Analysis of the structure of a natural alternating d(TA)(n) sequence in yeast chromatin

Yeast

Volumn 13, Issue 4, 1997, Pages 313-326

  Aranda, Agustín ^a   Pérez Ortín, José E ^a   Benham, Craig J ^b   Lí Del Olmo, Marcel ^a  

^a UNIVERSITY OF VALENCIA   (Spain)

^b MOUNT SINAI SCHOOL OF MEDICINE   (United States)

Author keywords

chromatin; cruciform; destabilized site; Saccharomyces cerevisiae; TA tract

Indexed keywords

ARTICLE; CHROMATIN; CONTROLLED STUDY; DENATURATION; DNA SEQUENCE; DNA STRUCTURE; NONHUMAN; NUCLEOSOME; PRIORITY JOURNAL; SACCHAROMYCES CEREVISIAE; YEAST;

ASPERGILLUS NUCLEASE S1; BASE SEQUENCE; CHROMATIN; DINUCLEOTIDE REPEATS; DNA, FUNGAL; ENDODEOXYRIBONUCLEASES; GENES, FUNGAL; MOLECULAR SEQUENCE DATA; MUTATION; NUCLEIC ACID CONFORMATION; SACCHAROMYCES CEREVISIAE;

EID: 0030891087     PISSN: 0749503X     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0061(19970330)13:4<313::AID-YEA93>3.0.CO;2-8     Document Type: Article

References (61)

1. Amati, B. B. and Gasser, S. M. (1988). Chromosomal ARS and CEN elements bind specifically to the yeast nuclear scaffold. Cell 54, 967-978.
2. Ausubel, S. F., Brent, R., Kingston, R., Moore, D., Seidman, J. S. and Struhl, K. (1987-1993). Current Protocols in Molecular Biology. John Wiley and Sons, New York.
3. Axelrod, J. D. and Majors, J. (1989). An improved method for photofootprinting yeast genes in vivo using Tug polymerase. Nucl. Acids Res. 17, 171-183.
4. Battistani, A., Leoni, L., Sampaolese, B. and Savino, M. (1988). Kinetic persistence of cruciform structures in reconstituted nucleosomes. Biochim. Biophys. Acta. 950, 161-171.
5. Benham, C. J. (1982). Stable cruciform formation at inverted repeat sequences in supercoiled DNA. Biopolymers 21, 679-696.
6. Benham, C. J. (1993). Sites of predicted stress-induced DNA duplex destabilization occur preferentially at regulatory loci. Proc. Natl. Acad. Sci. USA 90, 2999-3003.
7. Benham, C. J. (1996). Duplex destabilisation in superhelical DNA is predicted to occur at specific iranscriptional regulatory regions. J. Mol. Biol. 255, 425-434.
8. Berkhout, B., Klaver, B. and Das, A. T. (1995). A conserved hairpin structure predicted for the poly(A) signal of human and simian immunodeficiency viruses. Virology 207, 276-281.
9. Bode, J., Kohwi, Y., Dickinson, L., et al. (1992). Biological significance of unwinding capability of nuclear matrix-associating DNAs. Science 255, 195-197.
10. Bowater, R. P., Aboul-ela, F. and Lilley, D. M. J. (1994). Large-scale opening of A+T rich regions within supercoiled DNA molecules is suppressed by salt. Nucl. Acids Res. 22, 2042-2050.
11. Courcy, A. J. and Wang, J. C. (1983). Cruciform formation in a negatively supercoiled DNA may be kinetically forbidden under physiological conditions. Cell 13, 817-829.
12. del Olmo, M. and Pérez-Ortín, J. E. (1993). A natural A/T-rich sequence from the yeast FBP1 gene exists as a cruciform in Escherichia coli cells. Plasmid 29, 222-232.
13. del Olmo, M., Sogo, J. M., Franco, L. and Pérez-Ortín, J. E. (1993). Chromatin structure of the Saccharomyces cerevisiae FBP1 gene: Transcription-dependent changes in the regulatory and coding regions. Yeast 9, 1229-1240.
14. Dujon, B., et al. (1994). Complete DNA sequence of yeast chromosome XI. Nature 369, 371-378.
15. Estruch, F., Pérez-Ortín, J. E., Matallana, E. and Franco, L. (1989). In vivo assembly of chromatin on pBR322 sequences cloned into yeast plasmids. Plasmid 21, 113-119.
16. Funk, M., Hegemann, H. and Philippsen, P. (1989). Chromatin digestion with restriction endonuclease reveals 150-160 bp of protected DNA in the centromere of chromosome XIV in Saccharomyces cerevisiae. Mol. Gen. Genet. 219, 153-160.
17. 24 sequence from a Xenopus globin gene. J. Mol. Biol. 185, 461-478.
18. Inouye, S. and Inouye, M. (1987). Oligonucleotide-directed site-specific mutagenesis using double stranded plasmid DNA. In Narang, S. (Hd.), DNA and RNA Synthesis. vol. 1. Academic Press Inc, New York, pp. 181-206.
19. Irniger, S. and Braus, G. H. (1994). Saturation mutagenesis of a polyadenylation signal reveals a hexanucleotide element essential for mRNA 3′-end formation in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 91, 257-261.
20. Ito, H., Fukuda, Y., Murata, K. and Kimura, A. (1983). Transformation of intact yeast cells treated with alkali cations. J. Bacteriol. 153, 163-168.
21. Iver, V. and Struhl, K. (1995). Poly(dA : dT), a uniquitous promoter element that stimulates transcription via its intrinsic DNA structure. EMBO J. 14, 2570-2579.
22. Kent, N. A., Bird, L. E. and Mellor, J. (1993). Chromatin analysis in yeast using NP-40 permeabilised sphaeroplasts. Nucl. Acids Res. 21, 4653-4654.
23. Kowalski, D. and Eddy, M. J. (1988). The DNA unwinding element: a novel, cis acting component that facilitates opening of the E. coli replication origin. EMBO J. 8, 4335-4344.
24. Kowalski, D., Natale, D. A. and Eddy, M. J. (1988). Stable DNA unwinding, not "breathing", accounts for single-strand-specific nuclease hypersensitivity of specific A+T rich sequences. Proc. Natl. Acad. Sci. USA 85, 9464-9468.
25. Larsen, A. and Weintraub, H. (1982). An altered DNA conformation detected by S1 nuclease occurs at specific regions in active chick globin chromatin. Cell 29, 609-622.
26. Leach, D. R. F. (1994). Long DNA palindromes, cruciform structures, genetic instability and secondary structure repair. BioEssays 16, 893-900.
27. Lee, M.-S. and Garrard, W. T. (1991). Transcription-induced nucleosome "splitting" an underlying structure for DNase I sensitive chromatin. EMBO J. 10, 607-610.
28. Lilley, D. M. J. (1980). The inverted repeat as a recognizable structural feature in supercoiled DNA molecules. Proc. Natl. Acad. Sci. USA 77, 6468-6472.
29. Lilley, D. M. J. and Markham, A. F. (1983). Dynamics of cruciform extrusion in supercoiled DNA: use of a synthetic repeat to study conformational populations. EMBO J. 2, 527-533.
30. Liu, L. F. and Wang, J. C. (1987). Supercoiling of the DNA template during transcription. Proc. Natl. Acad. Sci. USA 84, 7024-7027.
31. Lohr, D. and Ide, G. (1979). Comparison of the structure and transcriptional activity of growing phase and stationary yeast chromatin: a model for reversible gene activation. Nucl. Acids Res. 6, 1909-1927.
32. Martínez-García, J. F., Estruch, F. and Pérez-Ortin, J. E. (1989). Chromatin structure of the 5′ flanking region of the yeast LEU2 gene. Mol. Gen. Genet. 217, 464-470.
33. Mizuuchi, K., Mizuuchi, M. and Gellert, M. (1982). Cruciform structures in palindromic DNA are favoured by DNA supercoiling. J. Mol. Biol. 156, 229-243.
34. Natale, D. A., Umek, R. M. and Kowalski, D. (1993). Ease of DNA unwinding is a conserved property of yeast replication origins. Nucl. Acids Res. 21, 555-560.
35. Nickol, J. M. and Felsenfeld, G. (1983). DNA conformation at the 5′ end of the chicken adult β-globin gene. Cell 35, 467-477.
36. Nickol, J. and Martin, R. G. (1983). DNA stem-loop structures bind poorly to histone octamer cores. Proc. Natl. Acad. Sci. USA 80, 4669-4673.
37. Nobile, C., Nickol, J. and Martin, R. G. (1986). Nucleosome phasing on a DNA fragment from the replication origin of simian virus 40 and rephasing upon cruciform formation of the DNA. Mol. Cell. Biol. 6, 2916-2922.
38. Palecek, E. (1991). Local supercoil-stabilized DNA structures. Crit. Rev. Biochem. Mol. Biol. 26, 151-226.
39. Panayotatos, N. and Wells, R. D. (1981). Cruciform structures in supercoiled DNA. Nature 289, 466-470.
40. Pérez-Ortín, J. E., Estruch, F., Matallana, E. and Franco, L. (1986). DNase I sensitivity of the chromatin of the yeast SUC2 gene for invertase. Mol. Gen. Genet. 205, 422-427.
41. Pottmeyer, S. and Kemper, B. (1992). T4 Endonuclease VII resolves cruciform DNA with nick and counternick and its activity is directed by local nucleotide sequence. J. Mol. Biol. 223, 607-615.
42. Pulleyblank, D. E., Haniford, D. B. and Morgan, A. R. (1985). A structural basis for S1 nuclease sensitivity of double-stranded DNA. Cell 42, 271-280.
43. Russo, P. (1995). mRNA 3′-end forming signals are also involved in transcription termination. Yeast 11, 447-453.
44. Russo, P. and Sherman, F. (1989). Transcription terminates near the poly(A) site in the CYC1 gene of the yeast Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 86, 8348-8352.
45. Russo, P., Li, W.-Z., Hampsey, D. M., Zaret, K. S. and Sherman, F. (1991). Distinct cis-acting signals enhance 3′ endpoint formation of CYC1 mRNA in the yeast Saccharomyces cerevisae. EMBO J. 10, 563-571.
46. Sambrook, J., Fritsch, E. F. and Maniatis. T. (1989). The Molecular Cloning: A Laboratory Manual. Cold Spring Harbor Laboratory, Cold Spring Harbor, New York.
47. Sander, M. and Hsieh, T.-S. (1985). Drosophila topoisomerase II double-strand DNA cleavage: analysis of DNA sequence homology at the cleavage site. Nucl. Acids Res. 13, 1057-1072.
48. Sinden, R. R., Broyles, S. S. and Pettijohn, D. E. (1983). Perfect palindromic lac operator DNA sequence exists as a stable cruciform structure in vitro but not in vivo. Proc. Natl. Acad. Sci. USA 80, 1797-1801.
49. Sinden, R. R., Zheng, G., Brankamp, R. G. and Allen, K. N. (1991). On the deletion of inverted repeated DNA in Escherichia coli: Effects of length, thermal stability and cruciform formation in vivo. Genetics 129, 991-1005.
50. Singleton, C. K., Klysik, J., Stirdivant, S. M. and Wells, R. D. (1982). Left-handed Z-DNA is induced by supercoiling in physiological ionic conditions. Nature 299, 312-316.
51. Snyder, M., Sapolsky, R. J. and Davis, R. W. (1988). Transcription interferes with elements important for chromosome maintenance in Saccharomyces cerevisiae. Mol. Cell Biol. 8, 2184-2194.
52. Szent-Györgyi, C., Finkelstein, D. B. and Garrard, W. T. (1987). Sharp boundaries demarcate the chromatin structure of a yeast heat shock gene. J. Mol. Biol. 193, 71-80.
53. Thoma, F. (1986). Protein-DNA interactions and nuclease-sensitive regions determine nucleosome positions on yeast plasmid chromatin. J. Mol. Biol. 190, 177-190.
54. Thoma, F. (1992). Nucleosome positioning. Biochim. Biophys. Acta 1130, 1-19.
55. Thoma, F., Bergman, L. W. and Simpson, R. T. (1984). Nuclease digestions of circular TRP1ARS1 chromatin reveals positioned nucleosomes separated by nuclease-sensitive regions. J. Mol. Biol. 177, 715-733.
56. Van Holde, K. and Zlatanova, J. (1993). Unusual DNA structures, chromatin and transcription. BioEssavs 16, 59-68.
57. Van Houten, J. V. and Newlon, C. S. (1990). Mutational analysis of the consensus sequence of a replication origin from yeast chromosome III. Mol. Cell. Biol. 10, 3917-3925.
58. Vologodskii, A. V. and Frank-Kemenetskii, M. D. (1982). Theoretical study of cruciform states in superhelical DNAs. FEBS Lett. 143, 257-260.
59. Ward, G. K., McKenzie, R., Zannis-Hadjopoulos, M. and Price, G.B. (1990). The dynamic distribution and quantification of DNA cruciforms in eukaryotic nuclei. Exp. Cell Res. 188, 235-246.
60. Wu, C. (1980). The 5′ ends of Drosophila heat shock genes in chromatin are hypersensitive to DNase I. Nature 286, 854-860.
61. Zaret, K. S. and Sherman, F. (1982). DNA sequence required for efficient transcription termination in yeast. Cell 28, 563-573.