In vivo and in vitro footprinting of nucleosomes and transcriptional activators using an infrared-fluorescence DNA sequencer

Biological and Pharmaceutical Bulletin

Volumn 31, Issue 2, 2008, Pages 187-192

  Morohashi, Nobuyuki ^a   Nakajima, Kumiko ^a   Kuwana, Shunsuke ^a   Tachiwana, Hiroaki ^b   Kurumizaka, Hitoshi ^b   Shimizu, Mitsuhiro ^a  

^a MEISEI UNIVERSITY   (Japan)

^b WASEDA UNIVERSITY   (Japan)

Author keywords

Chromatin; DNA footprinting; DNA sequencer; DNA protein interaction; Nucleosome; Transcription factor

Indexed keywords

DNA BINDING PROTEIN; DNA FRAGMENT; PROTEIN HAP1; PROTEIN HAP2; PROTEIN HAP3; PROTEIN HAP4; PROTEIN HAP5; UNCLASSIFIED DRUG;

ARTICLE; CHROMATIN STRUCTURE; CONTROLLED STUDY; DNA FOOTPRINTING; DNA SEQUENCE; FLUORESCENCE ANALYSIS; IN VITRO STUDY; IN VIVO STUDY; NONHUMAN; NUCLEOSOME; PROTEIN DNA INTERACTION; SEQUENCE ANALYSIS; YEAST;

CHROMATIN; CHROMOSOMES, FUNGAL; DNA REPAIR; DNA REPLICATION; DNA, FUNGAL; LAC OPERON; NUCLEOSOMES; PLASMIDS; PROTEIN FOOTPRINTING; RECOMBINATION, GENETIC; SACCHAROMYCES CEREVISIAE; SEQUENCE ANALYSIS, DNA; SPECTROMETRY, FLUORESCENCE; SPECTROPHOTOMETRY, INFRARED; TRANS-ACTIVATORS;

EID: 38849112444     PISSN: 09186158     EISSN: 13475215     Source Type: Journal    
DOI: 10.1248/bpb.31.187     Document Type: Article

References (22)

1. Carey B. Li. M., Workman J. L., Cell, 128, 707-719 (2007).
2. Sambrook J., Russel D. W., "Molecular Cloning, A Laboratory Manual," 3rd ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, 1998.
3. Sandaltzopoulos R., Ansorge W., Becker P. B., Voss H., Biotechniques, 17, 474-478 (1994).
4. Machida M., Kamio H., Sorensen D., Biotechniques, 23, 300-303 (1997).
5. Yindeeyoungyeon W., Schell M. A., Biotechniques, 29, 1034-1041 (2000).
6. Wilson D. O., Johnson P., McCord B. R., Electrophoresis, 22, 1979-1086 (2001).
7. Dai S. M., Chen H. H., Chang C., Riggs A. D., Flanagan S. D., Nature Biotechnol., 18, 1108-1111 (2000).
8. Guarente L., Ptashne M., Proc. Natl. Acad. Sci. U.S.A., 78, 2199-2203 (1981).
9. Shimizu M., Takahashi K., Lamb T. M., Shindo H., Mitchell A. P., Nucleic Acids Res., 31, 3033-3037 (2003).
10. Shimizu M., Mitchell A. P., Methods Enzymol., 370, 479-487 (2003).
11. Roth S. Y., Dean A., Simpson R. T., Mol. Cell. Biol., 10, 2247-2260 (1990).
12. Burke D., Dawson D., Stearns T., "Methods in Yeast Genetics, A Cold Spring Harbor Laboratory Course Manual," Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, 2000.
13. Axelrod J. D., Majors J., Nucleic Acids Res., 17, 171-183 (1989).
14. Murphy M. R., Shimizu M., Roth S. Y., Dranginis A. M., Simpson R. T., Nucleic Acids Res., 21, 3295-3300 (1993).
15. Shimizu M., Roth S. Y., Szent-Gyorgyi C., Simpson R. T., EMBO J., 10, 3033-3041 (1991).
16. Tanaka Y., Tawaramoto-Sasanuma M., Kawaguchi S., Ohta T., Yoda K., Kurumizaka H., Yokoyama S., Methods, 33, 3-11 (2004).
17. Roth S. Y., Shimizu M., Johnson L., Grunstein M., Simpson R. T., Genes Dev., 6, 411-425 (1992).
18. Shimizu M., Li W., Shindo H., Mitchell A. P., Proc. Natl. Acad. Sci. U.S.A., 94, 790-795 (1997).
19. Morohashi N., Yamamoto Y., Kuwana S., Morita W., Shindo H., Mitchell A. P., Shimizu M., Eukaryotic Cell, 5, 1925-1933 (2006).
20. Shimizu M., Mori T., Sakurai T., Shindo H., EMBO J., 19, 3358-3365 (2000).
21. Park Y. J., Chodaparambil J. V., Bao Y., McBryant S. J., Luger K., J. Biol. Chem., 280, 1817-1825 (2005).
22. Simpson R. T., Stafford D. W., Proc. Natl. Acad. Sci. U.S.A., 80, 51-55 (1983).