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. 1987 Feb 11;15(3):1245–1258. doi: 10.1093/nar/15.3.1245

Structure of the Bombyx mori rDNA: initiation site for its transcription.

H Fujiwara, H Ishikawa
PMCID: PMC340521  PMID: 3029701

Abstract

The initiation site of rDNA transcription in Bombyx mori was determined to be located at 909bp upstream from the 5'- end of mature 18s rRNA by S1-nuclease mapping and primer extension experiment. An in vitro transcription system, which was constructed using posterior silk glands of Bombyx larvae, initiated the transcription of cloned rDNA at exactly the same site as determined for the in vivo transcription above. The primary transcript seemed to be processed at about 200b downstream of the initiation site both in vivo and in vitro. Sequence analyses of the flanking region of the initiation site revealed that short repetitive sequences are widely distributed throughout the NTS region, and that a highly AT-rich region resides immediately upstream of the initiation region.

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Selected References

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

  1. Bayev A. A., Georgiev O. I., Hadjiolov A. A., Kermekchiev M. B., Nikolaev N., Skryabin K. G., Zakharyev V. M. The structure of the yeast ribosomal RNA genes. 2. The nucleotide sequence of the initiation site for ribosomal RNA transcription. Nucleic Acids Res. 1980 Nov 11;8(21):4919–4926. doi: 10.1093/nar/8.21.4919. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Berk A. J., Sharp P. A. Spliced early mRNAs of simian virus 40. Proc Natl Acad Sci U S A. 1978 Mar;75(3):1274–1278. doi: 10.1073/pnas.75.3.1274. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Blum B., Pierron G., Seebeck T., Braun R. Processing in the external transcribed spacer of ribosomal RNA from Physarum polycephalum. Nucleic Acids Res. 1986 Apr 25;14(8):3153–3166. doi: 10.1093/nar/14.8.3153. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Blum B., Seebeck T., Braun R., Ferris P., Vogt V. Localization and DNA sequence around the initiation site of ribosomal RNA transcription in Physarum polycephalum. Nucleic Acids Res. 1983 Dec 10;11(23):8519–8533. doi: 10.1093/nar/11.23.8519. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Boseley P., Moss T., Mächler M., Portmann R., Birnstiel M. Sequence organization of the spacer DNA in a ribosomal gene unit of Xenopus laevis. Cell. 1979 May;17(1):19–31. doi: 10.1016/0092-8674(79)90291-5. [DOI] [PubMed] [Google Scholar]
  6. Cassidy B. G., Subrahmanyan C. S., Rothblum L. I. The nucleotide sequence of the 5' region of rat 18S rDNA and adjoining spacer. Biochem Biophys Res Commun. 1982 Aug 31;107(4):1571–1576. doi: 10.1016/s0006-291x(82)80179-4. [DOI] [PubMed] [Google Scholar]
  7. Challoner P. B., Amin A. A., Pearlman R. E., Blackburn E. H. Conserved arrangements of repeated DNA sequences in nontranscribed spacers of ciliate ribosomal RNA genes: evidence for molecular coevolution. Nucleic Acids Res. 1985 Apr 11;13(7):2661–2680. doi: 10.1093/nar/13.7.2661. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Corden J., Wasylyk B., Buchwalder A., Sassone-Corsi P., Kedinger C., Chambon P. Promoter sequences of eukaryotic protein-coding genes. Science. 1980 Sep 19;209(4463):1406–1414. doi: 10.1126/science.6251548. [DOI] [PubMed] [Google Scholar]
  9. Engberg J., Din N., Saiga H., Higashinakagawa T. Nucleotide sequence of the 5'-terminal coding region for pre-rRNA and mature 17S rRNA in Tetrahymena thermophila rDNA. Nucleic Acids Res. 1984 Jan 25;12(2):959–972. doi: 10.1093/nar/12.2.959. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Financsek I., Mizumoto K., Mishima Y., Muramatsu M. Human ribosomal RNA gene: nucleotide sequence of the transcription initiation region and comparison of three mammalian genes. Proc Natl Acad Sci U S A. 1982 May;79(10):3092–3096. doi: 10.1073/pnas.79.10.3092. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Financsek I., Tora L., Kelemen G., Hidvégi E. J. Supercoil induced S1 hypersensitive sites in the rat and human ribosomal RNA genes. Nucleic Acids Res. 1986 Apr 25;14(8):3263–3277. doi: 10.1093/nar/14.8.3263. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Fujiwara H., Ishikawa H. Molecular mechanism of introduction of the hidden break into the 28S rRNA of insects: implication based on structural studies. Nucleic Acids Res. 1986 Aug 26;14(16):6393–6401. doi: 10.1093/nar/14.16.6393. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Fujiwara H., Ogura T., Takada N., Miyajima N., Ishikawa H., Maekawa H. Introns and their flanking sequences of Bombyx mori rDNA. Nucleic Acids Res. 1984 Sep 11;12(17):6861–6869. doi: 10.1093/nar/12.17.6861. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Galli G., Hofstetter H., Birnstiel M. L. Two conserved sequence blocks within eukaryotic tRNA genes are major promoter elements. Nature. 1981 Dec 17;294(5842):626–631. doi: 10.1038/294626a0. [DOI] [PubMed] [Google Scholar]
  15. Grosveld G. C., de Boer E., Shewmaker C. K., Flavell R. A. DNA sequences necessary for transcription of the rabbit beta-globin gene in vivo. Nature. 1982 Jan 14;295(5845):120–126. doi: 10.1038/295120a0. [DOI] [PubMed] [Google Scholar]
  16. Grummt I. Mapping of a mouse ribosomal DNA promoter by in vitro transcription. Nucleic Acids Res. 1981 Nov 25;9(22):6093–6102. doi: 10.1093/nar/9.22.6093. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Grummt I. Specific transcription of mouse ribosomal DNA in a cell-free system that mimics control in vivo. Proc Natl Acad Sci U S A. 1981 Feb;78(2):727–731. doi: 10.1073/pnas.78.2.727. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Hoshikawa Y., Iida Y., Iwabuchi M. Nucleotide sequence of the transcriptional initiation region of Dictyostelium discoideum rRNA gene and comparison of the initiation regions of three lower eukaryotes' genes. Nucleic Acids Res. 1983 Mar 25;11(6):1725–1734. doi: 10.1093/nar/11.6.1725. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Iida C. T., Kownin P., Paule M. R. Ribosomal RNA transcription: proteins and DNA sequences involved in preinitiation complex formation. Proc Natl Acad Sci U S A. 1985 Mar;82(6):1668–1672. doi: 10.1073/pnas.82.6.1668. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Kohorn B. D., Rae P. M. Accurate transcription of truncated ribosomal DNA templates in a Drosophila cell-free system. Proc Natl Acad Sci U S A. 1982 Mar;79(5):1501–1505. doi: 10.1073/pnas.79.5.1501. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Kohorn B. D., Rae P. M. Nontranscribed spacer sequences promote in vitro transcription of Drosophila ribosomal DNA. Nucleic Acids Res. 1982 Nov 11;10(21):6879–6886. doi: 10.1093/nar/10.21.6879. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Learned R. M., Tjian R. In vitro transcription of human ribosomal RNA genes by RNA polymerase I. J Mol Appl Genet. 1982;1(6):575–584. [PubMed] [Google Scholar]
  23. 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]
  24. Maden B. E., Moss M., Salim M. Nucleotide sequence of an external transcribed spacer in Xenopus laevis rDNA: sequences flanking the 5' and 3' ends of 18S rRNA are non-complementary. Nucleic Acids Res. 1982 Apr 10;10(7):2387–2398. doi: 10.1093/nar/10.7.2387. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Maekawa H., Suzuki Y. Repeated turn-off and turn-on of fibroin gene transcription during silk gland development of Bombyx mori. Dev Biol. 1980 Aug;78(2):394–406. doi: 10.1016/0012-1606(80)90343-7. [DOI] [PubMed] [Google Scholar]
  26. Manley J. L., Fire A., Cano A., Sharp P. A., Gefter M. L. DNA-dependent transcription of adenovirus genes in a soluble whole-cell extract. Proc Natl Acad Sci U S A. 1980 Jul;77(7):3855–3859. doi: 10.1073/pnas.77.7.3855. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. 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]
  28. Miller K. G., Sollner-Webb B. Transcription of mouse rRNA genes by RNA polymerase I: in vitro and in vivo initiation and processing sites. Cell. 1981 Nov;27(1 Pt 2):165–174. doi: 10.1016/0092-8674(81)90370-6. [DOI] [PubMed] [Google Scholar]
  29. Mishima Y., Financsek I., Kominami R., Muramatsu M. Fractionation and reconstitution of factors required for accurate transcription of mammalian ribosomal RNA genes: identification of a species-dependent initiation factor. Nucleic Acids Res. 1982 Nov 11;10(21):6659–6670. doi: 10.1093/nar/10.21.6659. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Mroczka D. L., Cassidy B., Busch H., Rothblum L. I. Characterization of rat ribosomal DNA. The highly repetitive sequences that flank the ribosomal RNA transcription unit are homologous and contain RNA polymerase III transcription initiation sites. J Mol Biol. 1984 Mar 25;174(1):141–162. doi: 10.1016/0022-2836(84)90369-3. [DOI] [PubMed] [Google Scholar]
  31. Paule M. R., Iida C. T., Perna P. J., Harris G. H., Brown Shimer S. L., Kownin P. Faithful initiation of ribosomal RNA transcription from cloned DNA by purified RNA polymerase I. Biochemistry. 1984 Aug 28;23(18):4167–4172. doi: 10.1021/bi00313a025. [DOI] [PubMed] [Google Scholar]
  32. Qu H. L., Michot B., Bachellerie J. P. Improved methods for structure probing in large RNAs: a rapid 'heterologous' sequencing approach is coupled to the direct mapping of nuclease accessible sites. Application to the 5' terminal domain of eukaryotic 28S rRNA. Nucleic Acids Res. 1983 Sep 10;11(17):5903–5920. doi: 10.1093/nar/11.17.5903. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Rubtsov P. M., Musakhanov M. M., Zakharyev V. M., Krayev A. S., Skryabin K. G., Bayev A. A. The structure of the yeast ribosomal RNA genes. I. The complete nucleotide sequence of the 18S ribosomal RNA gene from Saccharomyces cerevisiae. Nucleic Acids Res. 1980 Dec 11;8(23):5779–5794. doi: 10.1093/nar/8.23.5779. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Saiga H., Mizumoto K., Matsui T., Higashinakagawa T. Determination of the transcription initiation site of Tetrahymena pyriformis rDNA using in vitro capping of 35S pre-rRNA. Nucleic Acids Res. 1982 Jul 24;10(14):4223–4236. doi: 10.1093/nar/10.14.4223. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Sakonju S., Bogenhagen D. F., Brown D. D. A control region in the center of the 5S RNA gene directs specific initiation of transcription: I. The 5' border of the region. Cell. 1980 Jan;19(1):13–25. doi: 10.1016/0092-8674(80)90384-0. [DOI] [PubMed] [Google Scholar]
  36. Shortle D., Nathans D. Local mutagenesis: a method for generating viral mutants with base substitutions in preselected regions of the viral genome. Proc Natl Acad Sci U S A. 1978 May;75(5):2170–2174. doi: 10.1073/pnas.75.5.2170. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Tsuda M., Suzuki Y. Faithful transcription initiation of fibroin gene in a homologous cell-free system reveals an enhancing effect of 5' flanking sequence far upstream. Cell. 1981 Nov;27(1 Pt 2):175–182. doi: 10.1016/0092-8674(81)90371-8. [DOI] [PubMed] [Google Scholar]
  38. Tyler B. M., Giles N. H. Structure of a Neurospora RNA polymerase I promoter defined by transcription in vitro with homologous extracts. Nucleic Acids Res. 1985 Jun 25;13(12):4311–4332. doi: 10.1093/nar/13.12.4311. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Walseth T. F., Johnson R. A. The enzymatic preparation of [alpha-(32)P]nucleoside triphosphates, cyclic [32P] AMP, and cyclic [32P] GMP. Biochim Biophys Acta. 1979 Mar 28;562(1):11–31. doi: 10.1016/0005-2787(79)90122-9. [DOI] [PubMed] [Google Scholar]

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