Epigenomic Modification and Epigenetic Regulation in Rice

Journal of Genetics and Genomics

Volumn 39, Issue 7, 2012, Pages 307-315

  Zhao, Yu ^a   Zhou, Dao Xiu ^b  

^a HUAZHONG AGRICULTURAL UNIVERSITY   (China)

^b UNIVERSITÉ PARIS SACLAY   (France)

Author keywords

Epigenetics; Epigenomics; Oryza sativa

Indexed keywords

HISTONE;

AGRONOMIC TRAIT; ALLELE; CEREAL; CHROMATIN; CROP; DNA METHYLATION; EPIGENETICS; GENE CONTROL; GENE EXPRESSION; GENE EXPRESSION REGULATION; GENE LOCUS; GENE REPRESSION; GENETIC VARIABILITY; GENOTYPE; HERITABILITY; HETEROSIS; NONHUMAN; PLANT DEVELOPMENT; PLANT GROWTH; PLANT STRESS; PROTEIN MODIFICATION; REVIEW; RICE; TRANSPOSON;

CHIMERA; DNA TRANSPOSABLE ELEMENTS; EPIGENESIS, GENETIC; GENE EXPRESSION REGULATION, PLANT; GENOME, PLANT; ORYZA SATIVA;

ORYZA SATIVA;

EID: 84864310445     PISSN: 16738527     EISSN: 18735533     Source Type: Journal    
DOI: 10.1016/j.jgg.2012.02.009     Document Type: Review

References (82)

1. Akimoto K., Katakami H., Kim H.J., Ogawa E., Sano C.M., Wada Y., Sano H. Epigenetic inheritance in rice plants. Ann. Bot. 2007, 100:205-217.
2. Arteaga-Vazquez M.A., Chandler V.L. Paramutation in maize: RNA mediated trans-generational gene silencing. Curr. Opin. Genet. Dev. 2010, 20:156-163.
3. Baroux C., Pien S., Grossniklaus U. Chromatin modification and remodeling during early seed development. Curr. Opin. Genet. Dev. 2007, 17:473-479.
4. Becker C., Hagmann J., Muller J., Koenig D., Stegle O., Borgwardt K., Weigel D. Spontaneous epigenetic variation in the Arabidopsis thaliana methylome. Nature 2011, 480:245-249.
5. Berger S.L. The complex language of chromatin regulation during transcription. Nature 2007, 447:407-412.
6. Birchler J.A., Auger D.L., Riddle N.C. In search of the molecular basis of heterosis. Plant Cell 2003, 15:2236-2239.
7. Boyko A., Blevins T., Yao Y., Golubov A., Bilichak A., Ilnytskyy Y., Hollunder J., Meins F., Kovalchuk I. Transgenerational adaptation of Arabidopsis to stress requires DNA methylation and the function of Dicer-like proteins. PLoS ONE 2010, 5(3):e9514.
8. Cao X., Jacobsen S.E. Locus-specific control of asymmetric and CpNpG methylation by the DRM and CMT3 methyltransferase genes. Proc. Natl. Acad. Sci. USA 2002, 99(Suppl. 4):16491-16498.
9. Chan S.W., Henderson I.R., Jacobsen S.E. Gardening the genome: DNA methylation in Arabidopsis thaliana. Nat. Rev. Genet. 2005, 6:351-360.
10. Chen H., Gu X., Su I.H., Bottino R., Contreras J.L., Tarakhovsky A., Kim S.K. Polycomb protein Ezh2 regulates pancreatic beta-cell Ink4a/Arf expression and regeneration in diabetes mellitus. Genes Dev. 2009, 23:975-985.
11. Chen X., Hu Y., Zhou D.X. Epigenetic gene regulation by plant Jumonji group of histone demethylase. Biochim. Biophys. Acta 2011, 1809:421-426.
12. Chen Z.J., Tian L. Roles of dynamic and reversible histone acetylation in plant development and polyploidy. Biochim. Biophys. Acta 2007, 1769:295-307.
13. Cheng C., Daigen M., Hirochika H. Epigenetic regulation of the rice retrotransposon Tos17. Mol. Genet. Genomics 2006, 276:378-390.
14. 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.
15. Chung P.J., Kim Y.S., Jeong J.S., Park S.H., Nahm B.H., Kim J.K. The histone deacetylase OsHDAC1 epigenetically regulates the OsNAC6 gene that controls seedling root growth in rice. Plant J. 2009, 59:764-776.
16. Cubas P., Vincent C., Coen E. An epigenetic mutation responsible for natural variation in floral symmetry. Nature 1999, 401:157-161.
17. Ding Y., Wang X., Su L., Zhai J., Cao S., Zhang D., Liu C., Bi Y., Qian Q., Cheng Z., Chu C., Cao X. SDG714, a histone H3K9 methyltransferase, is involved in Tos17 DNA methylation and transposition in rice. Plant Cell 2007, 19:9-22.
18. Eichten S.R., Swanson-Wagner R.A., Schnable J.C., Waters A.J., Hermanson P.J., Liu S., Yeh C.T., Jia Y., Gendler K., Freeling M., Schnable P., Vaughn M., Springer N. Heritable epigenetic variation among maize inbreds. PLoS Genet. 2011, 7(11):e1002372.
19. 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., Ukomadu C., Sadler K.C., Pradhan S., Pellegrini M., Jacobsen S.E. Conservation and divergence of methylation patterning in plants and animals. Proc. Natl. Acad. Sci. USA 2010, 107:8689-8694.
20. Feschotte C., Jiang N., Wessler S.R. Plant transposable elements: where genetics meets genomics. Nat. Rev. Genet. 2002, 3:329-341.
21. Gehring M., Bubb K.L., Henikoff S. Extensive demethylation of repetitive elements during seed development underlies gene imprinting. Science 2009, 324:1447-1451.
22. Gehring M., Henikoff S. DNA methylation dynamics in plant genomes. Biochim. Biophys. Acta 2007, 1769:276-286.
23. Goff S.A., Ricke D., Lan T.H., Presting G., Wang R., Dunn M., Glazebrook J., Sessions A., Oeller P., Varma H., Hadley D., Hutchison D., Martin C., Katagiri F., Lange B.M., Moughamer T., Xia Y., Budworth P., Zhong J., Miguel T., Paszkowski U., Zhang S., Colbert M., Sun W.L., Chen L., Cooper B., Park S., Wood T.C., Mao L., Quail P., Wing R., Dean R., Yu Y., Zharkikh A., Shen R., Sahasrabudhe S., Thomas A., Cannings R., Gutin A., Pruss D., Reid J., Tavtigian S., Mitchell J., Eldredge G., Scholl T., Miller R.M., Bhatnagar S., Adey N., Rubano T., Tusneem N., Robinson R., Feldhaus J., Macalma T., Oliphant A., Briggs S. A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 2002, 296:92-100.
24. Gong Z., Morales-Ruiz T., Ariza R.R., Roldan-Arjona T., David L., Zhu J.K. ROS1, a repressor of transcriptional gene silencing in Arabidopsis, encodes a DNA glycosylase/lyase. Cell 2002, 111:803-814.
25. He G., Zhu X., Elling A.A., Chen L., Wang X., Guo L., Liang M., He H., Zhang H., Chen F., Qi Y., Chen R., Deng X.W. Global epigenetic and transcriptional trends among two rice subspecies and their reciprocal hybrids. Plant Cell 2010, 22:17-33.
26. Hennig L., Derkacheva M. Diversity of polycomb group complexes in plants: same rules, different players?. Trends Genet. 2009, 25:414-423.
27. Hirochika H., Sugimoto K., Otsuki Y., Tsugawa H., Kanda M. Retrotransposons of rice involved in mutations induced by tissue culture. Proc. Natl. Acad. Sci. USA 1996, 93:7783-7788.
28. 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.
29. Hu Y., Qin F., Huang L., Sun Q., Li C., Zhao Y., Zhou D.X. Rice histone deacetylase genes display specific expression patterns and developmental functions. Biochem. Biophys. Res. Commun. 2009, 388:266-271.
30. Hu Y., Shen Y., Conde E.S.N., Zhou D.X. The role of histone methylation and H2A.Z occupancy during rapid activation of ethylene responsive genes. PLoS ONE 2011, 6(11):e28224.
31. Hu Y., Liu D., Zhong X., Zhang C., Zhang Q., Zhou D.X. A CHD3 protein recognizes and regulates methylated histone H3 lysines 4 and 27 over a subset of targets in the rice genome. Proc. Natl. Acad. Sci. USA 2012, 109:5773-5778.
32. Huang L., Sun Q., Qin F., Li C., Zhao Y., Zhou D.X. Down-regulation of a SILENT INFORMATION REGULATOR2-related histone deacetylase gene, OsSRT1, induces DNA fragmentation and cell death in rice. Plant Physiol. 2007, 144:1508-1519.
33. Ishikawa R., Kinoshita T. Epigenetic programming: the challenge to species hybridization. Mol. Plant 2009, 2:589-599.
34. Jacobsen S.E., Meyerowitz E.M. Hypermethylated SUPERMAN epigenetic alleles in Arabidopsis. Science 1997, 277:1100-1103.
35. Jang I.C., Pahk Y.M., Song S.I., Kwon H.J., Nahm B.H., Kim J.K. Structure and expression of the rice class-I type histone deacetylase genes OsHDAC1-3: OsHDAC1 overexpression in transgenic plants leads to increased growth rate and altered architecture. Plant J. 2003, 33:531-541.
36. Jenuwein T., Laible G., Dorn R., Reuter G. SET domain proteins modulate chromatin domains in eu- and heterochromatin. Cell. Mol. Life Sci. 1998, 54:80-93.
37. Jiang N., Bao Z., Zhang X., Hirochika H., Eddy S.R., McCouch S.R., Wessler S.R. An active DNA transposon family in rice. Nature 2003, 421:163-167.
38. Josefsson C., Dilkes B., Comai L. Parent-dependent loss of gene silencing during interspecies hybridization. Curr. Biol. 2006, 16:1322-1328.
39. Kikuchi K., Terauchi K., Wada M., Hirano H.Y. The plant MITE mPing is mobilized in anther culture. Nature 2003, 421:167-170.
40. Komiya R., Ikegami A., Tamaki S., Yokoi S., Shimamoto K. Hd3a and RFT1 are essential for flowering in rice. Development 2008, 135:767-774.
41. Kou H.P., Li Y., Song X.X., Ou X.F., Xing S.C., Ma J., von Wettstein D., Liu B. Heritable alteration in DNA methylation induced by nitrogen-deficiency stress accompanies enhanced tolerance by progenies to the stress in rice (Oryza sativa L.). J. Plant Physiol. 2011, 168:1685-1693.
42. La H., Ding B., Mishra G.P., Zhou B., Yang H., Bellizzi Mdel R., Chen S., Meyers B.C., Peng Z., Zhu J.K., Wang G.L. A 5-methylcytosine DNA glycosylase/lyase demethylates the retrotransposon Tos17 and promotes its transposition in rice. Proc. Natl. Acad. Sci. USA 2011, 108:15498-15503.
43. Li C., Huang L., Xu C., Zhao Y., Zhou D.X. Altered levels of histone deacetylase OsHDT1 affect differential gene expression patterns in hybrid rice. PLoS ONE 2011, 6(7):e21789.
44. Li X., Wang X., He K., Ma Y., Su N., He H., Stolc V., Tongprasit W., Jin W., Jiang J., Terzaghi W., Li S., Deng X.W. High-resolution mapping of epigenetic modifications of the rice genome uncovers interplay between DNA methylation, histone methylation, and gene expression. Plant Cell 2008, 20:259-276.
45. Liang Y.K., Wang Y., Zhang Y., Li S.G., Lu X.C., Li H., Zou C., Xu Z.H., Bai S.N. OsSET1, a novel SET-domain-containing gene from rice. J. Exp. Bot. 2003, 54:1995-1996.
46. Lin X., Long L., Shan X., Zhang S., Shen S., Liu B. In planta mobilization of mPing and its putative autonomous element Pong in rice by hydrostatic pressurization. J. Exp. Bot. 2006, 57:2313-2323.
47. Liu C., Lu F., Cui X., Cao X. Histone methylation in higher plants. Annu. Rev. Plant Biol. 2010, 61:395-420.
48. Liu Z.L., Han F.P., Tan M., Shan X.H., Dong Y.Z., Wang X.Z., Fedak G., Hao S., Liu B. Activation of a rice endogenous retrotransposon Tos17 in tissue culture is accompanied by cytosine demethylation and causes heritable alteration in methylation pattern of flanking genomic regions. Theor. Appl. Genet. 2004, 109:200-209.
49. Luo M., Platten D., Chaudhury A., Peacock W.J., Dennis E.S. Expression, imprinting, and evolution of rice homologs of the polycomb group genes. Mol. Plant 2009, 2:711-723.
50. Manning K., Tor M., Poole M., Hong Y., Thompson A.J., King G.J., Giovannoni J.J., Seymour G.B. A naturally occurring epigenetic mutation in a gene encoding an SBP-box transcription factor inhibits tomato fruit ripening. Nat. Genet. 2006, 38:948-952.
51. Miura K., Agetsuma M., Kitano H., Yoshimura A., Matsuoka M., Jacobsen S.E., Ashikari M. A metastable DWARF1 epigenetic mutant affecting plant stature in rice. Proc. Natl. Acad. Sci. USA 2009, 106:11218-11223.
52. Miura K., Ikeda M., Matsubara A., Song X.J., Ito M., Asano K., Matsuoka M., Kitano H., Ashikari M. OsSPL14 promotes panicle branching and higher grain productivity in rice. Nat. Genet. 2010, 42:545-549.
53. Mosammaparast N., Shi Y. Reversal of histone methylation: biochemical and molecular mechanisms of histone demethylases. Annu. Rev. Biochem. 2010, 79:155-179.
54. Nakazaki T., Okumoto Y., Horibata A., Yamahira S., Teraishi M., Nishida H., Inoue H., Tanisaka T. Mobilization of a transposon in the rice genome. Nature 2003, 421:170-172.
55. Paszkowski J., Grossniklaus U. Selected aspects of transgenerational epigenetic inheritance and resetting in plants. Curr. Opin. Plant Biol. 2011, 14:195-203.
56. Paterson A.H., Bowers J.E., Bruggmann R., Dubchak I., Grimwood J., Gundlach H., Haberer G., Hellsten U., Mitros T., Poliakov A., Schmutz J., Spannagl M., Tang H., Wang X., Wicker T., Bharti A.K., Chapman J., Feltus F.A., Gowik U., Grigoriev I.V., Lyons E., Maher C.A., Martis M., Narechania A., Otillar R.P., Penning B.W., Salamov A.A., Wang Y., Zhang L., Carpita N.C., Freeling M., Gingle A.R., Hash C.T., Keller B., Klein P., Kresovich S., McCann M.C., Ming R., Peterson D.G., Mehboob-ur-Rahman, Ware D., Westhoff P., Mayer K.F., Messing J., Rokhsar D.S. The Sorghum bicolor genome and the diversification of grasses. Nature 2009, 457:551-556.
57. Pien S., Grossniklaus U. Polycomb group and trithorax group proteins in Arabidopsis. Biochim. Biophys. Acta 2007, 1769:375-382.
58. Qin F., Sun Q., Huang L., Chen X., Zhou D.X. Rice SUVH histone methyltransferase genes display specific functions in chromatin modification and retrotransposon repression. Mol. Plant 2010, 3:773-782.
59. Richards E.J. Natural epigenetic variation in plant species: a view from the field. Curr. Opin. Plant Biol. 2011, 14:204-209.
60. Rigal M., Mathieu O. A " mille-feuille" of silencing: epigenetic control of transposable elements. Biochim. Biophys. Acta 2011, 1809:452-458.
61. Schmitz R.J., Schultz M.D., Lewsey M.G., O'Malley R.C., Urich M.A., Libiger O., Schork N.J., Ecker J.R. Transgenerational epigenetic instability is a source of novel methylation variants. Science 2011, 334:369-373.
62. Servet C., Conde e Silva N., Zhou D.X. Histone acetyltransferase AtGCN5/HAG1 is a versatile regulator of developmental and inducible gene expression in Arabidopsis. Mol. Plant 2010, 3:670-677.
63. Shan X., Liu Z., Dong Z., Wang Y., Chen Y., Lin X., Long L., Han F., Dong Y., Liu B. Mobilization of the active MITE transposons mPing and Pong in rice by introgression from wild rice (Zizania latifolia Griseb.). Mol. Biol. Evol. 2005, 22:976-990.
64. Springer N.M., Stupar R.M. Allele-specific expression patterns reveal biases and embryo-specific parent-of-origin effects in hybrid maize. Plant Cell 2007, 19:2391-2402.
65. Springer N.M., Stupar R.M. Allelic variation and heterosis in maize: how do two halves make more than a whole?. Genome Res. 2007, 17:264-275.
66. Sui P., Jin J., Ye S., Mu C., Gao J., Feng H., Shen W.H., Yu Y., Dong A. H3K36 methylation is critical for brassinosteroid-regulated plant growth and development in rice. Plant J 2011, 10.1111/j.1365-313X.2011.04873.x.
67. Sun Q., Zhou D.X. Rice jmjC domain-containing gene JMJ706 encodes H3K9 demethylase required for floral organ development. Proc. Natl. Acad. Sci. USA 2008, 105:13679-13684.
68. 1 hybrid and its inbred parents. Proc. Natl. Acad. Sci. USA 2006, 103:6805-6810.
69. Thakur J.K., Malik M.R., Bhatt V., Reddy M.K., Sopory S.K., Tyagi A.K., Khurana J.P. A POLYCOMB group gene of rice (Oryza sativa L. subspecies indica), OsiEZ1, codes for a nuclear-localized protein expressed preferentially in young seedlings and during reproductive development. Gene 2003, 314:1-13.
70. Tsuji H., Saika H., Tsutsumi N., Hirai A., Nakazono M. Dynamic and reversible changes in histone H3-Lys4 methylation and H3 acetylation occurring at submergence-inducible genes in rice. Plant Cell Physiol. 2006, 47:995-1003.
71. Turck F., Roudier F., Farrona S., Martin-Magniette M.L., Guillaume E., Buisine N., Gagnot S., Martienssen R.A., Coupland G., Colot V. Arabidopsis TFL2/LHP1 specifically associates with genes marked by trimethylation of histone H3 lysine 27. PLoS Genet. 2007, 3(6):e86.
72. Vaughn M.W., Tanurdzic M., Lippman Z., Jiang H., Carrasquillo R., Rabinowicz P.D., Dedhia N., McCombie W.R., Agier N., Bulski A., Colot V., Doerge R.W., Martienssen R.A. Epigenetic natural variation in Arabidopsis thaliana. PLoS Biol. 2007, 5(7):e174.
73. Verhoeven K.J., Jansen J.J., van Dijk P.J., Biere A. Stress-induced DNA methylation changes and their heritability in asexual dandelions. New Phytol. 2010, 185:1108-1118.
74. Wang N., Wang H., Zhang D., Wu Y., Ou X., Liu S., Dong Z., Liu B. Transpositional reactivation of the Dart transposon family in rice lines derived from introgressive hybridization with Zizania latifolia. BMC Plant Biol. 2010, 10:190.
75. Wang W., Zhao X., Pan Y., Zhu L., Fu B., Li Z. DNA methylation changes detected by methylation-sensitive amplified polymorphism in two contrasting rice genotypes under salt stress. J. Genet. Genomics 2011, 38:419-424.
76. Wei G., Tao Y., Liu G., Chen C., Luo R., Xia H., Gan Q., Zeng H., Lu Z., Han Y., Li X., Song G., Zhai H., Peng Y., Li D., Xu H., Wei X., Cao M., Deng H., Xin Y., Fu X., Yuan L., Yu J., Zhu Z., Zhu L. A transcriptomic analysis of superhybrid rice LYP9 and its parents. Proc. Natl. Acad. Sci. USA 2009, 106:7695-7701.
77. Wu Y., Kikuchi S., Yan H., Zhang W., Rosenbaum H., Iniguez A.L., Jiang J. Euchromatic subdomains in rice centromeres are associated with genes and transcription. Plant Cell 2011, 23:4054-4064.
78. Yan H., Kikuchi S., Neumann P., Zhang W., Wu Y., Chen F., Jiang J. Genome-wide mapping of cytosine methylation revealed dynamic DNA methylation patterns associated with genes and centromeres in rice. Plant J. 2010, 63:353-365.
79. Yu J., Hu S., Wang J., Wong G.K., Li S., Liu B., Deng Y., Dai L., Zhou Y., Zhang X., Cao M., Liu J., Sun J., Tang J., Chen Y., Huang X., Lin W., Ye C., Tong W., Cong L., Geng J., Han Y., Li L., Li W., Hu G., Huang X., Li W., Li J., Liu Z., Li L., Liu J., Qi Q., Liu J., Li L., Li T., Wang X., Lu H., Wu T., Zhu M., Ni P., Han H., Dong W., Ren X., Feng X., Cui P., Li X., Wang H., Xu X., Zhai W., Xu Z., Zhang J., He S., Zhang J., Xu J., Zhang K., Zheng X., Dong J., Zeng W., Tao L., Ye J., Tan J., Ren X., Chen X., He J., Liu D., Tian W., Tian C., Xia H., Bao Q., Li G., Gao H., Cao T., Wang J., Zhao W., Li P., Chen W., Wang X., Zhang Y., Hu J., Wang J., Liu S., Yang J., Zhang G., Xiong Y., Li Z., Mao L., Zhou C., Zhu Z., Chen R., Hao B., Zheng W., Chen S., Guo W., Li G., Liu S., Tao M., Wang J., Zhu L., Yuan L., Yang H. A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 2002, 296:79-92.
80. 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. USA 2010, 107:18729-18734.
81. Zhang X., Clarenz O., Cokus S., Bernatavichute Y.V., Pellegrini M., Goodrich J., Jacobsen S.E. Whole-genome analysis of histone H3 lysine 27 trimethylation in Arabidopsis. PLoS Biol. 2007, 5:e129.
82. Zhu J.K. Active DNA demethylation mediated by DNA glycosylases. Annu. Rev. Genet. 2009, 43:143-166.