Mapping and characterization of DNase I hypersensitive sites in Arabidopsis chromatin

Plant and Cell Physiology

Volumn 48, Issue 3, 2007, Pages 459-470

  Kodama, Yuichi ^a   Nagaya, Shingo ^a   Shinmyo, Atsuhiko ^a   Kato, Ko ^a  

^a NARA INSTITUTE OF SCIENCE AND TECHNOLOGY   (Japan)

Author keywords

Arabidopsis thaliana; Chromatin structure; DNase I hypersensitive site; Gene expression; Histone acetylation; Transcription regulation

Indexed keywords

ARABIDOPSIS; ARABIDOPSIS THALIANA; EUKARYOTA;

ARABIDOPSIS PROTEIN; DEOXYRIBONUCLEASE I; HEAT SHOCK PROTEIN; HISTONE; HSP18.2 PROTEIN, ARABIDOPSIS; PLANT DNA; PRIMER DNA; UNCLASSIFIED DRUG;

ACETYLATION; ARABIDOPSIS; ARTICLE; BINDING SITE; CHROMATIN; CHROMOSOME MAP; GENE; GENETICS; GENOME; METABOLISM; NUCLEOTIDE SEQUENCE; PROMOTER REGION; TRANSACTIVATION;

ACETYLATION; ARABIDOPSIS; ARABIDOPSIS PROTEINS; BASE SEQUENCE; BINDING SITES; CHROMATIN; CHROMOSOME MAPPING; DEOXYRIBONUCLEASE I; DNA PRIMERS; DNA, PLANT; GENES, PLANT; GENOME, PLANT; HEAT-SHOCK PROTEINS; HISTONES; PROMOTER REGIONS (GENETICS); TRANS-ACTIVATION (GENETICS);

EID: 34249744467     PISSN: 00320781     EISSN: 14719053     Source Type: Journal    
DOI: 10.1093/pcp/pcm017     Document Type: Article

References (49)

1. Anderson, J.D. and Widom, J. (2000) Sequence and position-dependence of the equilibrium accessibility of nucleosomal DNA target sites. J. Mol. Biol. 296: 979-987.
2. Axelos, M., Curie, C., Mazzolini, L., Bardet, C. and Lescure, B. (1992) A protocol for transient gene expression in Arabidopsis thaliana protoplasts isolated from cell suspension cultures. Plant Physiol. Biochem. 30: 123-128.
3. Bernstein, B.E., Liu, C.L., Humphrey, E.L., Perlstein, E.O. and Schreiber, S.L. (2004) Global nucleosome occupancy in yeast. Genome Biol. 5: R62.
4. Brown, J.A., Holmes, S.G. and Smith, M.M. (1991) The chromatin structure of Saccharomyces cerevisiae autonomously replicating sequences changes during the cell division cycle. Mol. Cell Biol. 11: 5301-5311.
5. Cartwright, I.L. and Elgin, S.C. (1986) Nucleosomal instability and induction of new upstream protein-DNA associations accompany activation of four small heat shock protein genes in Drosophila melanogaster. Mol. Cell. Biol. 6: 779-791.
6. Conconi, A. and Ryan, C.A. (1993) DNase I and micrococcal nuclease analysis of the tomato proteinase inhibitor I gene in chromatin. J. Biol. Chem. 268: 430-435.
7. Crawford, G.E., Davis, S., Scacheri, P.C., Renaud, G., Halawi, M.J., Erdos, M.R., Green, R., Meltzer, P.S., Wolfsberg, T.G. and Collins, F.S. (2006a) DNase-chip: a high-resolution method to identify DNase I hypersensitive sites using tiled microarrays. Nat. Methods 3: 503-509.
8. Crawford, G.E., Holt, I.E., Mullikin, J.C., Tai, D., et al.; National Institutes Of Health Intramural Sequencing Center (2004) Identifying gene regulatory elements by genome-wide recovery of DNase hypersensitive sites. Proc. Natl Acad. Sci. USA 101: 992-997.
9. Crawford, G.E., Holt, I.E., Whittle, J., Webb, B.D., Tai, D., et al. (2006b) Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS). Genome Res. 16: 123-131.
10. Dean, A. (2006) On a chromosome far, far away: LCRs and gene expression. Trends Genet. 22: 38-45.
11. Deutsch, M. and Long, M. (1999) Intron-exon structures of eukaryotic model organisms. Nucleic Acids Res. 27: 3219-3228.
12. Dorschner, M.O., Hawrylycz, M., Humbert, R., Wallace, J.C., Shafer, A., et al. (2004) High-throughput localization of functional elements by quantitative chromatin profiling. Nat. Methods 1: 219-225.
13. Ercan, S. and Simpson, R.T. (2004) Global chromatin structure of 45,000 base pairs of chromosome III in a- and alpha-cell yeast and during mating-type switching. Mol. Cell Biol. 24: 10026-10035.
14. Erkine, A.M., Adams, C.C., Diken, T. and Gross, D.S. (1996) Heat shock factor gains access to the yeast HSC82 promoter independently of other sequence-specific factors and antagonizes nucleosomal repression of basal and induced transcription. Mol. Cell. Biol. 16: 7004-7017.
15. Gendrel, A.V., Lippman, Z., Yordan, C., Colot, V. and Martienssen, R.A. (2002) Dependence of heterochromatic histone H3 methylation patterns on the Arabidopsis gene DDM1. Science 297: 1871-1873.
16. Gross, D.S., Adams, C.C., Lee, S. and Stentz, B. (1993) A critical role for heat shock transcription factor in establishing a nucleosome-free region over the TATA-initiation site of the yeast HSP82 heat shock gene. EMBO J. 12: 3931-3945.
17. Gross, D.S. and Garrard, W.T. (1988) Nuclease hypersensitive sites in chromatin. Annu. Rev. Biochem. 57: 159-197.
18. Hanano, S., Amagai, M., Kaneko, T., Kuwata, C., Tsugane, T., Sakurai, N., Nakamura, Y., Shibata, D. and Tabata, S. (2002) Analysis of gene expression in Arabidopsis thaliana by array hybridization with genomic DNA fragments aligned along chromosomal regions. Plant J. 30: 247-255.
19. Higo, K., Ugawa, Y., Iwamoto, M. and Korenaga, T. (1999) Plant cis-acting regulatory DNA elements (PLACE) database: 1999. Nucleic Acids Res. 27: 297-300.
20. Kosugi, S. and Ohashi, Y. (2002) E2F sites that can interact with E2F proteins cloned from rice are required for meristematic tissue-specific expression of rice and tobacco proliferating cell nuclear antigen promoters. Plant J. 29: 45-59.
21. Leibovitch, B.A., Lu, Q., Benjamin, L.R., Liu, Y., Gilmour, D.S. and Elgin, S.C. (2002) GAGA factor and the TFIID complex collaborate in generating an open chromatin structure at the Drosophila melanogaster hsp26 promoter. Mol. Cell. Biol. 22: 6148-6157.
22. Lodha, M. and Schroda, M. (2005) Analysis of chromatin structure in the control regions of the Chlamydomonas HSP70A and RBCS2 genes. Plant Mol. Biol. 59: 501-513.
23. Lohmann, C., Eggers-Schumacher, G., Wunderlich, M. and Schoffl, F. (2004) Two different heat shock transcription factors regulate immediate early expression of stress genes in Arabidopsis. Mol. Genet. Genom. 271: 11-21.
24. Lu, Q., Wallrath, L.L., Granok, H. and Elgin, S.C. (1993) (CT)n·(GA)n repeats and heat shock elements have distinct roles in chromatin structure and transcriptional activation of the Drosophila hsp26 gene. Mol. Cell. Biol. 13: 2802-2814.
25. Luger, K., Mader, A.W., Richmond, R.K., Sargent, D.F. and Richmond, T.J. (1997) Crystal structure of the nucleosome core particle at 2.8 Å resolution. Nature 389: 251-260.
26. Magnotta, S.M. and Gogarten, J.P. (2002) Multi site polyadenylation and transcriptional response to stress of a vacuolar type H+-ATPase subunit A gene in Arabidopsis thaliana. BMC Plant Biol. 2: 3.
27. Nagata, T., Nemoto, Y. and Hasezawa, S. (1992) Tobacco BY-2 cell line as the 'Hela' cell in the cell biology of higher plants. Int. Rev. Cytol. 132: 1-30.
28. Nagaya, S., Kato, K., Ninomiya, Y., Horie, R., Sekine, M., Yoshida, K. and Shinmyo, A. (2004) Expression of randomly integrated single complete copy transgenes does not vary in Arabidopsis thaliana. Plant Cell Physiol. 46: 438-444.
29. Nakayama, H., Yoshida, K., Ono, H., Murooka, Y. and Shinmyo, A. (2000) Ectoine, the compatible solute of Halomonas elongate, confers hyperosmotic tolerance in cultured tobacco cells. Plant Physiol. 122: 1239-1247.
30. Ng, D.W., Chandrasekharan, M.B. and Hall, T.C. (2006) Ordered histone modifications are associated with transcriptional poising and activation of the phaseolin promoter. Plant Cell 18: 119-132.
31. Reinke, H. and Horz, W. (2003) Histones are first hyperacetylated and then lose contact with the activated PHO5 promoter. Mol. Cell 11: 1599-1607.
32. Sabo, P.J., Humbert, R., Hawrylycz, M., Wallace, J.C., Dorschner, M.O., McArthur, M. and Stamatoyannopoulos, J.A. (2004) Genome-wide identification of DNase I hypersensitive sites using active chromatin sequence libraries. Proc. Natl Acad. Sci. USA 101: 4537-4542.
33. Sabo, P.J., Kuehn, M.S., Thurman, R., Johnson, B.E., Johnson, E.M., et al. (2006) Genome-scale mapping of DNase I sensitivity in vivo using tiling DNA microarrays. Nat. Methods 3: 511-518.
34. Segal, E., Fondufe-Mittendorf, Y., Chen, L., Thastrom, A., Field, Y., Moore, I.K., Wang, J.P. and Widom, J. (2006) A genomic code for nucleosome positioning. Nature 442: 772-778.
35. Svaren, J., Schmitz, J. and Horz, W. (1994) The transactivation domain of Pho4 is required for nucleosome disruption at the PHO5 promoter. EMBO J. 13: 4856-4862.
36. Takahashi, T. and Komeda, Y. (1989) Characterization of two genes encoding small heat-shock proteins in Arabidopsis thaliana. Mol. Gen. Genet. 219: 365-372.
37. Tremousaygue, D., Manevski, A., Bardet, C., Lescure, N. and Lescure, B. (1999) Plant interstitial telomere motifs participate in the control of gene expression in root meristems. Plant J. 20: 553-561.
38. Tremousaygue, D., Garnier, L., Bardet, C., Dabos, P., Herve, C. and Lescure, B. (2003) Internal telomeric repeats and 'TCP domain' protein-binding sites co-operate to regulate gene expression in Arabidopsis thaliana cycling cells. Plant J. 33: 957-966.
39. Udvardy, A., Maine, E. and Schedl, P. (1985) The 87A7 chromomere. Identification of novel chromatin structures flanking the heat shock locus that may define the boundaries of higher order domains. J. Mol. Biol. 185: 341-358.
40. Uemukai, K., Iwakawa, H., Kosugi, S., de Jager, S., Kato, K., Kondorosi, E., Murray, J.A., Ito, M., Shinmyo, A. and Sekine, M. (2005) Transcriptional activation of tobacco E2F is repressed by co-transfection with the retinoblastoma-related protein: cyclin D expression overcomes this repressor activity. Plant Mol. Biol. 57: 83-100.
41. Uno, Y., Furihata, T., Abe, H., Yoshida, R., Shinozaki, K. and Yamaguchi-Shinozaki, K. (2000) Arabidopsis basic leucine zipper transcription factors involved in an abscisic acid-dependent signal transduction pathway under drought and high-salinity conditions. Proc. Natl Acad. Sci. USA 97: 11632-11637.
42. Vega-Palas, M.A. and Ferl, R.J. (1995) The Arabidopsis Adh gene exhibits diverse nucleosome arrangements within a small DNase I-sensitive domain. Plant Cell 7: 1923-1932.
43. Venter, U., Svaren, J., Schmitz, J., Schmid, A. and Horz, W. (1994) A nucleosome precludes binding of the transcription factor Pho4 in vivo to a critical target site in the PHO5 promoter. EMBO J. 13: 4848-4855.
44. Wallrath, L.L., Lu, Q., Granok, H. and Elgin, S.C. (1994) Architectural variations of inducible eukaryotic promoters: preset and remodeling chromatin structures. Bioessays 16: 165-170.
45. Wu, C. (1980) The 5′ ends of Drosophila heat shock genes in chromatin are hypersensitive to DNase I. Nature 286: 854-860.
46. Yuan, G.C., Liu, Y.J., Dion, M.F., Slack, M.D., Wu, L.F., Altschuler, S.J. and Rando, O.J. (2005) Genome-scale identification of nucleosome positions in S. cerevisiae. Science 309: 626-630.
47. Zhang, L., Eggers-Schumacher, G., Schoffl, F. and Prandl, R. (2001) Analysis of heat-shock transcription factor-DNA binding in Arabidopsis suspension cultures by UV laser crosslinking. Plant J. 28: 217-223.
48. Zhang, L., Lohmann, C., Prandl, R. and Schoffl, F. (2003) Heat stress-dependent DNA binding of Arabidopsis heat shock transcription factor HSF1 to heat shock gene promoters in Arabidopsis suspension culture cells in vivo. Biol. Chem. 384: 959-963.
49. Zhao, K., Hart, C.M. and Laemmli, U.K. (1995) Visualization of chromosomal domains with boundary element-associated factor BEAF-32. Cell 81: 879-889.