Skip to main content
SpringerLink
Log in

DNA Demethylation and Gene Imprinting in Flowering Plants

  • Chapter
  • First Online:
Epigenetic Memory and Control in Plants

Part of the book series: Signaling and Communication in Plants ((SIGCOMM,volume 18))

Abstract

Gene imprinting is the monoallelic gene expression in a parent-of-origin-dependent manner that results from differential epigenetic states of the parental alleles. It is important for plant reproduction, in particular, the development of endosperm that provides nutrients to the embryo in flowering plants. With a few exceptions, all known plant gene imprinting occurs in the endosperm. The distinctive mechanisms of gene imprinting in the endosperm involve DNA demethylation and histone modifications. Notably, regulation of many imprinted genes begins prior to fertilization of the central cell member of the female gametophyte, where active DNA demethylation, the process which removes DNA methylation independently of DNA replication, is initiated by a plant-specific DNA demethylase. Recent genome-wide studies revealed the “imprintome”—the whole set of imprinted genes—in Arabidopsis thaliana endosperm. From the evolutionary point of view, lines of evidence suggest that both double fertilization and gene imprinting might have coevolved in flowering plants for their reproductive success.

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

  • Agius F, Kapoor A, Zhu JK (2006) Role of the Arabidopsis DNA glycosylase/lyase ROS1 in active DNA demethylation. Proc Natl Acad Sci U S A 103:11796–11801

    PubMed  CAS  Google Scholar 

  • Barlow DP (2011) Genomic imprinting: a mammalian epigenetic discovery model. Annu Rev Genet 45:379–403

    PubMed  CAS  Google Scholar 

  • Baroux C, Gagliardini V, Page DR, Grossniklaus U (2006) Dynamic regulatory interactions of Polycomb group genes: MEDEA autoregulation is required for imprinted gene expression in Arabidopsis. Genes Dev 20:1081–1086

    PubMed  CAS  Google Scholar 

  • Barreto G, Schafer A, Marhold J, Stach D, Swaminathan SK, Handa V, Doderlein G, Maltry N, Wu W, Lyko F, Niehrs C (2007) Gadd45a promotes epigenetic gene activation by repair-mediated DNA demethylation. Nature 445:671–675

    PubMed  CAS  Google Scholar 

  • Baylin SB, Ohm JE (2006) Epigenetic gene silencing in cancer—a mechanism for early oncogenic pathway addiction? Nat Rev Cancer 6:107–116

    PubMed  CAS  Google Scholar 

  • Berger F, Fitz Gerald J, Ingouff M (2007) Arabidopsis as a model for understanding the basics of endosperm development. Endosperm 8:91–110

    CAS  Google Scholar 

  • Bhutani N, Burns DM, Blau HM (2011) DNA demethylation dynamics. Cell 146:866–872

    PubMed  CAS  Google Scholar 

  • Bicknell RA, Koltunow AM (2004) Understanding apomixis: recent advances and remaining conundrums. Plant Cell 16:S228–S245

    PubMed  CAS  Google Scholar 

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

    PubMed  CAS  Google Scholar 

  • Bratzel F, Yang C, Angelova A, Lopez-Torrejon G, Koch M, del Pozo JC, Calonje M (2012) Regulation of the new Arabidopsis imprinted gene AtBMI1C requires the interplay of different epigenetic mechanisms. Mol Plant 5:260–269

    PubMed  CAS  Google Scholar 

  • Brown R, Lemmon B (2007) The developmental biology of cereal endosperm. In: Olsen OA (ed) Endosperm. Springer, Berlin, pp 1–20

    Google Scholar 

  • Brown R, Lemmon B, Nguyen H (2003) Events during the first four rounds of mitosis establish three developmental domains in the syncytial endosperm of Arabidopsis thaliana. Protoplasma 222:167–174

    PubMed  CAS  Google Scholar 

  • Calonje M, Sung ZR (2006) Complexity beneath the silence. Curr Opin Plant Biol 9:530–537

    PubMed  CAS  Google Scholar 

  • Carlson LL, Page AW, Bestor TH (1992) Properties and localization of DNA methyltransferase in preimplantation mouse embryos: implications for genomic imprinting. Genes Dev 6:2536–2541

    PubMed  CAS  Google Scholar 

  • Chanvivattana Y, Bishopp A, Schubert D, Stock C, Moon YH, Sung ZR, Goodrich J (2004) Interaction of polycomb-group proteins controlling flowering in Arabidopsis. Development 131:5263–5276

    PubMed  CAS  Google Scholar 

  • Chaudhuri S, Messing J (1994) Allele-specific parental imprinting of dzr1, a posttranscriptional regulator of zein accumulation. Proc Natl Acad Sci U S A 91:4867–4871

    PubMed  CAS  Google Scholar 

  • Chaudhury AM, Ming L, Miller C, Craig S, Dennis ES, Peacock WJ (1997) Fertilization-independent seed development in Arabidopsis thaliana. Proc Natl Acad Sci U S A 94:4223–4228

    PubMed  CAS  Google Scholar 

  • Choi Y, Gehring M, Johnson L, Hannon M, Harada JJ, Goldberg RB, Jacobsen SE, Fischer RL (2002) DEMETER, a DNA glycosylase domain protein, is required for endosperm gene imprinting and seed viability in Arabidopsis. Cell 110:33–42

    PubMed  CAS  Google Scholar 

  • Choi Y, Harada JJ, Goldberg RB, Fischer RL (2004) An invariant aspartic acid in the DNA glycosylase domain of DEMETER is necessary for transcriptional activation of the imprinted MEDEA gene. Proc Natl Acad Sci U S A 101:7481–7486

    PubMed  CAS  Google Scholar 

  • Cortellino S, Xu J, Sannai M, Moore R, Caretti E, Cigliano A, Le Coz M, Devarajan K, Wessels A, Soprano D, Abramowitz LK, Bartolomei MS, Rambow F, Bassi MR, Bruno T, Fanciulli M, Renner C, Klein-Szanto AJ, Matsumoto Y, Kobi D, Davidson I, Alberti C, Larue L, Bellacosa A (2011) Thymine DNA glycosylase is essential for active DNA demethylation by linked deamination-base excision repair. Cell 146:67–79

    PubMed  CAS  Google Scholar 

  • Danilevskaya ON, Hermon P, Hantke S, Muszynski MG, Kollipara K, Ananiev EV (2003) Duplicated fie genes in maize: expression pattern and imprinting suggest distinct functions. Plant Cell 15:425–438

    PubMed  CAS  Google Scholar 

  • David SS, O’Shea VL, Kundu S (2007) Base-excision repair of oxidative DNA damage. Nature 447:941–950

    PubMed  CAS  Google Scholar 

  • Dresselhaus T (2006) Cell–cell communication during double fertilization. Curr Opin Plant Biol 9:41–47

    PubMed  CAS  Google Scholar 

  • Duroux M, Houben A, Ruzicka K, Friml J, Grasser KD (2004) The chromatin remodelling complex FACT associates with actively transcribed regions of the Arabidopsis genome. Plant J 40:660–671

    PubMed  CAS  Google Scholar 

  • Ebel C, Mariconti L, Gruissem W (2004) Plant retinoblastoma homologues control nuclear proliferation in the female gametophyte. Nature 429:776–780

    Google Scholar 

  • Formosa T (2008) FACT and the reorganized nucleosome. Mol Biosyst 4:1085–1093

    PubMed  CAS  Google Scholar 

  • Friedman WE (2001) Developmental and evolutionary hypotheses for the origin of double fertilization and endosperm. C R Acad Sci III 324:559–567

    PubMed  CAS  Google Scholar 

  • Friedman WE (2006) Embryological evidence for developmental lability during early angiosperm evolution. Nature 441:337–340

    PubMed  CAS  Google Scholar 

  • Gehring M, Henikoff S (2007) DNA methylation dynamics in plant genomes. Biochim Biophys Acta 1769:276–286

    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

    PubMed  CAS  Google Scholar 

  • Gehring M, Bubb KL, Henikoff S (2009a) Extensive demethylation of repetitive elements during seed development underlies gene imprinting. Science 324:1447–1451

    PubMed  CAS  Google Scholar 

  • Gehring M, Reik W, Henikoff S (2009b) DNA demethylation by DNA repair. Trends Genet 25:82–90

    PubMed  CAS  Google Scholar 

  • Gerald JNF, Hui PS, Berger F (2009) Polycomb group-dependent imprinting of the actin regulator AtFH5 regulates morphogenesis in Arabidopsis thaliana. Development 136:3399–3404

    Google Scholar 

  • Gong Z, Morales-Ruiz T, Ariza RR, Roldan-Arjona T, David L, Zhu JK (2002) ROS1, a repressor of transcriptional gene silencing in Arabidopsis, encodes a DNA glycosylase/lyase. Cell 111:803–814

    PubMed  CAS  Google Scholar 

  • Grossniklaus U, Vielle-Calzada JP, Hoeppner MA, Gagliano WB (1998) Maternal control of embryogenesis by MEDEA, a polycomb group gene in Arabidopsis. Science 280:446–450

    PubMed  CAS  Google Scholar 

  • Guitton AE, Page DR, Chambrier P, Lionnet C, Faure JE, Grossniklaus U, Berger F (2004) Identification of new members of fertilisation independent seed polycomb group pathway involved in the control of seed development in Arabidopsis thaliana. Development 131:2971–2981

    PubMed  CAS  Google Scholar 

  • Guo M, Rupe MA, Danilevskaya ON, Yang 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

    PubMed  CAS  Google Scholar 

  • Guo JU, Su Y, Zhong C, Ming GL, Song H (2011) Hydroxylation of 5-methylcytosine by TET1 promotes active DNA demethylation in the adult brain. Cell 145:423–434

    PubMed  CAS  Google Scholar 

  • Gutierrez-Marcos JF, Pennington PD, Costa LM, Dickinson HG (2003) Imprinting in the endosperm: a possible role in preventing wide hybridization. Philos Trans R Soc Lond B Biol Sci 358:1105–1111

    PubMed  CAS  Google Scholar 

  • Gutierrez-Marcos JF, Costa LM, Biderre-Petit C, Khbaya B, O’Sullivan DM, Wormald M, Perez P, Dickinson HG (2004) Maternally 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

    PubMed  CAS  Google Scholar 

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

    PubMed  Google Scholar 

  • Haerizadeh F, Singh MB, Bhalla PL (2006) Transcriptional repression distinguishes somatic from germ cell lineages in a plant. Science 313:496–499

    PubMed  CAS  Google Scholar 

  • Haig D, Westoby M (1989) Selective forces in the emergence of the seed habit. Biol J Linn Soc 38:215–238

    Google Scholar 

  • Hajkova P, Erhardt S, Lane N, Haaf T, El-Maarri O, Reik W, Walter J, Surani MA (2002) Epigenetic reprogramming in mouse primordial germ cells. Mech Dev 117:15–23

    PubMed  CAS  Google Scholar 

  • Haun WJ, Springer NM (2008) Maternal and paternal alleles exhibit differential histone methylation and acetylation at maize imprinted genes. Plant J 56:903–912

    PubMed  CAS  Google Scholar 

  • Haun WJ, Laoueillé-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

    PubMed  CAS  Google Scholar 

  • Hayashi K, de Sousa Lopes SM, Surani MA (2007) Germ cell specification in mice. Science 316:394–396

    PubMed  CAS  Google Scholar 

  • Henderson IR, Jacobsen SE (2007) Epigenetic inheritance in plants. Nature 447:418–424

    PubMed  CAS  Google Scholar 

  • Hsieh TF, Ibarra CA, Silva P, Zemach A, Eshed-Williams L, Fischer RL, Zilberman D (2009) Genome-wide demethylation of Arabidopsis endosperm. Science 324:1451–1454

    PubMed  CAS  Google Scholar 

  • Hsieh TF, Shin J, Uzawa R, Silva P, Cohen S, Bauer MJ, Hashimoto M, Kirkbride RC, Harada JJ, Zilberman D, Fischer RL (2011) Regulation of imprinted gene expression in Arabidopsis endosperm. Proc Natl Acad Sci U S A 108:1755–1762

    PubMed  CAS  Google Scholar 

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

    PubMed  CAS  Google Scholar 

  • Ikeda Y, Kinoshita Y, Susaki D, Iwano M, Takayama S, Higashiyama T, Kakutani T, Kinoshita T (2011) HMG domain containing SSRP1 is required for DNA demethylation and genomic imprinting in Arabidopsis. Dev Cell 21:589–596

    PubMed  CAS  Google Scholar 

  • Ingouff M, Fitz Gerald JN, Guerin C, Robert H, Sorensen MB, Van Damme D, Geelen D, Blanchoin L, Berger F (2005) Plant formin AtFH5 is an evolutionarily conserved actin nucleator involved in cytokinesis. Nat Cell Biol 7:374–380

    PubMed  CAS  Google Scholar 

  • Iwakawa H, Shinmyo A, Sekine M (2006) Arabidopsis CDKA;1, a cdc2 homologue, controls proliferation of generative cells in male gametogenesis. Plant J 45:819–831

    PubMed  CAS  Google Scholar 

  • Jahnke S, Scholten S (2009) Epigenetic resetting of a gene imprinted in plant embryos. Curr Biol 19:1677–1681

    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

    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

    PubMed  CAS  Google Scholar 

  • Jullien PE, Mosquna A, Ingouff M, Sakata T, Ohad N, Berger F (2008) Retinoblastoma and its binding partner MSI1 control imprinting in Arabidopsis. PLoS Biol 6:e194

    PubMed  Google Scholar 

  • Kermicle J (1970) Dependence of the R-mottled aleurone phenotype in maize on mode of sexual transmission. Genetics 66:69–85

    PubMed  CAS  Google Scholar 

  • Kinoshita T, Yadegari R, Harada JJ, Goldberg RB, Fischer RL (1999) Imprinting of the MEDEA polycomb gene in the Arabidopsis endosperm. Plant Cell 11:1945–1952

    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

    PubMed  CAS  Google Scholar 

  • Kiyosue T, Ohad N, Yadegari R, Hannon M, Dinneny J, Wells D, Katz A, Margossian L, Harada JJ, Goldberg RB, Fischer RL (1999) Control of fertilization-independent endosperm development by the MEDEA polycomb gene in Arabidopsis. Proc Natl Acad Sci U S A 96:4186–4191

    PubMed  CAS  Google Scholar 

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

    PubMed  CAS  Google Scholar 

  • Kohler C, Hennig L, Bouveret R, Gheyselinck J, Grossniklaus U, Gruissem W (2003a) Arabidopsis MSI1 is a component of the MEA/FIE polycomb group complex and required for seed development. EMBO J 22:4804–4814

    PubMed  Google Scholar 

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

    PubMed  Google Scholar 

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

    PubMed  Google Scholar 

  • Kohler C, Wolff P, Spillane C (2012) Epigenetic mechanisms underlying genomic imprinting in plants. Annu Rev Plant Biol 63:331–352

    PubMed  Google Scholar 

  • Law JA, Jacobsen SE (2010) Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat Rev Genet 11:204–220

    PubMed  CAS  Google Scholar 

  • Le BH, Wagmaister JA, Kawashima T, Bui AQ, Harada JJ, Goldberg RB (2007) Using genomics to study legume seed development. Plant Physiol 144:562–574

    PubMed  CAS  Google Scholar 

  • Li Y, Sasaki H (2011) Genomic imprinting in mammals: its life cycle, molecular mechanisms and reprogramming. Cell Res 21:466–473

    PubMed  CAS  Google Scholar 

  • Lister R, O’Malley RC, Tonti-Filippini J, Gregory BD, Berry CC, Millar AH, Ecker JR (2008) Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133:523–536

    PubMed  CAS  Google Scholar 

  • Lohmann JU, Weigel D (2002) Building beauty: the genetic control of floral patterning. Dev Cell 2:135–142

    PubMed  CAS  Google Scholar 

  • Lolas IB, Himanen K, Gronlund JT, Lynggaard C, Houben A, Melzer M, Van Lijsebettens M, Grasser KD (2010) The transcript elongation factor FACT affects Arabidopsis vegetative and reproductive development and genetically interacts with HUB1/2. Plant J 61:686–697

    PubMed  CAS  Google Scholar 

  • Ludwig SR, Habera LF, Dellaporta SL, Wessler SR (1989) Lc, a member of the maize R gene family responsible for tissue-specific anthocyanin production, encodes a protein similar to transcriptional activators and contains the myc-homology region. Proc Natl Acad Sci U S A 86:7092–7096

    PubMed  CAS  Google Scholar 

  • Lund G, Ciceri P, Viotti A (1995a) Maternal-specific demethylation and expression of specific alleles of zein genes in the endosperm of Zea mays L. Plant J 8:571–581

    PubMed  CAS  Google Scholar 

  • Lund G, Messing J, Viotti A (1995b) Endosperm-specific demethylation and activation of specific alleles of alpha-tubulin genes of Zea mays L. Mol Gen Genet 246:716–722

    PubMed  CAS  Google Scholar 

  • Luo M, Bilodeau P, Koltunow A, Dennis ES, Peacock WJ, Chaudhury AM (1999) Genes controlling fertilization-independent seed development in Arabidopsis thaliana. Proc Natl Acad Sci U S A 96:296–301

    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 U S A 97:10637–10642

    PubMed  CAS  Google Scholar 

  • Makarevich G, Leroy O, Akinci U, Schubert D, Clarenz O, Goodrich J, Grossniklaus U, Kohler C (2006) Different polycomb group complexes regulate common target genes in Arabidopsis. EMBO Rep 7:947–952

    PubMed  CAS  Google Scholar 

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

    PubMed  CAS  Google Scholar 

  • Matzke M, Kanno T, Huettel B, Daxinger L, Matzke AJ (2007) Targets of RNA-directed DNA methylation. Curr Opin Plant Biol 10:512–519

    PubMed  CAS  Google Scholar 

  • Mok YG, Uzawa R, Lee J, Weiner GM, Eichman BF, Fischer RL, Huh JH (2010) Domain structure of the DEMETER 5-methylcytosine DNA glycosylase. Proc Natl Acad Sci U S A 107:19225–19230

    PubMed  CAS  Google Scholar 

  • Morales-Ruiz T, Ortega-Galisteo AP, Ponferrada-Marin MI, Martinez-Macias MI, Ariza RR, Roldan-Arjona T (2006) DEMETER and REPRESSOR OF SILENCING 1 encode 5-methylcytosine DNA glycosylases. Proc Natl Acad Sci U S A 103:6853–6858

    PubMed  CAS  Google Scholar 

  • Mosher RA, Melnyk CW, Kelly KA, Dunn RM, Studholme DJ, Baulcombe DC (2009) Uniparental expression of PolIV-dependent siRNAs in developing endosperm of Arabidopsis. Nature 460:283–286

    PubMed  CAS  Google Scholar 

  • Nguyen H, Brown R, Lemmon B (2000) The specialized chalazal endosperm in Arabidopsis thaliana and Lepidium virginicum (Brassicaceae). Protoplasma 212:99–110

    Google Scholar 

  • Nowack MK, Grini PE, Jakoby MJ, Lafos M, Koncz C, Schnittger A (2006) A positive signal from the fertilization of the egg cell sets off endosperm proliferation in angiosperm embryogenesis. Nat Genet 38:63–67

    PubMed  CAS  Google Scholar 

  • Nowack MK, Shirzadi R, Dissmeyer N, Dolf A, Endl E, Grini PE, Schnittger A (2007) Bypassing genomic imprinting allows seed development. Nature 447:312–315

    PubMed  CAS  Google Scholar 

  • Ohad N, Margossian L, Hsu YC, Williams C, Repetti P, Fischer RL (1996) A mutation that allows endosperm development without fertilization. Proc Natl Acad Sci U S A 93:5319–5324

    PubMed  CAS  Google Scholar 

  • Ohad N, Yadegari R, Margossian L, Hannon M, Michaeli D, Harada JJ, Goldberg RB, Fischer RL (1999) Mutations in FIE, a WD polycomb group gene, allow endosperm development without fertilization. Plant Cell 11:407–416

    PubMed  CAS  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

    PubMed  CAS  Google Scholar 

  • Okada T, Singh MB, Bhalla PL (2007) Transcriptome profiling of Lilium longiflorum generative cells by cDNA microarray. Plant Cell Rep 26:1045–1052

    PubMed  CAS  Google Scholar 

  • Orphanides G, Wu WH, Lane WS, Hampsey M, Reinberg D (1999) The chromatin-specific transcription elongation factor FACT comprises human SPT16 and SSRP1 proteins. Nature 400:284–288

    PubMed  CAS  Google Scholar 

  • Penterman J, Uzawa R, Fischer RL (2007) Genetic interactions between DNA demethylation and methylation in Arabidopsis. Plant Physiol 145:1549–1557

    PubMed  CAS  Google Scholar 

  • Pien S, Grossniklaus U (2007) Polycomb group and trithorax group proteins in Arabidopsis. Biochim Biophys Acta 1769:375–382

    PubMed  CAS  Google Scholar 

  • Raissig MT, Baroux C, Grossniklaus U (2011) Regulation and flexibility of genomic imprinting during seed development. Plant Cell 23:16–26

    PubMed  CAS  Google Scholar 

  • Rea M, Zheng W, Chen M, Braud C, Bhangu D, Rognan TN, Xiao W (2012) Histone H1 affects gene imprinting and DNA methylation in Arabidopsis. Plant J 71:776–786

    PubMed  CAS  Google Scholar 

  • Reik W (2007) Stability and flexibility of epigenetic gene regulation in mammalian development. Nature 447:425–432

    PubMed  CAS  Google Scholar 

  • Scharer OD, Jiricny J (2001) Recent progress in the biology, chemistry and structural biology of DNA glycosylases. Bioessays 23:270–281

    PubMed  CAS  Google Scholar 

  • Schuettengruber B, Chourrout D, Vervoort M, Leblanc B, Cavalli G (2007) Genome regulation by polycomb and trithorax proteins. Cell 128:735–745

    PubMed  CAS  Google Scholar 

  • Schwartz YB, Pirrotta V (2007) Polycomb silencing mechanisms and the management of genomic programmes. Nat Rev Genet 8:9–22

    PubMed  CAS  Google Scholar 

  • Skinner DJ, Hill TA, Gasser CS (2004) Regulation of ovule development. Plant Cell 16:S32–S45

    PubMed  CAS  Google Scholar 

  • Soppe WJ, Jacobsen SE, Alonso-Blanco C, Jackson JP, Kakutani T, Koornneef M, Peeters AJ (2000) The late flowering phenotype of fwa mutants is caused by gain-of-function epigenetic alleles of a homeodomain gene. Mol Cell 6:791–802

    PubMed  CAS  Google Scholar 

  • Sung S, He Y, Eshoo TW, Tamada Y, Johnson L, Nakahigashi K, Goto K, Jacobsen SE, Amasino RM (2006) Epigenetic maintenance of the vernalized state in Arabidopsis thaliana requires LIKE HETEROCHROMATIN PROTEIN 1. Nat Genet 38:706–710

    PubMed  CAS  Google Scholar 

  • Tahiliani M, Koh KP, Shen Y, Pastor WA, Bandukwala H, Brudno Y, Agarwal S, Iyer LM, Liu DR, Aravind L, Rao A (2009) Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science 324:930–935

    PubMed  CAS  Google Scholar 

  • Tiwari S, Schulz R, Ikeda Y, Dytham L, Bravo J, Mathers L, Spielman M, Guzman P, Oakey RJ, Kinoshita T, Scott RJ (2008) MATERNALLY EXPRESSED PAB C-TERMINAL, a novel imprinted gene in Arabidopsis, encodes the conserved C-terminal domain of polyadenylate binding proteins. Plant Cell 20:2387–2398

    PubMed  CAS  Google Scholar 

  • Williams JH, Friedman WE (2002) Identification of diploid endosperm in an early angiosperm lineage. Nature 415:522–526

    PubMed  Google Scholar 

  • Williams K, Christensen J, Pedersen MT, Johansen JV, Cloos PA, Rappsilber J, Helin K (2011) TET1 and hydroxymethylcytosine in transcription and DNA methylation fidelity. Nature 473:343–348

    PubMed  CAS  Google Scholar 

  • Wolff P, Weinhofer I, Seguin J, Roszak P, Beisel C, Donoghue MTA, Spillane C, Nordborg M, Rehmsmeier M, Köhler C (2011) High-resolution analysis of parent-of-origin allelic expression in the Arabidopsis endosperm. PLoS Genet 7:e1002126

    PubMed  CAS  Google Scholar 

  • Wu SC, Zhang Y (2010) Active DNA demethylation: many roads lead to Rome. Nat Rev Mol Cell Biol 11:607–620

    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

    PubMed  CAS  Google Scholar 

  • Xu Y, Wu F, Tan L, Kong L, Xiong L, Deng J, Barbera AJ, Zheng L, Zhang H, Huang S, Min J, Nicholson T, Chen T, Xu G, Shi Y, Zhang K, Shi YG (2011) Genome-wide regulation of 5hmC, 5mC, and gene expression by Tet1 hydroxylase in mouse embryonic stem cells. Mol Cell 42:451–464

    PubMed  CAS  Google Scholar 

  • Yadegari R, Drews GN (2004) Female gametophyte development. Plant Cell 16:S133–S141

    PubMed  CAS  Google Scholar 

  • Yadegari R, Kinoshita T, Lotan O, Cohen G, Katz A, Choi Y, Nakashima K, Harada JJ, Goldberg RB (2000) Mutations in the FIE and MEA genes that encode interacting polycomb proteins cause parent-of-origin effects on seed development by distinct mechanisms. Plant Cell 12:2367–2382

    PubMed  CAS  Google Scholar 

  • Yao Q, Song CX, He C, Kumaran D, Dunn JJ (2012) Heterologous expression and purification of Arabidopsis thaliana VIM1 protein: in vitro evidence for its inability to recognize hydroxymethylcytosine, a rare base in Arabidopsis DNA. Prot Expr Purif 83:104–111

    CAS  Google Scholar 

  • Zheng X, Pontes O, Zhu J, Miki D, Zhang F, Li WX, Iida K, Kapoor A, Pikaard CS, Zhu JK (2008) ROS3 is an RNA-binding protein required for DNA demethylation in Arabidopsis. Nature 455:1259–1262

    PubMed  CAS  Google Scholar 

  • Zhu JK (2009) Active DNA demethylation mediated by DNA glycosylases. Annu Rev Genet 43:143–166

    PubMed  CAS  Google Scholar 

  • Zhu J, Kapoor A, Sridhar VV, Agius F, Zhu JK (2007) The DNA glycosylase/lyase ROS1 functions in pruning DNA methylation patterns in Arabidopsis. Curr Biol 17:54–59

    PubMed  CAS  Google Scholar 

Download references

Acknowledgements

We thank all members in the Huh laboratory for their critical reading of the manuscript. We also apologize to colleagues whose work cannot be cited owing to space constraints. Work in the laboratory is supported by the Next Generation BioGreen21 Program (TAGC) of the Rural Development Administration, Korea.

Author information

Authors and Affiliations

  1. Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agricultural Life Sciences, Seoul National University, Seoul, 151-921, South Korea

    Jin Hoe Huh & Hyun Jung Rim

Authors
  1. Jin Hoe Huh
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Hyun Jung Rim
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Jin Hoe Huh .

Editor information

Editors and Affiliations

  1. Agriculture and Biotech. of Drylands, Jacob Blaustein Inst. for Desert Res., French Associates Institute for, Sede Boqer Campus, 84990, Israel

    Gideon Grafi

  2. Britannia Building, Department of Molecular Biology, Tel-Aviv University, Tel Aviv, 69978, Tel Aviv, Israel

    Nir Ohad

Rights and permissions

Reprints and permissions

Copyright information

© 2013 Springer-Verlag Berlin Heidelberg

About this chapter

Cite this chapter

Huh, J.H., Rim, H.J. (2013). DNA Demethylation and Gene Imprinting in Flowering Plants. In: Grafi, G., Ohad, N. (eds) Epigenetic Memory and Control in Plants. Signaling and Communication in Plants, vol 18. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-35227-0_10

Download citation

Publish with us

Policies and ethics

Search

Navigation