Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Review
  • Published:

Arabidopsis histone deacetylase 6: a green link to RNA silencing

Oncogene volume 26, pages 5477–5488 (2007)Cite this article

Abstract

Epigenetic reprogramming is at the base of cancer initiation and progression. Generally, genome-wide reduction in cytosine methylation contrasts with the hypermethylation of control regions of functionally well-established tumor suppressor genes and many other genes whose role in cancer biology is not yet clear. While insight into mechanisms that induce aberrant cytosine methylation in cancer cells is just beginning to emerge, the initiating signals for analogous promoter methylation in plants are well documented. In Arabidopsis, the silencing of promoters requires components of the RNA interference machinery and promoter double-stranded RNA (dsRNA) to induce a repressive chromatin state that is characterized by cytosine methylation and histone deacetylation catalysed by the RPD3-type histone deacetylase AtHDA6. Similar mechanisms have been shown to occur in fission yeast and mammals. This review focuses on the connections between cytosine methylation, dsRNA and AtHDA6-controlled histone deacetylation during promoter silencing in Arabidopsis and discusses potential mechanistic similarities of these silencing events in cancer and plant cells.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1
Figure 2

Similar content being viewed by others

References

  • Aasland R, Stewart AF, Gibson T . (1996). The SANT domain: a putative DNA-binding domain in the SWI-SNF and ADA complexes, the transcriptional co-repressor N-CoR and TFIIIB. Trends Biochem Sci 21: 87–88.

    CAS  PubMed  Google Scholar 

  • Aravind L, Koonin EV, Dangl M, Lusser A, Brosch G, Loidl A et al. (1998). Second family of histone deacetylases. Science 280: 1167a.

    Google Scholar 

  • Aufsatz W, Mette MF, Matzke AJ, Matzke M . (2004). The role of MET1 in RNA-directed de novo and maintenance methylation of CG dinucleotides. Plant Mol Biol 54: 793–804.

    CAS  PubMed  Google Scholar 

  • Aufsatz W, Mette MF, van der Winden J, Matzke AJM, Matzke M . (2002a). RNA-directed DNA methylation in Arabidopsis. Proc Natl Acad Sci USA 99: 16499–16506.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Aufsatz W, Mette MF, van der Winden J, Matzke M, Matzke AJ . (2002b). HDA6, a putative histone deacetylase needed to enhance DNA methylation induced by double-stranded RNA. EMBO J 21: 6832–6841.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Battaglioli E, Andres ME, Rose DW, Chenoweth JG, Rosenfeld MG, Anderson ME et al. (2002). REST repression of neuronal genes requires components of the hSWI.SNF complex. J Biol Chem 277: 41038–41045.

    CAS  PubMed  Google Scholar 

  • Baylin SB, Herman JG . (2000). DNA hypermethylation in tumorigenesis: epigenetics joins genetics. Trends Genet 16: 168–174.

    CAS  PubMed  Google Scholar 

  • Belinsky SA, Nikula KJ, Palmisano WA, Michels R, Saccomanno G, Gabrielson E et al. (1998). Aberrant methylation of p16INK4A is an early event in lung cancer and a potential biomarker for early diagnosis. Proc Natl Acad Sci USA 95: 11891–11896.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Benhamed M, Bertrand C, Servet C, Zhou D-X . (2006). Arabidopsis GCN5, HD1, and TAF1/HAF2 interact to regulate histone acetylation required for light-responsive gene expression. Plant Cell 18: 2893–2903.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Bestor TH . (2000). The DNA methyltransferases of mammals. Hum Mol Genet 9: 2395–2402.

    CAS  PubMed  Google Scholar 

  • Billy E, Brondani V, Zhang H, Muller U, Filipowicz W . (2001). Specific interference with gene expression induced by long, double-stranded RNA in mouse embryonal teratocarcinoma cell lines. Proc Natl Acad Sci USA 98: 14428–14433.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Bird AP, Wolffe AP . (1999). Methylation-induced repression – Belts, braces and chromatin. Cell 99: 451–454.

    CAS  PubMed  Google Scholar 

  • Boyes J, Bird A . (1992). Repression of genes by DNA methylation depends on CpG density and promoter strength: evidence for involvement of a methyl-CpG binding protein. EMBO J 11: 327–333.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Bracken AP, Pasini D, Capra M, Prosperini E, Colli E, Helin K . (2003). EZH2 is downstream of the pRB-E2F pathway, essential for proliferation and amplified in cancer. EMBO J 22: 5323–5335.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Cameron EE, Bachman KE, Myohanen S, Herman JG, Baylin SB . (1999). Synergy of demethylation and histone deacetylase inhibition in the re-expression of genes silenced in cancer. Nat Genet 21: 103–107.

    CAS  PubMed  Google Scholar 

  • Cao X, Aufsatz W, Zilberman D, Mette MF, Huang MS, Matzke M et al. (2003). Role of the DRM and CMT3 methyltransferases in RNA-directed DNA methylation. Curr Biol 13: 2212–2217.

    CAS  PubMed  Google Scholar 

  • Cao X, Jacobsen SE . (2002). Role of the Arabidopsis DRM methyltransferases in de novo DNA methylation and gene silencing. Curr Biol 12: 1138–1144.

    CAS  PubMed  Google Scholar 

  • Castanotto D, Tommasi S, Li M, Li H, Yanow S, Pfeifer GP et al. (2005). Short hairpin RNA-directed cytosine (CpG) methylation of the RASSF1A gene promoter in HeLa cells. Mol Ther 12: 179–183.

    CAS  PubMed  Google Scholar 

  • Chan SW-L, Henderson IR, Jacobsen SE . (2005). Gardening the genome: DNA methylation in Arabidopsis thaliana. Nat Rev Genet 6: 351–360.

    CAS  PubMed  Google Scholar 

  • Chan SW, Zilberman D, Xie Z, Johansen LK, Carrington JC, Jacobsen SE . (2004). RNA silencing genes control de novo DNA methylation. Science 303: 1336.

    CAS  PubMed  Google Scholar 

  • Chang S, Pikaard CS . (2005). Transcript profiling in Arabidopsis reveals complex responses to global inhibition of DNA methylation and histone deacetylation. J Biol Chem 280: 796–804.

    CAS  PubMed  Google Scholar 

  • Chen ZJ, Pikaard CS . (1997). Epigenetic silencing of RNA polymerase I transcription: a role for DNA methylation and histone modification in nucleolar dominance. Genes Dev 11: 2124–2136.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Cigan AM, Unger-Wallace E, Haug-Collet K . (2005). Transcriptional gene silencing as a tool for uncovering gene function in maize. Plant J 43: 929–940.

    CAS  PubMed  Google Scholar 

  • Coulondre C, Miller JH, Farabaugh PJ, Gilbert W . (1978). Molecular basis of base substitution hotspots in Escherichia coli. Nature 274: 775–780.

    CAS  PubMed  Google Scholar 

  • Cress WD, Seto E . (2000). Histone deacetylases, transcriptional control and cancer. J Cell Physiol 184: 1–16.

    CAS  PubMed  Google Scholar 

  • Datta J, Ghoshal K, Sharma SM, Tajima S, Jacob ST . (2003). Biochemical fractionation reveals association of DNA methyltransferase (Dnmt) 3b with Dnmt1 and that of Dnmt 3a with a histone methyltransferase and Hdac1. J Cell Biochem 88: 855–864.

    CAS  PubMed  Google Scholar 

  • De Marzo AM, Marchi VL, Yang ES, Veeraswamy R, Lin X, Nelson WG . (1999). Abnormal regulation of DNA methyltransferase expression during colorectal carcinogenesis. Cancer Res 59: 3855–3860.

    CAS  PubMed  Google Scholar 

  • De Ruijter AJM, Van Gennip AH, Caron HN, Kemp S, Van Kuilenburg ABP . (2003). Histone deacetylases (HDACs): characterization of the classical HDAC family. Biochem J 370: 737–749.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Dobosy JR, Selker EU . (2001). Emerging connections between DNA methylation and histone acetylation. Cell Mol Life Sci 58: 721–727.

    CAS  PubMed  Google Scholar 

  • Earley K, Lawrence RJ, Pontes O, Reuther R, Enciso AJ, Silva M et al. (2006). Erasure of histone acetylation by Arabidopsis HDA6 mediates large-scale gene silencing in nucleolar dominance. Genes Dev 20: 1283–1293.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Fahrner JA, Eguchi S, Herman JG, Baylin SB . (2002). Dependence of histone modifications and gene expression on DNA hypermethylation in cancer. Cancer Res 62: 7213–7218.

    CAS  PubMed  Google Scholar 

  • Finnin MS, Donigian JR, Cohen A, Richon VM, Rifkind RA, Marks PA et al. (1999). Structures of a histone deacetylase homologue bound to the TSA and SAHA inhibitors. Nature 401: 188–193.

    CAS  PubMed  Google Scholar 

  • Fuks F, Burgers WA, Brehm A, Hughes-Davies L, Kouzarides T . (2000). DNA methyltransferase Dnmt1 associates with histone deacetylase activity. Nat Genet 24: 88–91.

    CAS  PubMed  Google Scholar 

  • Fuks F, Burgers WA, Godin N, Kasai M, Kouzarides T . (2001). Dnmt3a binds deacetylases and is recruited by a sequence-specific repressor to silence transcription. EMBO J 20: 2536–2544.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Fuks F, Hurd PJ, Deplus R, Kouzarides T . (2003). The DNA methyltransferases associate with HP1 and the SUV39H1 histone methyltransferase. Nucleic Acids Res 31: 2305–2312.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Furner IJ, Sheikh MA, Collett CE . (1998). Gene silencing and homology-dependent gene silencing in Arabidopsis: genetic modifiers and DNA methylation. Genetics 149: 651–662.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Gartenberg MR . (2000). The Sir proteins of Saccharomyces cerevisiae: mediators of transcriptional silencing and much more. Curr Opin Microbiol 3: 132–137.

    CAS  PubMed  Google Scholar 

  • Goll MG, Bestor TH . (2005). Eukaryotic cytosine methyltransferases. Annu Rev Biochem 74: 481–514.

    CAS  PubMed  Google Scholar 

  • Grimaud C, Bantignies F, Pal-Bhadra M, Ghana P, Bhadra U, Cavalli G . (2006). RNAi components are required for nuclear clustering of Polycomb response elements. Cell 124: 957–971.

    CAS  PubMed  Google Scholar 

  • Grozinger CM, Chao ED, Blackwell HE, Moazed D, Schreiber SL . (2001). Identification of a class of small molecule inhibitors of the sirtuin family of NAD-dependent deacetylases by phenotypic screening. J Biol Chem 42: 38837–38843.

    Google Scholar 

  • Guarente L . (2000). Sir2 links chromatin silencing, metabolism, and aging. Genes Dev 14: 1021–1026.

    CAS  PubMed  Google Scholar 

  • Herman JG, Baylin SB . (2003). Gene silencing in cancer in association with promoter hypermethylation. N Engl J Med 349: 2042–2054.

    CAS  PubMed  Google Scholar 

  • Herr AJ, Jensen MB, Dalmay T, Baulcombe DC . (2005). RNA polymerase IV directs silencing of endogenous DNA. Science 308: 118–120.

    CAS  PubMed  Google Scholar 

  • Holst CR, Nuovo GJ, Esteller M, Chew K, Baylin SB, Herman JG et al. (2003). Methylation of p16INK4A promoters occurs in vivo in histologically normal human mammary epithelia. Cancer Res 63: 1596–1601.

    CAS  PubMed  Google Scholar 

  • Huettel B, Kanno T, Daxinger L, Aufsatz W, Matzke AJM, Matzke M . (2006). Endogenous targets of RNA-directed DNA methylation and Pol IV in Arabidopsis. EMBO J 25: 2828–2836.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Jacobsen SE, Sakai H, Finnegan EJ, Cao X, Meyerowitz EM . (2000). Ectopic hypermethylation of flower-specific genes in Arabidopsis. Curr Biol 10: 179–186.

    CAS  PubMed  Google Scholar 

  • Jones PA, Baylin SB . (2002). The fundamental role of epigenetic events in cancer. Nat Rev Genet 3: 415–428.

    CAS  PubMed  Google Scholar 

  • Jones PA, Laird PW . (1999). Cancer epigenetics comes of age. Nat Genet 21: 163–167.

    CAS  PubMed  Google Scholar 

  • Kanellopoulou C, Muljo SA, Kung AL, Ganesan S, Drapkin R, Jenuwein T et al. (2005). Dicer-deficient mouse embryonic stem cells are defective in differentiation and centromeric silencing. Genes Dev 19: 489–501.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Kanno T, Huettel B, Mette MF, Aufsatz W, Jaligot E, Daxinger L et al. (2005). Atypical RNA polymerase subunits required for RNA-directed DNA methylation. Nat Genet 37: 761–765.

    CAS  PubMed  Google Scholar 

  • Kanno T, Mette MF, Kreil DP, Aufsatz W, Matzke M, Matzke AJ . (2004). Involvement of putative SNF2 chromatin remodeling protein DRD1 in RNA-directed DNA methylation. Curr Biol 14: 801–805.

    CAS  PubMed  Google Scholar 

  • Kawai T, Akira S . (2006). Innate immune recognition of viral infection. Nat Immunol 7: 131–137.

    CAS  PubMed  Google Scholar 

  • Keshet I, Schlesinger Y, Farkash S, Rand E, Hecht M, Segal E et al. (2006). Evidence for an instructive mechanism of de novo methylation in cancer cells. Nat Genet 38: 149–153.

    CAS  PubMed  Google Scholar 

  • Kim DH, Villeneuve LM, Morris KV, Rossi JJ . (2006). Argonaute-1 directs siRNA-mediated transcriptional gene silencing in human cells. Nat Struct Mol Biol 13: 793–797.

    CAS  PubMed  Google Scholar 

  • Klimov D, Skoblov M, Ryazantzev A, Tyazhelova T, Baranova A . (2006). In silico search for natural antisense transcripts reveals their differential expression in human tumors. J Bioinform Comput Biol 4: 515–521.

    CAS  PubMed  Google Scholar 

  • Klose RJ, Bird AP . (2006). Genomic DNA methylation: the mark and its mediators. Trends Biochem Sci 31: 89–97.

    CAS  PubMed  Google Scholar 

  • Kondo Y, Shen L, Issa J-PJ . (2003). Critical role of histone methylation in tumor suppressor gene silencing in colorectal cancer. Mol Cell Biol 23: 206–215.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Lawrence RJ, Earley K, Pontes O, Silva M, Chen ZJ, Neves N et al. (2004). A concerted DNA methylation/histone methylation switch regulates rRNA gene dosage control and nucleolar dominance. Mol Cell 13: 599–609.

    CAS  PubMed  Google Scholar 

  • Li CF, Pontes O, El-Shami M, Henderson IR, Bernatavichute YV, Chan SW et al. (2006b). An ARGONAUTE4-containing nuclear processing center colocalized with Cajal bodies in Arabidopsis thaliana. Cell 126: 93–106.

    CAS  PubMed  Google Scholar 

  • Li H, Rauch T, Chen ZX, Szabo PE, Riggs AD, Pfeifer GP . (2006a). The histone methyltransferase SETDB1 and the DNA methyltransferase DNMT3A interact directly and localize to promoters silenced in cancer cells. J Biol Chem 281: 19489–19500.

    CAS  PubMed  Google Scholar 

  • Lippman Z, Martienssen R . (2004). The role of RNA interference in heterochromatic silencing. Nature 431: 364–370.

    CAS  PubMed  Google Scholar 

  • Lippman Z, May B, Yordan C, Singer T, Martienssen R . (2003). Distinct mechanisms determine transposon inheritance and methylation via small interfering RNA and histone methylation. PLOS Biol 1: 420–428.

    CAS  Google Scholar 

  • Long JA, Ohno C, Smith ZR, Meyerowitz EM . (2006). TOPLESS regulates apical embryonic fate in Arabidopsis. Science 312: 1520–1523.

    CAS  PubMed  Google Scholar 

  • Lu C, Tej SS, Luo S, Haudenschild CD, Meyers BC, Green PJ . (2005). Elucidation of the small RNA component of the transcriptome. Science 309: 1567–1569.

    CAS  PubMed  Google Scholar 

  • Lusser A, Brosch G, Loidl A, Haas H, Loidl P . (1997). Identification of maize histone deacetylase HD2 as an acidic nucleolar phosphoprotein. Science 277: 88–91.

    CAS  PubMed  Google Scholar 

  • Martienssen RA, Zaratiegui M, Goto DB . (2005). RNA interference and heterochromatin in the fission yeast Schizosaccharomyces pombe. Trends Genet 21: 450–456.

    CAS  PubMed  Google Scholar 

  • Mathieu O, Bender J . (2004). RNA-directed DNA methylation. J Cell Sci 117: 4881–4888.

    CAS  PubMed  Google Scholar 

  • Matzke MA, Birchler JA . (2005). RNAi mediated pathways in the nucleus. Nat Rev Genet 6: 24–35.

    CAS  PubMed  Google Scholar 

  • McGarvey KM, Fahrner JA, Green E, Martens J, Jenuwein T, Baylin SB . (2006). Silenced tumor suppressor genes reactivated by DNA demethylation do not return to a fully euchromatic chromatin state. Cancer Res 66: 3541–3549.

    CAS  PubMed  Google Scholar 

  • Melquist S, Bender J . (2003). Transcription from an upstream promoter controls methylation signaling from an inverted repeat of endogenous genes in Arabidopsis. Genes Dev 17: 2036–2047.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Momparler RL . (2003). Cancer epigenetics. Oncogene 22: 6479–6483.

    CAS  PubMed  Google Scholar 

  • Morris KV, Chan S-L, Jacobsen SE, Looney DJ . (2004). Small interfering RNA-induced transcriptional gene silencing in human cells. Science 305: 1289–1292.

    CAS  PubMed  Google Scholar 

  • Muller J, Hart CM, Francis NJ, Vargas ML, Sengupta A, Wild B et al. (2002). Histone methyltransferase activity of a Drosophila Polycomb group repressor complex. Cell 111: 197–208.

    CAS  PubMed  Google Scholar 

  • Murfett J, Wang XJ, Hagen G, Guilfoyle TJ . (2001). Identification of Arabidopsis histone deacetylase HDA6 mutants that affect transgene expression. Plant Cell 13: 1047–1061.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Nguyen CT, Gonzales FA, Jones PA . (2001). Altered chromatin structure associated with methylation-induced gene silencing in cancer cells: correlation of accessibility, methylation, MeCP2 binding and acetylation. Nucleic Acids Res 29: 4598–4606.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Nicolai M, Roncato MA, Canoy AS, Rouquié D, Sarda X, Freyssinet G et al. (2006). Large-scale analysis of mRNA translation states during sucrose starvation in Arabidopsis cells identifies cell proliferation and chromatin structure as targets of translational control. Plant Physiol 141: 663–673.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Onodera Y, Haag JR, Ream T, Nunes PC, Pontes O, Pikaard CS . (2005). Plant nuclear RNA polymerase IV mediates siRNA and DNA methylation-dependent heterochromatin formation. Cell 120: 613–622.

    CAS  PubMed  Google Scholar 

  • Pandey R, Müller A, Napoli CA, Selinger DA, Pikaard CS, Richards EJ 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.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Pontes O, Li CF, Nunes PC, Haag J, Ream T, Vitins A et al. (2006). The Arabidopsis chromatin-modifying nuclear siRNA pathway involves a nucleolar RNA processing center. Cell 126: 79–92.

    CAS  PubMed  Google Scholar 

  • Pontier D, Yahubyan G, Vega D, Bulski A, Saez-Vasquez J, Hakimi MA et al. (2005). Reinforcement of silencing at transposons and highly repeated sequences requires the concerted action of two distinct RNA polymerases IV in Arabidopsis. Genes Dev 19: 2030–2040.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Probst AV, Fagard M, Proux F, Mourrain P, Boutet S, Ealey K 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.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Rideout III WM, Coetzee GA, Olumi AF, Jones PA . (1990). 5-Methylcytosine as an endogenous mutagen in the human LDL receptor and p53 genes. Science 249: 1288–1290.

    CAS  PubMed  Google Scholar 

  • Robertson KD, Uzvolgyi E, Liang G, Talmadge C, Sumegi J, Gonzales FA et al. (1999). The human DNA methyltransferase (DNMTs) 1, 3a and 3b: coordinate mRNA expression in normal tissues and overexpression in tumors. Nucleic Acids Res 27: 2291–2298.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Rountree MR, Bachman KE, Baylin SB . (2000). DNMT1 binds HDAC2 and a new co-repressor, DMAP1, to form a complex at replication foci. Nat Genet 25: 269–277.

    CAS  PubMed  Google Scholar 

  • Schlesinger Y, Straussman R, Keshet I, Farkash S, Hecht M, Zimmerman J et al. (2006). Polycomb-mediated methylation on Lys27 of histone H3 pre-marks genes for de novo methylation in cancer. Nat Genet 39: 232–236.

    PubMed  Google Scholar 

  • Selker EU . (1998). Trichostatin A causes selective loss of DNA methylation in Neurospora. Proc Natl Acad Sci USA 95: 9430–9435.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Song C-P, Agarwal M, Ohta M, Guo Y, Halfter U, Wang P et al. (2005). Role of an Arabidopsis AP2/EREBP-type transcriptional repressor in abscisic acid and drought stress responses. Plant Cell 17: 2384–2396.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Song C-P, Galbraith DW . (2006). AtSAP18, an orthologue of human SAP18, is involved in the regulation of salt stress and mediates transcriptional repression in Arabidopsis. Plant Mol Biol 60: 241–257.

    CAS  PubMed  Google Scholar 

  • Sridha S, Wu K . (2006). Identification of AtHD2C as a novel regulator of abscisic acid responses in Arabidopsis. Plant J 46: 124–133.

    CAS  PubMed  Google Scholar 

  • Suzuki H, Gabrielson E, Chen W, Anbazhagan R, van Engeland M, Weijenberg MP et al. (2002). A genomic screen for genes upregulated by demethylation and histone deacetylase inhibition in human colorectal cancer. Nat Genet 31: 141–149.

    CAS  PubMed  Google Scholar 

  • Tian L, Chen ZJ . (2001). Blocking histone deacetylation in Arabidopsis induce pleiotropic effects on plant gene regulation and development. Proc Natl Acad Sci USA 98: 200–205.

    CAS  PubMed  Google Scholar 

  • Tian L, Wang J, Fong MP, Chen M, Cao H, Gelvin SB et al. (2003). Genetic control of developmental changes induced by disruption of Arabidopsis histone deacetylase 1 (AtHD1) expression. Genetics 165: 399–409.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Ting AH, Schuebel KE, Herman JG, Baylin SB . (2005). Short double-stranded RNA induces transcriptional gene silencing in human cancer cells in the absence of DNA methylation. Nat Genet 37: 906–910.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Tran RK, Henikoff JG, Zilberman D, Ditt RF, Jacobsen SE, Henikoff S . (2005). DNA methylation profiling identifies CG methylation clusters in Arabidopsis genes. Curr Biol 15: 154–159.

    CAS  PubMed  Google Scholar 

  • Ueno Y, Ishikawa T, Watanabe K, Terakura S, Iwakawa H, Okada K et al. (2007). Histone deacetylases and ASYMMETRIC LEAVES2 are involved in the establishment of polarity in leaves of Arabidopsis. Plant Cell 19: 445–457.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Varambally S, Dhanasekaran SM, Zhou M, Barrette TR, Kumar-Sinha C, Sanda MG et al. (2002). The polycomb group protein EZH2 is involved in progression of prostate cancer. Nature 419: 624–629.

    CAS  PubMed  Google Scholar 

  • Verdel A, Moazed D . (2005). RNAi-directed assembly of heterochromatin in fission yeast. FEBS Lett 579: 5872–5878.

    CAS  PubMed  Google Scholar 

  • Viré E, Brenner C, Deplus R, Blanchon L, Fraga M, Didelot C et al. (2006). The polycomb group protein EZH2 directly controls DNA methylation. Nature 439: 871–874.

    PubMed  Google Scholar 

  • Wade PA, Gegonne A, Jones PL, Ballestar E, Aubry F, Wolffe AP . (1999). Mi-2 complex couples DNA methylation to chromatin remodelling and histone deacetylation. Nat Genet 23: 62–66.

    CAS  PubMed  Google Scholar 

  • Wassenegger M . (2000). RNA-directed DNA methylation. Plant Mol Biol 43: 203–220.

    CAS  PubMed  Google Scholar 

  • Weinberg MS, Villeneuve LM, Ehsani A, Amarzguioui M, Aagaard L, Chen ZX et al. (2006). The antisense strand of small interfering RNAs directs histone methylation and transcriptional gene silencing in human cells. RNA 12: 256–262.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Widschwendter M, Fiegl H, Egle D, Mueller-Holzner E, Spizzo G, Marth C et al. (2007). Epigenetic stem cell signature in cancer. Nat Genet 39: 157–158.

    CAS  PubMed  Google Scholar 

  • Wu K, Tian L, Malik K, Brown D, Miki B . (2000). Functional analysis of HD2 histone deacetylase homologues in Arabidopsis thaliana. Plant J 22: 19–27.

    CAS  PubMed  Google Scholar 

  • Xie Z, Johansen LK, Gustafson AM, Kasschau KD, Lellis AD, Zilberman D et al. (2004). Genetic and functional diversification of small RNA pathways in plants. PLoS Biol 2: 642–652.

    CAS  Google Scholar 

  • Xu C-R, Liu C, Wang Y-L, Li L-C, Chen W-Q, Xu Z-H et al. (2005). Histone acetylation affects expression of cellular patterning genes in the Arabidopsis root epidermis. Proc Natl Acad Sci USA 102: 14469–14474.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Zemach A, Grafi G . (2007). Methyl-CpG-binding domain proteins in plants: interpreters of DNA methylation. Trends Plant Sci 12: 80–85.

    CAS  PubMed  Google Scholar 

  • Zhang X, Yazaki J, Sundaresan A, Cokus S, Chan SW-L, Chen H et al. (2006). Genome-wide high-resolution mapping and functional analysis of DNA methylation in Arabidopsis. Cell 126: 1189–1201.

    CAS  PubMed  Google Scholar 

  • Zhao Y, Dai X, Blackwell HE, Schreiber SL, Chory J . (2003). SIR1, an upstream component in auxin signaling identified by chemical genetics. Science 301: 1107–1110.

    CAS  PubMed  Google Scholar 

  • Zhou C, Labbe H, Sridha S, Wang L, Tian L, Latoszek-Green M et al. (2004). Expression and function of HD2-type histone deacetylases in Arabidopsis development. Plant J 38: 715–724.

    CAS  PubMed  Google Scholar 

  • Zhou C, Zhang L, Duan J, Miki B, Wu K . (2005). HISTONE DEACETYLASE19 is involved in jasmonic acid and ethylene signaling of pathogen response in Arabidopsis. Plant Cell 17: 1196–1204.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Zilberman D, Cao X, Jacobsen SE . (2003). ARGONAUTE4 control of locus-specific siRNA accumulation and DNA and histone methylation. Science 299: 716–719.

    CAS  PubMed  Google Scholar 

  • Zilberman D, Gehring M, Tran RK, Ballinger T, Henikoff S . (2007). Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. Nat Genet 39: 61–69.

    CAS  PubMed  Google Scholar 

Download references

Acknowledgements

We thank Ortrun Mittelsten Scheid, Dieter Schweizer and two anonymous reviewers for critical comments and Maria Siomos for scientific editing of the manuscript. The authors are grateful to Thomas Jenuwein for donating antibodies specific for H3K9me2 and H3K27me1. Part of the work in the Aufsatz laboratory discussed in this review is supported by the GEN-AU program of the Austrian Ministry for Science and Research (BMWF).

Author information

Authors and Affiliations

  1. Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna, Austria

    W Aufsatz, T Stoiber, B Rakic & K Naumann

Authors
  1. W Aufsatz
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. T Stoiber
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. B Rakic
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. K Naumann
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to W Aufsatz.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Aufsatz, W., Stoiber, T., Rakic, B. et al. Arabidopsis histone deacetylase 6: a green link to RNA silencing. Oncogene 26, 5477–5488 (2007). https://doi.org/10.1038/sj.onc.1210615

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/sj.onc.1210615

Keywords

This article is cited by

Search

Advanced search

Quick links