Population Analysis of Subsaturated 172-12 Nucleosomal Arrays by Atomic Force Microscopy Detects Nonrandom Behavior That Is Favored by Histone Acetylation and Short Repeat Length

Journal of Biological Chemistry

Volumn 276, Issue 51, 2001, Pages 48362-48370

  Bash, Ralph C ^a   Yodh, Jaya ^b   Lyubchenko, Yuri ^a   Woodbury, Neal ^a   Lohr, D ^a  

^a ARIZONA STATE UNIVERSITY   (United States)

^b MIDWESTERN UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACETYLATION; ATOMIC FORCE MICROSCOPY; DNA; GENES; POPULATION STATISTICS;

CHROMATIN;

PROTEINS;

HISTONE; RIBOSOME DNA; DNA;

ACETYLATION; ARTICLE; ATOMIC FORCE MICROSCOPY; CHROMATIN; GENOME; MODEL; NUCLEOSOME; PRIORITY JOURNAL; TANDEM REPEAT; CHEMISTRY; DNA MICROARRAY; HELA CELL; HUMAN; METABOLISM; METHODOLOGY; NUCLEOTIDE REPEAT; ULTRASTRUCTURE;

ACETYLATION; DNA; HELA CELLS; HISTONES; HUMAN; MICROSCOPY, ATOMIC FORCE; NUCLEOSOMES; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; REPETITIVE SEQUENCES, NUCLEIC ACID; SUPPORT, U.S. GOV'T, P.H.S.;

EID: 0035930512     PISSN: 00219258     EISSN: None     Source Type: Journal    
DOI: 10.1074/jbc.M104916200     Document Type: Article

References (57)

1. Compton, J. L., Bellard, M., and Chambon, P. (1976) Proc. Natl. Acad. Sci. U. S. A. 73, 4382-4386
2. Lohr, D., Corden, J., Kovacic, T., Tatchell, K., and van Holde, K. E. (1977) Proc. Natl. Acad. Sci. U. S. A. 74, 79-83
3. Van Holde, K. (1988) Chromatin, Springer-Verlag New York Inc, New York
4. Widom, J. (1998) Annu. Rev. Biophys. Biomol. Struct. 27, 285-327
5. Berkowitz, E. M., and Riggs, E. A. (1981) Biochemistry 20, 7284-7290
6. Villeponteau, B., Brawley, J., and Martinson, H. G. (1992) Biochemistry 31, 1554-1563
7. Bash, R., and Lohr, D. (2001) Progr. Nuc. Acids Res. Mol. Biol. 65, 197-259
8. Simpson, R. T., Thoma, F., and Brubaker, J. M. (1985) Cell 42, 799-808
9. Dong, F., Hansen, J., and van Holde, K. (1990) Proc. Natl Acad. Sci. U. S. A. 87, 5724-5728
10. Meersseman, G., Pennings, S., and Bradbury, E. (1991) J. Mol. Biol. 220, 89-100
11. Hansen, J., Van Holde, and Lohr, D. (1991) J. Biol. Chem. 266, 4276-4282
12. Hansen, J., and Lohr, D. (1993) J. Biol. Chem. 268, 5840-5848
13. Hansen, J., Ausio, J., Stanik, V., and van Holde, K. (1989) Biochemistry 28, 9129-9136
14. Garcia-Ramirez, M., Dong, F., and Ausio, J. (1992) J. Biol. Chem. 267, 19587-19595
15. Garcia-Ramirez, M., Rocchini, C., and Ausio, J. (1995) J. Biol. Chem. 270, 17923-17928
16. Hansen, J., and Wolffe, A. (1992) Biochemistry 31, 7977-7988
17. Hansen, J., and Wolffe, A. (1994) Proc. Natl. Acad. Sci. U. S. A. 91, 2339-2343
18. Howe, L., Iskandar, M., and Ausio, J. (1998) J. Biol. Chem. 273, 11625-11629
19. Carruthers, L., Bednar, J. Woodcock, C., and Hansen, J. (1998) Biochemistry 37, 14776-14787
20. Tse, C., Sera, T., Wolffe, A., and Hansen, J. (1998) Mol. Cell. Biol. 18, 4629-4638
21. Logie, C., Tse, C., Hansen, J. C., and Peterson, C. L. (1999) Biochemistry 38, 2514-2522
22. Sendra, R., Tse, C., and Hansen, J. C. (2000) J. Biol. Chem. 275, 24928-24934
23. Lyubchenko, Y. L., Jacobs, B. L., Lindsay, S. M., and Stasiak, A. (1995) Scanning Microsc. 9, 705-727
24. Lyubchenko, Y. L., Gall, A. A., and Shlyakhtenko, L. S. (2001) Methods Mol. Biol. 148, 569-578
25. Allen, M. J., Dong, X. F, O'Neill, T. E., Yau, P., Kowalczykowski, S. C., Gatewood, J., Balhorn, R., and Bradbury, E. M. (1993) Biochemistry 32, 8390-8396
26. Leuba, S., Yang, G., Robert, C., Samori, B., van Holde, K., Zlatanova, J., and Bustamante. (1994) Proc. Natl. Acad. Sci. U. S. A. 91, 11621-11625
27. Martin, L. Vesenka, J., Henderson, E., and Dobbs, D. (1995) Biochemistry 34, 4610-4616
28. Fritzsche, W. and Henderson, E. (1997) Scanning 1942-47
29. Sato, M. Ura, K., Hohmura, K. Tokumasu, F., Yoshimura, S., Hanaoka, F., and Takeyasu, K. (1999) FEBS Letters 452, 267-271
30. Yodh, J., Lyubchenko, Y., Shlyakhtenko, L., Woodbury, N., and Lohr, D. (1999) Biochemistry 38, 15756-15763
31. Sogo, J. M., Stahl, H., Koller, T., and Knippers, R. (1986) J. Mol. Biol. 189, 189-204
32. Lohr, D., and Torchia, T. (1988) Biochemistry 27, 3961-3965
33. Lohr, D. (1984) Nucleic Acids Res. 12, 8457-8479
34. Lohr, D. (1997) J. Biol. Chem. 272, 26795-26798
35. Jeppesen, P., and Turner, B. M. (1993) Cell 74, 281-289
36. Braunstein, M., Rose, A. B., Holmes, S. G., Allis, C. D., and Broach, J. R. (1993) Genes Dev. 7, 592-604
37. Brownell, J., and Allis, D. (1996) Curr. Opin. Genet. Dev. 6, 176-184
38. Davie, J., and Saunders C. (1981) J. Bibl. Chem. 256, 12574-12580
39. Waterborg, J. H.(2000) J. Biol. Chem. 275, 13007-13011
40. Lyubchenko, Y. L., Gall, A. A., Shlyakhtenko, L. S., Harrington, R. E., Jacobs, B. L., Oden, P. I., and Lindsay, S. M. (1992a) J. Biomol. Struct. Dyn. 10, 589-606
41. Lyubchenko, Y. L., Blankenskip, R. E., Gall, A. A., Lindsay, S. M., Thiemann, O., Simpson, L., and Shlyakhtenko, L. S. (1996) Scanning Microsc. 10, (suppl.) 97-107
42. Burgoyne, L. A., and Skinner, J. D. (1981) Biochem. Biophys. Res. Commun. 99, 893-899
43. Lohr, D., and van Holde, K. E. (1979) Proc. Natl. Acad. Sci. U. S. A. 76, 6326-6330
44. Woodcock, C. L. F., Frado, L. L., and Rattner, J. B. (1984) J. Cell Biol. 99, 42-52
45. Staynov, D. Z. (2000) Nucleic Acids Res. 28, 3092-3099
46. Widlund, H., Vitolo, H., Thiriet, C., and Hayes, J. (2000) Bicchemistry 39, 3835-3841
47. Thåström, A., Lowary, P., Widlund, H., Cao, H., Kubista, M., and Widom, J. (1999) J. Mol. Biol. 288, 213-229
48. Shrader, T., and Crothers, D. (1989) Proc. Natl. Acad. Sci. U. S. A. 86, 7418-7422
49. Lowary, P., and Widom, J. (1998) J. Mol. Biol. 276, 19-42
50. Gruss, C., and Sogo, J. M. (1992) Bioessays 14, 1-8
51. Annunziato, A. T., and Hansen, J. C. (2000) Gene Expr. 9, 37-61
52. Lohr, D., and Lopez, J. (1995) J. Biol. Chem. 270, 27671-27678
53. Wolffe, A., and Hayes, J. (1999) Nucleic Acids Res. 27, 711-720
54. Workman, J. L., and Kingston, R. E. (1998) Annu. Rev. Biochem. 67, 549-579
55. Lohr, D. (1986) J. Biol. Chem. 261, 9904-9914
56. Grunstein, M. (1997) Nature 389, 349-352
57. Strahl, B., and Allis, C. (2000) Nature 403, 41-45