In vivo footprinting by LMPCR procedure

  • Pierre Brignon
  • Claude Gigot
  • Nicole Chaubet


A number of approaches have been developed to elucidate molecular mechanisms of gene regulation at the transcriptional level. In vivo footprinting, however, is the only method providing information of when and how proteins actually occupy a given regulatory region of the DNA in the living cell.


Xylene Cyanol Saran Wrap Phenol Blue Longe Oligomer Nucleus Isolation Buffer 
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  1. 1.
    Cartwright IL, Kelly SE (1991) Probing the nature of chromosomal DNA-protein contacts by in vivo footprinting. Biotechniques 11: 188–203.PubMedGoogle Scholar
  2. 2.
    Maxam AM, Gilbert W (1980) Sequencing end-labelled DNA with base-specific chemical cleavages. Meth Enzymol 65, 499–560.PubMedCrossRefGoogle Scholar
  3. 3.
    Church GM, Ephrussi A, Gilbert W, Tonegawa S (1985) Cell-type-specific contacts to immunoglobulin enhancers in nuclei. Nature 313: 798–801.PubMedCrossRefGoogle Scholar
  4. 4.
    Wu C (1980) The 5’ ends of Drosophila heat shock genes in chromatin are hypersensitive to DNAse I. Nature 286: 854–860.PubMedCrossRefGoogle Scholar
  5. 5.
    Gralla JD (1985) Rapid footprinting on supercoiled DNA. Proc Natl Acad Sci USA 82: 3078–3081.PubMedCrossRefGoogle Scholar
  6. 6.
    Weintraub H (1985) High resolution mapping of S1- and DNAse I-hypersensitive sites in chromatin. Mol Cell Biol 5: 1538–1539.PubMedGoogle Scholar
  7. 7.
    Saluz HP, Jost JP (1989) A simple, high-resolution procedure to study DNA methylation and in vivo DNA-protein interactions on a single-copy gene level in higher eukaryotes. Proc Natl Acad Sci USA 86: 2602–2606.PubMedCrossRefGoogle Scholar
  8. 8.
    Mueller PR, Wold B (1989) In vivo footprinting of a muscle specific enhancer by ligation mediated PCR. Science 246: 780–786.PubMedCrossRefGoogle Scholar
  9. 9.
    Ferl RJ, Nick HN (1987) In vivo detection of regulatory factor binding sites in the 5’ flanking region of maize Adh1. J Biol Chem 262: 7947–7950.PubMedGoogle Scholar
  10. 10.
    Ferl RJ, Laughner B (1989) In vivo detection of regulatory factor binding sites of Arabidopsis thaliana Adh. Plant Mol Biol 12: 357–366.CrossRefGoogle Scholar
  11. 11.
    Schulze-Lefert P, Dangl JL, Becker-André M, Hahlbrock K, Schulz W (1989) Inducible in vivo DNA footprints define sequences necessary for UV light activation of the parsley chalcone synthase gene. EMBO J 8: 651–656.PubMedGoogle Scholar
  12. 12.
    Lois R, Dietrich A, Hahlbrock K, Schulz W (1989) A phenylalanine ammonia-lyase gene from parsley: structure, regulation and identification of elicitor and light responsive cis-acting elements. EMBO J 8: 1641–1648.PubMedGoogle Scholar
  13. 13.
    Schulze-Lefert P, Becker-André M, Schulz W, Hahlbrock K, Dangl JL (1989) Functional architecture of the light-responsive chalcone synthase promoter from parsley. Plant Cell 1: 707–714.PubMedGoogle Scholar
  14. 14.
    Mc Kendree W, Paul AL, DeLisle AJ, Ferl RJ (1990) In vivo and in vitro characterization of protein interactions with the dyad G-box of the Arabidopsis Adh gene. Plant Cell 2: 207–214.Google Scholar
  15. 15.
    Paul AL, Ferl RJ (1991) In vivo footprinting reveals unique cis-elements and different modes of hypoxic induction in maize Adh1 and Adh2. Plant Cell 3: 159–168.PubMedGoogle Scholar
  16. 16.
    Meier J, Hahlbrock K, Somssich JE (1991) Elicitor-inducible and constitutive in vivo DNA footprints indicate novel cis-acting elements in the promoter of a parsley gene encoding pathogenesis-related protein 1. Plant Cell 3: 309–315.PubMedGoogle Scholar
  17. 17.
    Ferl RJ (1989) In vivo detection of protein-DNA interactions. Plant Molecular Biology Manual, pp B12/1-B12/11. Kluwer Academic Publishers, Dordrecht.Google Scholar
  18. 18.
    Sorrensen MB (1992) Methylation of B-hordein genes in barley endosperm is inversely correlated with gene activity and affected by the regulatory gene Lys 3. Proc Natl Acad Sci USA 89: 4119–4123.CrossRefGoogle Scholar
  19. 19.
    Ott T, Nelsen-Salz B, Döring HP (1992) PCR-aided genomic sequencing of 5’ subterminal sequences of the maize transposable element activator ( Ac) in transgenic tobacco plants. The Plant J 2: 705–711.Google Scholar
  20. 20.
    Mueller PR, Wold B (1991) Ligation-mediated PCR: applications to genomic footprinting. Methods 2: 20–31.CrossRefGoogle Scholar
  21. 21.
    Zimmerman JI, Golberg RB (1977) DNA sequence organization in the genome of Nicotiana tabacum. Chromosoma 59: 227–252.CrossRefGoogle Scholar
  22. 22.
    Dellaporta SL, Woods J, Hicks R (1983) A plant DNA minipreparation: Version II. Plant Mol Biol Rep 1: 19–21.CrossRefGoogle Scholar
  23. 23.
    Guillemaut P, Maréchal-Drouard L (1992) Isolation of plant DNA: A fast, inexpensive and reliable method. Plant Mol Biol Rep 10: 60–65.CrossRefGoogle Scholar
  24. 24.
    Saluz HP, Jost JP (1990) A laboratory guide for in vivo studies of DNA methylation and protein/DNA interactions. Birkhaüser Verlag, Basel.CrossRefGoogle Scholar
  25. 25.
    Rigaud G, Roux J, Pictet R, Grange T (1991) In vivo footprinting of rat TAT gene: dynamic interplay between the glucocorticoïd receptor and liver-specific factor. Cell 67: 977–986.PubMedCrossRefGoogle Scholar
  26. 26.
    Sambrook J, Frisch EF, Maniatis T (1989) Molecular cloning: A laboratory manual, second edition. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY.Google Scholar

Copyright information

© Springer Science+Business Media Dordrecht 1993

Authors and Affiliations

  • Pierre Brignon
    • 1
  • Claude Gigot
    • 1
  • Nicole Chaubet
    • 1
  1. 1.Institut de Biologie Moléculaire des Plantes du C.N.R.S.Université Louis PasteurStrasbourgFrance

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