Quantitative whole-genome analysis of DNA-protein interactions by in vivo methylase protection in E. coli (original) (raw)

References

  1. Cartwright, I.L., and Kelly, S.E. 1991. Probing the nature of chromosomal DNA-protein contacts by in vivofootprinting. Biotechniques 11: 188–203.
    CAS PubMed Google Scholar
  2. Barras, F., and Marinus, M.G. 1989. The Great GATC:DNA methylation in E. coli. Trends Genet. 5: 139–143.
    Article CAS Google Scholar
  3. Rinquist, S., and Smith, C.L. 1992. The Escherichia coli chromosome contains specific, unmethylated dam and dcm sites. Proc. Natl. Acad. Sci. USA 89: 4539–4543.
    Article Google Scholar
  4. Wang, M.X., and Church, G.M. 1992. A whole genome approach to in vivo DNA-protein interactions in E. coli. Nature 360: 606–610.
    Article CAS Google Scholar
  5. Hale, W.B., van der Woude M.W., and Low D.A. 1994. Analysis of Nonmethylated GATC sites in the Escherichia coli chromosome and identification of sites that are differentially methylated in response to environmental stimuli. J. Bact. 176: 3438–3441.
    Article CAS Google Scholar
  6. Prashar, Y., and Weissman, S.M. 1996. Analysis of differential gene expression by display of 3′ end restriction fragments of cDNAs. Proc. Natl. Acad. Sci. USA 93: 659–663.
    Article CAS Google Scholar
  7. Sabourin, D., and Beckwith, J. 1975. Deletion of Escherichia coli crp gene. J. Bacteriol. 122: 338–340.
    CAS PubMed PubMed Central Google Scholar
  8. Kolb, A., Busby, X., Buc, H., Garges, S., and Adhya, S. 1993. Transcriptional regulation by cAMP and its receptor protein. Annu. Rev. Biochem. 62: 749–795.
    Article CAS Google Scholar
  9. Renbaum, P., Abrahamove, D., Fainsod, A., Wilson, G.G., Rottem, S., and Razin, A. 1990. Cloning, characterization, and expression in Escherichia coli of the gene coding for the CpG DNA methylase from Spiroplasma sp. strain MQ1 (M.SssI). Nucleic Acids Res. 18: 1145–1152.
    Article CAS Google Scholar
  10. Zhang, X., and Mathews, C.K. 1994. Effect of DNA cytosine methylation upon deamination-induced mutagenesis in a natural target sequence in duplex DNA. J. Biol. Chem. 269: 7066–7069.
    CAS PubMed Google Scholar
  11. Kelleher, J., and Raleigh, E.A. 1991. A novel activity in Escherichia coli K-12 that directs restriction of DNA modified at CG dinucleotides. J. Bacteriol. 173: 5220–5223.
    Article CAS Google Scholar
  12. Hall, B.G., and Xu, L. 1992. Nucleotide sequence, function, activation, and evolution of the cryptic asc operon of Escherichia coli K12. Mol. Biol. Evol. 9: 688–706.
    CAS PubMed Google Scholar
  13. Irani, M.H., Orosz, L.M., and Adhya, S. 1983. A control element within a structural gene: The gal operon of Escherichia coli. Cell 32: 783–788.
    CAS PubMed Google Scholar
  14. Weinstein, J.N., Myers, T.G., O'Connor, P.M., Friend, S.H., Fornace, A.J., Jr Kohn, K.W. et al. 1997. An information-intensive approach to the molecular pharmacology of cancer. Science 275: 343–349.
    Article CAS Google Scholar
  15. Kendall, M. 1980. Multivariate analysis. Macmillan, New York.
    Google Scholar
  16. Norregaard-Madsen, M., Mygind, B., Pedersen, R., Valentin-Hansen, P., and Sogaard-Anderson, L. 1994. The gene encoding the periplasmic cyclophilin homologue, PPIase A, in Escherichia coli, is expressed from four promoters, three of which are activated by the cAMP-CRP complex and negatively regulated by the CytR repressor. Mol. Microbiol. 14: 989–997.
    Article CAS Google Scholar
  17. Ramseier, T.M., and Saier, M.H., Jr. 1995. cAMP-cAMP receptor protein complex: five binding sites in the control region of the Escherichia coli mannitol operon. Microbiology 141: 1901–1907.
    CAS PubMed Google Scholar
  18. Blattner, F.R., Plunkett, G., Bloch, C.A., Perna, N.T., Burland, V., Riley, M. et al. 1997. The complete sequence of Eschericia coli K-12. Science 277: 1453–1462.
    Article CAS Google Scholar
  19. Barras, F., and Marinus, M.G. 1988. Arrangement of Dam methylation sites (GATC) in the Escherichia coli chromosome. Nucleic Acids Res. 16: 9821–9838.
    Article CAS Google Scholar
  20. Charlier, D., Gigot, D., Huysveld, N., Roovers, M., Pierard, A., and Glansdorff, N. 1995. Pyrimidine regulation of the Escherichia coli and Salmonella typhimurium carAB operon: CarP and Intergration Host Factor (IHF) modulate the methylation status of a GATC site present in the control region. J. Mol. Biol. 250: 391–391.
    Google Scholar
  21. Jovanovic, G., Weiner, L., and Model, P. 1996. Identification, nucleotide sequence, and characterization of PspF, the transcriptional activator of the Escherichia coli stress-induced psp operon. J. Bacteriol. 178: 1936–1945.
    Article CAS Google Scholar
  22. Hoist, B., Sogaard-Anderson, L., Pedersen, H., and Valentin-Hansen, P. 1992. The cAMP-CRP/CytR nucleoprotein complex in Escherichia coli: two pairs of closely linked binding sites for the cAMP-CRP activator complex are involved in combinatorial regulation of the odd promoter. EMBO J. 11: 3635–3643.
    Article Google Scholar
  23. Shea, C.M. and Mclntosh, M.A. 1991. Nucleotide sequence and genetic organization of the ferric enterobactin transport system: homology to other periplasmic binding protein-dependent systems in Escherichia coli. Mol. Microbiol. 5: 1 415–1428.
    Article Google Scholar
  24. Yamada, M., Asaoka, S., Saier, M.H., and Yamada, Y. 1993. Characterization of the gcd gene from Escherichia coli K-12 W3110 and regulation of its expression. J. Bacteriol. 175: 568–571.
    Article CAS Google Scholar
  25. Kutsukake, K., Ohya, Y. and lino, T. 1989. Transcriptional analysis of the flagellar regulon of Salmonella typhimurium. J. Bacteriol. 177: 741–747.
    Google Scholar
  26. Andrews, S.C., Harrison, P.M., and Guest, J.R. 1991. A molecular analysis of the 53.4 minute of the Escherichia coli linkage map. J. Gen. Microbiol. 137: 361–367.
    Article CAS Google Scholar
  27. Yamada, M., Saier, M.H., and Yamada, Y. 1988. Positive and negative regulators for glucitol (gut) operon expression in Escherichia coli. J. Mol. Biol. 203: 569–583.
    Article CAS Google Scholar
  28. Xu, J., and Johnson, R.C. 1995. Fis activates the RpoS-dependent stationary-phase expression of proP in Escherichia coli. J. Bacteriol. 177: 5222–5231.
    Article CAS Google Scholar
  29. Weiner, L., Brissette, J.L., Ramani, N., and Model, P. 1995. Analysis of the proteins and c/s-acting elements regulating the stress-induced phage shock protein operon. Nucleic Acid Res. 23: 2030–2036.
    Article CAS Google Scholar
  30. Goodrich, J.A., Schwartz, M.L., and McClure W.R. 1990. Searching for and predicting the activity of sites for DNA binding proteins: compilation and analysis of the binding sites for Escherichia coli integration host factor (IHF). Nucleic Acids Res. 18: 4993–5000.
    Article CAS Google Scholar
  31. Lockhart, D.J., Dong, H.L., Byrne, M.C., Follettie, M.T., Gallo, M.V., Chee, M.S. et al. 1996. Expression monitoring by hybridizatiion to high-density oligonucleotide arrays. Nature Biotechnology 14: 1675–1680.
    Article CAS Google Scholar
  32. DeRisi, J.L., Iyer, V.R., and Brown, P.O. 1997. Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 278: 680–686.
    Article CAS Google Scholar
  33. Gottshcling, D.E. 1992. Telomere-proximal DNA in Saccharomyces cerevisiae is refractory to methyltransferase activity in vivo. Proc. Natl. Acad. Sci. USA 89: 4062–4065.
    Article Google Scholar
  34. Ausubel, F.M., Brent, R., Kingston, R.E., Moore, D.D., Seidman, J.G., Smith, J.A. et al. 1989. Current protocols in molecular biology. John Wiley and Sons, New York.

Download references