Epigenomic Modification and Epigenetic Regulation in Rice

Yu Zhao; Dao-Xiu Zhou

doi:10.1016/j.jgg.2012.02.009

Volume 39 Issue 7

Jul. 2012

Turn off MathJax

Article Contents

Article Navigation > Journal of Genetics and Genomics > 2012 > 39(7): 307-315

PDF( 393 KB)

Epigenomic Modification and Epigenetic Regulation in Rice

doi: 10.1016/j.jgg.2012.02.009

Yu Zhao^a,
Dao-Xiu Zhou^b

a
National Key Laboratory for Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
b
Institut de Biologie des Plantes, Université Paris sud, Orsay 91405, France

More Information

Corresponding author: E-mail address: dao-xiu.zhou@u-psud.fr (Dao-Xiu Zhou)
Received Date: 2011-12-26
Accepted Date: 2012-02-04
Rev Recd Date: 2012-02-03

Available Online: 2012-04-02

Publish Date: 2012-07-20

Abstract

Abstract

Epigenomes including genome-wide histone modification and DNA methylation profiles are important for genome activity and for defining gene expression patterns of plant development and responses to various environmental conditions. Rice is the most important crop plant and serves as a model for cereal genomics. Rice epigenomic landscape is emerging and the function of chromatin modification regulators in gene expression, transposon repression and plant development is being characterized. Epigenomic variation that gives rise to stable or transgenerational heritable epialleles related to variation of important agronomical traits or stress responses is being characterized in rice. Implication of epigenomic variation in rice heterosis is being exploited.
- Epigenetics,
- Epigenomics

FullText(HTML)

References(82)

References

[1]	Akimoto, K., Katakami, H., Kim, H.J. et al. Epigenetic inheritance in rice plants Ann. Bot., 100 (2007),pp. 205-217
[2]	Arteaga-Vazquez, M.A., Chandler, V.L. Paramutation in maize: RNA mediated trans-generational gene silencing Curr. Opin. Genet. Dev., 20 (2010),pp. 156-163
[3]	Baroux, C., Pien, S., Grossniklaus, U. Chromatin modification and remodeling during early seed development Curr. Opin. Genet. Dev., 17 (2007),pp. 473-479
[4]	Becker, C., Hagmann, J., Muller, J. et al. Nature, 480 (2011),pp. 245-249
[5]	Berger, S.L. The complex language of chromatin regulation during transcription Nature, 447 (2007),pp. 407-412
[6]	Birchler, J.A., Auger, D.L., Riddle, N.C. In search of the molecular basis of heterosis Plant Cell, 15 (2003),pp. 2236-2239
[7]	Boyko, A., Blevins, T., Yao, Y. et al. PLoS ONE, 5 (2010),p. 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, 99 (2002),pp. 16491-16498
[9]	Chan, S.W., Henderson, I.R., Jacobsen, S.E. Nat. Rev. Genet., 6 (2005),pp. 351-360
[10]	Chen, H., Gu, X., Su, I.H. et al. Polycomb protein Ezh2 regulates pancreatic beta-cell Ink4a/Arf expression and regeneration in diabetes mellitus Genes Dev., 23 (2009),pp. 975-985
[11]	Chen, X., Hu, Y., Zhou, D.X. Epigenetic gene regulation by plant Jumonji group of histone demethylase Biochim. Biophys. Acta, 1809 (2011),pp. 421-426
[12]	Chen, Z.J., Tian, L. Roles of dynamic and reversible histone acetylation in plant development and polyploidy Biochim. Biophys. Acta, 1769 (2007),pp. 295-307
[13]	Cheng, C., Daigen, M., Hirochika, H. Mol. Genet. Genomics, 276 (2006),pp. 378-390
[14]	Choi, Y., Gehring, M., Johnson, L. et al. Cell, 110 (2002),pp. 33-42
[15]	Chung, P.J., Kim, Y.S., Jeong, J.S. et al. Plant J., 59 (2009),pp. 764-776
[16]	Cubas, P., Vincent, C., Coen, E. An epigenetic mutation responsible for natural variation in floral symmetry Nature, 401 (1999),pp. 157-161
[17]	Ding, Y., Wang, X., Su, L. et al. Plant Cell, 19 (2007),pp. 9-22
[18]	Eichten, S.R., Swanson-Wagner, R.A., Schnable, J.C. et al. Heritable epigenetic variation among maize inbreds PLoS Genet., 7 (2011),p. e1002372
[19]	Feng, S., Cokus, S.J., Zhang, X. et al. Conservation and divergence of methylation patterning in plants and animals Proc. Natl. Acad. Sci. USA, 107 (2010),pp. 8689-8694
[20]	Feschotte, C., Jiang, N., Wessler, S.R. Plant transposable elements: where genetics meets genomics Nat. Rev. Genet., 3 (2002),pp. 329-341
[21]	Gehring, M., Bubb, K.L., Henikoff, S. Extensive demethylation of repetitive elements during seed development underlies gene imprinting Science, 324 (2009),pp. 1447-1451
[22]	Gehring, M., Henikoff, S. DNA methylation dynamics in plant genomes Biochim. Biophys. Acta, 1769 (2007),pp. 276-286
[23]	Goff, S.A., Ricke, D., Lan, T.H. et al. Science, 296 (2002),pp. 92-100
[24]	Gong, Z., Morales-Ruiz, T., Ariza, R.R. et al. Cell, 111 (2002),pp. 803-814
[25]	He, G., Zhu, X., Elling, A.A. et al. Global epigenetic and transcriptional trends among two rice subspecies and their reciprocal hybrids Plant Cell, 22 (2010),pp. 17-33
[26]	Hennig, L., Derkacheva, M. Diversity of polycomb group complexes in plants: same rules, different players? Trends Genet., 25 (2009),pp. 414-423
[27]	Hirochika, H., Sugimoto, K., Otsuki, Y. et al. Retrotransposons of rice involved in mutations induced by tissue culture Proc. Natl. Acad. Sci. USA, 93 (1996),pp. 7783-7788
[28]	Hsieh, T.F., Ibarra, C.A., Silva, P. et al. Science, 324 (2009),pp. 1451-1454
[29]	Hu, Y., Qin, F., Huang, L. et al. Rice histone deacetylase genes display specific expression patterns and developmental functions Biochem. Biophys. Res. Commun., 388 (2009),pp. 266-271
[30]	Hu, Y., Shen, Y., Conde, E.S.N. et al. The role of histone methylation and H2A.Z occupancy during rapid activation of ethylene responsive genes PLoS ONE, 6 (2011),p. e28224
[31]	Hu, Y., Liu, D., Zhong, X. et al. 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, 109 (2012),pp. 5773-5778
[32]	Huang, L., Sun, Q., Qin, F. et al. Plant Physiol., 144 (2007),pp. 1508-1519
[33]	Ishikawa, R., Kinoshita, T. Epigenetic programming: the challenge to species hybridization Mol. Plant, 2 (2009),pp. 589-599
[34]	Jacobsen, S.E., Meyerowitz, E.M. Science, 277 (1997),pp. 1100-1103
[35]	Jang, I.C., Pahk, Y.M., Song, S.I. et al. Plant J., 33 (2003),pp. 531-541
[36]	Jenuwein, T., Laible, G., Dorn, R. et al. SET domain proteins modulate chromatin domains in eu- and heterochromatin Cell. Mol. Life Sci., 54 (1998),pp. 80-93
[37]	Jiang, N., Bao, Z., Zhang, X. et al. An active DNA transposon family in rice Nature, 421 (2003),pp. 163-167
[38]	Josefsson, C., Dilkes, B., Comai, L. Parent-dependent loss of gene silencing during interspecies hybridization Curr. Biol., 16 (2006),pp. 1322-1328
[39]	Kikuchi, K., Terauchi, K., Wada, M. et al. The plant MITE mPing is mobilized in anther culture Nature, 421 (2003),pp. 167-170
[40]	Komiya, R., Ikegami, A., Tamaki, S. et al. Hd3a and RFT1 are essential for flowering in rice Development, 135 (2008),pp. 767-774
[41]	Kou, H.P., Li, Y., Song, X.X. et al. J. Plant Physiol., 168 (2011),pp. 1685-1693
[42]	La, H., Ding, B., Mishra, G.P. et al. Proc. Natl. Acad. Sci. USA, 108 (2011),pp. 15498-15503
[43]	Li, C., Huang, L., Xu, C. et al. Altered levels of histone deacetylase OsHDT1 affect differential gene expression patterns in hybrid rice PLoS ONE, 6 (2011),p. e21789
[44]	Li, X., Wang, X., He, K. et al. High-resolution mapping of epigenetic modifications of the rice genome uncovers interplay between DNA methylation, histone methylation, and gene expression Plant Cell, 20 (2008),pp. 259-276
[45]	Liang, Y.K., Wang, Y., Zhang, Y. et al. J. Exp. Bot., 54 (2003),pp. 1995-1996
[46]	Lin, X., Long, L., Shan, X. et al. In planta mobilization of mPing and its putative autonomous element Pong in rice by hydrostatic pressurization J. Exp. Bot., 57 (2006),pp. 2313-2323
[47]	Liu, C., Lu, F., Cui, X. et al. Histone methylation in higher plants Annu. Rev. Plant Biol., 61 (2010),pp. 395-420
[48]	Liu, Z.L., Han, F.P., Tan, M. et al. Theor. Appl. Genet., 109 (2004),pp. 200-209
[49]	Luo, M., Platten, D., Chaudhury, A. et al. Expression, imprinting, and evolution of rice homologs of the polycomb group genes Mol. Plant, 2 (2009),pp. 711-723
[50]	Manning, K., Tor, M., Poole, M. et al. A naturally occurring epigenetic mutation in a gene encoding an SBP-box transcription factor inhibits tomato fruit ripening Nat. Genet., 38 (2006),pp. 948-952
[51]	Miura, K., Agetsuma, M., Kitano, H. et al. Proc. Natl. Acad. Sci. USA, 106 (2009),pp. 11218-11223
[52]	Miura, K., Ikeda, M., Matsubara, A. et al. Nat. Genet., 42 (2010),pp. 545-549
[53]	Mosammaparast, N., Shi, Y. Reversal of histone methylation: biochemical and molecular mechanisms of histone demethylases Annu. Rev. Biochem., 79 (2010),pp. 155-179
[54]	Nakazaki, T., Okumoto, Y., Horibata, A. et al. Mobilization of a transposon in the rice genome Nature, 421 (2003),pp. 170-172
[55]	Paszkowski, J., Grossniklaus, U. Selected aspects of transgenerational epigenetic inheritance and resetting in plants Curr. Opin. Plant Biol., 14 (2011),pp. 195-203
[56]	Paterson, A.H., Bowers, J.E., Bruggmann, R. et al. Nature, 457 (2009),pp. 551-556
[57]	Pien, S., Grossniklaus, U. Biochim. Biophys. Acta, 1769 (2007),pp. 375-382
[58]	Qin, F., Sun, Q., Huang, L. et al. Rice SUVH histone methyltransferase genes display specific functions in chromatin modification and retrotransposon repression Mol. Plant, 3 (2010),pp. 773-782
[59]	Richards, E.J. Natural epigenetic variation in plant species: a view from the field Curr. Opin. Plant Biol., 14 (2011),pp. 204-209
[60]	Rigal, M., Mathieu, O. A “mille-feuille” of silencing: epigenetic control of transposable elements Biochim. Biophys. Acta, 1809 (2011),pp. 452-458
[61]	Schmitz, R.J., Schultz, M.D., Lewsey, M.G. et al. Transgenerational epigenetic instability is a source of novel methylation variants Science, 334 (2011),pp. 369-373
[62]	Servet, C., Conde e Silva, N., Zhou, D.X. Mol. Plant, 3 (2010),pp. 670-677
[63]	Shan, X., Liu, Z., Dong, Z. et al. Mol. Biol. Evol., 22 (2005),pp. 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, 19 (2007),pp. 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., 17 (2007),pp. 264-275
[66]	Sui, P., Jin, J., Ye, S. et al. H3K36 methylation is critical for brassinosteroid-regulated plant growth and development in rice Plant J (2011)
[67]	Sun, Q., Zhou, D.X. Proc. Natl. Acad. Sci. USA, 105 (2008),pp. 13679-13684
[68]	Swanson-Wagner, R.A., Jia, Y., deCook, R. et al. Proc. Natl. Acad. Sci. USA, 103 (2006),pp. 6805-6810
[69]	Thakur, J.K., Malik, M.R., Bhatt, V. et al. Gene, 314 (2003),pp. 1-13
[70]	Tsuji, H., Saika, H., Tsutsumi, N. et al. Dynamic and reversible changes in histone H3-Lys4 methylation and H3 acetylation occurring at submergence-inducible genes in rice Plant Cell Physiol., 47 (2006),pp. 995-1003
[71]	Turck, F., Roudier, F., Farrona, S. et al. PLoS Genet., 3 (2007),p. e86
[72]	Vaughn, M.W., Tanurdzic, M., Lippman, Z. et al. PLoS Biol., 5 (2007),p. e174
[73]	Verhoeven, K.J., Jansen, J.J., van Dijk, P.J. et al. Stress-induced DNA methylation changes and their heritability in asexual dandelions New Phytol., 185 (2010),pp. 1108-1118
[74]	Wang, N., Wang, H., Zhang, D. et al. BMC Plant Biol., 10 (2010),p. 190
[75]	Wang, W., Zhao, X., Pan, Y. et al. DNA methylation changes detected by methylation-sensitive amplified polymorphism in two contrasting rice genotypes under salt stress J. Genet. Genomics, 38 (2011),pp. 419-424
[76]	Wei, G., Tao, Y., Liu, G. et al. A transcriptomic analysis of superhybrid rice LYP9 and its parents Proc. Natl. Acad. Sci. USA, 106 (2009),pp. 7695-7701
[77]	Wu, Y., Kikuchi, S., Yan, H. et al. Euchromatic subdomains in rice centromeres are associated with genes and transcription Plant Cell, 23 (2011),pp. 4054-4064
[78]	Yan, H., Kikuchi, S., Neumann, P. et al. Genome-wide mapping of cytosine methylation revealed dynamic DNA methylation patterns associated with genes and centromeres in rice Plant J., 63 (2010),pp. 353-365
[79]	Yu, J., Hu, S., Wang, J. et al. Science, 296 (2002),pp. 79-92
[80]	Zemach, A., Kim, M.Y., Silva, P. et al. Local DNA hypomethylation activates genes in rice endosperm Proc. Natl. Acad. Sci. USA, 107 (2010),pp. 18729-18734
[81]	Zhang, X., Clarenz, O., Cokus, S. et al. PLoS Biol., 5 (2007),p. e129
[82]	Zhu, J.K. Active DNA demethylation mediated by DNA glycosylases Annu. Rev. Genet., 43 (2009),pp. 143-166