Skip to main content

Chromosomal Distribution and Functional Interpretation of Epigenetic Histone Marks in Plants

  • Chapter
  • First Online:
Plant Cytogenetics

Part of the book series: Plant Genetics and Genomics: Crops and Models ((PGG,volume 4))

Abstract

Histones, the main protein component of the chromatin, are subjected to several different posttranslational modifications that control the structure and/or function of the chromatin fiber. Together with DNA methylation, these modifications constitute the “epigenetic code.” Here, we survey current knowledge on the nuclear and chromosomal distribution of histone acetylation, phosphorylation, and methylation marks in plants, discuss functional consequences, and point out similarities and differences between nonplant eukaryotes and plants.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 249.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Abbreviations

NORs:

Nucleolar organizing regions

References

  • Aagaard L, Laible G, Selenko P, Schmid M, Dorn R, Schotta G, Kuhfittig S, Wolf A, Lebersorger A, Singh PB, Reuter G, Jenuwein T (1999) Functional mammalian homologues of the Drosophila PEV-modifier Su(var)3-9 encode centromere-associated proteins which complex with the heterochromatin component M31. EMBO J 18:1923–1938

    CAS  PubMed  Google Scholar 

  • Adams RR, Maiato H, Earnshaw WC, Carmena M (2001) Essential roles of Drosophila inner centromere protein (INCENP) and aurora B in histone H3 phosphorylation, metaphase chromosome alignment, kinetochore disjunction, and chromosome segregation. J Cell Biol 153:865–880

    CAS  PubMed  Google Scholar 

  • Adhvaryu KK, Morris SA, Strahl BD, Selker EU (2005) Methylation of histone H3 lysine 36 is required for normal development in Neurospora crassa. Eukaryot Cell 4:1455–1464

    CAS  PubMed  PubMed Central  Google Scholar 

  • Allfrey VG, Faulkner R, Mirsky AE (1964) Acetylation and methylation of histones and their possible role in the regulation of RNA synthesis. Proc Natl Acad Sci USA 51:786–794

    CAS  PubMed  Google Scholar 

  • Allshire RC, Selker EU (2007) Fungal models for epigenetic research: Schizosaccharomyces pombe and Neurospora crassa. In: Allis CD, Jenuwein T, Reinberg D, Caparros M-L (eds) Epigenetics. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, pp 101–125

    Google Scholar 

  • Bannister AJ, Zegerman P, Partridge JF, Miska EA, Thomas JO, Allshire RC, Kouzarides T (2001) Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domain. Nature 410:120–124

    CAS  PubMed  Google Scholar 

  • Bartee L, Malagnac F, Bender J (2001) Arabidopsis cmt3 chromomethylase mutations block non-CG methylation and silencing of an endogenous gene. Genes Dev 15:1753–1758

    CAS  PubMed  Google Scholar 

  • Bedford MT, Richard S (2005) Arginine methylation an emerging regulator of protein function. Mol Cell 18:263–272

    CAS  PubMed  Google Scholar 

  • Belyaev N, Keohane AM, Turner BM (1996) Differential underacetylation of histones H2A, H3 and H4 on the inactive X chromosome in human female cells. Hum. Genet 97:573–578

    CAS  PubMed  Google Scholar 

  • Belyaev ND, Houben A, Baranczewski P, Schubert I (1997) Histone H4 acetylation in plant ­heterochromatin is altered during the cell cycle. Chromosoma 106:193–197

    CAS  PubMed  Google Scholar 

  • Belyaev ND, Houben A, Baranczewski P, Schubert I (1998) The acetylation patterns of histones H3 and H4 along Vicia faba chromosomes are different. Chromosome Res 6:59–63

    CAS  PubMed  Google Scholar 

  • Bergmüller E, Gehrig PM, Gruissem W (2007) Characterization of post-translational modifications of histone H2B-variants isolated from Arabidopsis thaliana. J Proteome Res 6:3655–3668

    PubMed  Google Scholar 

  • Bird A (2002) DNA methylation patterns and epigenetic memory. Genes Dev 16:6–21

    CAS  PubMed  Google Scholar 

  • Bird AW, Yu DY, Pray-Grant MG, Qiu Q, Harmon KE, Megee PC, Grant PA, Smith MM, Christman MF (2002) Acetylation of histone H4 by Esa1 is required for DNA double-strand break repair. Nature 419:411–415

    CAS  PubMed  Google Scholar 

  • Cao X, Jacobsen SE (2002) Locus-specific control of asymmetric and CpNpG methylation by the DRM and CMT3 methyltransferase genes. Proc Natl Acad Sci USA 99 Suppl 4:16491–16498

    CAS  PubMed  Google Scholar 

  • Carchilan M, Delgado M, Ribeiro T, Costa-Nunes P, Caperta A, Morais-Cecílio L, Jones RN, Viegas W, Houben A (2007) Transcriptionally active heterochromatin in rye B chromosomes. Plant Cell 19:1738–1749

    CAS  PubMed  PubMed Central  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 

  • Cheung WL, Briggs SD, Allis CD (2000) Acetylation and chromosomal functions. Curr Opin Cell Biol 12:326–333

    CAS  PubMed  Google Scholar 

  • Cloos PAC, Christensen J, Agger K, Maiolica A, Rappsilber J, Antal T, Hansen KH, Helin K (2006) The putative oncogene GASC1 demethylates tri- and dimethylated lysine 9 on histone H3. Nature 442:307–311

    CAS  PubMed  Google Scholar 

  • Dacwag CS, Ohkawa Y, Pal S, Sif S, Imbalzano AN (2007) The protein arginine methyltransferase Prmt5 is required for myogenesis because it facilitates ATP-dependent chromatin remodeling. Mol Cell Biol 27:384–394

    CAS  PubMed  PubMed Central  Google Scholar 

  • Daujat S, Bauer UM, Shah V, Turner B, Berger S, Kouzarides T (2002) Crosstalk between CARM1 methylation and CBP acetylation on histone H3. Curr Biol 12:2090–2097

    CAS  PubMed  Google Scholar 

  • De Santa F, Totaro MG, Prosperini E, Notarbartolo S, Testa G, Natoli G (2007) The histone H3 lysine-27 demethylase Jmjd3 links inflammation to inhibition of polycomb-mediated gene silencing. Cell 130:1083–1094

    PubMed  Google Scholar 

  • Delattre M, Spierer A, Tonka C-H, Spierer P (2000) The genomic silencing of position-effect variegation in Drosophila melanogaster: interaction between the heterochromatin-associated proteins Su(var)3-7 and HP1. J Cell Sci 113 Pt 23:4253–4261

    CAS  PubMed  Google Scholar 

  • Di Stefano L, Ji J-Y, Moon N-S, Herr A, Dyson N (2007) Mutation of Drosophila Lsd1 disrupts H3-K4 methylation, resulting in tissue-specific defects during development. Curr Biol 17:808–812

    PubMed  PubMed Central  Google Scholar 

  • Döbel P, Schubert I, Rieger R (1978) Distribution of heterochromatin in a reconstructed karyotype of Vicia faba as identified by banding- and DNA-late replication patterns. Chromosoma 69:193–209

    Google Scholar 

  • Ebbs ML, Bartee L, Bender J (2005) H3 lysine 9 methylation is maintained on a transcribed inverted repeat by combined action of SUVH6 and SUVH4 methyltransferases. Mol Cell Biol 25:10507–10515

    CAS  PubMed  PubMed Central  Google Scholar 

  • Ebbs ML, Bender J (2006) Locus-specific control of DNA methylation by the Arabidopsis SUVH5 histone methyltransferase. Plant Cell 18:1166–1176

    CAS  PubMed  PubMed Central  Google Scholar 

  • Ebert A, Schotta G, Lein S, Kubicek S, Krauss V, Jenuwein T, Reuter G (2004) Su(var) genes ­regulate the balance between euchromatin and heterochromatin in Drosophila. Genes Dev 18: 2973–2983

    CAS  PubMed  Google Scholar 

  • Ebert A, Lein S, Schotta G, Reuter G (2006) Histone modification and the control of heterochromatic gene silencing in Drosophila. Chromosome Res 14:377–392

    CAS  PubMed  Google Scholar 

  • Eissenberg JC, Lee MG, Schneider J, Ilvarsonn A, Shiekhattar R, Shilatifard A (2007) The trithorax-group gene in Drosophila little imaginal discs encodes a trimethylated histone H3 Lys4 demethylase. Nat Struct Mol Biol 14:344–346

    CAS  PubMed  Google Scholar 

  • Finnegan EJ, Kovac KA (2000) Plant DNA methyltransferases. Plant Mol Biol 43:189–201

    CAS  PubMed  Google Scholar 

  • Fischle W, Tseng BS, Dormann HL, Ueberheide BM, Garcia BA, Shabanowitz J, Hunt DF, Funabiki H, Allis CD (2005) Regulation of HP1-chromatin binding by histone H3 methylation and phosphorylation. Nature 438:1116–1122

    CAS  PubMed  Google Scholar 

  • Fodor BD, Kubicek S, Yonezawa M, O’Sullivan RJ, Sengupta R, Perez-Burgos L, Opravil S, Mechtler K, Schotta G, Jenuwein T (2006) Jmjd2b antagonizes H3K9 trimethylation at pericentric heterochromatin in mammalian cells. Genes Dev 20:1557–1562

    CAS  PubMed  Google Scholar 

  • Freitag M, Hickey PC, Khlafallah TK, Read ND, Selker EU (2004) HP1 is essential for DNA methylation in Neurospora. Mol Cell 13:427–434

    CAS  PubMed  Google Scholar 

  • Friesner JD, Liu B, Culligan K, Britt AB (2005) Ionizing radiation-dependent gamma-H2AX focus formation requires ataxia telangiectasia mutated and ataxia telangiectasia mutated and Rad3-related. Mol Biol Cell 16:2566–2576

    CAS  PubMed  PubMed Central  Google Scholar 

  • Fuchs J, Jovtchev G, Schubert I (2008) The chromosomal distribution of histone methylation marks in gymnosperms differs from that of angiosperms. Chromosome Res 16:891–898

    CAS  PubMed  Google Scholar 

  • Fuchs J, Pich U, Meister A, Schubert I (1994) Differentiation of field bean heterochromatin by in situ hybridization with a repeated FokI sequence. Chromosome Res 2:25–28

    CAS  PubMed  Google Scholar 

  • Fuchs J, Strehl S, Brandes A, Schweizer D, Schubert I (1998) Molecular-cytogenetic characterization of the Vicia faba genome-heterochromatin differentiation, replication patterns and sequence localization. Chromosome Res 6:219–230

    CAS  PubMed  Google Scholar 

  • Fuchs J, Demidov D, Houben A, Schubert I (2006) Chromosomal histone modification patterns-from conservation to diversity. Trends Plant Sci 11:199–208

    CAS  PubMed  Google Scholar 

  • Gernand D, Demidov D, Houben A (2003) The temporal and spatial pattern of histone H3 phosphorylation at serine 28 and serine 10 is similar in plants but differs between mono- and polycentric chromosomes. Cytogenet Genome Res 101:172–176

    CAS  PubMed  Google Scholar 

  • Goto H, Tomono Y, Ajiro K, Kosako H, Fujita M, Sakurai M, Okawa K, Iwamatsu A, Okigaki T, Takahashi T, Inagaki M (1999) Identification of a novel phosphorylation site on histone H3 coupled with mitotic chromosome condensation. J Biol Chem 274:25543–25549

    CAS  PubMed  Google Scholar 

  • Grewal SIS, Moazed D (2003) Heterochromatin and epigenetic control of gene expression. Science 301:798–802

    CAS  PubMed  Google Scholar 

  • Grunstein M (1997) Histone acetylation in chromatin structure and transcription. Nature 389:349–352

    CAS  PubMed  Google Scholar 

  • Guerra M, Brasileiro-Vidal AC, Arana P, Puertas MJ (2006) Mitotic microtubule development and histone H3 phosphorylation in the holocentric chromosomes of Rhynchospora tenuis (Cyperaceae). Genetica 126:33–41

    CAS  PubMed  Google Scholar 

  • Gurtley LR, Walters RA, Tobey RA (1975) Sequential phosphorylation of histone subfraction in the Chinese hamster cell cycle. J Biol Chem 250:3936–3944

    Google Scholar 

  • Hanson KK, Kelley AC, Bienz M (2005) Loss of Drosophila borealin causes polyploidy, delayed apoptosis and abnormal tissue development. Development 132:4777–4787

    CAS  PubMed  Google Scholar 

  • Heard E (2005) Delving into the diversity of facultative heterochromatin: the epigenetics of the inactive X chromosome. Curr Opin Genet Dev 15:482–489

    CAS  PubMed  Google Scholar 

  • Hendzel MJ, Wei Y, Mancini MA, Van Hooser A, Ranalli T, Brinkley BR, Bazett-Jones DP, Allis CD (1997) Mitosis-specific phosphorylation of histone H3 initiates primarily within pericentromeric heterochromatin during G2 and spreads in an ordered fashion coincident with mitotic chromosome condensation. Chromosoma 106:348–360

    CAS  PubMed  Google Scholar 

  • Hizume K, Yoshimura SH, Kumeta M, Takeyasu K (2007) Structural organization of dynamic chromatin. Subcell Biochem 41:3–28

    PubMed  Google Scholar 

  • Houben A, Belyaev ND, Turner BM, Schubert I (1996) Differential immunostaining of plant chromosomes by antibodies recognizing acetylated histone H4 variants. Chromosome Res 4:191–194

    CAS  PubMed  Google Scholar 

  • Houben A, Wako T, Furushima-Shimogawara R, Presting G, Künzel G, Schubert I, Fukui K (1999) Short communication: the cell cycle dependent phosphorylation of histone H3 is correlated with the condensation of plant mitotic chromosomes. Plant J 18:675–679

    CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • Houben A, Demidov D, Rutten T, Scheidtmann KH (2005) Novel phosphorylation of histone H3 at threonine 11 that temporally correlates with condensation of mitotic and meiotic chromosomes in plant cells. Cytogenet Genome Res 109:148–155

    CAS  PubMed  Google Scholar 

  • Houben A, Demidov D, Caperta AD, Karimi R, Agueci F, Vlasenko L (2007) Phosphorylation of histone H3 in plants-a dynamic affair. Biochim Biophys Acta 1769:308–315

    CAS  PubMed  Google Scholar 

  • Ikura T, Ogryzko VV, Grigoriev M, Groisman R, Wang J, Horikoshi M, Scully R, Qin J, Nakatani Y (2000) Involvement of the TIP60 histone acetylase complex in DNA repair and apoptosis. Cell 102:463–473

    CAS  PubMed  Google Scholar 

  • Jackson JP, Lindroth AM, Cao X, Jacobsen SE (2002) Control of CpNpG DNA methylation by the KRYPTONITE histone H3 methyltransferase. Nature 416:556–560

    CAS  PubMed  Google Scholar 

  • Jackson JP, Johnson L, Jasencakova Z, Zhang X, Perez-Burgos L, Singh PB, Cheng X, Schubert I, Jenuwein T, Jacobsen SE (2004) Dimethylation of histone H3 lysine 9 is a critical mark for DNA methylation and gene silencing in Arabidopsis thaliana. Chromosoma 112:308–315

    CAS  PubMed  Google Scholar 

  • James TC, Elgin SCR (1986) Identification of a nonhistone chromosomal protein associated with heterochromatin in Drosophila melanogaster and its gene. Mol Cell Biol 6:3862–3872

    CAS  PubMed  PubMed Central  Google Scholar 

  • Jasencakova Z, Meister A, Walter J, Turner BM, Schubert I (2000) Histone H4 acetylation of euchromatin and heterochromatin is cell cycle dependent and correlated with replication rather than with transcription. Plant Cell 12:2087–2100

    CAS  PubMed  PubMed Central  Google Scholar 

  • Jasencakova Z, Meister A, Schubert I (2001) Chromatin organization and its relation to replication and histone acetylation during the cell cycle in barley. Chromosoma 110:83–92

    CAS  PubMed  Google Scholar 

  • Jasencakova Z, Soppe WJJ, 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

    CAS  PubMed  Google Scholar 

  • Jenuwein T, Allis CD (2001) Translating the histone code. Science 293:1074–1080

    CAS  PubMed  Google Scholar 

  • Jeppesen P, Mitchell A, Turner B, Perry P (1992) Antibodies to defined histone epitopes reveal variations in chromatin conformation and underacetylation of centric heterochromatin in human metaphase chromosomes. Chromosoma 101:322–332

    CAS  PubMed  Google Scholar 

  • Jeppesen P, Turner BM (1993) The inactive X chromosome in female mammals is distinguished by a lack of histone H4 acetylation, a cytogenetic marker for gene expression. Cell 74:281–289

    CAS  PubMed  Google Scholar 

  • Jia S, Kobayashi R, Grewal SIS (2005) Ubiquitin ligase component Cul4 associates with Clr4 histone methyltransferase to assemble heterochromatin. Nat Cell Biol 7:1007–1013

    CAS  PubMed  Google Scholar 

  • Jiang D, Yang W, He Y, Amasino RM (2007) Arabidopsis relatives of the human lysine specific demethylase1 repress the expression of FWA and FLOWERING LOCUS C and thus promote the floral transition. Plant Cell 19:2975–2987

    CAS  PubMed  PubMed Central  Google Scholar 

  • Johnson LM, Cao X, Jacobsen SE (2002) Interplay between two epigenetic marks. DNA methylation and histone H3 lysine 9 methylation. Curr Biol 12:1360–1367

    CAS  PubMed  Google Scholar 

  • Johnson LM, Mollah S, Garcia BA, Muratore TL, Shabanowitz J, Hunt DF, Jacobsen SE (2004) Mass spectrometry analysis of Arabidopsis histone H3 reveals distinct combinations of post-translational modifications. Nucleic Acids Res 32:6511–6518

    CAS  PubMed  PubMed Central  Google Scholar 

  • Johnson LM, Bostick M, Zhang X, Kraft E, Henderson I, Callis J, Jacobsen SE (2007) The SRA methyl-cytosine-binding domain links DNA and histone methylation. Curr Biol 17:379–384

    CAS  PubMed  PubMed Central  Google Scholar 

  • Kaszás É, Cande WZ (2000) Phosphorylation of histone H3 is correlated with changes in the maintenance of sister chromatid cohesion during meiosis in maize, rather than the condensation of the chromatin. J Cell Sci 113 ( Pt 18):3217–3226

    PubMed  Google Scholar 

  • Kirmizis A, Santos-Rosa H, Penkett CJ, Singer MA, Vermeulen M, Mann M, Bähler J, Green RD, Kouzarides T (2007) Arginine methylation at histone H3R2 controls deposition of H3K4 trimethylation. Nature 449:928–932

    CAS  PubMed  PubMed Central  Google Scholar 

  • Klose RJ, Yamane K, Bae Y, Zhang D, Erdjument-Bromage H, Tempst P, Wong J, Zhang Y (2006) The transcriptional repressor JHDM3A demethylates trimethyl histone H3 lysine 9 and lysine 36. Nature 442:312–316

    CAS  PubMed  Google Scholar 

  • Klose RJ, Yan Q, Tothova Z, Yamane K, Erdjument-Bromage H, Tempst P, Gilliland DG, Zhang Y, Kaelin WG, Jr (2007) The retinoblastoma binding protein RBP2 is an H3K4 demethylase. Cell 128:889–900

    CAS  PubMed  Google Scholar 

  • Kornberg RD (1974) Chromatin structure: a repeating unit of histones and DNA. Science 184:868–871

    CAS  PubMed  Google Scholar 

  • Kornberg RD, Lorch Y (1999) Twenty-five years of the nucleosome, fundamental particle of the eukaryote chromosome. Cell 98:285–294

    CAS  PubMed  Google Scholar 

  • Lachner M, O’Carroll D, Rea S, Mechtler K, Jenuwein T (2001) Methylation of histone H3 lysine 9 creates a binding site for HP1 proteins. Nature 410:116–120

    CAS  PubMed  Google Scholar 

  • Lachner M, Sengupta R, Schotta G, Jenuwein T (2004) Trilogies of histone lysine methylation as epigenetic landmarks of the eukaryotic genome. Cold Spring Harb Symp Quant Biol 69:209–218

    CAS  PubMed  Google Scholar 

  • Lan F, Bayliss PE, Rinn JL, Whetstine JR, Wang JK, Chen S, Iwase S, Alpatov R, Issaeva I, Canaani E, Roberts TM, Chang HY, Shi Y (2007) A histone H3 lysine 27 demethylase regulates animal posterior development. Nature 449:689–694

    CAS  PubMed  Google Scholar 

  • Latham JA, Dent SY (2007) Cross-regulation of histone modifications. Nat Struct Mol Biol 14:1017–1024

    CAS  PubMed  Google Scholar 

  • Lee DY, Hayes JJ, Pruss D, Wolffe AP (1993) A positive role for histone acetylation in transcription factor access to nucleosomal DNA. Cell 72:73–84

    CAS  PubMed  Google Scholar 

  • Lee MG, Villa R, Trojer P, Norman J, Yan K-P, Reinberg D, Croce LD, Shiekhattar R (2007a) Demethylation of H3K27 regulates polycomb recruitment and H2A ubiquitination. Science 318:447–450

    CAS  PubMed  Google Scholar 

  • Lee N, Zhang J, Klose RJ, Erdjument-Bromage H, Tempst P, Jones RS, Zhang Y (2007b) The trithorax-group protein Lid is a histone H3 trimethyl-Lys4 demethylase. Nat Struct Mol Biol 14:341–343

    CAS  PubMed  Google Scholar 

  • Libault M, Tessadori F, Germann S, Snijder B, Fransz P, Gaudin V (2005) The Arabidopsis LHP1 protein is a component of euchromatin. Planta 222:910–925

    CAS  PubMed  Google Scholar 

  • Lindroth AM, Cao X, Jackson JP, Zilberman D, McCallum CM, Henikoff S, Jacobsen SE (2001) Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation. Science 292:2077–2080

    CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • Loidl P (2004) A plant dialect of the histone language. Trends Plant Sci 9:84–90

    CAS  PubMed  Google Scholar 

  • Loury R, Sassone-Corsi P (2004) Analysis of histone phosphorylation: coupling intracellular signaling to chromatin remodeling. Methods Enzymol 377:197–212

    CAS  PubMed  Google Scholar 

  • Luger K, Richmond TJ (1998) The histone tails of the nucleosome. Curr Opin Genet Dev 8:140–146

    CAS  PubMed  Google Scholar 

  • Lusser A, Kölle D, Loidl P (2001) Histone acetylation: lessons from the plant kingdom. Trends Plant Sci 6:59–65

    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

    CAS  PubMed  Google Scholar 

  • Manzanero S, Arana P, Puertas MJ, Houben A (2000) The chromosomal distribution of phosphorylated histone H3 differs between plants and animals at meiosis. Chromosoma 109:308–317

    CAS  PubMed  Google Scholar 

  • Marschner S, Meister A, Blattner FR, Houben A (2007) Evolution and function of B chromosome 45 S rDNA sequences in Brachycome dichromosomatica. Genome 50:638–644

    CAS  PubMed  Google Scholar 

  • Mathieu O, Probst AV, Paszkowski J (2005) Distinct regulation of histone H3 methylation at lysines 27 and 9 by CpG methylation in Arabidopsis. EMBO J 24:2783–2791

    CAS  PubMed  Google Scholar 

  • Mathieu O, Reinders J, Čaikovski M, Smathajitt C, Paszkowski J (2007) Transgenerational stability of the Arabidopsis epigenome is coordinated by CG methylation. Cell 130:851–862

    CAS  PubMed  Google Scholar 

  • McBlane F, Boyes J (2000) Stimulation of V(D)J recombination by histone acetylation. Curr Biol 10:483–486

    CAS  PubMed  Google Scholar 

  • McMurry MT, Krangel MS (2000) A role for histone acetylation in the developmental regulation of VDJ recombination. Science 287:495–458

    CAS  PubMed  Google Scholar 

  • Metzger E, Wissmann M, Yin N, Müller JM, Schneider R, Peters AHFM, Günther T, Buettner R, Schüle R (2005) LSD1 demethylates repressive histone marks to promote androgen-receptor-dependent transcription. Nature 437:436–439

    CAS  PubMed  Google Scholar 

  • Morris SA, Shibata Y, Noma K, Tsukamoto Y, Warren E, Temple B, Grewal SIS, Strahl BD (2005) Histone H3 K36 methylation is associated with transcription elongation in Schizosaccharomyces pombe. Eukaryot Cell 4:1446–1454

    CAS  PubMed  PubMed Central  Google Scholar 

  • Morris SA, Rao B, Garcia BA, Hake SB, Diaz RL, Shabanowitz J, Hunt DF, Allis CD, Lieb JD, Strahl BD (2007) Identification of histone H3 lysine 36 acetylation as a highly conserved histone modification. J Biol Chem 282:7632–7640

    CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • Nakayama J, Rice JC, Strahl BD, Allis CD, Grewal SIS (2001) Role of histone H3 lysine 9 methylation in epigenetic control of heterochromatin assembly. Science 292:110–113

    CAS  PubMed  Google Scholar 

  • Naumann K, Fischer A, Hofmann I, Krauss V, Phalke S, Irmler K, Hause G, Aurich A-C, Dorn R, Jenuwein T, Reuter G (2005) Pivotal role of AtSUVH2 in heterochromatic histone methylation and gene silencing in Arabidopsis. EMBO J 24:1418–1429

    CAS  PubMed  Google Scholar 

  • Noma K, Allis CD, Grewal SIS (2001) Transitions in distinct histone H3 methylation patterns at the heterochromatin domain boundaries. Science 293:1150–1155

    CAS  PubMed  Google Scholar 

  • Nowak SJ, Corces VG (2000) Phosphorylation of histone H3 correlates with transcriptionally active loci. Genes Dev 14:3003–3013

    CAS  PubMed  Google Scholar 

  • Okada T, Endo M, Singh MB, Bhalla PL (2005) Analysis of the histone H3 gene family in Arabidopsis and identification of the male-gamete-specific variant AtMGH3. Plant J 44:557–568

    CAS  PubMed  Google Scholar 

  • Peters AHFM, Kubicek S, Mechtler K, O’Sullivan RJ, Derijck AAHA, Perez-Burgos L, Kohlmaier A, Opravil S, Tachibana M, Shinkai Y, Martens JHA, Jenuwein T (2003) Partitioning and plasticity of repressive histone methylation states in mammalian chromatin. Mol Cell 12:1577–1589

    CAS  PubMed  Google Scholar 

  • Plath K, Fang J, Mlynarczyk-Evans SK, Cao R, Worringer KA, Wang H, de la Cruz CC, Otte AP, Panning B, Zhang Y (2003) Role of histone H3 lysine 27 methylation in X inactivation. Science 300:131–135

    CAS  PubMed  Google Scholar 

  • Polioudaki H, Markaki Y, Kourmouli N, Dialynas G, Theodoropoulos PA, Singh PB, Georgatos SD (2004) Mitotic phosphorylation of histone H3 at threonine 3. FEBS Lett 560:39–44

    CAS  PubMed  Google Scholar 

  • Preuss U, Landsberg G, Scheidtmann KH (2003) Novel mitosis-specific phosphorylation of histone H3 at Thr11 mediated by Dlk/ZIP kinase. Nucleic Acids Res 31:878–885

    CAS  PubMed  PubMed Central  Google Scholar 

  • Prigent C, Dimitrov S (2003) Phosphorylation of serine 10 in histone H3, what for? J Cell Sci 116:3677–3685

    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 SCR (2002) Epigenetic codes for heterochromatin formation and silencing: rounding up the usual suspects. Cell 108:489–500

    CAS  PubMed  Google Scholar 

  • Rossi V, Locatelli S, Varotto S, Donn G, Pirona R, Henderson DA, Hartings H, Motto M (2007) Maize histone deacetylase hda101 is involved in plant development, gene transcription, and sequence-specific modulation of histone modification of genes and repeats. Plant Cell 19:1145–1162

    CAS  PubMed  PubMed Central  Google Scholar 

  • Rudolph T, Yonezawa M, Lein S, Heidrich K, Kubicek S, Schäfer C, Phalke S, Walther M, Schmidt A, Jenuwein T, Reuter G (2007) Heterochromatin formation in Drosophila is initiated through active removal of H3K4 methylation by the LSD1 homolog SU(VAR)3-3. Mol Cell 26:103–115

    CAS  PubMed  Google Scholar 

  • Salvador LM, Park Y, Cottom J, Maizels ET, Jones JCR, Schillace RV, Carr DW, Cheung P, Allis CD, Jameson JL, Hunzicker-Dunn M (2001) Follicle-stimulating hormone stimulates protein kinase A-mediated histone H3 phosphorylation and acetylation leading to select gene activation in ovarian granulosa cells. J Biol Chem 276:40146–40155

    CAS  PubMed  Google Scholar 

  • Sanders SL, Portoso M, Mata J, Bähler J, Allshire RC, Kouzarides T (2004) Methylation of histone H4 lysine 20 controls recruitment of Crb2 to sites of DNA damage. Cell 119:603–614

    CAS  PubMed  Google Scholar 

  • Saze H, Mittelsten Scheid O, Paszkowski J (2003) Maintenance of CpG methylation is essential for epigenetic inheritance during plant gametogenesis. Nat Genet 34:65–69

    CAS  PubMed  Google Scholar 

  • Schotta G, Lachner M, Sarma K, Ebert A, Sengupta R, Reuter G, Reinberg D, Jenuwein T (2004) A silencing pathway to induce H3-K9 and H4-K20 trimethylation at constitutive heterochromatin. Genes Dev 18:1251–1262

    CAS  PubMed  Google Scholar 

  • Secombe J, Li L, Carlos L, Eisenman RN (2007) The Trithorax group protein Lid is a trimethyl histone H3K4 demethylase required for dMyc-induced cell growth. Genes Dev 21:537–551

    CAS  PubMed  Google Scholar 

  • Shi J, Dawe RK (2006) Partitioning of the maize epigenome by the number of methyl groups on histone H3 lysines 9 and 27. Genetics 173:1571–1583

    CAS  PubMed  Google Scholar 

  • Shi Y-J, Matson C, Lan F, Iwase S, Baba T, Shi Y (2005) Regulation of LSD1 histone demethylase activity by its associated factors. Mol Cell 19:857–864

    CAS  PubMed  Google Scholar 

  • Shi Y, Lan F, Matson C, Mulligan P, Whetstine JR, Cole PA, Casero RA, Shi Y (2004) Histone demethylation mediated by the nuclear amine oxidase homolog LSD1. Cell 119:941–953

    CAS  PubMed  Google Scholar 

  • Silva J, Mak W, Zvetkova I, Appanah R, Nesterova TB, Webster Z, Peters AHFM, Jenuwein T, Otte AP, Brockdorff N (2003) Establishment of histone h3 methylation on the inactive X chromosome requires transient recruitment of Eed-Enx1 polycomb group complexes. Dev Cell 4:481–495

    CAS  PubMed  Google Scholar 

  • Siroky J, Castiglione MR, Vyskot B (1998) DNA methylation patterns of Melandrium album chromosomes. Chromosome Res 6:441–446

    CAS  PubMed  Google Scholar 

  • Soppe WJJ, 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

    CAS  PubMed  Google Scholar 

  • Sridhar VV, Kapoor A, Zhang K, Zhu J, Zhou T, Hasegawa PM, Bressan RA, Zhu J-K (2007) Control of DNA methylation and heterochromatic silencing by histone H2B deubiquitination. Nature 447:735–738

    CAS  PubMed  Google Scholar 

  • Strahl BD, Allis CD (2000) The language of covalent histone modifications. Nature 403:41–45

    CAS  PubMed  Google Scholar 

  • Sun Z-W, Allis CD (2002) Ubiquitination of histone H2B regulates H3 methylation and gene silencing in yeast. Nature 418:104–108

    CAS  PubMed  Google Scholar 

  • Taddei A, Roche D, Sibarita J-B, Turner BM, Almouzni G (1999) Duplication and maintenance of heterochromatin domains. J Cell Biol 147:1153–1166

    CAS  PubMed  Google Scholar 

  • Tamaru H, Selker EU (2001) A histone H3 methyltransferase controls DNA methylation in Neurospora crassa. Nature 414:277–283

    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

    CAS  PubMed  Google Scholar 

  • Tariq M, Saze H, Probst AV, Lichota J, Habu Y, Paszkowski J (2003) Erasure of CpG methylation in Arabidopsis alters patterns of histone H3 methylation in heterochromatin. Proc Natl Acad Sci USA 100:8823–8827

    CAS  PubMed  Google Scholar 

  • Thiriet C, Hayes JJ (2005) Chromatin in need of a fix: phosphorylation of H2AX connects chromatin to DNA repair. Mol Cell 18:617–622

    CAS  PubMed  Google Scholar 

  • Tsukada Y, Fang J, Erdjument-Bromage H, Warren ME, Borchers CH, Tempst P, Zhang Y (2006) Histone demethylation by a family of JmjC domain-containing proteins. Nature 439:811–816

    CAS  PubMed  Google Scholar 

  • Turck F, Roudier F, Farrona S, Martin-Magniette M-L, Guillaume E, Buisine N, Gagnot S, Martienssen RA, Coupland G, Colot V (2007) Arabidopsis TFL2/LHP1 specifically associates with genes marked by trimethylation of histone H3 lysine 27. PLoS Genet 3:e86

    PubMed  PubMed Central  Google Scholar 

  • Turner BM, Birley AJ, Lavender J (1992) Histone H4 isoforms acetylated at specific lysine residues define individual chromosomes and chromatin domains in Drosophila polytene nuclei. Cell 69:375–384

    CAS  PubMed  Google Scholar 

  • Turner BM (2000) Histone acetylation and an epigenetic code. BioEssays 22:836–845

    CAS  PubMed  Google Scholar 

  • Vongs A, Kakutani T, Martienssen RA, Richards EJ (1993) Arabidopsis thaliana DNA methylation mutants. Science 260:1926–1928

    CAS  PubMed  Google Scholar 

  • Vyskot B, Araya A, Veuskens J, Negrutiu I, Mouras A (1993) DNA methylation of sex chromosomes in a dioecious plant, Melandrium album. Mol Gen Genet 239:219–224

    CAS  PubMed  Google Scholar 

  • Vyskot B, Siroky J, Hladilova R, Belyaev ND, Turner BM (1999) Euchromatic domains in plant chromosomes as revealed by H4 histone acetylation and early DNA replication. Genome 42:343–350

    CAS  PubMed  Google Scholar 

  • Wade PA, Pruss D, Wolffe AP (1997) Histone acetylation: chromatin in action. Trends Biochem Sci 22:128–132

    CAS  PubMed  Google Scholar 

  • Wang X, Zhang Y, Ma Q, Zhang Z, Xue Y, Bao S, Chong K (2007) SKB1-mediated symmetric dimethylation of histone H4R3 controls flowering time in Arabidopsis. EMBO J 26:1934–1941

    CAS  PubMed  Google Scholar 

  • Whetstine JR, Nottke A, Lan F, Huarte M, Smolikov S, Chen Z, Spooner E, Li E, Zhang G, Colaiacovo M, Shi Y (2006) Reversal of histone lysine trimethylation by the JMJD2 family of histone demethylases. Cell 125:467–481

    CAS  PubMed  Google Scholar 

  • Wilkinson CRM, Bartlett R, Nurse P, Bird AP (1995) The fission yeast gene pmt1+ encodes a DNA methyltransferase homologue. Nucleic Acids Res 23:203–210

    CAS  PubMed  PubMed Central  Google Scholar 

  • Xiang Y, Zhu Z, Han G, Lin H, Xu L, Chen CD (2007) JMJD3 is a histone H3K27 demethylase. Cell Res 17:850–857

    CAS  PubMed  Google Scholar 

  • Yamada T, Fischle W, Sugiyama T, Allis CD, Grewal SIS (2005) The nucleation and maintenance of heterochromatin by a histone deacetylase in fission yeast. Mol Cell 20:173–185

    CAS  PubMed  Google Scholar 

  • Yamane K, Toumazou C, Tsukada Y, Erdjument-Bromage H, Tempst P, Wong J, Zhang Y (2006) JHDM2A, a JmjC-containing H3K9 demethylase, facilitates transcription activation by androgen receptor. Cell 125:483–495

    CAS  PubMed  Google Scholar 

  • Zhang X, Li X, Marshall JB, Zhong CX, Dawe RK (2005) Phosphoserines on maize CENTROMERIC HISTONE H3 and histone H3 demarcate the centromere and pericentromere during chromosome segregation. Plant Cell 17:572–583

    CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang X, Clarenz O, Cokus S, Bernatavichute YV, Pellegrini M, Goodrich J, Jacobsen SE (2007a) Whole-genome analysis of histone H3 lysine 27 trimethylation in Arabidopsis. PLoS Biol 5:e129

    PubMed  PubMed Central  Google Scholar 

  • Zhang X, Germann S, Blus BJ, Khorasanizadeh S, Gaudin V, Jacobsen SE (2007b) The Arabidopsis LHP1 protein colocalizes with histone H3 Lys27 trimethylation. Nat Struct Mol Biol 14:869–871

    CAS  PubMed  Google Scholar 

  • Zhu P, Zhou W, Wang J, Puc J, Ohgi KA, Erdjument-Bromage H, Tempst P, Glass CK, Rosenfeld MG (2007) A histone H2A deubiquitinase complex coordinating histone acetylation and H1 dissociation in transcriptional regulation. Mol Cell 27:609–621

    CAS  PubMed  PubMed Central  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

Acknowledgments

This work was supported by a grant of the Land Sachsen-Anhalt to J.F. and I.S.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Jörg Fuchs .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2012 Springer Science+Business Media, LLC

About this chapter

Cite this chapter

Fuchs, J., Schubert, I. (2012). Chromosomal Distribution and Functional Interpretation of Epigenetic Histone Marks in Plants. In: Bass, H., Birchler, J. (eds) Plant Cytogenetics. Plant Genetics and Genomics: Crops and Models, vol 4. Springer, New York, NY. https://doi.org/10.1007/978-0-387-70869-0_9

Download citation

Publish with us

Policies and ethics