Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Review Article
  • Published:

STEM Footprints and Bound Mass Distributions for DNA Control Proteins

Abstract

We review a current methodology which analyzes quantitative scattering data from Scanning Transmission Electron Microscopy to establish footprints—positions of DNA-binding proteins on cloned genes—and mass distributions for the bound protein. Recognition by computer of the DNA path and the extent of the bound protein leads to an analysis rate which is high for image-based data. The methods have been applied in the study of eukaryotic transcription initiation and T antigen interaction with the SV40 control region.

This is a preview of subscription content, access via your institution

Access options

Buy this article

Prices may be subject to local taxes which are calculated during checkout

Similar content being viewed by others

References

  1. Matsui, T., Segall, J., Weil, P.A. and Roeder, R.G. 1980. Multiple factors required for accurate initiation of transcription by purified RNA polymerase II. J. Biol. Chem. 255: 11,992–11,996.

    CAS  Google Scholar 

  2. Samuels, M., Fire, A. and Sharp, P.A. 1982. Separation and characterization of factors mediating accurate transcription by RNA polymerase II. J. Biol. Chem. 257: 14,419–14,427.

    CAS  Google Scholar 

  3. Dignam, J.D., Martin, P.L., Shastry, B.S. and Roeder, R.G. 1983. Eukaryotic gene transcription with purified components. Meth. Enzymol. 101: 583–598.

    Google Scholar 

  4. Davison, B.L., Egly, J.-M., Mulvihill, E.R. and Chambon, P. 1983. Formation of stable preinitiation complexes between eukaryotic class B transcription factors and promoter sequences. Nature 301: 680–686.

    Article  CAS  Google Scholar 

  5. Parker, C.S. and Topol, J. 1984. A Drosophila RNA polymerase II transcription factor contains a promoter-region-specific DNA-binding activity. Cell 36: 357–369.

    Article  CAS  Google Scholar 

  6. Wu, C. 1984. Two protein-binding sites in chromatin implicated in the activation of heat-shock genes. Nature 309: 229–234.

    Article  CAS  Google Scholar 

  7. Gidoni, D., Dynan, W.S. and Tjian, R. 1984. Multiple specific contacts between a mammalian transcription factor and its cognate promoters. Nature 312: 409–413.

    Article  CAS  Google Scholar 

  8. Fire, A., Samuels, M. and Sharp, P.A. 1984. Interactions between RNA polymerase II, factors, and template leading to accurate transcription. J. Biol. Chem. 259: 2509–2516.

    CAS  PubMed  Google Scholar 

  9. Bogenhagen, D.F., Wormington, W.M. and Brown, D.D. 1982. Stable transcription complexes of Xenopus 5S RNA genes: a means to maintain the differentiated state. Cell 28: 413–421.

    Article  CAS  Google Scholar 

  10. Lassar, A.B., Martin, P.L. and Roeder, R.G. 1983. Transcription of class III genes: formation of preinitiation complexes. Science 222: 740–748.

    Article  CAS  Google Scholar 

  11. Brown, D.D. 1984. The role of stable complexes that repress and activate eucaryotic genes. Cell 37: 359–365.

    Article  CAS  Google Scholar 

  12. Bieker, J.J., Martin, P.L. and Roeder, R.G. 1985. Formation of a rate-limiting intermediate in 5S RNA gene transcription. Cell 40: 119–127.

    Article  CAS  Google Scholar 

  13. Hough, P.V.C., Mastrangelo, I.A., Wall, J.S., Hainfeld, J.F., Simon, M.N. and Manley, J.L. 1982. DNA-protein complexes spread on N2-discharged carbon film and characterized by molecular weight and its projected distribution. J. Mol. Biol. 160: 375–386.

    Article  CAS  Google Scholar 

  14. Hough, P.V.C., Simon, M.N. and Mastrangelo, I.A. 1984. Analysis of eukaryotic control proteins at their recognition sequences by scanning transmission electron microscopy, p. 279–307. In: Genetic Engineering, Vol. 6. Hollaender A. and Setlow, J. K. (eds.), Plenum Publ. Corp., N.Y.

    Chapter  Google Scholar 

  15. Mastrangelo, I.A., Hough, P.V.C., Wilson, V.G., Wall, J.S., Hainfeld, J.F. and Tegtmeyer, P. 1985. Monomers through trimers of large T antigen in region I and monomers through tetramers in region II bind to SV40 origin DNA as stable structures in solution. Proc. Natl. Acad. Sci. USA in press.

    Google Scholar 

  16. Wall, J.S. 1979. Biological scanning transmission electron microscopy, p. 333–342. In: Introduction to Analytical Electron Microscopy. Hren, J.J., Goldstein, J. I., and Joy, D. C. (eds.), Plenum Publ. Co., N.Y.

    Chapter  Google Scholar 

  17. Mosesson, M.W., Hainfeld, J., Wall, J. and Haschemeyer, R.H. 1981. Identification and mass analysis of human fibrinogen molecules and their domains by scanning transmission electron microscopy. J. Mol. Biol. 153: 695–718.

    Article  CAS  Google Scholar 

  18. Langmore, J.P., Wall, J. and Isaacson, M.S. 1973. The collection of scattered electrons in dark field electron microscopy. 1. Elastic scattering. Optik 38: 335–350.

    Google Scholar 

  19. Buchman, A.R., Burnett, L. and Berg, P. 1980. The SV40 nucleotide sequence, p. 799–818. In: DNA Tumor Viruses. Tooze, J. (ed.), Cold Spring Harbor Laboratory, N.Y.

    Google Scholar 

  20. Henderson, R. 1975. Structure of the purple membrane from Halobacterium halobrum: analysis of the x-ray diffraction pattern. J. Mol. Biol. 93: 123–138.

    Article  CAS  Google Scholar 

  21. Wall, J.S., Hainfeld, J.F., Bartlett, P.A. and Singer, S.J. 1982. Observation of an undecagold cluster compound in the scanning transmission electron microscope. Ultramicros. 8: 397–402.

    Article  CAS  Google Scholar 

  22. Hough, P.V.C. 1962. General purpose visual input for a computer. Ann. N.Y. Acad. Sci. 99: 323–334.

    Article  CAS  Google Scholar 

  23. Weil, P.A., Luse, D.S., Segall, J. and Roeder, R.G. 1979. Selective and accurate initiation of transcription at the Ad2 major late promoter in a soluble system dependent on purified RNA polymerase II and DNA. Cell 18: 469–484.

    Article  CAS  Google Scholar 

  24. Manley, J.L., Fire, A., Cano, A., Sharp, P.A. and Gefter, M.L. 1980. DNA-dependent transcription of adenovirus genes in a soluble whole-cell extract. Proc. Natl. Acad. Sci. USA 77: 3855–3859.

    Article  CAS  Google Scholar 

  25. Dignam, J.D., Lebovitz, R.M. and Roeder, R.G. 1984. Accurate transcription initiation by RNA polymerase II in a soluble extract from isolated mammalian nuclei. Nucleic Acids Res. 11: 1475–1489.

    Article  Google Scholar 

  26. Slattery, E., Dignam, J.D., Matsui, T. and Roeder, R.G. 1983. Purification and analysis of a factor which suppresses nick-induced transcription by RNA polymerase II and its identity with poly(ADP-ribose) polymerase. J. Biol. Chem. 258: 5955–5959.

    CAS  PubMed  Google Scholar 

  27. Sawadogo, M. and Roeder, R.G. 1984. Energy requirement for specific transcription initiation by the human polymerase II system. J. Biol. Chem. 259: 5321–5326.

    CAS  PubMed  Google Scholar 

  28. Tegtmeyer, P. 1975. Altered patterns of protein synthesis in infection by SV40 mutants. Cold Spring Harbor Symp. Quant. Biol. 39: 9–15.

    Article  Google Scholar 

  29. Myers, R.M. and Tjian, R. 1980. Construction and analysis of simian virus origins defective in tumor antigen binding and DNA replication. Proc. Natl. Acad. Sci. USA 77: 6491–6495.

    Article  CAS  Google Scholar 

  30. Shortle, D.R., Margolskee, R.F. and Nathans, D. 1979. Mutational analysis of the simian virus 40 replicon: pseudorevertants of mutants with a defective replication origin. Proc. Natl. Acad. Sci. USA 76: 6128–6131.

    Article  CAS  Google Scholar 

  31. Wilson, V.G., Tevethia, M.J., Lewton, B.A. and Tegtmeyer, P. 1982. DNA-binding properties of simian virus 40 temperature-sensitive A proteins. J. Virol. 44: 458–468.

    CAS  PubMed  PubMed Central  Google Scholar 

  32. Hansen, U., Tenen, D.G., Livingston, D.M. and Sharp, P. 1981. T antigen repression of SV40 early transcription from two promoters. Cell 27: 603–612.

    Article  CAS  Google Scholar 

  33. Rio, D.C. and Tjian, R. 1983. SV40 T antigen binding site mutations that affect autoregulation. Cell 32: 1227–1240.

    Article  CAS  Google Scholar 

  34. Tjian, R. 1978. Protein-DNA interactions at the origin of simian virus 40 DNA replication. Cold Spring Harbor Symp. Quant. Biol. 43: 655–662.

    Article  Google Scholar 

  35. DeLucia, A.L., Lewton, B.A., Tjian, R. and Tegtmeyer, P. 1983. Topography of simian virus A protein-DNA complexes: arrangement of pentanucleotide interaction sites at the origin of replication. J. Virol. 46: 143–150.

    CAS  PubMed  PubMed Central  Google Scholar 

  36. Tegtmeyer, P., Lewton, B.A., DeLucia, A.L., Wilson, V.G. and Ryder, K. 1983.Topography of simian virus 40 A protein-DNA complexes: arrangement of protein bound to the origin of replication. J. Virol. 46: 151–161.

    CAS  PubMed  PubMed Central  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Rights and permissions

Reprints and permissions

About this article

Cite this article

Hough, P., Mastrangelo, I., Wall, J. et al. STEM Footprints and Bound Mass Distributions for DNA Control Proteins. Nat Biotechnol 3, 549–553 (1985). https://doi.org/10.1038/nbt0685-549

Download citation

  • Issue Date:

  • DOI: https://doi.org/10.1038/nbt0685-549

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing