Distinct DNase I hypersensitive sites are absent from promoters of transcriptionally incompetent genes in Arabidopsis

Plant Biotechnology

Volumn 24, Issue 4, 2007, Pages 383-392

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

^a NARA INSTITUTE OF SCIENCE AND TECHNOLOGY   (Japan)

^b IDEMITSU KOSAN CO LTD   (Japan)

Author keywords

Arabidopsis thaliana; Chromatin accessibility; DNase I hypersensitive site; Tissue specific gene expression; Transcriptional competency

Indexed keywords

ANIMALIA; ARABIDOPSIS; ARABIDOPSIS THALIANA;

EID: 34548856233     PISSN: 13424580     EISSN: 13476114     Source Type: Journal    
DOI: 10.5511/plantbiotechnology.24.383     Document Type: Article

References (45)

1. Angermayr M, Oechsner U, Gregor K, Schroth GP, Bandlow W (2002) Transcription initiation in vivo without classical transactivators: DNA kinks flanking the core promoter of the housekeeping yeast adenylate kinase gene, AKY2, position nucleosomes and constitutively activate transcription. Nucl Acids Res 30: 4199-4207
2. Angermayr M, Oechsner U, Bandlow W (2003) Reb1p-dependent DNA bending effects nucleosome positioning and constitutive transcription at the yeast profilin promoter. J Biol Chem 278: 17918-17926
3. Axelos M, Curie C, Mazzolini L, Bardet C, Lescure B (1992) A protocol for transient gene expression in Arabidopsis thaliana protoplasts isolated from cell suspension cultures. Plant Physiol Biochem 30: 123-128
4. Bowman JL, Drews GN, Meyerowitz EM (1991) Expression of the Arabidopsis floral homeotic gene AGAMOUS is restricted to specific cell types late in flower development. Plant Cell 3: 749-758
5. Brocard IM, Lynch TJ, Finkelstein RR (2002) Regulation and role of the Arabidopsis abscisic acid-insensitive 5 gene in abscisic acid, sugar, and stress response. Plant Physiol 129: 1533-1543
6. Carles C, Bies-Etheve N, Aspart L, Leon-Kloosterziel KM, Koornneef M, Echeverria M, Delseny M (2002) Regulation of Arabidopsis thaliana Em genes: role of ABI5. Plant J 30: 373-383
7. Crawford GE, Holt IE, Mullikin JC, Tai D, Blakesley R, Bouffard G, Young A, Masiello C, Green ED, Wolfsberg TG, Collins FS; 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
8. Crawford GE, Davis S, Scacheri PC, Renaud G, Halawi MJ, Erdos MR, Green R, Meltzer PS, Wolfsberg TG, Collins FS (2006) DNase-chip: a high-resolution method to identify DNase I hypersensitive sites using tiled microarrays. Nature Methods 3: 503-509
9. de Bruxelles GL, Peacock WJ, Dennis ES, Dolferus R (1996) Abscisic acid induces the alcohol dehydrogenase gene in Arabidopsis. Plant Physiol 111: 381-391
10. Dolferus R, Jacobs M, Peacock WJ, Dennis ES (1994) Differential interactions of promoter elements in stress responses of the Arabidopsis Adh gene. Plant Physiol 105: 1075-1087
11. Ercan S, Simpson RT (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
12. Fritton HP, Igo-Kemenes T, Nowock J, Strech-Jurk U, Theisen M, Sippel AE (1984) Alternative sets of DNase I-hypersensitive sites characterize the various functional states of the chicken lysozyme gene. Nature 311: 163-165
13. Goodrich J, Puangsomlee P, Martin M, Long D, Meyerowitz EM, Coupland G (1997) A Polycomb-group gene regulates homeotic gene expression in Arabidopsis. Nature 386: 44-51
14. Gross DS, Garrard WT (1988) Nuclease hypersensitive sites in chromatin. Annu Rev Biochem 57: 159-197
15. Gross DS, Adams CC, Lee S, 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
16. Higo K, Ugawa Y, Iwamoto M, Korenaga T (1999) Plant cis-acting regulatory DNA elements (PLACE) database: 1999. Nucl Acids Res 27: 297-300
17. Houben A, Demidov D, Gernand D, Meister A, Leach CR, Schubert I (2003) Methylation of histone H3 in euchromatin of plant chromosomes depends on basic nuclear DNA content. Plant J 33: 967-973
18. Ito T, Sakai H, Meyerowitz EM (2003) Whorl-specific expression of the SUPERMAN gene of Arabidopsis is mediated by cis elements in the transcribed region. Curr Biol 13: 1524-1530
19. Jacobsen SE, Meyerowitz EM (1997) Hypermethylated SUPERMAN epigenetic alleles in arabidopsis. Science 277: 1100-1103
20. Kinoshita T, Miura A, Choi Y, Kinoshita Y, Cao X, Jacobsen SE, Fischer RL, Kakutani T (2004) One-way control of FWA imprinting in Arabidopsis endosperm by DNA methylation. Science 303: 521-523
21. Kodama Y, Nagaya S, Sakurai N, Shibata D, Shinmyo A, Kato K (2006) Analysis of chromatin condensation states by DNase I sensitivity assay at 500-base resolution in Arabidopsis. Plant Biotechnol 23: 451-457
22. Kodama Y, Nagaya S, Shinmyo A, Kato K (2007) Mapping and characterization of DNase I hypersensitive sites in Arabidopsis chromatin. Plant Cell Physiol 48: 459-470
23. Kotake T, Takada S, Nakahigashi K, Ohto M, Goto K (2003) Arabidopsis TERMINAL FLOWER 2 gene encodes a heterochromatin protein 1 homolog and represses both FLOWERING LOCUS T to regulate flowering time and several floral homeotic genes. Plant Cell Physiol 44: 555-564
24. Lachner M, Jenuwein T (2002) The many faces of histone lysine methylation. Curr Opin Cell Biol 14: 286-298
25. Leibovitch BA, Lu Q, Benjamin LR, Liu Y, Gilmour DS, Elgin, SC (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
26. Lindroth AM, Shultis D, Jasencakova Z, Fuchs J, Johnson L, Schubert D, Patnaik D, Pradhan S, Goodrich J, Schubert I, Jenuwein T, Khorasanizadeh S, Jacobsen SE (2004) Dual histone H3 methylation marks at lysines 9 and 27 required for interaction with CHROMOMETHYLASE3. EMBO J 23: 4286-4296
27. Litt MD, Simpson M, Gaszner M, Allis CD, Felsenfeld G (2001) Correlation between histone lysine methylation and developmental changes at the chicken beta-globin locus. Science 293: 2453-2455
28. Lopez-Molina L, Mongrand S, McLachlin DT, Chait BT, Chua NH (2002) ABI5 acts downstream of ABI3 to execute an ABA-dependent growth arrest during germination. Plant J 32: 317-328
29. Lu Q, Wallrath LL, Granok H, Elgin SC (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
30. Magnotta SM, Gogarten JP (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
31. Naito S, Yokota-Hirai M, Chino M, Komeda Y (1994) Expression of a soybean (Glycine max [L.] Merr.) seed storage protein gene in transgenic Arabidopsis thaliana and its response to nutritional stress and to abscisic acid mutations. Plant Physiol 104: 497-503
32. Nakahigashi K, Jasencakova Z, Schubert I, Goto K (2005) The Arabidopsis heterochromatin protein1 homolog (TERMINAL FLOWER2) silences genes within the euchromatic region but not genes positioned in heterochromatin. Plant Cell Physiol 46: 1747-1756
33. Parcy F, Valon C, Raynal M, Gaubier-Comella P, Delseny M, Giraudat J (1994) Regulation of gene expression programs during Arabidopsis seed development: roles of the ABI3 locus and of endogenous abscisic acid. Plant Cell 6: 1567-1582
34. Pischke MS, Huttlin EL, Hegeman AD, Sussman MR (2006) A transcriptome-based characterization of habituation in plant tissue culture. Plant Physiol 140: 1255-1278
35. Sabo PJ, Humbert R, Hawrylycz M, Wallace JC, Dorschner MO, McArthur M, Stamatoyannopoulos JA (2004) Genome-wide identification of DNaseI hypersensitive sites using active chromatin sequence libraries. Proc Natl Acad Sci USA 101: 4537-4542
36. Sabo PJ, Kuehn MS, Thurman R, Johnson BE, Johnson EM, Cao H, Yu M, Rosenzweig E, Goldy J, Haydock A, Weaver M, Shafer A, Lee K, Neri F, Humbert R, Singer MA, Richmond TA, Dorschner MO, McArthur M, Hawrylycz M, Green RD, Navas PA, Noble WS, Stamatoyannopoulos JA (2006) Genome-scale mapping of DNase I sensitivity in vivo using tiling DNA microarrays. Nature Methods 3: 511-518
37. Sakai H, Medrano LJ, Meyerowitz EM (1995) Role of SUPERMAN in maintaining Arabidopsis floral whorl boundaries Nature 378: 199-203
38. Schubert D, Primavesi L, Bishopp A, Roberts G, Doonan J, Jenuwein T, Goodrich J (2006) Silencing by plant Polycombgroup genes requires dispersed trimethylation of histone H3 at lysine 27. EMBO J 25: 4638-4649
39. Soppe WJ, Jacobsen SE, Alonso-Blanco C, Jackson JP, Kakutani T, Koornneef M, Peeters AJ (2000) The late flowering phenotype of fwa mutants is caused by gain-of-function epigenetic alleles of a homeodomain gene. Mol Cell 6: 791-802
40. Svaren J, Schmitz J, Horz W (1994) The transactivation domain of Pho4 is required for nucleosome disruption at the PHO5 promoter. EMBO J 13: 4856-4862
41. Vega-Palas MA, Ferl RJ (1995) The Arabidopsis Adh gene exhibits diverse nucleosome arrangements within a small DNase I-sensitive domain. Plant Cell 7: 1923-1932
42. Venter U, Svaren J, Schmitz J, Schmid A, 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
43. Wallrath LL, Lu Q, Granok H, Elgin SC (1994) Architectural variations of inducible eukaryotic promoters: preset and remodeling chromatin structures. Bioessays 16: 165-170
44. Yanofsky MF, Ma H, Bowman JL, Drews GN, Feldmann KA, Meyerowitz EM (1990) The protein encoded by the Arabidopsis homeotic gene agamous resembles transcription factors. Nature 346: 35-39
45. Yuan GC, Liu YJ, Dion MF, Slack MD, Wu LF, Altschuler SJ, Rando OJ (2005) Genome-Scale Identification of Nucleosome Positions in S. Cerevisiae. Science 309: 626-630