Epigenetic reprogramming during plant reproduction and seed development

Current Opinion in Plant Biology

Volumn 15, Issue 1, 2012, Pages 63-69

  Wollmann, Heike ^a   Berger, Frédéric ^a  

^a NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

Author keywords

[No Author keywords available]

Indexed keywords

DNA METHYLATION; GENETIC EPIGENESIS; GENETICS; GROWTH, DEVELOPMENT AND AGING; NUCLEAR REPROGRAMMING; PLANT; PLANT SEED; REPRODUCTION; REVIEW;

DNA METHYLATION; EPIGENESIS, GENETIC; NUCLEAR REPROGRAMMING; PLANTS; REPRODUCTION; SEEDS;

MAGNOLIOPHYTA;

EID: 84856232863     PISSN: 13695266     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.pbi.2011.10.001     Document Type: Review

References (50)

1. Chan S.W., Henderson I.R., Jacobsen S.E. Gardening the genome: DNA methylation in Arabidopsis thaliana. Nat Rev Genet 2005, 6:351-360.
2. Boyko A., Kovalchuk I. Epigenetic control of plant stress response. Environ Mol Mutagen 2008, 49:61-72.
3. Cokus S.J., Feng S., Zhang X., Chen Z., Merriman B., Haudenschild C.D., Pradhan S., Nelson S.F., Pellegrini M., Jacobsen S.E. Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature 2008, 452:215-219.
4. Law J.A., Jacobsen S.E. Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat Rev Genet 2010, 11:204-220.
5. Simon S.A., Meyers B.C. Small RNA-mediated epigenetic modifications in plants. Curr Opin Plant Biol 2010, 14:148-155.
6. Zemach A., McDaniel I.E., Silva P., Zilberman D. Genome-wide evolutionary analysis of eukaryotic DNA methylation. Science 2010, 328:916-919.
7. Feng S., Cokus S.J., Zhang X., Chen P.Y., Bostick M., Goll M.G., Hetzel J., Jain J., Strauss S.H., Halpern M.E., et al. Conservation and divergence of methylation patterning in plants and animals. Proc Natl Acad Sci U S A 2010, 107:8689-8694.
8. Ahmed I., Sarazin A., Bowler C., Colot V., Quesneville H. Genome-wide evidence for local DNA methylation spreading from small RNA-targeted sequences in Arabidopsis. Nucleic Acids Res 2011, 39:6919-6931.
9. Berger F., Twell D. Germline specification and function in plants. Annu Rev Plant Biol 2011, 62:461-484.
10. Berger F., Chaudhury A. Parental memories shape seeds. Trends Plant Sci 2009, 14:550-556.
11. de Jong T.J., Scott R.J. Parental conflict does not necessarily lead to the evolution of imprinting. Trends Plant Sci 2007, 12:439-443.
12. Slotkin R.K., Vaughn M., Borges F., Tanurdzic M., Becker J.D., Feijo J.A., Martienssen R.A. Epigenetic reprogramming and small RNA silencing of transposable elements in pollen. Cell 2009, 136:461-472.
13. Schoft V.K., Chumak N., Mosiolek M., Slusarz L., Komnenovic V., Brownfield L., Twell D., Kakutani T., Tamaru H. Induction of RNA-directed DNA methylation upon decondensation of constitutive heterochromatin. EMBO Rep 2009, 10:1015-1021.
14. Lippman Z., Gendrel A.V., Black M., Vaughn M.W., Dedhia N., McCombie W.R., Lavine K., Mittal V., May B., Kasschau K.D., et al. Role of transposable elements in heterochromatin and epigenetic control. Nature 2004, 430:471-476.
15. Jullien P.E., Berger F. Gamete-specific epigenetic mechanisms shape genomic imprinting. Curr Opin Plant Biol 2009, 12:637-642.
16. Schoft V.K., Chumak N., Choi Y., Hannon M., Garcia-Aguilar M., Machlicova A., Slusarz L., Mosiolek M., Park J.S., Park G.T., et al. Function of the DEMETER DNA glycosylase in the Arabidopsis thaliana male gametophyte. Proc Natl Acad Sci U S A 2011, 108:8042-8047.
17. Choi Y., Gehring M., Johnson L., Hannon M., Harada J.J., Goldberg R.B., Jacobsen S.E., Fischer R.L. DEMETER, a DNA glycosylase domain protein, is required for endosperm gene imprinting and seed viability in arabidopsis. Cell 2002, 110:33-42.
18. Kinoshita T., Miura A., Choi Y., Kinoshita Y., Cao X., Jacobsen S.E., Fischer R.L., Kakutani T. One-way control of FWA imprinting in Arabidopsis endosperm by DNA methylation. Science 2004, 303:521-523.
19. Borges F., Gomes G., Gardner R., Moreno N., McCormick S., Feijo J.A., Becker J.D. Comparative transcriptomics of Arabidopsis sperm cells. Plant Physiol 2008, 148:1168-1181.
20. Wuest S.E., Vijverberg K., Schmidt A., Weiss M., Gheyselinck J., Lohr M., Wellmer F., Rahnenfuhrer J., von Mering C., Grossniklaus U. Arabidopsis female gametophyte gene expression map reveals similarities between plant and animal gametes. Curr Biol 2010, 20:506-512.
21. Jullien P.E., Mosquna A., Ingouff M., Sakata T., Ohad N., Berger F. Retinoblastoma and its binding partner MSI1 control imprinting in Arabidopsis. PLoS Biol 2008, 6:e194.
22. Jullien P.E., Kinoshita T., Ohad N., Berger F. Maintenance of DNA methylation during the Arabidopsis life cycle is essential for parental imprinting. Plant Cell 2006, 18:1360-1372.
23. Gehring M., Huh J.H., Hsieh T.F., Penterman J., Choi Y., Harada J.J., Goldberg R.B., Fischer R.L. DEMETER DNA glycosylase establishes MEDEA polycomb gene self-imprinting by allele-specific demethylation. Cell 2006, 124:495-506.
24. Gutierrez-Marcos J.F., Costa L.M., Dal Pra M., Scholten S., Kranz E., Perez P., Dickinson H.G. Epigenetic asymmetry of imprinted genes in plant gametes. Nat Genet 2006, 38:876-878.
25. Jahnke S., Scholten S. Epigenetic resetting of a gene imprinted in plant embryos. Curr Biol 2009, 19:1677-1681.
26. Jullien P.E., Berger F. DNA methylation reprogramming during plant sexual reproduction?. Trends Genet 2010, 26:394-399.
27. Gehring M., Bubb K.L., Henikoff S. Extensive demethylation of repetitive elements during seed development underlies gene imprinting. Science 2009, 324:1447-1451.
28. Zemach A., Kim M.Y., Silva P., Rodrigues J.A., Dotson B., Brooks M.D., Zilberman D. Local DNA hypomethylation activates genes in rice endosperm. Proc Natl Acad Sci U S A 2010, 107:18729-18734.
29. Hsieh T.F., Ibarra C.A., Silva P., Zemach A., Eshed-Williams L., Fischer R.L., Zilberman D. Genome-wide demethylation of Arabidopsis endosperm. Science 2009, 324:1451-1454.
30. Mosher R.A., Melnyk C.W., Kelly K.A., Dunn R.M., Studholme D.J., Baulcombe D.C. Uniparental expression of PolIV-dependent siRNAs in developing endosperm of Arabidopsis. Nature 2009, 460:283-286.
31. Weinhofer I., Hehenberger E., Roszak P., Hennig L., Kohler C. H3K27me3 profiling of the endosperm implies exclusion of polycomb group protein targeting by DNA methylation. PLoS Genet 2010, 6.
32. Bouyer D., Roudier F., Heese M., Andersen E.D., Gey D., Nowack M.K., Goodrich J., Renou J.P., Grini P.E., Colot V., et al. Polycomb repressive complex 2 controls the embryo-to-seedling phase transition. PLoS Genet 2011, 7:e1002014.
33. Jacob Y., Stroud H., Leblanc C., Feng S., Zhuo L., Caro E., Hassel C., Gutierrez C., Michaels S.D., Jacobsen SE Regulation of heterochromatic DNA replication by histone H3 lysine 27 methyltransferases. Nature 2010, 466:987-991.
34. Ingouff M., Hamamura Y., Gourgues M., Higashiyama T., Berger F. Distinct dynamics of HISTONE3 variants between the two fertilization products in plants. Curr Biol 2007, 17:1032-1037.
35. Ingouff M., Rademacher S., Holec S., Soljic L., Xin N., Readshaw A., Foo S.H., Lahouze B., Sprunck S., Berger F. Zygotic resetting of the HISTONE 3 variant repertoire participates in epigenetic reprogramming in Arabidopsis. Curr Biol 2010, 20:2137-2143.
36. Gregg C., Zhang J., Butler J.E., Haig D., Dulac C. Sex-specific parent-of-origin allelic expression in the mouse brain. Science 2010, 329:682-685.
37. Gregg C., Zhang J., Weissbourd B., Luo S., Schroth G.P., Haig D., Dulac C. High-resolution analysis of parent-of-origin allelic expression in the mouse brain. Science 2010, 329:643-648.
38. Gehring M., Missirian V., Henikoff S. Genomic analysis of parent-of-origin allelic expression in Arabidopsis thaliana seeds. PLoS One 2011, 6:e23687.
39. Hsieh T.F., Shin J., Uzawa R., Silva P., Cohen S., Bauer M.J., Hashimoto M., Kirkbride R.C., Harada J.J., Zilberman D., et al. Regulation of imprinted gene expression in Arabidopsis endosperm. Proc Natl Acad Sci U S A 2011, 108:1755-1762.
40. Wolff P., Weinhofer I., Seguin J., Roszak P., Beisel C., Donoghue M.T., Spillane C., Nordborg M., Rehmsmeier M., Kohler C. High-resolution analysis of parent-of-origin allelic expression in the Arabidopsis endosperm. PLoS Genet 2011, 7:e1002126.
41. Luo M., Taylor J.M., Spriggs A., Zhang H., Wu X., Russell S., Singh M., Koltunow A. A genome-wide survey of imprinted genes in rice seeds reveals imprinting primarily occurs in the endosperm. PLoS Genet 2011, 7:e1002125.
42. Feil R., Berger F. Convergent evolution of genomic imprinting in plants and mammals. Trends Genet 2007, 23:192-199.
43. Erilova A., Brownfield L., Exner V., Rosa M., Twell D., Mittelsten Scheid O., Hennig L., Kohler C. Imprinting of the polycomb group gene MEDEA serves as a ploidy sensor in Arabidopsis. PLoS Genet 2009, 5:e1000663.
44. Jullien P.E., Berger F. Parental genome dosage imbalance deregulates imprinting in Arabidopsis. PLoS Genet 2010, 6. e1000885.
45. Vielle-Calzada J.P., Thomas J., Spillane C., Coluccio A., Hoeppner M.A., Grossniklaus U. Maintenance of genomic imprinting at the Arabidopsis medea locus requires zygotic DDM1 activity. Genes Dev 1999, 13:2971-2982.
46. Kinoshita T., Yadegari R., Harada J.J., Goldberg R.B., Fischer R.L. Imprinting of the MEDEA polycomb gene in the Arabidopsis endosperm. Plant Cell 1999, 11:1945-1952.
47. Luo M., Bilodeau P., Dennis E.S., Peacock W.J., Chaudhury A. 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 2000, 97:10637-10642.
48. Tiwari S., Schulz R., Ikeda Y., Dytham L., Bravo J., Mathers L., Spielman M., Guzman P., Oakey R.J., Kinoshita T., et al. Maternally expressed PAB C-terminal, a novel imprinted gene in Arabidopsis, encodes the conserved C-terminal domain of polyadenylate binding proteins. Plant Cell 2008, 20:2387-2398.
49. Fitz Gerald J.N., Hui P.S., Berger F. Polycomb group-dependent imprinting of the actin regulator AtFH5 regulates morphogenesis in Arabidopsis thaliana. Development 2009, 136:3399-3404.
50. Kohler C., Page D.R., Gagliardini V., Grossniklaus U. The Arabidopsis thaliana MEDEA polycomb group protein controls expression of PHERES1 by parental imprinting. Nat Genet 2005, 37:28-30.