Mapping sequence specific DNA-protein interactions: A versatile, quantitative method and its application to transcription factor XF1

Journal of Molecular Biology

Volumn 266, Issue 3, 1997, Pages 479-492

  Luo, Bo ^a   Perry, David J ^a   Zhang, Leying ^a   Kharat, Indira ^a   Basic, Mirjana ^a   Fagan, John B ^a  

^a MAHARISHI UNIVERSITY OF MANAGEMENT   (United States)

Author keywords

DNA binding proteins; in vitro oligonucleotide selection; Mapping DNA protein interactions; Oligonucleotide library; Transcription factors

Indexed keywords

CHLORAMPHENICOL ACETYLTRANSFERASE; DNA; DNA BINDING PROTEIN; OLIGONUCLEOTIDE; TRANSCRIPTION FACTOR;

ANIMAL CELL; ARTICLE; BINDING AFFINITY; CONSENSUS SEQUENCE; CONTROLLED STUDY; DNA SEQUENCE; ELECTROPHORETIC MOBILITY; GENETIC TRANSFECTION; MOLECULAR CLONING; MOLECULAR RECOGNITION; NONHUMAN; PRIORITY JOURNAL; PROTEIN DNA BINDING; RAT; REPORTER GENE; STRUCTURE ACTIVITY RELATION; TRANSCRIPTION REGULATION;

EID: 0031588739     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1996.0722     Document Type: Article

References (46)

1. Aoyama T., Yamano S., Guzelian P. S., Gelboin H. V., Gonzalez F. J. Five of 12 forms of vaccinia virus-expressed human hepatic cytochrome P450 metabolically activate aflatoxin B1. Proc. Natl Acad. Sci. USA. 87:1990;4790-4793.
2. Blackwell T. K., Weintraub H. Differences and similarities in DNA-binding preferences of MyoD and E2A protein complexes revealed by binding site selection. Science. 250:1990;1104-1110.
3. Blackwell T. K., Kretzner L., Blackwood E. M., Eisenman R. N., Weintraub H. Sequence-specific DNA binding by the c-Myc protein. Science. 250:1990;1149-1151.
4. Butler M. A., Guengerich F. P., Kadlubar F. F. Metabolic oxidation of the carcinogens 4-aminobiphenyl and 4,4′-methylene-bis(2-chloroaniline) by human hepatic microsomes and by purified rat hepatic cytochrome P-450 monooxygenases. Cancer Res. 49:1989a;25-31.
5. Butler M. A., Iwasaki M., Guengerich F. P., Kadlubar F. F. Human cytochrome P-450PA (P-450IA2), the phenacetin O-deethylase, is primarily responsible for the hepatic 3-demethylation of caffeine and N-oxidation of carcinogenic acrylamines. Proc. Natl Acad. Sci. USA. 86:1989b;7696-7700.
6. Chou J. Y. Temperature-sensitive adult liver cell line dependent on glucocorticoid for differentiation. Mol. Cell Biol. 3:1983;1013-1020.
7. Chou J. Y., Schlegel-Haueter S. E. Study of liver differentiation in vitro. J. Cell Biol. 89:1981;216-222.
8. Ekker S. C., von Kessler D. P., Beachy P. A. Differential DNA sequence recognition is a determinant of specificity in homeotic gene action. EMBO J. 11:1992;4059-4072.
9. Ellington A. D., Szostak J. W. In vitro selection of RNA molecules that bind specific ligands. Nature. 346:1990;818-822.
10. Faletto M. B., Koser P. L., Battula N., Townsend G. K., Maccubbin A. E., Gelboin H. V., Gurtoo H. L. Cytochrome P3-450 cDNA encodes aflatoxin B1-4-hydroxylase. J. Biol. Chem. 263:1988;12187-12789.
11. Famulok M., Szostak J. W. Yeast HAP1 activator competes with the factor RC2 for binding to the upstream activation site UAS1 of the CYC1 gene. Angew. Chem. Int. Ed. Engl. 31:1992;979-988.
12. Fujisawa-Sehara A., Sogawa K., Nishi C., Fujii-Kuriyama Y. Regulatory DNA elements localized remotely upstream from the drug-metabolizing cytochrome P-450c gene. Nucl. Acids Res. 14:1986;1465-1477.
13. Fujisawa-Segawa A., Sogawa K., Yamane M., Fujii-Kuriyama Y. Characterization of xenobiotic responsive elements upstream from the drug-metabolizing cytochrome P-450c gene: a similarity to glucocorticoid regulatory elements. Nucl. Acids Res. 15:1987;4179-4191.
14. Funk W. D., Wright W. E. Cyclic amplification and selection of targets for multicomponent complexes: myogenin interacts with factors recognizing binding sites for basic helix-loop-helix, nuclear factor 1, myocyte-specific enhancer-binding factor 2, and COMP1 factor. Proc. Natl Acad. Sci. USA. 89:1992;9484-9488.
15. Gelboin H. V. Benzo[alpha]pyrene metabolism, activation and carcinogenesis: role and regulation of mixed-function oxidases and related enzymes. Physiol. Rev. 60:1980;1107-1166.
16. Gonzalez F. J., Nebert D. W. Autoregulation plus upstream positive and negative control regions associated with transcriptional activation of the mouse P1 (450) gene. Nucl. Acids Res. 13:1985;7269-7288.
17. Hankinson O., Andersen R. D., Birren B. W., Sander F., Negishi M., Nebert D. W. Mutations affecting the regulation of transcription of the cytochrome P1-450 gene in the mouse Hepa-1 cell line. J. Biol. Chem. 260:1985;1790-1795.
18. Hines R. N., Mathis J. M., Jacob C. S. Identification of multiple regulatory elements on the human cytochrome P450IA1 gene. Carcinogenesis. 9:1988;1599-1605.
19. Horwitz M. S., Loeb L. A. Promoters selected from random DNA sequences. Proc. Natl Acad. Sci. USA. 83:1986;7405-7409.
20. Jones K. W., Whitlock J., Jr. Functional analysis of the transcriptional promoter for the CYP1A1 gene. Mol. Cell Biol. 10:1990;5098-5105.
21. Jones P. B., Galeazzi D. R., Fisher J. M., Whitlock J., Jr. Control of cytochrome P1-450 gene expression by dioxin. Science. 227:1985;1499-1502.
22. Jones P. B., Durrin L. K., Fisher J. M., Whitlock J., Jr. Control of gene expression by 2,3,7,8-tetrachlorodibenzo-p-dioxine. Multiple dioxin-responsive domains 5′-ward of the cytochrome P1-450 gene. J. Biol. Chem. 261:1986a;6647-6650.
23. Jones P. B., Durrin L. K., Galeazzi D. R., Whitlock J., Jr. Control of cytochrome P1-450 gene expression: analysis of a dioxin-responsive enhancer system. Proc. Natl Acad. Sci. USA. 83:1986b;2802-2806.
24. Kinzler K. W., Vogelstein B. Whole genome PCR: application to the identification of sequences bound by gene regulatory proteins. Nucl. Acids Res. 17:1989;3645-3653.
25. Kinzler K. W., Vogelstein B. The GLI gene encodes a nuclear protein which binds specific sequences in the human genome. Mol. Cell Biol. 10:1990;634-642.
26. Neuhold L. A., Gonzalez F. J., Jaiswal A. K., Nebert D. W. Dioxin-inducible enhancer region upstream from the mouse P(1)450 gene and interaction with a heterologous SV40 promoter. DNA. 5:1986;403-411.
27. Oliphant A. R., Struhl K. The use of random-sequence oligonucleotides for determining consensus sequences. Methods Enzymol. 155:1987;568-582.
28. Pelkonen O., Nebert D. W. Metabolism of polycyclic aromatic hydrocarbons: etiologic role in carcinogenesis. Phamacol. Rev. 34:1982;189-222.
29. Pollock R., Treisman R. A sensitive method for the determination of protein-DNA binding specificities. Nucl. Acids Res. 18:1990;6197-6204.
30. Reick M., Robertson R. W., Pasco D. S., Fagan J. B. Down-regulation of nuclear aryl hydrocarbon receptor DNA-binding and transactivation functions: requirement for a labile or inducible factor. Mol. Cell Biol. 14:1994;5653-5660.
31. Robertson R. W., Zhang L., Pasco D. S., Fagan J. B. Aryl hydrocarbon-induced interactions at multiple DNA elements of diverse sequence-A multicomponent mechanism for activation of cytochrome P4501A1 (CYP1A1) gene transcription. Nucl. Acids Res. 9:1994;1741-1749.
32. Saatcioglu F., Perry D. J., Pasco D. S., Fagan J. B. Multiple DNA-binding factors interact with overlapping specificities at the aryl hydrocarbon response element of the cytochrome P450IA1 gene. Mol. Cell Biol. 10:1990;6408-6416.
33. Sambrook J., Fritsch E. F., Maniatis T. Molecular Cloning: 1989;Cold Spring Harbor Laboratory Press, Cold Spring Harbor.
34. Shapiro D. J., Sharp P. A., Wahli W. W., Keller M. J. A high-efficiency HeLa cell nuclear transcription extract. DNA. 7:1988;47-55.
35. Shen E. S., Whitlock J., Jr. Protein-DNA interactions at a dioxin-responsive enhancer. Mutational analysis of the DNA-binding site for the liganded Ah receptor. J. Biol. Chem. 267:1992;6815-6819.
36. Sogawa K., Fujisawa-Sehara A., Yamane M., Fujii-Kuriyama Y. Location of regulatory elements responsible for drug induction in the rat cytochrome P-450c gene. Proc. Natl Acad. Sci. USA. 83:1986;8044-8048.
37. Szosta J. W. In vitro genetics. Trends Biochem. Sci. 17:1992;89-93.
38. Thiesen H. J., Bach C. Target Detection Assay (TDA): a versatile procedure to determine DNA binding sites as demonstrated on SP1 protein. Nucl. Acids Res. 18:1990;3203-3209.
39. Tuerk C., Gold L. Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science. 249:1990;505-510.
40. Ueda H., Hirose S. Defining the sequence recognized with BmFTZ-F1, a sequence specific DNA binding factor in the silkworm, Bombyx mori, as revealed by direct sequencing of bound oligonucleotides and gel mobility shift competition analysis. Nucl. Acids Res. 19:1991;3689-3693.
41. Wen L. P., Koeiman N., Whitlock J. P., Jr. Dioxin-inducible Ah receptor-dependent transcription in vitro. Proc. Natl Acad. Sci. USA. 87:1990;8545-8549.
42. Wen L. P., Jones K. W., Whitlock J., Jr. Analysis of CYP1A1 promoter function by transcription in vitro. Mol. Carcinog. 4:1991;93-96.
43. Whitlock J., Jr, Galeazzi D. R. 2,3,7,8-Tetrachlorodibenzo-p-dioxin receptors in wild-type and mouse hepatoma cells. Nuclear location and strength of nuclear binding. J. Biol. Chem. 259:1984;980-985.
44. Wright W. E., Funk W. D. CASTing for multicomponent DNA-binding complexes. Trends Biochem. Sci. 18:1993;77-80.
45. Wright W. E., Binder M., Funk W. Cyclic amplification and selection of targets (CASTing) for the myogenin consensus binding site. Mol. Cell Biol. 11:1991;4104-4110.
46. Wu L., Whitlock J., Jr. Mechanism of dioxin action: Ah receptor-mediated increase in promoter accessibility in vivo. Proc. Natl Acad. Sci. USA. 89:1992;4811-4815.