Skip to main content
NCBI home page
Proceedings of the National Academy of Sciences of the United States of America logoLink to Proceedings of the National Academy of Sciences of the United States of America
. 1983 Dec;80(23):7090–7094. doi: 10.1073/pnas.80.23.7090

7S-K nuclear RNA from simian virus 40-transformed cells has sequence homology to the viral early promoter.

U Sohn, J Szyszko, D Coombs, M Krause
PMCID: PMC389998  PMID: 6196783

Abstract

Previous findings in our laboratory have identified a specific small nuclear RNA (7S-K) that promotes transcription initiation by RNA polymerase II in isolated mammalian nuclei. The present study was designed to investigate the homology between 7S-K RNAs and host and viral sequences in simian virus 40 (SV40)-transformed and in untransformed mouse 3T3 cells, with the object of testing the hypothesis that these RNAs take part in the transcription initiation complex by base pairing to promoter/enhancer regions of active genes. DNA . RNA hybridization experiments, using either Southern or RNA blotting techniques, indicated that both 7S-K and 7S-L RNAs hybridize to midrepetitive fractions of the mouse genome. However, only 7S-K RNA from transformed cells hybridized to SV40 DNA. Restriction mapping and nuclease S1 treatment of the hybridized region of SV40 yielded a 45-nucleotide-long hybrid duplex. Partial sequence analysis of the 5' end of the DNA in this duplex revealed sequence homology with the 21-base-pair repeat sequence, identified as the SV40 early promoter. Because the viral early gene is expressed in transformed cells, we conclude that 7S-K RNAs in these cells contain a species that has sequence homology to a promoter of an active gene. Taking these results together with previous ones, we postulate that the observed stimulatory activity of 7S-K RNA on transcription initiation is due to its recognition of promoter sequences, either to facilitate the formation or as part of the transcription initiation complex.

Full text

PDF
7090

Images in this article

7091Image
on p.7091
7091Image
on p.7091
7092Image
on p.7092
7092Image
on p.7092
7093Image
on p.7093
7093Image
on p.7093

Selected References

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

  1. Alwine J. C., Kemp D. J., Stark G. R. Method for detection of specific RNAs in agarose gels by transfer to diazobenzyloxymethyl-paper and hybridization with DNA probes. Proc Natl Acad Sci U S A. 1977 Dec;74(12):5350–5354. doi: 10.1073/pnas.74.12.5350. [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. Bonner J., Widholm J. Molecular complementarity between nuclear DNA and organ-specific chromosomal RNA. Proc Natl Acad Sci U S A. 1967 May;57(5):1379–1385. doi: 10.1073/pnas.57.5.1379. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Britten R. J., Davidson E. H. Gene regulation for higher cells: a theory. Science. 1969 Jul 25;165(3891):349–357. doi: 10.1126/science.165.3891.349. [DOI] [PubMed] [Google Scholar]
  5. Britten R. J., Kohne D. E. Repeated sequences in DNA. Hundreds of thousands of copies of DNA sequences have been incorporated into the genomes of higher organisms. Science. 1968 Aug 9;161(3841):529–540. doi: 10.1126/science.161.3841.529. [DOI] [PubMed] [Google Scholar]
  6. Busch H., Reddy R., Rothblum L., Choi Y. C. SnRNAs, SnRNPs, and RNA processing. Annu Rev Biochem. 1982;51:617–654. doi: 10.1146/annurev.bi.51.070182.003153. [DOI] [PubMed] [Google Scholar]
  7. Byrne B. J., Davis M. S., Yamaguchi J., Bergsma D. J., Subramanian K. N. Definition of the simian virus 40 early promoter region and demonstration of a host range bias in the enhancement effect of the simian virus 40 72-base-pair repeat. Proc Natl Acad Sci U S A. 1983 Feb;80(3):721–725. doi: 10.1073/pnas.80.3.721. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Davidson E. H., Jacobs H. T., Britten R. J. Very short repeats and coordinate induction of genes. Nature. 1983 Feb 10;301(5900):468–470. doi: 10.1038/301468a0. [DOI] [PubMed] [Google Scholar]
  9. Deshpande A. K., Jakowlew S. B., Arnold H. H., Crawford P. A., Siddiqui M. A. A novel RNA affecting embryonic gene functions in early chick glastoderm. J Biol Chem. 1977 Sep 25;252(18):6521–6527. [PubMed] [Google Scholar]
  10. Frenster J. H. Nuclear polyanions as de-repressors of synthesis of ribonucleic acid. Nature. 1965 May 15;206(985):680–683. doi: 10.1038/206680a0. [DOI] [PubMed] [Google Scholar]
  11. Frenster J. H. Selective control of DNA helix openings during gene regulation. Cancer Res. 1976 Sep;36(9 Pt 2):3394–3398. [PubMed] [Google Scholar]
  12. Georgiev G. P. On the structural organization of operon and the regulation of RNA synthesis in animal cells. J Theor Biol. 1969 Dec;25(3):473–490. doi: 10.1016/s0022-5193(69)80034-2. [DOI] [PubMed] [Google Scholar]
  13. Gottesfeld J., Bloomer L. S. Assembly of transcriptionally active 5S RNA gene chromatin in vitro. Cell. 1982 Apr;28(4):781–791. doi: 10.1016/0092-8674(82)90057-5. [DOI] [PubMed] [Google Scholar]
  14. Kanehisa T., Fujitani H., Sano M., Tanaka T. Studies on low molecular weight RNA of chromatin. Effects of template activity of chick liver chromatin. Biochim Biophys Acta. 1971 Jun 17;240(1):46–55. doi: 10.1016/0005-2787(71)90511-9. [DOI] [PubMed] [Google Scholar]
  15. Kanehisa T., Kitazume Y., Ikuta K., Tanaka Y. Release of template restriction in chromatin by nuclear 4.5s RNA. Biochim Biophys Acta. 1977 Apr 4;475(3):501–513. doi: 10.1016/0005-2787(77)90065-x. [DOI] [PubMed] [Google Scholar]
  16. Kolodny A. Tissue Changes after Experimental Deep Roentgen Irradiation. Am J Pathol. 1925 May;1(3):285–294.1. [PMC free article] [PubMed] [Google Scholar]
  17. Krause M. O., Ringuette M. Low molecular weight nuclear RNA from SV40-transformed WI38 cells; effect on transcription of WI38 chromatin in vitro. Biochem Biophys Res Commun. 1977 Jun 6;76(3):796–803. doi: 10.1016/0006-291x(77)91571-6. [DOI] [PubMed] [Google Scholar]
  18. Lerner M. R., Steitz J. A. Antibodies to small nuclear RNAs complexed with proteins are produced by patients with systemic lupus erythematosus. Proc Natl Acad Sci U S A. 1979 Nov;76(11):5495–5499. doi: 10.1073/pnas.76.11.5495. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Liu W. C., Godbout R., Jay E., Yu K. K., Krause M. O. Tissue and species-specific effects of small molecular weight nuclear RNA's on transcription in isolated mammalian nuclei. Can J Biochem. 1981 May;59(5):343–352. doi: 10.1139/o81-048. [DOI] [PubMed] [Google Scholar]
  20. Maxam A. M., Gilbert W. A new method for sequencing DNA. Proc Natl Acad Sci U S A. 1977 Feb;74(2):560–564. doi: 10.1073/pnas.74.2.560. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Nordheim A., Rich A. Negatively supercoiled simian virus 40 DNA contains Z-DNA segments within transcriptional enhancer sequences. Nature. 1983 Jun 23;303(5919):674–679. doi: 10.1038/303674a0. [DOI] [PubMed] [Google Scholar]
  22. Pelham H. R., Wormington W. M., Brown D. D. Related 5S RNA transcription factors in Xenopus oocytes and somatic cells. Proc Natl Acad Sci U S A. 1981 Mar;78(3):1760–1764. doi: 10.1073/pnas.78.3.1760. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Rigby P. W., Dieckmann M., Rhodes C., Berg P. Labeling deoxyribonucleic acid to high specific activity in vitro by nick translation with DNA polymerase I. J Mol Biol. 1977 Jun 15;113(1):237–251. doi: 10.1016/0022-2836(77)90052-3. [DOI] [PubMed] [Google Scholar]
  24. Ringuette M. J., Gordon K., Szyszko J., Krause M. O. Specific small nuclear RNAs from SV40-transformed cells stimulate transcription initiation in nontransformed isolated nuclei. Can J Biochem. 1982 Mar;60(3):252–262. doi: 10.1139/o82-030. [DOI] [PubMed] [Google Scholar]
  25. Ringuette M., Liu W. C., Jay E., Yu K. K., Krause M. O. Stimulation of transcription of chromatin by specific small nuclear RNAs. Gene. 1980 Jan;8(2):211–224. doi: 10.1016/0378-1119(80)90038-4. [DOI] [PubMed] [Google Scholar]
  26. Saris C. J., Franssen H. J., Heuyerjans J. H., van Eenbergen J., Bloemers H. P. Blotting of RNA onto ion exchange paper allowing subsequent characterization by in situ translation in addition to blot hybridization. Nucleic Acids Res. 1982 Aug 25;10(16):4831–4843. doi: 10.1093/nar/10.16.4831. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Sharp P. A., Pettersson U., Sambrook J. Viral DNA in transformed cells. I. A study of the sequences of adenovirus 2 DNA in a line of transformed rat cells using specific fragments of the viral genome. J Mol Biol. 1974 Jul 15;86(4):709–726. doi: 10.1016/0022-2836(74)90348-9. [DOI] [PubMed] [Google Scholar]
  28. Sohn U., Rothfels K. H., Straus N. A. DNA: DNA hybridization studies in black flies. J Mol Evol. 1975 Jun 9;5(1):75–85. doi: 10.1007/BF01732015. [DOI] [PubMed] [Google Scholar]
  29. Southern E. M. Detection of specific sequences among DNA fragments separated by gel electrophoresis. J Mol Biol. 1975 Nov 5;98(3):503–517. doi: 10.1016/s0022-2836(75)80083-0. [DOI] [PubMed] [Google Scholar]
  30. Subramanian K. N., Dhar R., Weissman S. M. Nucleotide sequence of a fragment of SV40 DNA that contains the origin of DNA replication and specifies the 5' ends of "early" and "late" viral RNA. I. Mapping of the restriction endonuclease sites within the EcoRII-G fragment and strategy employed for its sequence analysis. J Biol Chem. 1977 Jan 10;252(1):333–339. [PubMed] [Google Scholar]
  31. Walter P., Blobel G. Signal recognition particle contains a 7S RNA essential for protein translocation across the endoplasmic reticulum. Nature. 1982 Oct 21;299(5885):691–698. doi: 10.1038/299691a0. [DOI] [PubMed] [Google Scholar]
  32. Weinberg R., Penman S. Metabolism of small molecular weight monodisperse nuclear RNA. Biochim Biophys Acta. 1969 Sep 17;190(1):10–29. doi: 10.1016/0005-2787(69)90150-6. [DOI] [PubMed] [Google Scholar]
  33. Winberg G., Hammarskjöld M. L. Isolation of DNA from agarose gels using DEAE-paper. Application to restriction site mapping of adenovirus type 16 DNA. Nucleic Acids Res. 1980 Jan 25;8(2):253–264. doi: 10.1093/nar/8.2.253. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Zieve G., Penman S. Small RNA species of the HeLa cell: metabolism and subcellular localization. Cell. 1976 May;8(1):19–31. doi: 10.1016/0092-8674(76)90181-1. [DOI] [PubMed] [Google Scholar]

Articles from Proceedings of the National Academy of Sciences of the United States of America are provided here courtesy of National Academy of Sciences

RESOURCES