Skip to main content
SpringerLink
Log in

Molecular Mechanisms in Epigenetic Regulation of Plant Growth and Development

  • Chapter
  • First Online:
Plant Developmental Biology - Biotechnological Perspectives

Abstract

The extraordinary flexibility and plasticity of growth and development play a fundamental role in plant adaptation to environmental changes. Reversible epigenetic changes at the level of histone covalent modifications (e.g. methylation, acetylation and ubiquitylation), DNA methylation and ATP-dependent chromatin remodelling can rapidly establish a differential pattern of genome expression that can be stably maintained through cell divisions. During the past few years, there has been an exponential increase in the number of genes that have been characterized and shown to function according to different epigenetic mechanisms, particularly in the model plant Arabidopsis thaliana. Diverse biological processes including flowering time control, seed development, cell fate maintenance and plant responses to environmental factors were shown to be regulated by epigenetic mechanisms.

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

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 169.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 219.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 219.99
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

References

  • Aida M, Beis D, Heidstra R, Willemsen V, Blilou I, Galinha C, Nussaume L, Noh YS, Amasino R, Scheres B (2004) The PLETHORA genes mediate patterning of the Arabidopsis root stem cell niche. Cell 119:109–120

    Article  PubMed  CAS  Google Scholar 

  • Alvarez-Venegas R, Pien S, Sadder M, Witmer X, Grossniklaus U, Avramova Z (2003) ATX-1, an Arabidopsis homolog of trithorax, activates flower homeotic genes. Curr Biol 13:627–637

    Article  PubMed  CAS  Google Scholar 

  • Bastow R, Mylne JS, Lister C, Lippman Z, Martienssen RA, Dean C (2004) Vernalization requires epigenetic silencing of FLC by histone methylation. Nature 427:164–167

    Article  PubMed  CAS  Google Scholar 

  • Bäurle I, Dean C (2006) The timing of developmental transitions in plants. Cell 125:655–664

    Article  PubMed  CAS  Google Scholar 

  • Bharti K, Von Koskull-Döring P, Bharti S, Kumar P, Tintschl-Körbitzer A, Treuter E, Nover L (2004) Tomato heat stress transcription factor HsfB1 represents a novel type of general transcription coactivator with a histone-like motif interacting with the plant CREB binding protein ortholog HAC1. Plant Cell 16:1521–1535

    Article  PubMed  CAS  Google Scholar 

  • Byrne ME, Barley R, Curtis M, Arroyo JM, Dunham M, Hudson A, Martienssen RA (2000) ASYMMETRIC LEAVES1 mediates leaf patterning and stem cell function in Arabidopsis. Nature 408:967–971

    Article  PubMed  CAS  Google Scholar 

  • Choi K, Kim S, Kim SY, Kim M, Hyun Y, Lee H, Choe S, Kim SG, Michaels S, Lee I (2005) SUPPRESSOR OF FRIGIDA3 encodes a nuclear ACTIN-RELATED PROTEIN6 required for floral repression in Arabidopsis. Plant Cell 17:2647–2660

    Article  PubMed  CAS  Google Scholar 

  • Choi K, Park C, Lee J, Oh M, Noh B, Lee I (2007) Arabidopsis homologs of components of the SWR1 complex regulate flowering and plant development. Development 134:1931–1941

    Article  PubMed  CAS  Google Scholar 

  • Costa S, Shaw P (2006) Chromatin organization and cell fate switch respond to positional information in Arabidopsis. Nature 439:493–496

    Article  PubMed  CAS  Google Scholar 

  • Deal RB, Kandasamy MK, McKinney EC, Meagher RB (2005) The nuclear actin-related protein ARP6 is a pleiotropic developmental regulator required for the maintenance of FLOWERING LOCUS C expression and repression of flowering in Arabidopsis. Plant Cell 17:2633–2646

    Article  PubMed  CAS  Google Scholar 

  • Deng W, Liu C, Pei Y, Deng X, Niu L, Cao X (2007) Involvement of the histone acetyltransferase AtHAC1 in the regulation of flowering time via repression of FLOWERING LOCUS C in Arabidopsis. Plant Physiol 143:1660–1668

    Article  PubMed  CAS  Google Scholar 

  • Devoto A, Nieto-Rostro M, Xie D, Ellis C, Harmston R, Patrick E, Davis J, Sherratt L, Coleman M, Turner JG (2002) COI1 links jasmonate signalling and fertility to the SCF ubiquitin-ligase complex in Arabidopsis. Plant J 32:457–466

    Article  PubMed  CAS  Google Scholar 

  • Di Laurenzio L, Wysocka-Diller J, Malamy JE, Pysh L, Helariutta Y, Freshour G, Hahn MG, Feldmann KA, Benfey PN (1996) The SCARECROW gene regulates an asymmetric cell division that is essential for generating the radial organization of the Arabidopsis root. Cell 86:423–433

    Article  PubMed  CAS  Google Scholar 

  • Farrona S, Hurtado L, Bowman JL, Reyes JC (2004) The Arabidopsis thaliana SNF2 homolog AtBRM controls shoot development and flowering. Development 131:4965–4975

    Article  PubMed  CAS  Google Scholar 

  • Fleury D, Himanen K, Cnops G, Nelissen H, Boccardi TM, Maere S, Beemster GT, Neyt P, Anami S, Robles P, Micol JL, Inzé D, Van Lijsebettens M (2007) The Arabidopsis thaliana homolog of yeast BRE1 has a function in cell cycle regulation during early leaf and root growth. Plant Cell 19:417–432

    Article  PubMed  CAS  Google Scholar 

  • Fu W, Wu K, Duan J (2007) Sequence and expression analysis of histone deacetylases in rice. Biochem Biophys Res Comm 356:843–850

    Article  PubMed  CAS  Google Scholar 

  • Gehring M, Huh JH, Hsieh TF, Penterman J, Choi Y, Harada JJ, Goldberg RB, Fischer RL (2006) DEMETER DNA glycosylase establishes MEDEA Polycomb gene self-imprinting by allele-specific demethylation. Cell 124:495–506

    Article  PubMed  CAS  Google Scholar 

  • Gendall AR, Levy YY, Wilson A, Dean C (2001) The VERNALIZATION 2 gene mediates the epigenetic regulation of vernalization in Arabidopsis. Cell 107:525–535

    Article  PubMed  CAS  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • Greb T, Mylne JS, Crevillen P, Geraldo N, An H, Gendall AR, Dean C (2007) The PHD finger protein VRN5 functions in the epigenetic silencing of Arabidopsis. Curr Biol 17:73–78

    Article  PubMed  CAS  Google Scholar 

  • Guo M, Rupe MA, Danilevskaya ON, Yan X, Hu Z (2003) Genome-wide mRNA profiling reveals heterochronic allelic variation and a new imprinted gene in hybrid maize endosperm. Plant J 36:30–44

    Article  PubMed  CAS  Google Scholar 

  • Guo M, Thomas J, Collins G, Timmermans MC (2008) Direct repression of KNOX loci by the ASYMMETRIC LEAVES1 complex of Arabidopsis. Plant Cell 20:48–58

    Article  PubMed  CAS  Google Scholar 

  • Gutierrez-Marcos JF, Costa LM, Biderre-Petit C, Khbaya B, O’Sullivan DM, Wormald M, Perez P, Dickinson HG (2004) Amaternally expressed gene1 is a novel maize endosperm transfer cell specific gene with a maternal parent-of-origin pattern of expression. Plant Cell 16:1288–1301

    Article  PubMed  CAS  Google Scholar 

  • Gutierrez-Marcos JF, Costa LM, Dal Pra M, Scholten S, Kranz E, Perez P, Dickinson HG (2006) Epigenetic asymmetry of imprinted genes in plant gametes. Nature Genet 38:876–878

    Article  PubMed  CAS  Google Scholar 

  • Hamilton A, Voinnet O, Chappell L, Baulcombe D (2002) Two classes of short interfering RNA in RNA silencing. EMBO J 21:4671–4679

    Article  PubMed  CAS  Google Scholar 

  • Han SK, Song JD, Noh YS, Noh B (2007) Role of plant CBP/p300-like genes in the regulation of flowering time. Plant J 49:103–114

    Article  PubMed  CAS  Google Scholar 

  • Haun WJ, Laoueille-Duprat S, O’Connell MJ, Spillane C, Grossniklaus U, Phillips AR, Kaeppler SM, Springer NM (2007) Genomic imprinting, methylation and molecular evolution of maize enhancer of zeste (Mez) homologs. Plant J 49:325–337

    Article  PubMed  CAS  Google Scholar 

  • He Y, Doyle MR, Amasino RM (2004) PAF1-complex-mediated histone methylation of FLOWERING LOCUS C chromatin is required for the vernalization-responsive, winter-annual habit in Arabidopsis. Genes Dev 18:2774–2784

    Article  PubMed  CAS  Google Scholar 

  • Hermon P, Srilunchang KO, Zou J, Dresselhaus T, Danilevskaya ON (2007) Activation of the imprinted Polycomb Group Fie1 gene in maize endosperm requires demethylation of the maternal allele. Plant Mol Biol 64:387–395

    Article  PubMed  CAS  Google Scholar 

  • Horsthemke B, Buiting K (2008) Genomic imprinting and imprinting defects in humans. Adv Genet 61:225–246

    Article  PubMed  CAS  Google Scholar 

  • Huang L, Sun Q, Qin F, Li C, Zhao Y, Zhou DX (2007) Down-regulation of a SILENT INFORMATION REGULATOR2-related histone deacetylase gene, OsSRT1, induces DNA fragmentation and cell death in rice. Plant Physiol 144:1508–1519

    Article  PubMed  CAS  Google Scholar 

  • Huh JH, Bauer MJ, Hsieh TF, Fischer RL (2008) Cellular programming of plant gene imprinting. Cell 132:735–744

    Article  PubMed  CAS  Google Scholar 

  • Jullien PE, Katz A, Oliva M, Ohad N, Berger F (2006a) Polycomb group complexes self-regulate imprinting of the Polycomb group gene MEDEA in Arabidopsis. Curr Biol 16:486–492

    Article  PubMed  CAS  Google Scholar 

  • Jullien PE, Kinoshita T, Ohad N, Berger F (2006b) Maintenance of DNA methylation during the Arabidopsis life cycle is essential for parental imprinting. Plant Cell 18:1360–1372

    Article  PubMed  CAS  Google Scholar 

  • Kamakaka RT, Biggins S (2005) Histone variants: deviants? Genes Dev 19:295–316

    Article  PubMed  CAS  Google Scholar 

  • Kandasamy MK, Deal RB, McKinney EC, Meagher RB (2005) Silencing the nuclear actin-related protein AtARP4 in Arabidopsis has multiple effects on plant development, including early flowering and delayed floral senescence. Plant J 41:845–858

    Article  PubMed  CAS  Google Scholar 

  • Kaya H, Shibahara KI, Taoka KI, Iwabuchi M, Stillman B, Araki T (2001) FASCIATA genes for chromatin assembly factor-1 in Arabidopsis maintain the cellular organization of apical meristems. Cell 104:131–142

    Article  PubMed  CAS  Google Scholar 

  • Kim HJ, Hyun Y, Park JY, Park MJ, Park MK, Kim MD, Kim HJ, Lee MH, Moon J, Lee I, Kim J (2004) A genetic link between cold responses and flowering time through FVE in Arabidopsis thaliana. Nature Genet 36:167–171

    Article  PubMed  CAS  Google Scholar 

  • Kim SY, He Y, Jacob Y, Noh YS, Michaels S, Amasino R (2005) Establishment of the vernalization-responsive, winter-annual habit in Arabidopsis requires a putative histone H3 methyl transferase. Plant Cell 17:3301–3310

    Article  PubMed  CAS  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • Kinoshita Y, Saze H, Kinoshita T, Miura A, Soppe WJ, Koornneef M, Kakutani T (2007) Control of FWA gene silencing in Arabidopsis thaliana by SINE-related direct repeats. Plant J 49:38–45

    Article  PubMed  CAS  Google Scholar 

  • Klymenko T, Papp B, Fischle W, Köcher T, M. Schelder M, Fritsch C, Wild B, Wilm M, Müller J (2006) A Polycomb group protein complex with sequence-specific DNA-binding and selective methyl-lysine-binding activities. Genes Dev 20:1110–1122

    CAS  Google Scholar 

  • Köhler C, Hennig L, Spillane C, Pien S, Gruissem W, Grossniklaus U (2003) The Polycomb-group protein MEDEA regulates seed development by controlling expression of the MADS-box gene PHERES1. Genes Dev 17:1540–1553

    Article  PubMed  CAS  Google Scholar 

  • Köhler C, Page DR, Gagliardini V, Grossniklaus U (2005) The Arabidopsis thaliana MEDEA Polycomb group protein controls expression of PHERES1 by parental imprinting. Nature Genet 37:28–30

    PubMed  Google Scholar 

  • Kwon CS, Chen C, Wagner D (2005) WUSCHEL is a primary target for transcriptional regulation by SPLAYED in dynamic control of stem cell fate in Arabidopsis. Genes Dev 19:992–1003

    Article  PubMed  CAS  Google Scholar 

  • Lázaro A, Gómez-Zambrano A, López-González L, Piñeiro M, Jarillo JA (2008) Mutations in the Arabidopsis SWC6 gene, encoding a component of the SWR1 chromatin remodelling complex, accelerate flowering time and alter leaf and flower development. J Exp Bot 59:653–666

    Article  PubMed  CAS  Google Scholar 

  • Lee B, Henderson DA, Zhu JK (2005) The Arabidopsis cold-responsive transcriptome and its regulation by ICE1. Plant Cell 17:3155–3175

    Article  PubMed  CAS  Google Scholar 

  • Levy YY, Mesnage S, Mylne JS, Gendall AR, Dean C (2002) Multiple roles of Arabidopsis VRN1 in vernalization and flowering time control. Science 297:243–246

    Article  PubMed  CAS  Google Scholar 

  • Li H, He Z, Lu G, Lee SC, Alonso J, Ecker JR, Luan S (2007) A WD40 domain cyclophilin interacts with histone H3 and functions in gene repression and organogenesis in Arabidopsis. Plant Cell 19:2403–2416

    Article  PubMed  CAS  Google Scholar 

  • Liu J, He Y, Amasino R, Chen X (2004) siRNAs targeting an intronic transposon in the regulation of natural flowering behaviour in Arabidopsis thaliana. Genes Dev 18:2873–2878

    Article  PubMed  CAS  Google Scholar 

  • Liu Y, Koornneef M, Soppe WJ (2007) The absence of histone H2B monoubiquitination in the Arabidopsis hub1 (rdo4) mutant reveals a role for chromatin remodeling in seed dormancy. Plant Cell 19:433–444

    Article  PubMed  CAS  Google Scholar 

  • Luo M, Bilodeau P, Dennis ES, Peacock WJ, Chaudhury A (2000) Expression and parent-of-origin effects for FIS2, MEA, and FIE in the endosperm and embryo of developing Arabidopsis seeds. Proc Natl Acad Sci USA 97:10637–10642

    Article  CAS  Google Scholar 

  • Makarevich G, Villar CB, Erilova A, Köhler C (2008) Mechanism of PHERES1 imprinting in Arabidopsis. J Cell Sci 121:906–912

    Article  PubMed  CAS  Google Scholar 

  • March-Diaz R, Garcia-Dominguez M, Florencio FJ, Reyes JC (2007) SEF, a new protein required for flowering repression in Arabidopsis, interacts with PIE1 and ARP6. Plant Physiol 143:893–901

    Article  PubMed  CAS  Google Scholar 

  • Martin-Trillo M, Lazaro A, Poethig RS, Gomez-Mena C, Pineiro MA, Martinez-Zapater JM, Jarillo JA (2006) EARLY IN SHORT DAYS 1 (ESD1) encodes ACTIN-RELATED PROTEIN 6 (AtARP6), a putative component of chromatin remodelling complexes that positively regulates FLC accumulation in Arabidopsis. Development 133:1241–1252

    Article  PubMed  CAS  Google Scholar 

  • Mlynárová L, Nap JP, Bisseling T (2007) The SWI/SNF chromatin-remodeling gene AtCHR12 mediates temporary growth arrest in Arabidopsis thaliana upon perceiving environmental stress. Plant J 51:874–885

    Article  PubMed  CAS  Google Scholar 

  • Mylne JS, Barrett L, Tessadori F, Mesnage S, Johnson L, Bernatavichute YV, Jacobsen SE, Fransz P, Dean C (2006) LHP1, the Arabidopsis homologue of HETEROCHROMATIN PROTEIN1, is required for epigenetic silencing of FLC. Proc Natl Acad Sci USA 103:5012–5017

    Article  PubMed  CAS  Google Scholar 

  • Niu L, Lu F, Pei Y, Liu C, Cao X (2007) Regulation of flowering time by the protein arginine methyltransferase AtPRMT10. EMBO Rep 12:1190–1195

    Article  CAS  Google Scholar 

  • Noh YS, Amasino RM (2003) PIE1, an ISWI family gene, is required for FLC activation and floral repression in Arabidopsis. Plant Cell 15:1671–1682

    Article  PubMed  CAS  Google Scholar 

  • Noh B, Lee SH, Kim HJ, Yi G, Shin EA, Lee M, Jung KJ, Doyle MR, Amasino RM, Noh YS (2004) Divergent roles of a pair of homologous jumonji/zinc-finger-class transcription factor proteins in the regulation of Arabidopsis flowering time. Plant Cell 16:2601–2613

    Article  PubMed  CAS  Google Scholar 

  • Novillo F, Medina J, Salinas J (2007) Arabidopsis CBF1 and CBF3 have a different function than CBF2 in cold acclimation and define different gene classes in the CBF regulon. Proc Natl Acad Sci USA 104:21002–21007

    Article  PubMed  CAS  Google Scholar 

  • Oh S, Zhang H, Ludwig P, van Nocker S (2004) A mechanism related to the yeast transcriptional regulator Paf1c is required for expression of the Arabidopsis FLC/MAF MADS box gene family. Plant Cell 16:2940–2953

    Article  PubMed  CAS  Google Scholar 

  • Ohashi Y, Oka A, Rodrigues-Pousada R, Possenti M, Ruberti I, Morelli G, Aoyama T (2003) Modulation of phospholipid signaling by GLABRA2 in root-hair pattern formation. Science 300:1427–1430

    Article  PubMed  CAS  Google Scholar 

  • Pei Y, Niu L, Lu F, Liu C, Zhai J, Kong X, Cao X (2007) Mutations in the Type II protein arginine methyltransferase AtPRMT5 result in pleiotropic developmental defects in Arabidopsis. Plant Physiol 144:1913–1923

    Article  PubMed  CAS  Google Scholar 

  • Perruc E, Kinoshita N, Lopez-Molina L (2007) The role of chromatin-remodeling factor PKL in balancing osmotic stress responses during Arabidopsis seed germination. Plant J 52:927–936

    Article  PubMed  CAS  Google Scholar 

  • Phelps-Durr TL, Thomas J, Vahab P, Timmermans MCP (2005) Maize ROUGH SHEATH2 and its Arabidopsis orthologue ASYMMETRIC LEAVES1 interact with HIRA, a predicted histone chaperone, to maintain knox gene silencing and determinacy during organogenesis. Plant Cell 17:2886–2898

    Article  PubMed  CAS  Google Scholar 

  • Pien S, Fleury D, Mylne JS, Crevillen P, Inzé D, Avramova Z, Dean C, Grossniklaus U (2008) ARABIDOPSIS TRITHORAX1 dynamically regulates FLOWERING LOCUS C activation via histone 3 lysine 4 trimethylation. Plant Cell 20:580–588

    Article  PubMed  CAS  Google Scholar 

  • Polo SE, Almouzni G (2006) Chromatin assembly: a basic recipe with various flavours. Curr Opin Genet Dev 16:104–111

    Article  PubMed  CAS  Google Scholar 

  • Saleh A, Al-Abdallat A, Ndamukong I, Alvarez-Venegas R, Avramova Z (2007) The Arabidopsis homologs of trithorax (ATX1) and enhancer of zeste (CLF) establish ‘bivalent chromatin marks’ at the silent AGAMOUS locus. Nucleic Acids Res 35:6290–6296

    Article  PubMed  CAS  Google Scholar 

  • Scheres B, van den Toorn H, Heidstra R (2004) Root genomics: towards digital in situ hybridization. Genome Biol 5:e227

    Article  PubMed  Google Scholar 

  • Schmitz RJ, Amasino RM (2007) Vernalization: a model for investigating epigenetics and eukaryotic gene regulation in plants. Biochim Biophys Acta 1769:269–275

    PubMed  CAS  Google Scholar 

  • Schmitz RJ, Hong L, Fitzpatrick KE, Amasino RM (2007) DICER-LIKE 1 and DICER-LIKE 3 redundantly act to promote flowering via repression of FLOWERING LOCUS C in Arabidopsis thaliana. Genetics 176:1359–1362

    Article  PubMed  CAS  Google Scholar 

  • Schmitz RJ, Sung S, Amasino RM (2008) Histone arginine methylation is required for vernalization-induced epigenetic silencing of FLC in winter-annual Arabidopsis thaliana. Proc Natl Acad Sci USA 105:411–416

    Article  PubMed  CAS  Google Scholar 

  • Schönrock N, Bouveret R, Leroy O, Borghi L, Köhler C, Gruissem W, Hennig L (2006) Polycomb-group proteins repress the floral activator AGL19 in the FLC-independent vernalization pathway. Genes Dev 20:1667–1678

    Article  PubMed  CAS  Google Scholar 

  • Schubert D, Primavesi L, Bishopp A, Roberts G, Doonan J, Jenuwein T, Goodrich J (2006) Silencing by plant Polycomb-group genes requires dispersed trimethylation of histone H3 at lysine 27. EMBO J 25:4638–4649

    Article  PubMed  CAS  Google Scholar 

  • Scofield S, Murray JAH (2006) KNOX gene function in plant stem cell niches. Plant Mol Biol 60:929–946

    Article  PubMed  CAS  Google Scholar 

  • Shi Y (2007) Histone lysine demethylases: emerging roles in development, physiology and disease. Nature Rev Genet 8:829–833

    Article  PubMed  CAS  Google Scholar 

  • Shilatifard A (2006) Chromatin modifications by methylation and ubiquitination: implications in the regulation of gene expression. Annu Rev Biochem 75:243–269

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Soppe WJ, Bentsink L, Koornneef M (1999) The early-flowering mutant efs is involved in the autonomous promotion pathway of Arabidopsis thaliana. Development 126:4763–4770

    PubMed  CAS  Google Scholar 

  • Spillane C, Baroux C, Escobar-Restrepo JM, Page DR, Laoueille S, Grossniklaus U (2004) Transposons and tandem repeats are not involved in the control of genomic imprinting at the MEDEA locus in Arabidopsis. Cold Spring Harbor Symp Quant Biol 69:465–475

    Article  PubMed  CAS  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

    Article  PubMed  CAS  Google Scholar 

  • Stockinger EJ, Mao Y, Regier MK, Triezenberg SJ, Thomashow MF (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

    Article  PubMed  CAS  Google Scholar 

  • Sung S, Amasino RM (2004) Vernalization in Arabidopsis thaliana is mediated by the PHD finger protein VIN3. Nature 427:159–164

    Article  PubMed  CAS  Google Scholar 

  • Sung S, Schmitz RJ, Amasino RM (2006) A PHD finger protein involved in both the vernalization and photoperiod pathways in Arabidopsis. Genes Dev 20:3244–3248

    Article  PubMed  CAS  Google Scholar 

  • Swiezewski S, Crevillen P, Liu F, Ecker JR, Jerzmanowski A, Dean C (2007) Small RNA-mediated chromatin silencing directed to the 3′ region of the Arabidopsis gene encoding the developmental regulator, FLC. Proc Natl Acad Sci USA 104:3633–3638

    Article  PubMed  CAS  Google Scholar 

  • Tian L, Fong MP, Wang JJ, Wei NE, Jiang H, Doerge RW, Chen ZJ (2005) Reversible histone acetylation and deacetylation mediate genome-wide, promoter-dependent and locus-specific changes in gene expression during plant development. Genetics 169:337–345

    Article  PubMed  CAS  Google Scholar 

  • Tsuji H, Saika H, Tsutsumi N, Hirai A, Nakazono M (2006) Dynamic and reversible changes in histone H3-Lys4 methylation and H3 acetylation occurring at submergence-inducible genes in rice. Plant Cell Physiol 47:995–1003

    Article  PubMed  CAS  Google Scholar 

  • Turck F, Roudier F, Farrona S, Martin-Magniette ML, 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

    Article  CAS  Google Scholar 

  • Vlachonasios KE, Thomashow MF, Triezenberg SJ (2003) Disruption mutations of ADA2b and GCN5 transcriptional adaptor genes dramatically affect Arabidopsis growth, development, and gene expression. Plant Cell 15:626–638

    Article  PubMed  CAS  Google Scholar 

  • Volpe TA, Kidner C, Hall IM, Teng G, Grewal SI, Martienssen RA (2002) Regulation of heterochromatic silencing and histone H3 lysine-9 methylation by RNAi. Science 297:1833–1837

    Article  PubMed  CAS  Google Scholar 

  • Wagner D, Meyerowitz EM (2002) SPLAYED, a novel SWI/SNF ATPase homolog, controls reproductive development in Arabidopsis. Curr Biol 12:85–94

    Article  PubMed  CAS  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

    Article  PubMed  CAS  Google Scholar 

  • Wood CC, Robertson M, Tanner G, Peacock WJ, Dennis ES, Helliwell CA (2006) The Arabidopsis thaliana vernalization response requires a Polycomb-like protein complex that also includes VERNALIZATION INSENSITIVE 3. Proc Natl Acad Sci USA 103:14631–14636

    Article  PubMed  CAS  Google Scholar 

  • Wu K, Zhang L, Zhou C, Yu CW, Chaikam V (2008) HDA6 is required for jasmonate response, senescence and flowering in Arabidopsis. J Exp Bot 59:225–234

    Article  PubMed  CAS  Google Scholar 

  • Xiao W, Gehring M, Choi Y, Margossian L, Pu H, Harada JJ, Goldberg RB, Pennell RI, Fischer RL (2003) Imprinting of the MEA Polycomb gene is controlled by antagonism between MET1 methyltransferase and DME glycosylase. Dev Cell 5:891–901

    Article  PubMed  CAS  Google Scholar 

  • Xie Z, Johansen LK, Gustafson AM, Kasschau KD, Lellis AD, Zilberman D, Jacobsen SE, Carrington JC (2004) Genetic and functional diversification of small RNA pathways in plants. PLoS Biol 2:e107

    Article  Google Scholar 

  • Xu L, Xu Y, Dong AW, Sun Y, Pi LM, Xu YQ, Huang H (2003) Novel as1 and as2 defects in leaf adaxial-abaxial polarity reveal the requirement for ASYMMETRIC LEAVES1 and 2 and ERECTA functions in specifying adaxial identity. Development 130:4097–4107

    Article  PubMed  CAS  Google Scholar 

  • Xu CR, Liu C, Wang YL, Li LC, Chen WQ, Xu ZH, Bai SN (2005) Histone acetylation affects expression of cellular patterning genes in the Arabidopsis root epidermis. Proc Natl Acad Sci USA 102:14469–14474

    Article  PubMed  CAS  Google Scholar 

  • Xu L, Ménard, R, Berr A, Fuchs J, Cognat V, Meyer D, Shen WH (2009) The E2 ubiquitin-conjugating enzymes, AtUBC1 and AtUBC2, play redundant roles and are involved in activation of FLC expression and repression of flowering in Arabidopsis. Plant J 57:279–288

    Article  PubMed  CAS  Google Scholar 

  • Xu L, Zhao Z, Dong A, Soubigou-Taconnat L, Renou JP, Steinmetz A, Shen WH (2008) Di- and tri- but not monomethylation on histone H3 lysine 36 marks active transcription of genes involved in flowering time regulation and other processes in Arabidopsis thaliana. Mol Cell Biol 28:1348–1360

    Article  PubMed  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  • Zhao Z, Yu Y, Meyer D, Wu C, Shen WH (2005) Prevention of early flowering by expression of FLOWERING LOCUS C requires methylation of histone H3 K36. Nature Cell Biol 7:1156–1160

    Article  CAS  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

    Article  PubMed  CAS  Google Scholar 

  • Zhu Y, Dong A, Meyer D, Pichon O, Renou JP, Cao K, Shen WH (2006) Arabidopsis NRP1 and NRP2 encode histone chaperones and are required for maintaining postembryonic root growth. Plant Cell 18:2879–2892

    Article  PubMed  CAS  Google Scholar 

  • Zhu J, Jeong JC, Zhu Y, Sokolchik I, Miyazaki S, Zhu JK, Hasegawa PM, Bohnert HJ, Shi H, Yun DJ, Bressan RA (2008) Involvement of Arabidopsis HOS15 in histone deacetylation and cold tolerance. Proc Natl Acad Sci USA 105:4945–4950

    Article  PubMed  CAS  Google Scholar 

  • Zilberman D, Cao X, Jacobsen SE (2003) AARGONAUTE4 control of locus-specific siRNA accumulation and DNA and histone methylation. Science 299:716–719

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgements

The authors thank Lin Xu for helpful discussions and comments on the manuscript, and the French Agence Nationale de la Recherche (ANR) for financial support in the research project METHISTONARA. A. Berr is supported by a postdoctoral fellowship from ANR-06-Blanc-0054-01.

Author information

Authors and Affiliations

  1. Institut de Biologie Moléculaire des Plantes (IBMP) Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg (UdS), 12 rue du Général Zimmer, 67084, Strasbourg cedex, France

    A. Berr & W. H. Shen

Authors
  1. A. Berr
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. W. H. Shen
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to W. H. Shen .

Editor information

Editors and Affiliations

  1. New Era College, Jalan Bukit, Kajang, 43000, Malaysia

    Eng Chong Pua

  2. Dept. Plant Sciences Division, University of Nottingham, Loughborough, LE12 5RD, United Kingdom

    Michael R. Davey

Rights and permissions

Reprints and permissions

Copyright information

© 2010 Springer-Verlag Berlin Heidelberg

About this chapter

Cite this chapter

Berr, A., Shen, W.H. (2010). Molecular Mechanisms in Epigenetic Regulation of Plant Growth and Development. In: Pua, E., Davey, M. (eds) Plant Developmental Biology - Biotechnological Perspectives. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-04670-4_17

Download citation

Publish with us

Policies and ethics

Search

Navigation