evidence for transposition of dispersed repetitive DNA families in yeast. Cell. 1979 Apr;16(4):739–751. doi: 10.1016/0092-8674(79)90090-4. [DOI] [PubMed] [Google Scholar]
  6. Dawid I. B., Wellauer P. K., Long E. O. Ribosomal DNA in Drosophila melanogaster. I. Isolation and characterization of cloned fragments. J Mol Biol. 1978 Dec 25;126(4):749–768. doi: 10.1016/0022-2836(78)90018-9. [DOI] [PubMed] [Google Scholar]
  7. Dawid I. B., Wellauer P. K. Ribosomal DNA and related sequences in Drosophila melanogaster. Cold Spring Harb Symp Quant Biol. 1978;42(Pt 2):1185–1194. doi: 10.1101/sqb.1978.042.01.119. [DOI] [PubMed] [Google Scholar]
  8. Dover G., Coen E. Springcleaning ribosomal DNA: a model for multigene evolution? Nature. 1981 Apr 30;290(5809):731–732. doi: 10.1038/290731a0. [DOI] [PubMed] [Google Scholar]
  9. Dunsmuir P., Brorein W. J., Jr, Simon M. A., Rubin G. M. Insertion of the Drosophila transposable element copia generates a 5 base pair duplication. Cell. 1980 Sep;21(2):575–579. doi: 10.1016/0092-8674(80)90495-x. [DOI] [PubMed] [Google Scholar]
  10. Glover D. M. Cloned segment of Drosophila melanogaster rDNA containing new types of sequence insertion. Proc Natl Acad Sci U S A. 1977 Nov;74(11):4932–4936. doi: 10.1073/pnas.74.11.4932. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Hosbach H. A., Silberklang M., McCarthy B. J. Evolution of a D. melanogaster glutamate tRNA gene cluster. Cell. 1980 Aug;21(1):169–178. doi: 10.1016/0092-8674(80)90124-5. [DOI] [PubMed] [Google Scholar]
  12. Konkel D. A., Maizel J. V., Jr, Leder P. The evolution and sequence comparison of two recently diverged mouse chromosomal beta--globin genes. Cell. 1979 Nov;18(3):865–873. doi: 10.1016/0092-8674(79)90138-7. [DOI] [PubMed] [Google Scholar]
  13. Levis R., Dunsmuir P., Rubin G. M. Terminal repeats of the Drosophila transposable element copia: nucleotide sequence and genomic organization. Cell. 1980 Sep;21(2):581–588. doi: 10.1016/0092-8674(80)90496-1. [DOI] [PubMed] [Google Scholar]
  14. Long E. O., Dawid I. B. Expression of ribosomal DNA insertions in Drosophila melanogaster. Cell. 1979 Dec;18(4):1185–1196. doi: 10.1016/0092-8674(79)90231-9. [DOI] [PubMed] [Google Scholar]
  15. Long E. O., Dawid I. B. Repeated genes in eukaryotes. Annu Rev Biochem. 1980;49:727–764. doi: 10.1146/annurev.bi.49.070180.003455. [DOI] [PubMed] [Google Scholar]
  16. Long E. O., Dawid I. B. Restriction analysis of spacers in ribosomal DNA of Drosophila melanogaster. Nucleic Acids Res. 1979 Sep 11;7(1):205–215. doi: 10.1093/nar/7.1.205. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Long E. O., Rebbert M. L., Dawid I. B. Nucleotide sequence of the initiation site for ribosomal RNA transcription in Drosophila melanogaster: comparison of genes with and without insertions. Proc Natl Acad Sci U S A. 1981 Mar;78(3):1513–1517. doi: 10.1073/pnas.78.3.1513. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Maxam A. M., Gilbert W. Sequencing end-labeled DNA with base-specific chemical cleavages. Methods Enzymol. 1980;65(1):499–560. doi: 10.1016/s0076-6879(80)65059-9. [DOI] [PubMed] [Google Scholar]
  19. Queen C. L., Korn L. J. Computer analysis of nucleic acids and proteins. Methods Enzymol. 1980;65(1):595–609. doi: 10.1016/s0076-6879(80)65062-9. [DOI] [PubMed] [Google Scholar]
  20. Rae P. M., Kohorn B. D., Wade R. P. The 10 kb Drosophila virilis 28S rDNA intervening sequence is flanked by a direct repeat of 14 base pairs of coding sequence. Nucleic Acids Res. 1980 Aug 25;8(16):3491–3504. doi: 10.1093/nar/8.16.3491. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Roiha H., Glover D. M. Chracterisation of complete type II insertions in cloned segments of ribosomal DNA from Drosophila melanogaster. J Mol Biol. 1980 Jun 25;140(2):341–355. doi: 10.1016/0022-2836(80)90110-2. [DOI] [PubMed] [Google Scholar]
  22. Roiha H., Miller J. R., Woods L. C., Glover D. M. Arrangements and rearrangements of sequences flanking the two types of rDNA insertion in D. melanogaster. Nature. 1981 Apr 30;290(5809):749–753. doi: 10.1038/290749a0. [DOI] [PubMed] [Google Scholar]
  23. Smith G. P. Unequal crossover and the evolution of multigene families. Cold Spring Harb Symp Quant Biol. 1974;38:507–513. doi: 10.1101/sqb.1974.038.01.055. [DOI] [PubMed] [Google Scholar]
  24. Tu C. P., Cohen S. N. 3'-end labeling of DNA with [alpha-32P]cordycepin-5'-triphosphate. Gene. 1980 Jul;10(2):177–183. doi: 10.1016/0378-1119(80)90135-3. [DOI] [PubMed] [Google Scholar]
  25. Wellauer P. K., Dawid I. B., Brown D. D., Reeder R. H. The molecular basis for length heterogeneity in ribosomal DNA from Xenopus laevis. J Mol Biol. 1976 Aug 25;105(4):461–486. doi: 10.1016/0022-2836(76)90229-1. [DOI] [PubMed] [Google Scholar]
  26. Wellauer P. K., Dawid I. B. Ribosomal DNA in Drosophila melanogaster. II. Heteroduplex mapping of cloned and uncloned rDNA. J Mol Biol. 1978 Dec 25;126(4):769–782. doi: 10.1016/0022-2836(78)90019-0. [DOI] [PubMed] [Google Scholar]
  27. Wellauer P. K., Dawid I. B., Tartof K. D. X and Y chromosomal ribosomal DNA of Drosophila: comparison of spacers and insertions. Cell. 1978 Jun;14(2):269–278. doi: 10.1016/0092-8674(78)90113-7. [DOI] [PubMed] [Google Scholar]

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