Skip to main content
NCBI home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1982 Feb 11;10(3):871–887. doi: 10.1093/nar/10.3.871

Comparison of the polyoma virus early and late promoters by transcription in vitro.

P Jat, J W Roberts, A Cowie, R Kamen
PMCID: PMC326208  PMID: 6174941

Abstract

Polyoma virus DNA was transcribed in the HeLa whole cell extract in vitro system (1). Early region transcripts with the same 5'-ends as in vivo mRNAs, located 31 +/- 2bp from 'TATA'-boxes, were synthesized by RNA polymerase II. Sequences sufficient for efficient expression of the early promoter were present in a substitution mutant lacking viral DNA from a position 55bp before the principal cap sites. Late region transcripts were synthesised inefficiently. Only one (at nt5129 +/- 2) of the many late mRNA cap sites functioned as an in vitro initiation point. This was the one 5'-end located 31 +/- 2bp from a sequence resembling the 'TATA' consensus. The proportion of late to early region RNA polymerase II transcripts decreased dramatically at suboptimal template concentrations. An hypothesis to explain the regulation of late gene expression in vivo based on these results is proposed. A linear templates were transcribed only by RNA polymerase II, transcripts with the same sense as late mRNAs and 5'-ends at nt5076 +/- 2 were produced from superhelical template by an alpha amanitin resistant enzyme.

Full text

PDF
871

Images in this article

874Image
on p.874
877Image
on p.877
879Image
on p.879
881Image
on p.881

Selected References

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

  1. Benoist C., Chambon P. In vivo sequence requirements of the SV40 early promotor region. Nature. 1981 Mar 26;290(5804):304–310. doi: 10.1038/290304a0. [DOI] [PubMed] [Google Scholar]
  2. Berk A. J., Sharp P. A. Sizing and mapping of early adenovirus mRNAs by gel electrophoresis of S1 endonuclease-digested hybrids. Cell. 1977 Nov;12(3):721–732. doi: 10.1016/0092-8674(77)90272-0. [DOI] [PubMed] [Google Scholar]
  3. Bogenhagen D. F., Sakonju S., Brown D. D. A control region in the center of the 5S RNA gene directs specific initiation of transcription: II. The 3' border of the region. Cell. 1980 Jan;19(1):27–35. doi: 10.1016/0092-8674(80)90385-2. [DOI] [PubMed] [Google Scholar]
  4. Cogen B. Virus-specific early RNA in 3T6 cells infected by a tsA mutant of polyoma virus. Virology. 1978 Mar;85(1):222–230. doi: 10.1016/0042-6822(78)90426-9. [DOI] [PubMed] [Google Scholar]
  5. Condit R. C., Cowie A., Kamen R., Birg F. Polyoma virus transcription in vitro. J Mol Biol. 1977 Sep 15;115(2):215–235. doi: 10.1016/0022-2836(77)90098-5. [DOI] [PubMed] [Google Scholar]
  6. Cowie A., Tyndall C., Kamen R. Sequences at the capped 5'-ends of polyoma virus late region mRNAs: an example of extreme terminal heterogeneity. Nucleic Acids Res. 1981 Dec 11;9(23):6305–6322. doi: 10.1093/nar/9.23.6305. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Dierks P., van Ooyen A., Mantei N., Weissmann C. DNA sequences preceding the rabbit beta-globin gene are required for formation in mouse L cells of beta-globin RNA with the correct 5' terminus. Proc Natl Acad Sci U S A. 1981 Mar;78(3):1411–1415. doi: 10.1073/pnas.78.3.1411. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Favaloro J., Treisman R., Kamen R. Transcription maps of polyoma virus-specific RNA: analysis by two-dimensional nuclease S1 gel mapping. Methods Enzymol. 1980;65(1):718–749. doi: 10.1016/s0076-6879(80)65070-8. [DOI] [PubMed] [Google Scholar]
  9. Flavell A. J., Cowie A., Arrand J. R., Kamen R. Localization of three major cappe 5' ends of polyoma virus late mRNA's within a single tetranucleotide sequence in the viral genome. J Virol. 1980 Feb;33(2):902–908. doi: 10.1128/jvi.33.2.902-908.1980. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Flavell A. J., Cowie A., Legon S., Kamen R. Multiple 5' terminal cap structures in late polyoma virus RNA. Cell. 1979 Feb;16(2):357–371. doi: 10.1016/0092-8674(79)90012-6. [DOI] [PubMed] [Google Scholar]
  11. Ghosh P. K., Reddy V. B., Piatak M., Lebowitz P., Weissman S. M. Determination of RNA sequences by primer directed synthesis and sequencing of their cDNA transcripts. Methods Enzymol. 1980;65(1):580–595. doi: 10.1016/s0076-6879(80)65061-7. [DOI] [PubMed] [Google Scholar]
  12. Griffin B. E., Fried M., Cowie A. Polyoma DNA: a physical map. Proc Natl Acad Sci U S A. 1974 May;71(5):2077–2081. doi: 10.1073/pnas.71.5.2077. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Grosschedl R., Birnstiel M. L. Identification of regulatory sequences in the prelude sequences of an H2A histone gene by the study of specific deletion mutants in vivo. Proc Natl Acad Sci U S A. 1980 Mar;77(3):1432–1436. doi: 10.1073/pnas.77.3.1432. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Hagenbüchle O., Schibler U. Mouse beta-globin and adenovirus-2 major late transcripts are initiated at the cap site in vitro. Proc Natl Acad Sci U S A. 1981 Apr;78(4):2283–2286. doi: 10.1073/pnas.78.4.2283. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Hentschel C., Irminger J. C., Bucher P., Birnstiel M. L. Sea urchin histone mRNA termini are located in gene regions downstream from putative regulatory sequences. Nature. 1980 May 15;285(5761):147–151. doi: 10.1038/285147a0. [DOI] [PubMed] [Google Scholar]
  16. Herbomel P., Saragosti S., Blangy D., Yaniv M. Fine structure of the origin-proximal DNAase I-hypersensitive region in wild-type and EC mutant polyoma. Cell. 1981 Sep;25(3):651–658. doi: 10.1016/0092-8674(81)90172-0. [DOI] [PubMed] [Google Scholar]
  17. Kamen R., Favaloro J., Parker J. Topography of the three late mRNA's of polyoma virus which encode the virion proteins. J Virol. 1980 Feb;33(2):637–651. doi: 10.1128/jvi.33.2.637-651.1980. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Kamen R., Favaloro J., Parker J., Treisman R., Lania L., Fried M., Mellor A. Comparison of polyoma virus transcription in productively infected mouse cells and transformed rodent cell lines. Cold Spring Harb Symp Quant Biol. 1980;44(Pt 1):63–75. doi: 10.1101/sqb.1980.044.01.009. [DOI] [PubMed] [Google Scholar]
  19. Kamen R., Sedat J., Ziff E. Orientation of the complementary strands of polyoma virus DNA with respect to the DNA physical map. J Virol. 1975 Jan;17(1):212–218. doi: 10.1128/jvi.17.1.212-218.1976. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Lee D. C., Roeder R. G. Transcription of adenovirus type 2 genes in a cell-free system: apparent heterogeneity of initiation at some promoters. Mol Cell Biol. 1981 Jul;1(7):635–651. doi: 10.1128/mcb.1.7.635. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Legon S., Flavell A. J., Cowie A., Kamen R. Amplification in the leader sequence of late polyoma virus mRNAs. Cell. 1979 Feb;16(2):373–388. doi: 10.1016/0092-8674(79)90013-8. [DOI] [PubMed] [Google Scholar]
  22. Luse D. S., Haynes J. R., VanLeeuwen D., Schon E. A., Cleary M. L., Shapiro S. G., Lingrel J. B., Roeder R. G. Transcription of the beta-like globin genes and pseudogenes of the goat in a cell-free system. Nucleic Acids Res. 1981 Sep 11;9(17):4339–4354. doi: 10.1093/nar/9.17.4339. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. 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]
  24. Mathis D. J., Chambon P. The SV40 early region TATA box is required for accurate in vitro initiation of transcription. Nature. 1981 Mar 26;290(5804):310–315. doi: 10.1038/290310a0. [DOI] [PubMed] [Google Scholar]
  25. 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]
  26. McKnight S. L., Gavis E. R., Kingsbury R., Axel R. Analysis of transcriptional regulatory signals of the HSV thymidine kinase gene: identification of an upstream control region. Cell. 1981 Aug;25(2):385–398. doi: 10.1016/0092-8674(81)90057-x. [DOI] [PubMed] [Google Scholar]
  27. Moreau P., Hen R., Wasylyk B., Everett R., Gaub M. P., Chambon P. The SV40 72 base repair repeat has a striking effect on gene expression both in SV40 and other chimeric recombinants. Nucleic Acids Res. 1981 Nov 25;9(22):6047–6068. doi: 10.1093/nar/9.22.6047. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Sanger F., Coulson A. R. The use of thin acrylamide gels for DNA sequencing. FEBS Lett. 1978 Mar 1;87(1):107–110. doi: 10.1016/0014-5793(78)80145-8. [DOI] [PubMed] [Google Scholar]
  29. Saragosti S., Moyne G., Yaniv M. Absence of nucleosomes in a fraction of SV40 chromatin between the origin of replication and the region coding for the late leader RNA. Cell. 1980 May;20(1):65–73. doi: 10.1016/0092-8674(80)90235-4. [DOI] [PubMed] [Google Scholar]
  30. Shenk T. Transcriptional control regions: nucleotide sequence requirements for initiation by RNA polymerase II and III. Curr Top Microbiol Immunol. 1981;93:25–46. doi: 10.1007/978-3-642-68123-3_3. [DOI] [PubMed] [Google Scholar]
  31. Soeda E., Arrand J. R., Smolar N., Walsh J. E., Griffin B. E. Coding potential and regulatory signals of the polyoma virus genome. Nature. 1980 Jan 31;283(5746):445–453. doi: 10.1038/283445a0. [DOI] [PubMed] [Google Scholar]
  32. Sollner-Webb B., Reeder R. H. The nucleotide sequence of the initiation and termination sites for ribosomal RNA transcription in X. laevis. Cell. 1979 Oct;18(2):485–499. doi: 10.1016/0092-8674(79)90066-7. [DOI] [PubMed] [Google Scholar]
  33. Talkington C. A., Nishioka Y., Leder P. In vitro transcription of normal, mutant, and truncated mouse alpha-globin genes. Proc Natl Acad Sci U S A. 1980 Dec;77(12):7132–7136. doi: 10.1073/pnas.77.12.7132. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Treisman R. Characterisation of polyoma late mRNA leader sequences by molecular cloning and DNA sequence analysis. Nucleic Acids Res. 1980 Nov 11;8(21):4867–4888. doi: 10.1093/nar/8.21.4867. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Treisman R., Cowie A., Favaloro J., Jat P., Kamen R. The structures of the spliced mRNAs encoding polyoma virus early region proteins. J Mol Appl Genet. 1981;1(2):83–92. [PubMed] [Google Scholar]
  36. Treisman R., Kamen R. Structure of polyoma virus late nuclear RNA. J Mol Biol. 1981 May 25;148(3):273–301. doi: 10.1016/0022-2836(81)90539-8. [DOI] [PubMed] [Google Scholar]
  37. Twigg A. J., Sherratt D. Trans-complementable copy-number mutants of plasmid ColE1. Nature. 1980 Jan 10;283(5743):216–218. doi: 10.1038/283216a0. [DOI] [PubMed] [Google Scholar]
  38. Tyndall C., La Mantia G., Thacker C. M., Favaloro J., Kamen R. A region of the polyoma virus genome between the replication origin and late protein coding sequences is required in cis for both early gene expression and viral DNA replication. Nucleic Acids Res. 1981 Dec 11;9(23):6231–6250. doi: 10.1093/nar/9.23.6231. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Weaver R. F., Weissmann C. Mapping of RNA by a modification of the Berk-Sharp procedure: the 5' termini of 15 S beta-globin mRNA precursor and mature 10 s beta-globin mRNA have identical map coordinates. Nucleic Acids Res. 1979 Nov 10;7(5):1175–1193. doi: 10.1093/nar/7.5.1175. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Weil P. A., Luse D. S., Segall J., Roeder R. G. Selective and accurate initiation of transcription at the Ad2 major late promotor in a soluble system dependent on purified RNA polymerase II and DNA. Cell. 1979 Oct;18(2):469–484. doi: 10.1016/0092-8674(79)90065-5. [DOI] [PubMed] [Google Scholar]
  41. Weil P. A., Segall J., Harris B., Ng S. Y., Roeder R. G. Faithful transcription of eukaryotic genes by RNA polymerase III in systems reconstituted with purified DNA templates. J Biol Chem. 1979 Jul 10;254(13):6163–6173. [PubMed] [Google Scholar]
  42. Zuckermann M., Manor H., Parker J., Kamen R. Electron microscopic demonstration of the presence of amplified sequences at the 5'-ends of the polyoma virus late mRNAs. Nucleic Acids Res. 1980 Apr 11;8(7):1505–1519. doi: 10.1093/nar/8.7.1505. [DOI] [PMC free article] [PubMed] [Google Scholar]
  43. de Villiers J., Schaffner W. A small segment of polyoma virus DNA enhances the expression of a cloned beta-globin gene over a distance of 1400 base pairs. Nucleic Acids Res. 1981 Dec 11;9(23):6251–6264. doi: 10.1093/nar/9.23.6251. [DOI] [PMC free article] [PubMed] [Google Scholar]
  44. von Gabain A., Bujard H. Interaction of Escherichia coli RNA polymerase with promoters of several coliphage and plasmid DNAs. Proc Natl Acad Sci U S A. 1979 Jan;76(1):189–193. doi: 10.1073/pnas.76.1.189. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Nucleic Acids Research are provided here courtesy of Oxford University Press

RESOURCES