Reversible histone acetylation and deacetylation mediate genome-wide, promoter-dependent and locus-specific changes in gene expression during plant development

Genetics

Volumn 169, Issue 1, 2005, Pages 337-345

  Tian, Lu ^a   Fong, M Paulus ^a   Wang, Jiyuan J ^a   Wei, Ning E ^a   Jiang, Hongmei ^b   Doerge, R W ^b   Chen, Z Jeffrey ^a  

^a TEXAS A AND M UNIVERSITY   (United States)

^b PURDUE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACETYLATION; ARABIDOPSIS; ARTICLE; CHROMATIN STRUCTURE; DEACETYLATION; DNA MICROARRAY; GENE EXPRESSION; GENE EXPRESSION REGULATION; HOMEOSTASIS; NUCLEOTIDE SEQUENCE; PLANT DEVELOPMENT; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN SYNTHESIS;

ACETYLATION; ARABIDOPSIS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, DEVELOPMENTAL; GENE EXPRESSION REGULATION, PLANT; GENOME, PLANT; HISTONE DEACETYLASES; HISTONES; MICROARRAY ANALYSIS; PROMOTER REGIONS (GENETICS);

ARABIDOPSIS THALIANA;

EID: 13744260173     PISSN: 00166731     EISSN: None     Source Type: Journal    
DOI: 10.1534/genetics.104.033142     Document Type: Article

References (42)

1. ALLAND, L., R. MUHLE, H. HOU, JR., J. POTES, L. CHIN et al., 1997 Role for N-CoR and histone deacetylase in Sin3-mediated transcriptional repression. Nature 387: 49-55.
2. ARABIDOPSIS GENOME INITIATIVE, 2000 Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408: 796-815.
3. AUFSATZ, W., M. F. METTE, J. VAN DER WINDEN, M. MATZKE and A. J. MATZKE, 2002 HDA6, a putative histone deacetylase needed to enhance DNA methylation induced by double-stranded RNA. EMBO J. 21: 6832-6841.
4. AUSIN, I., C. ALONSO-BLANCO, J. A. JARILLO, L. RUIZ-GARCIA and J. M. MARTINEZ-ZAPATER, 2004 Regulation of flowering time by FVE, a retinoblastoma-associated protein. Nat. Genet. 36: 162-166.
5. BERNSTEIN, B. E., J. K. TONG and S. L. SCHREIBER, 2000 Genome-wide studies of histone deacetylase function in yeast. Proc. Natl. Acad. Sci. USA 97: 13708-13713.
6. BREHM, A., E. A. MISKA, D. J. MCCANCE, J. L. REID, A. J. BANNISTER et al., 1998 Retinoblastoma protein recruits histone deacetylase to repress transcription. Nature 391: 597-601.
7. BROWNELL, J. E., and C. D. ALLIS, 1996 Special HATs for special occasions: linking histone acetylation to chromatin assembly and gene activation. Curr. Opin. Genet. Dev. 6: 176-184.
8. BRUNET, A., L. B. SWEENEY, J. F. STURGILL, K. F. CHUA, P. L. GREER et al., 2004 Stress-dependent regulation of FOXO transcription factors by the SIRT1 deacetylase. Science 303: 2011-2015.
9. CHEN, Z. J., J. WANG, L. TIAN, H.-S. LEE, J. J. WANG et al., 2004 The development of an Arabidopsis model system for genome-wide analysis of polyploidy effects. Biol. J. Linn. Soc. Lond. 82: 689-700.
10. CHUA, Y. L., E. MOTT, A. P. BROWN, D. MACLEAN and J. C. GRAY, 2004 Microarray analysis of chromatin-immunoprecipitated DNA identifies specific regions of tobacco genes associated with acetylated histones. Plant J. 37: 789-800.
11. CLEVELAND, W. S., 1979 Robust locally weighted regression and smoothing scatterplots. J. Am. Stat. Assoc. 74: 829-836.
12. DE NADAL, E., M. ZAPATER, P. M. ALEPUZ, L. SUMOY, G. MAS et al., 2004 The MAPK Hog1 recruits Rpd3 histone deacetylase to activate osmoresponsive genes. Nature 427: 370-374.
13. FUKS, F., W. A. BURGERS, A. BREHM, L. HUGHES-DAVIES and T. KOUZARIDES, 2000 DNA methyltransferase Dnmtl associates with histone deacetylase activity. Nat. Genet. 24: 88-91.
14. HE, Y., S. D. MICHAELS and R. M. AMASINO, 2003 Regulation of flowering time by histone acetylation in Arabidopsis. Science 302: 1751-1754.
15. HEKIMI, S., and L. GUARENTE, 2003 Genetics and the specificity of the aging process. Science 299: 1351-1354.
16. IMAI, S., C. M. ARMSTRONG, M. KAEBERLEIN and L. GUARENTE, 2000 Transcriptional silencing and longevity protein Sir2 is an NAD-dependent histone deacetylase. Nature 403: 795-800.
17. JENUWEIN, T., and C. D. ALLIS, 2001 Translating the histone code. Science 293: 1074-1080.
18. KADOSH, D., and K. STRUHL, 1997 Repression by Ume6 involves recruitment of a complex containing Sin3 corepressor and Rpd3 histone deacetylase to target promoters. Cell 89: 365-371.
19. KIM, H. J., Y. HYUN, J. Y. PARK, M. J. PARK, M. K PARK et al., 2004 A genetic link between cold responses and flowering time through FVE in Arabidopsis thaliana. Nat. Genet. 36: 167-171.
20. KUO, M. H., and C. D. ALLIS, 1998 Roles of histone acetyltransferases and deacetylases in gene regulation. BioEssays 20: 615-626.
21. LAWRENCE, R. J., K. EARLEY, O. PONTES, M. SILVA, Z. J. CHEN et al., 2004 A concerted DNA methylation/histone methylation switch regulates rRNA gene dosage control and nucleolar dominance. Mol. Cell 13: 599-609.
22. LEE, H. S., J. WANG, L. TIAN, H. JIANG, M. A. BLACK et al., 2004 Sensitivity of 70-mer oligonucleotides and cDNAs for microarray analysis of gene expression in Arabidopsis and Brasssica. Plant Biotechnol. J. 2: 45-57.
23. LIPPMAN, Z., B. MAY, C. YORDAN, T. SINGER and R. MARTIENSSEN, 2003 Distinct mechanisms determine transposon inheritance and methylation via small interfering RNA and histone modification. PLoS Biol. 1: E67.
24. LUO, R. X., A. A. POSTIGO and D. C. DEAN, 1998 Rb interacts with histone deacetylase to repress transcription. Cell 92: 463-473.
25. MEYEROWITZ, E. M., 1996 Plant development: local control, global patterning. Curr. Opin. Genet. Dev. 6: 475-479.
26. MURFETT, J., X. J. WANG, G. HAGEN and T. J. GUILFOYLE, 2001 Identification of Arabidopsis histone deacetylase hda6 mutants that affect transgene expression. Plant Cell 13: 1047-1061.
27. NAN, X., H. H. NG, C. A. JOHNSON, C. D. LAHERTY, B. M. TURNER et al., 1998 Transcriptional repression by the methyl-CpG-binding protein MeCP2 involves a histone deacetylase complex. Nature 393: 386-389.
28. NOMA, K., C. D. ALLIS and S. I. GREWAL, 2001 Transitions in distinct histone H3 methylation patterns at the heterochromatin domain boundaries. Science 293: 1150-1155.
29. PANDEY, R., A. MULLER, C. A. NAPOLI, D. A. SELINGER, C. S. PIKAARD et al., 2002 Analysis of histone acetyltransferase and histone deacetylase families of Arabidopsis thaliana suggests functional diversification of chromatin modification among multicellular eukaryotes. Nucleic Acids Res. 30: 5036-5055.
30. PROBST, A. V., M. FAGARD, F. PROUX, P. MOURRAIN, S. BOUTET et al., 2004 Arabidopsis histone deacetylase HDA6 is required for maintenance of transcriptional gene silencing and determines nuclear organization of rDNA repeats. Plant Cell 16: 1021-1034.
31. RABINOWICZ, P. D., W. R. MCCOMBIE and R. A. MARTIENSSEN, 2003 Gene enrichment in plant genomic shotgun libraries. Curr. Opin. Plant Biol. 6: 150-156.
32. RICHARDS, E. J., and S. C. ELGIN, 2002 Epigenetic codes for heterochromatin formation and silencing: rounding up the usual suspects. Cell 108: 489-500.
33. ROBYR, D., Y. SUKA, I. XENARIOS, S. K. KURDISTANI, A. WANG et al., 2002 Microarray deacetylation maps determine genome-wide functions for yeast histone deacetylases. Cell 109: 437-446.
34. SMITH, J. S., C. B. BRACHMANN, I. CELIC, M. A. KENNA, S. MUHAMMAD et al., 2000 A phylogenetically conserved NAD+-dependent protein deacetylase activity in the Sir2 protein family. Proc. Natl. Acad. Sci. USA 97: 6658-6663.
35. STOCKINGER, E. J., Y. MAO, M. K. REGIER, S. J. TRIEZENBERG and M. F. THOMASHOW, 2001 Transcriptional adaptor and histone acetyltransferase proteins in Arabidopsis and their interactions with CBF1, a transcriptional activator involved in cold-regulated gene expression. Nucleic Acids Res. 29: 1524-1533.
36. STOKES, T. L., and E. J. RICHARDS, 2002 Induced instability of two Arabidopsis constitutive pathogen-response alleles. Proc. Natl. Acad. Sci. USA 99: 7792-7796.
37. STOKES, T. L., B. N. KUNKEL and E. J. RICHARDS, 2002 Epigenetic variation in Arabidopsis disease resistance. Genes Dev. 16: 171-182.
38. TIAN, L., and Z. J. CHEN, 2001 Blocking histone deacetylation in Arabidopsis induces pleiotropic effects on plant gene regulation and development. Proc. Natl. Acad. Sci. USA 98: 200-205.
39. TIAN, L., J. WANG, M. P. FONG, M. CHEN, H. CAO et al., 2003 Genetic control of developmental changes induced by disruption of Arabidopsis histone deacetylase 1 (AtHD1) expression. Genetics 165: 399-409.
40. VOGELAUER, M., J. WU, N. SUKA and M. GRUNSTEIN, 2000 Global histone acetylation and deacetylation in yeast. Nature 408: 495-498.
41. WU, K, L. TIAN, C. ZHOU, D. BROWN and B. MIKI, 2003 Repression of gene expression by Arabidopsis HD2 histone deacetylases. Plant J. 34: 241-247.
42. YANG, W. M., C. INOUYE, Y. ZENG, D. BEARSS and E. SETO, 1996 Transcriptional repression by YY1 is mediated by interaction with a mammalian homolog of the yeast global regulator RPD3. Proc. Natl. Acad. Sci. USA 93: 12845-12850.