Dimethylation of histone H3 lysine 9 is a critical mark for DNA methylation and gene silencing in Arabidopsis thaliana (original) (raw)

Abstract

The Arabidopsis KRYPTONITE gene encodes a member of the Su(var)3-9 family of histone methyltransferases. Mutations of kryptonite cause a reduction of methylated histone H3 lysine 9, a loss of DNA methylation, and reduced gene silencing. Lysine residues of histones can be either monomethylated, dimethylated or trimethylated and recent evidence suggests that different methylation states are found in different chromatin domains. Here we show that bulk Arabidopsis histones contain high levels of monomethylated and dimethylated, but not trimethylated histone H3 lysine 9. Using both immunostaining of nuclei and chromatin immunoprecipitation assays, we show that monomethyl and dimethyl histone H3 lysine 9 are concentrated in heterochromatin. In kryptonite mutants, dimethyl histone H3 lysine 9 is nearly completely lost, but monomethyl histone H3 lysine 9 levels are only slightly reduced. Recombinant KRYPTONITE can add one or two, but not three, methyl groups to the lysine 9 position of histone H3. Further, we identify a KRYPTONITE-related protein, SUVH6, which displays histone H3 lysine 9 methylation activity with a spectrum similar to that of KRYPTONITE. Our results suggest that multiple Su(var)3-9 family members are active in Arabidopsis and that dimethylation of histone H3 lysine 9 is the critical mark for gene silencing and DNA methylation.

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References

• Baumbusch LO, Thorstensen T, Krauss V, Fischer A, Naumann K, Assalkhou R, Schulz I, Reuter G, Aalen RB (2001) The Arabidopsis thaliana genome contains at least 29 active genes encoding SET domain proteins that can be assigned to four evolutionarily conserved classes. Nucleic Acids Res 29:4319–4333
  Article CAS PubMed Google Scholar
• Cowell IG, Aucott R, Mahadevaiah SK, Burgoyne PS, Huskisson N, Bongiorni S, Prantera G, Fanti L, Pimpinelli S, Wu R et al (2002) Heterochromatin, HP1 and methylation at lysine 9 of histone H3 in animals. Chromosoma 111:22–36
  Article CAS PubMed Google Scholar
• Dutnall RN (2003) Cracking the histone code: one, two, three methyls, you’re out! Mol Cell 12:3–4
• Jackson JP, Lindroth AM, Cao X, Jacobsen SE (2002) Control of CpNpG DNA methylation by the KRYPTONITE histone H3 methyltransferase. Nature 416:556–560
  PubMed Google Scholar
• Jasencakova Z, Soppe WJ, Meister A, Gernand D, Turner BM, Schubert I (2003) Histone modifications in Arabidopsis—high methylation of H3 lysine 9 is dispensable for constitutive heterochromatin. Plant J 33:471–480
  Article CAS PubMed Google Scholar
• Jenuwein T, Allis CD (2001) Translating the histone code. Science 293:1074–1080
  CAS PubMed Google Scholar
• Johnson L, Cao X, Jacobsen S (2002) Interplay between two epigenetic marks. DNA methylation and histone H3 lysine 9 methylation. Curr Biol 12:1360–1367
  Article CAS PubMed Google Scholar
• Krogan NJ, Dover J, Wood A, Schneider J, Heidt J, Boateng MA, Dean K, Ryan OW, Golshani A, Johnston M et al (2003) The Paf1 complex is required for histone H3 methylation by COMPASS and Dot1p: linking transcriptional elongation to histone methylation. Mol Cell 11:721–729
  CAS PubMed Google Scholar
• Malagnac F, Bartee L, Bender J (2002) An Arabidopsis SET domain protein required for maintenance but not establishment of DNA methylation. EMBO J 21:6842–6852
  Article CAS PubMed Google Scholar
• Martienssen RA, Colot V (2001) DNA methylation and epigenetic inheritance in plants and filamentous fungi. Science 293:1070–1074
  Article CAS PubMed Google Scholar
• Nakayama J, Rice JC, Strahl BD, Allis CD, Grewal SI (2001) Role of histone H3 lysine 9 methylation in epigenetic control of heterochromatin assembly. Science 292:110–113
  CAS PubMed Google Scholar
• Ng HH, Robert F, Young RA, Struhl K (2003) Targeted recruitment of Set1 histone methylase by elongating Pol II provides a localized mark and memory of recent transcriptional activity. Mol Cell 11:709–719
  CAS PubMed Google Scholar
• Peters AH, Kubicek S, Mechtler K, O’Sullivan RJ, Derijck AA, Perez-Burgos L, Kohlmaier A, Opravil S, Tachibana M, Shinkai Y et al (2003) Partitioning and plasticity of repressive histone methylation states in mammalian chromatin. Mol Cell 12:1577–1589
  CAS PubMed Google Scholar
• Rea S, Eisenhaber F, O’Carroll D, Strahl BD, Sun ZW, Schmid M, Opravil S, Mechtler K, Ponting CP, Allis CD, Jenuwein T (2000) Regulation of chromatin structure by site-specific histone H3 methyltransferases. Nature 406:593–599
  CAS PubMed Google Scholar
• Rice JC, Briggs SD, Ueberheide B, Barber CM, Shabanowitz J, Hunt DF, Shinkai Y, Allis CD (2003) Histone methyltransferases direct different degrees of methylation to define distinct chromatin domains. Mol Cell 12:1591–1598
  CAS PubMed Google Scholar
• Richards EJ, Elgin SC (2002) Epigenetic codes for heterochromatin formation and silencing: rounding up the usual suspects. Cell 108:489–500
  CAS PubMed Google Scholar
• Santos-Rosa H, Schneider R, Bannister AJ, Sherriff J, Bernstein BE, Emre NC, Schreiber SL, Mellor J, Kouzarides T (2002) Active genes are tri-methylated at K4 of histone H3. Nature 419:407–411
  Article CAS PubMed Google Scholar
• Soppe WJ, Jasencakova Z, Houben A, Kakutani T, Meister A, Huang MS, Jacobsen SE, Schubert I, Fransz PF (2002) DNA methylation controls histone H3 lysine 9 methylation and heterochromatin assembly in Arabidopsis. EMBO J 21:6549–6559
  Article CAS PubMed Google Scholar
• Strahl BD, Allis CD (2000) The language of covalent histone modifications. Nature 403:41–45
  CAS PubMed Google Scholar
• Tachibana M, Sugimoto K, Fukushima T, Shinkai Y (2001) Set domain-containing protein, G9a, is a novel lysine-preferring mammalian histone methyltransferase with hyperactivity and specific selectivity to lysines 9 and 27 of histone H3. J Biol Chem 276:25309–25317
  Article CAS PubMed Google Scholar
• Tachibana M, Sugimoto K, Nozaki M, Ueda J, Ohta T, Ohki M, Fukuda M, Takeda N, Niida H, Kato H, Shinkai Y (2002) G9a histone methyltransferase plays a dominant role in euchromatic histone H3 lysine 9 methylation and is essential for early embryogenesis. Genes Dev 16:1779–1791
  Article CAS PubMed Google Scholar
• Tamaru H, Selker EU (2001) A histone H3 methyltransferase controls DNA methylation in Neurospora crassa. Nature 414:277–283
  Article CAS PubMed Google Scholar
• Tamaru H, Zhang X, McMillen D, Singh PB, Nakayama J, Grewal SI, Allis CD, Cheng X, Selker EU (2003) Trimethylated lysine 9 of histone H3 is a mark for DNA methylation in Neurospora crassa. Nat Genet 34:75–79
  Article CAS PubMed Google Scholar
• Tschiersch B, Hofmann A, Krauss V, Dorn R, Korge G, Reuter G (1994) The protein encoded by the Drosophila position-effect variegation suppressor gene Su(var)3-9 combines domains of antagonistic regulators of homeotic gene complexes. EMBO J 13:3822–3831
  CAS PubMed Google Scholar
• Turner BM (2000) Histone acetylation and an epigenetic code. Bioessays 22:836–845
  CAS PubMed Google Scholar
• Turner BM (2002) Cellular memory and the histone code. Cell 111:285–291
  CAS PubMed Google Scholar
• Wang H, An W, Cao R, Xia L, Erdjument-Bromage H, Chatton B, Tempst P, Roeder RG, Zhang Y (2003) mAM facilitates conversion by ESET of dimethyl to trimethyl lysine 9 of histone H3 to cause transcriptional repression. Mol Cell 12:475–487
  CAS PubMed Google Scholar
• Waterborg JH (1990) Sequence analysis of acetylation and methylation in two histone H3 variants of alfalfa. J Biol Chem 265:17157–17161
  CAS PubMed Google Scholar
• Ying Z, Mulligan RM, Janney N, Houtz RL (1999) Rubisco small and large subunit _N_-methyltransferases. Bi- and mono-functional methyltransferases that methylate the small and large subunits of Rubisco. J Biol Chem 274:36750–36756
  Article CAS PubMed Google Scholar
• Zhang X, Yang Z, Khan SI, Horton JR, Tamaru H, Selker EU, Cheng X (2003) Structural basis for the product specificity of histone lysine methyltransferases. Mol Cell 12:177–185
  CAS PubMed Google Scholar

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Acknowledgments

We thank L. Cahoon, E. Huang, J. Bruder, and C. Hyun for technical assistance, A. Meister for flow-sorting of nuclei, E. Selker and H. Tamaru for providing the GST-DIM5 fusion construct, and members of the Jacobsen laboratory for discussions and critical review of the manuscript. This work was supported by NIH grant GM60398 (S.E.J.), NIH training grant GM07104 (J.P.J.), grants from the Land Sachsen-Anhalt (3233A/0020L) and DFG (Schu 951/8-2) (Z.J. and I.S.), and NIH grants GM49245 and GM61355 (X.Z. and X.C.).

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Authors and Affiliations

1. Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, 90095, USA
   James P. Jackson, Lianna Johnson & Steven E. Jacobsen
2. Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK), 06466, Gatersleben, Germany
   Zuzana Jasencakova & Ingo Schubert
3. Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
   Xing Zhang & Xiaodong Cheng
4. Research Institute of Molecular Pathology (IMP) at the Vienna Biocenter, Dr. Bohrgasse 7, 1030, Vienna, Austria
   Laura PerezBurgos & Thomas Jenuwein
5. Nuclear Reprogramming Laboratory, Division of Gene Expression and Development, The Roslin Institute, Edinburgh, Midlothian, EH25 9PS, UK
   Prim B. Singh
6. Molecular Biology Institute, University of California, P.O. Box 951606, Los Angeles, CA 90095-1606, USA
   Steven E. Jacobsen

Authors

1. James P. Jackson
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2. Lianna Johnson
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3. Zuzana Jasencakova
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4. Xing Zhang
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5. Laura PerezBurgos
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6. Prim B. Singh
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7. Xiaodong Cheng
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8. Ingo Schubert
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9. Thomas Jenuwein
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10. Steven E. Jacobsen
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Correspondence toSteven E. Jacobsen.

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Communicated by P. Shaw

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Jackson, J.P., Johnson, L., Jasencakova, Z. et al. Dimethylation of histone H3 lysine 9 is a critical mark for DNA methylation and gene silencing in Arabidopsis thaliana .Chromosoma 112, 308–315 (2004). https://doi.org/10.1007/s00412-004-0275-7

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• Received: 02 January 2004
• Accepted: 17 February 2004
• Published: 10 March 2004
• Issue Date: March 2004
• DOI: https://doi.org/10.1007/s00412-004-0275-7

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