The epigenome and plant development

Annual Review of Plant Biology

Volumn 62, Issue , 2011, Pages 411-435

  He, Guangming ^a,b   Elling, Axel A ^b,c   Deng, Xing Wang ^a,b  

^a PEKING UNIVERSITY   (China)

^b YALE UNIVERSITY   (United States)

^c WASHINGTON STATE UNIVERSITY   (United States)

Author keywords

endosperm; epigenomic reprogramming; epigenomic variation; gametogenesis; heterosis; imprinting; light response; plant epigenome

Indexed keywords

VEGETABLE PROTEIN;

ARTICLE; CHROMATIN ASSEMBLY AND DISASSEMBLY; DNA METHYLATION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETIC EPIGENESIS; GENETIC VARIABILITY; GENETICS; GENOME IMPRINTING; GROWTH, DEVELOPMENT AND AGING; LIGHT; METABOLISM; PLANT; RADIATION EXPOSURE;

CHROMATIN ASSEMBLY AND DISASSEMBLY; DNA METHYLATION; EPIGENESIS, GENETIC; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; GENETIC VARIATION; GENOMIC IMPRINTING; LIGHT; PLANT PROTEINS; PLANTS;

EID: 79955592294     PISSN: 15435008     EISSN: 15452123     Source Type: Book Series    
DOI: 10.1146/annurev-arplant-042110-103806     Document Type: Article

References (148)

1. Alabadi D, Gallego-Bartoloḿe J, Orlando L, Garcia-Ćarcel L, Rubio V, et al. 2008. Gibberellins modulate light signaling pathways to prevent Arabidopsis seedling de-etiolation in darkness. Plant J. 53:324-35.
2. Barski A, Cuddapah S, Cui K, Roh TY, Schones DE, et al. 2007. High-resolution profiling of histone methylations in the human genome. Cell 129:823-37. (Pubitemid 46802390)
3. Beck S, Rakyan VK. 2008. The methylome: approaches for global DNA methylation profiling. Trends Genet. 24:231-37.
4. Benfey PN, Mitchell-Olds T. 2008. From genotype to phenotype: systems biology meets natural variation. Science 320:495-97. (Pubitemid 351590634)
5. Benhamed M, Bertrand C, Servet C, Zhou DX. 2006. Arabidopsis GCN5, HD1, and TAF1/HAF2 interact to regulate histone acetylation required for light-responsive gene expression. Plant Cell 18:2893-903. (Pubitemid 46013264)
6. Berger SL. 2007. The complex language of chromatin regulation during transcription. Nature 447:407-12. (Pubitemid 46816746)
7. Bernatavichute YV, Zhang X, Cokus S, Pellegrini M, Jacobsen SE. 2008. Genome-wide association of histone H3 lysine nine methylation with CHG DNA methylation in Arabidopsis thaliana. PLoS ONE 3:e3156.
8. Bernstein BE, Meissner A, Lander ES. 2007. The mammalian epigenome. Cell 128:669-81. (Pubitemid 46273573)
9. Bertrand C, Benhamed M, Li YF, AyadiM, Lemonnier G, et al. 2005. Arabidopsis HAF2 gene encoding TATA-binding protein (TBP)-associated factor TAF1 is required to integrate light signals to regulate gene expression and growth. J. Biol. Chem. 280:1465-73.
10. Birchler JA, Auger DL, Riddle NC. 2003. In search of the molecular basis of heterosis. Plant Cell 15:2236-39. (Pubitemid 37261796)
11. Birchler JA, YaoH, Chudalayandi S. 2006. Unraveling the genetic basis of hybrid vigor. Proc. Natl. Acad. Sci. USA 103:12957-58. (Pubitemid 44338897)
12. Bowler C, BenvenutoG, Laflamme P, MolinoD, Probst AV, et al. 2004. Chromatin techniques for plant cells. Plant J. 39:776-89. (Pubitemid 39218784)
13. Chan SW. 2008. Inputs and outputs for chromatin-targeted RNAi. Trends Plant Sci. 13:383-89.
14. Chan SW, Henderson IR, Jacobsen SE. 2005. Gardening the genome: DNA methylation in Arabidopsis thaliana. Nat. Rev. Genet. 6:351-60. (Pubitemid 40577179)
15. Charron JB, He H, Elling AA, Deng XW. 2009. Dynamic landscapes of four histone modifications during deetiolation in Arabidopsis. Plant Cell 21:3732-48.
16. Chen M, Chory J, Fankhauser C. 2004. Light signal transduction in higher plants. Annu. Rev. Genet. 38:87-117. (Pubitemid 40013725)
17. Chen X. 2009. Small RNAs and their roles in plant development. Annu. Rev. Cell Dev. Biol. 25:21-44.
18. Choi Y, Gehring M, Johnson L, Hannon M, Harada JJ, et al. 2002. DEMETER, a DNA glycosylase domain protein, is required for endosperm gene imprinting and seed viability in Arabidopsis. Cell 110:33-42. (Pubitemid 34874604)
19. Chua YL, Brown AP,Gray JC. 2001. Targeted histone acetylation and altered nuclease accessibility over short regions of the pea plastocyanin gene. Plant Cell 13:599-612. (Pubitemid 32265378)
20. Chua YL, Watson LA, Gray JC. 2003. The transcriptional enhancer of the pea plastocyanin gene associates with the nuclear matrix and regulates gene expression through histone acetylation. Plant Cell 15:1468-79. (Pubitemid 36715186)
21. Clarke J, Wu HC, Jayasinghe L, Patel A, Reid S, Bayley H. 2009. Continuous base identification for single-molecule nanopore DNA sequencing. Nat. Nanotechnol. 4:265-70.
22. Cokus SJ, Feng S, Zhang X, Chen Z, Merriman B, et al. 2008. Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature 452:215-19. (Pubitemid 351380251)
23. Crow JF. 1948. Alternative hypotheses of hybrid vigor. Genetics 33:477-87.
24. Cubas P, Vincent C, Coen E. 1999. An epigenetic mutation responsible for natural variation in floral symmetry. Nature 401:157-61. (Pubitemid 29436317)
25. de Lucas M, Davíere JM, Rodríguez-Falćon M, Pontin M, Iglesias-Pedraz JM, et al. 2008. A molecular framework for light and gibberellin control of cell elongation. Nature 451:480-84. (Pubitemid 351158891)
26. Dunoyer P, Schott G, Himber C, Meyer D, Takeda A, et al. 2010. Small RNA duplexes function as mobile silencing signals between plant cells. Science 328:912-16.
27. Eckardt NA. 2009. Deep sequencing maps the maize epigenomic landscape. Plant Cell 21:1024-26.
28. Ecker JR. 2010. Zeroing in on DNA methylomes with no BS. Nat. Methods 7:435-37.
29. Elling AA, Deng XW. 2009. Next-generation sequencing reveals complex relationships between the epigenome and transcriptome in maize. Plant Signal. Behav. 4:760-62.
30. Feil R, Berger F. 2007. Convergent evolution of genomic imprinting in plants and mammals. Trends Genet. 23:192-99. (Pubitemid 46509542)
31. Feng S, Cokus SJ, ZhangX,Chen PY, Bostick M, et al. 2010. Conservation and divergence ofmethylation patterning in plants and animals. Proc. Natl. Acad. Sci. USA 107:8689-94.
32. Feng S, Martinez C, Gusmaroli G, Wang Y, Zhou J, et al. 2008. Coordinated regulation of Arabidopsis thaliana development by light and gibberellins. Nature 451:475-79. (Pubitemid 351158880)
33. Flusberg BA, Webster DR, Lee JH, Travers KJ, Olivares EC, et al. 2010. Direct detection of DNA methylation during single-molecule, real-time sequencing. Nat. Methods 7:461-65.
34. Gehring M, Bubb KL, Henikoff S. 2009. Extensive demethylation of repetitive elements during seed development underlies gene imprinting. Science 324:1447-51.
35. Gehring M, Choi Y, Fischer RL. 2004. Imprinting and seed development. Plant Cell 16:S203-13. (Pubitemid 38774229)
36. Gehring M, Huh JH, Hsieh TF, Penterman J, Choi Y, et al. 2006. DEMETER DNA glycosylase establishes MEDEA polycomb gene self-imprinting by allele-specific demethylation. Cell 124:495-506. (Pubitemid 43199436)
37. Gendrel AV, Lippman Z, Martienssen R,Colot V. 2005. Profiling histone modification patterns in plants using genomic tiling microarrays. Nat. Methods 2:213-18. (Pubitemid 41122129)
38. Goll MG, Bestor TH. 2005. Eukaryotic cytosine methyltransferases. Annu. Rev. Biochem. 74:481-514. (Pubitemid 40995515)
39. Gong Z, Morales-Ruiz T, Ariza RR, Rold́an-Arjona T, David L, Zhu JK. 2002. ROS1, a repressor of transcriptional gene silencing in Arabidopsis, encodes a DNA glycosylase/lyase. Cell 111:803-14. (Pubitemid 36106402)
40. Gregory BD, Yazaki J, Ecker JR. 2008. Utilizing tiling microarrays for whole-genome analysis in plants. Plant J. 53:636-44. (Pubitemid 351224691)
41. Guo L, Zhou J, Elling AA, Charron JB, Deng XW. 2008. Histone modifications and expression of lightregulated genes in Arabidopsis are cooperatively influenced by changing light conditions. Plant Physiol. 147:2070-83. (Pubitemid 352844246)
42. Gutíerrez-Marcos JF, Costa LM, Biderre-Petit C, Khbaya B, O'Sullivan DM, et al. 2004. Maternally expressed gene1 is a novel maize endosperm transfer cell-specific gene with a maternal parent-of-origin pattern of expression. Plant Cell 16:1288-301. (Pubitemid 38641521)
43. Gutíerrez-Marcos JF, Costa LM, Dal PraM, Scholten S, Kranz E, et al. 2006. Epigenetic asymmetry of imprinted genes in plant gametes. Nat. Genet. 38:876-78. (Pubitemid 44141654)
44. Ha M, Lu J, Tian L, Ramachandran V, Kasschau KD, et al. 2009. Small RNAs serve as a genetic buffer against genomic shock in Arabidopsis interspecific hybrids and allopolyploids. Proc. Natl. Acad. Sci. USA 106:17835-40.
45. He G, Zhu X, Elling AA, Chen L, Wang X, et al. 2010. Global epigenetic and transcriptional trends among two rice subspecies and their reciprocal hybrids. Plant Cell 22:17-33.
46. Henderson IR, Jacobsen SE. 2007. Epigenetic inheritance in plants. Nature 447:418-24. (Pubitemid 46816748)
47. Hofmann NR. 2009. Dynamic histone modifications in light-regulated gene expression. Plant Cell 21: 3717.
48. Holm M, Ma LG, Qu LJ, Deng XW. 2002. Two interacting bZIP proteins are direct targets of COP1- mediated control of light-dependent gene expression in Arabidopsis. Genes Dev. 16:1247-59. (Pubitemid 34553105)
49. Howell MD, Fahlgren N, Chapman EJ, Cumbie JS, Sullivan CM, et al. 2007. Genome-wide analysis of the RNA-DEPENDENT RNA POLYMERASE6/DICER-LIKE4 pathway in Arabidopsis reveals dependency on miRNA- and tasiRNA-directed targeting. Plant Cell 19:926-42. (Pubitemid 46953238)
50. Hsieh TF, Ibarra CA, Silva P, Zemach A, Eshed-Williams L, et al. 2009. Genome-wide demethylation of Arabidopsis endosperm. Science 324:1451-54.
51. Huh JH, Bauer MJ, Hsieh TF, Fischer RL. 2008. Cellular programming of plant gene imprinting. Cell 132:735-44. (Pubitemid 351312806)
52. Jeltsch A. 2010. Molecular biology. Phylogeny of methylomes. Science 328:837-38.
53. Jiao Y, Lau OS, Deng XW. 2007. Light-regulated transcriptional networks in higher plants. Nat. Rev. Genet. 8:217-30.
54. Jiao Y, Ma L, Strickland E, Deng XW. 2005. Conservation and divergence of light-regulated genome expression patterns during seedling development in rice and Arabidopsis. Plant Cell 17:3239-56.
55. Johannes F, Colot V, Jansen RC. 2008. Epigenome dynamics: a quantitative genetics perspective. Nat. Rev. Genet. 9:883-90.
56. Johannes F, Porcher E, Teixeira FK, Saliba-Colombani V, Simon M, et al. 2009. Assessing the impact of transgenerational epigenetic variation on complex traits. PLoS Genet. 5:e1000530.
57. Johnson MA, Bender J. 2009. Reprogramming the epigenome during germline and seed development. Genome Biol. 10:232.
58. Jullien PE, Katz A, OlivaM,OhadN, Berger F. 2006. Polycomb group complexes self-regulate imprinting of the Polycomb group gene MEDEA in Arabidopsis. Curr. Biol. 16:486-92. (Pubitemid 43343709)
59. Jullien PE, Kinoshita T, Ohad N, Berger F. 2006. Maintenance of DNA methylation during the Arabidopsis life cycle is essential for parental imprinting. Plant Cell 18:1360-72. (Pubitemid 43956102)
60. Kasschau KD, Fahlgren N, Chapman EJ, Sullivan CM, Cumbie JS, et al. 2007. Genome-wide profiling and analysis of Arabidopsis siRNAs. PLoS Biol. 5:e57.
61. Kinoshita T,Miura A, Choi Y, Kinoshita Y, Cao X, et al. 2004. One-way control of FWA imprinting in Arabidopsis endosperm by DNA methylation. Science 303:521-23. (Pubitemid 38120849)
62. Kinoshita Y, Saze H, Kinoshita T, Miura A, Soppe WJ, et al. 2007. Control of FWA gene silencing in Arabidopsis thaliana by SINE-related direct repeats. Plant J. 49:38-45. (Pubitemid 44952696)
63. Kohler C, Hennig L, Spillane C, Pien S,GruissemW,GrossniklausU. 2003. The Polycomb-group protein MEDEA regulates seed development by controlling expression of theMADS-box gene PHERES1. Genes Dev. 17:1540-53. (Pubitemid 36734710)
64. Kouzarides T. 2007. Chromatin modifications and their function. Cell 128:693-705. (Pubitemid 46273577)
65. Laird PW. 2010. Principles and challenges of genome-wide DNA methylation analysis. Nat. Rev. Genet. 11:191-203.
66. Lauria M, Rupe M, Guo M, Kranz E, Pirona R, et al. 2004. Extensive maternal DNA hypomethylation in the endosperm of Zea mays. Plant Cell 16:510-22. (Pubitemid 38192706)
67. Law JA, Jacobsen SE. 2010. Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat. Rev. Genet. 11:204-20.
68. Lee J, He K, Stolc V, Lee H, Figueroa P, et al. 2007. Analysis of transcription factor HY5 genomic binding sites revealed its hierarchical role in light regulation of development. Plant Cell 19:731-49. (Pubitemid 46953224)
69. Lee TF, Zhai J, Meyers BC. 2010. Conservation and divergence in eukaryotic DNA methylation. Proc. Natl. Acad. Sci. USA 107:9027-28.
70. Le Trionnaire G, Twell D. 2010. Small RNAs in angiosperm gametophytes: from epigenetics to gamete development. Genes Dev. 24:1081-85.
71. Li B, Carey M,Workman JL. 2007. The role of chromatin during transcription. Cell 128:707-19. (Pubitemid 46273570)
72. Li L, Lu K, Chen Z, Mu T, Hu Z, Li X. 2008. Dominance, overdominance and epistasis condition the heterosis in two heterotic rice hybrids. Genetics 180:1725-42.
73. Li X, Wang X, He K,MaY, Su N, et al. 2008. High-resolution mapping of epigenetic modifications of the rice genome uncovers interplay between DNA methylation, histone methylation, and gene expression. Plant Cell 20:259-76. (Pubitemid 352844011)
74. Lippman Z, Gendrel AV, Colot V, Martienssen R. 2005. Profiling DNA methylation patterns using genomic tiling microarrays. Nat. Methods 2:219-24. (Pubitemid 41122130)
75. Lister R, Ecker JR. 2009. Finding the fifth base: genome-wide sequencing of cytosine methylation. Genome Res. 19:959-66.
76. Lister R, Gregory BD, Ecker JR. 2009. Next is now: new technologies for sequencing of genomes, transcriptomes, and beyond. Curr. Opin. Plant Biol. 12:107-18.
77. Lister R, O'Malley RC, Tonti-Filippini J, Gregory BD, Berry CC, et al. 2008. Highly integrated singlebase resolution maps of the epigenome in Arabidopsis. Cell 133:523-36.
78. LiuC, Lu F,Cui X, CaoX. 2010. Histonemethylation in higher plants. Annu. Rev. Plant Biol. 61:395-420.
79. Lu C, Kulkarni K, Souret FF, MuthuValliappan R, Tej SS, et al. 2006. MicroRNAs and other small RNAs enriched in the Arabidopsis RNA-dependent RNA polymerase-2 mutant. Genome Res. 16:1276-88. (Pubitemid 44506961)
80. Lu C, Tej SS, Luo S, Haudenschild CD, Meyers BC, Green PJ. 2005. Elucidation of the small RNA component of the transcriptome. Science 309:1567-69. (Pubitemid 41266483)
81. Ma L, Li J, Qu L, Hager J, Chen Z, et al. 2001. Light control of Arabidopsis development entails coordinated regulation of genome expression and cellular pathways. Plant Cell 13:2589-607. (Pubitemid 34096106)
82. Makarevich G, Villar CB, Erilova A,K OhlerC. 2008. Mechanism of PHERES1 imprinting in Arabidopsis. J. Cell Sci. 121:906-12. (Pubitemid 351578126)
83. Manning K, Tor M, Poole M, Hong Y, Thompson AJ, et al. 2006. A naturally occurring epigenetic mutation in a gene encoding an SBP-box transcription factor inhibits tomato fruit ripening. Nat. Genet. 38:948-52. (Pubitemid 44141665)
84. Mardis ER. 2008. Next-generation DNA sequencing methods. Annu. Rev. Genomics Hum. Genet. 9:387-402.
85. Martienssen R. 2010. Molecular biology. Small RNA makes its move. Science 328:834-35.
86. Martienssen RA, Colot V. 2001. DNA methylation and epigenetic inheritance in plants and filamentous fungi. Science 293:1070-74. (Pubitemid 32758076)
87. Martienssen RA, Doerge RW, Colot V. 2005. Epigenomic mapping in Arabidopsis using tiling microarrays. Chromosome Res. 13:299-308.
88. MatzkeM,Kanno T, DaxingerL,HuettelB,Matzke AJ. 2009. RNA-mediated chromatin-based silencing in plants. Curr. Opin. Cell Biol. 21:367-76.
89. McCormick S. 1993. Male gametophyte development. Plant Cell 5:1265-75. (Pubitemid 2001862)
90. Mendenhall EM, Bernstein BE. 2008. Chromatin state maps: new technologies, new insights. Curr. Opin. Genet. Dev. 18:109-15. (Pubitemid 351749822)
91. Mikkelsen TS, Ku M, Jaffe DB, Issac B, Lieberman E, et al. 2007. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448:553-60. (Pubitemid 47206934)
92. Mockler TC, Chan S, Sundaresan A, Chen H, Jacobsen SE, Ecker JR. 2005. Applications of DNA tiling arrays for whole-genome analysis. Genomics 85:1-15. (Pubitemid 39655686)
93. Molnar A, Melnyk CW, Bassett A, Hardcastle TJ, Dunn R, BaulcombeDC. 2010. Small silencing RNAs in plants are mobile and direct epigenetic modification in recipient cells. Science 328:872-75.
94. Mosher RA, Melnyk CW. 2010. siRNAs and DNA methylation: seedy epigenetics. Trends Plant Sci. 15:204-10.
95. 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 460:283-86.
96. Ni Z, Kim ED, Ha M, Lackey E, Liu J, et al. 2009. Altered circadian rhythms regulate growth vigour in hybrids and allopolyploids. Nature 457:327-31.
97. NobutaK,LuC, Shrivastava R, PillayM,DePaoliE, et al. 2008. Distinct size distribution of endogeneous siRNAs in maize: evidence from deep sequencing in the mop1-1 mutant. Proc. Natl. Acad. Sci. USA 105:14958-63.
98. Nobuta K, Venu RC, Lu C, Belo A, Vemaraju K, et al. 2007. An expression atlas of rice mRNAs and small RNAs. Nat. Biotechnol. 25:473-77. (Pubitemid 46572851)
99. Offermann S,Dreesen B, Horst I,Danker T, Jaskiewicz M, Peterhansel C. 2008. Developmental and environmental signals induce distinct histone acetylation profiles on distal and proximal promoter elements of the C4-Pepc gene in maize. Genetics 179:1891-901.
100. Olmedo-Monfil V, Duran-Figueroa N, Arteaga-V́azquez M, Demesa-Aŕevalo E, Autran D, et al. 2010. Control of female gamete formation by a small RNA pathway in Arabidopsis. Nature 464:628-32.
101. Orlando V. 2000. Mapping chromosomal proteins in vivo by formaldehyde-crosslinked-chromatin immunoprecipitation. Trends Biochem. Sci. 25:99-104. (Pubitemid 30122417)
102. Park PJ. 2009. ChIP-seq: advantages and challenges of a maturing technology. Nat. Rev. Genet. 10:669-80.
103. Penterman J, Zilberman D, Huh JH, Ballinger T, Henikoff S, Fischer RL. 2007. DNA demethylation in the Arabidopsis genome. Proc. Natl. Acad. Sci. USA 104:6752-57. (Pubitemid 47175573)
104. Pfluger J, Wagner D. 2007. Histone modifications and dynamic regulation of genome accessibility in plants. Curr. Opin. Plant Biol. 10:645-52. (Pubitemid 350030606)
105. Qi Y, He X, Wang XJ, Kohany O, Jurka J, Hannon GJ. 2006. Distinct catalytic and non-catalytic roles of ARGONAUTE4 in RNA-directed DNA methylation. Nature 443:1008-12. (Pubitemid 44646179)
106. Reinders J, Delucinge Vivier C,TheilerG,CholletD,Descombes P, Paszkowski J. 2008. Genome-wide, high-resolution DNA methylation profiling using bisulfite-mediated cytosine conversion. Genome Res. 18:469-76. (Pubitemid 351347090)
107. Reinders J, Wulff BB, Mirouze M, Mari-Ordonez A, Dapp M, et al. 2009. Compromised stability of DNA methylation and transposon immobilization in mosaic Arabidopsis epigenomes. Genes Dev. 23:939-50.
108. Richards EJ. 2006. Inherited epigenetic variation-revisiting soft inheritance. Nat. Rev. Genet. 7:395-401.
109. Richards EJ. 2008. Population epigenetics. Curr. Opin. Genet. Dev. 18:221-26. (Pubitemid 351749826)
110. Roudier F, Teixeira FK, Colot V. 2009. Chromatin indexing in Arabidopsis: an epigenomic tale of tails and more. Trends Genet. 25:511-17.
111. Schena M, Shalon D, Davis RW, Brown PO. 1995. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270:467-70.
112. Schones DE, Zhao K. 2008. Genome-wide approaches to studying chromatin modifications. Nat. Rev. Genet. 9:179-91. (Pubitemid 351271798)
113. Servet C, Conde e Silva N, Zhou DX. 2010. Histone acetyltransferase AtGCN5/HAG1 is a versatile regulator of developmental and inducible gene expression in Arabidopsis. Mol. Plant 3:670-77.
114. Shahbazian MD, Grunstein M. 2007. Functions of site-specific histone acetylation and deacetylation. Annu. Rev. Biochem. 76:75-100.
115. Shendure J, Ji H. 2008. Next-generation DNA sequencing. Nat. Biotechnol. 26:1135-45.
116. Shindo C, Lister C, Crevillen P, Nordborg M, Dean C. 2006. Variation in the epigenetic silencing of FLC contributes to natural variation in Arabidopsis vernalization response. Genes Dev. 20:3079-83. (Pubitemid 44790623)
117. Slotkin RK, Martienssen R. 2007. Transposable elements and the epigenetic regulation of the genome. Nat. Rev. Genet. 8:272-85. (Pubitemid 46439291)
118. Slotkin RK, VaughnM, Borges F, Tanurdzic M, Becker JD, et al. 2009. Epigenetic reprogramming and small RNA silencing of transposable elements in pollen. Cell 136:461-72.
119. SolomonMJ, Larsen PL, Varshavsky A. 1988. Mapping protein-DNA interactions in vivo with formaldehyde: evidence that histone H4 is retained on a highly transcribed gene. Cell 53:937-47.
120. Springer NM, Stupar RM. 2007. Allelic variation and heterosis in maize: How do two halves make more than a whole? Genome Res. 17:264-75. (Pubitemid 46376735)
121. Suzuki MM, Bird A. 2008. DNA methylation landscapes: provocative insights from epigenomics. Nat. Rev. Genet. 9:465-76. (Pubitemid 351693975)
122. Swanson-Wagner RA, Jia Y, DeCook R, Borsuk LA,Nettleton D, Schnable PS. 2006. All possiblemodes of gene action are observed in a global comparison of gene expression in a maize F1 hybrid and its inbred parents. Proc. Natl. Acad. Sci. USA 103:6805-10.
123. Tanurdzic M, Vaughn MW, Jiang H, Lee TJ, Slotkin RK, et al. 2008. Epigenomic consequences of immortalized plant cell suspension culture. PLoS Biol. 6:2880-95.
124. Tiwari S, Schulz R, Ikeda Y, Dytham L, Bravo J, et al. 2008. MATERNALLY EXPRESSED PAB C-TERMINAL, a novel imprinted gene in Arabidopsis, encodes the conserved C-terminal domain of polyadenylate binding proteins. Plant Cell 20:2387-98. (Pubitemid 352844606)
125. Tompa R, McCallum CM, Delrow J, Henikoff JG, van Steensel B, Henikoff S. 2002. Genome-wide profiling of DNA methylation reveals transposon targets of CHROMOMETHYLASE3. Curr. Biol. 12:65-68. (Pubitemid 34063355)
126. Tran RK, Henikoff JG, Zilberman D, Ditt RF, Jacobsen SE, Henikoff S. 2005. DNA methylation profiling identifies CG methylation clusters in Arabidopsis genes. Curr. Biol. 15:154-59.
127. Tran RK, ZilbermanD, de Bustos C,Ditt RF, Henikoff JG, et al. 2005. Chromatin and siRNA pathways cooperate to maintain DNA methylation of small transposable elements in Arabidopsis. Genome Biol. 6:R90.
128. VaughnMW,Tanurdzic M, Lippman Z, JiangH,Carrasquillo R, et al. 2007. Epigenetic natural variation in Arabidopsis thaliana. PLoS Biol. 5:e174.
129. Vazquez F. 2006. Arabidopsis endogenous small RNAs: highways and byways. Trends Plant Sci. 11:460-68. (Pubitemid 44280036)
130. Wang X, Elling AA, Li X, Li N, Peng Z, et al. 2009. Genome-wide and organ-specific landscapes of epigenetic modifications and their relationships to mRNA and small RNA transcriptomes in maize. Plant Cell 21:1053-69.
131. Wei G, Tao Y, Liu G, Chen C, Luo R, et al. 2009. A transcriptomic analysis of superhybrid rice LYP9 and its parents. Proc. Natl. Acad. Sci. USA 106:7695-701.
132. Wilson ZA, YangC. 2004. Plant gametogenesis: conservation and contrasts in development. Reproduction 128:483-92. (Pubitemid 40124279)
133. Yadegari R, Kinoshita T, Lotan O, Cohen G, Katz A, et al. 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 12:2367-82.
134. Yan H, Kikuchi S, Neumann P, Zhang W, Wu Y, et al. 2010. Genome-wide mapping of cytosine methylation revealed dynamic DNAmethylation patterns associated with genes and centromeres in rice. Plant J. 63:353-65.
135. Yazaki J, Gregory BD, Ecker JR. 2007. Mapping the genome landscape using tiling array technology. Curr. Opin. Plant Biol. 10:534-42. (Pubitemid 47503881)
136. Yu SB, Li JX, Xu CG, Tan YF, Gao YJ, et al. 1997. Importance of epistasis as the genetic basis of heterosis in an elite rice hybrid. Proc. Natl. Acad. Sci. USA 94:9226-31. (Pubitemid 27357811)
137. Zemach A, McDaniel IE, Silva P, Zilberman D. 2010. Genome-wide evolutionary analysis of eukaryotic DNA methylation. Science 328:916-19.
138. Zhai J, Liu J, Liu B, Li P, Meyers BC, et al. 2008. Small RNA-directed epigenetic natural variation in Arabidopsis thaliana. PLoS Genet. 4:e1000056.
139. Zhang HY, He H, Chen LB, Li L, Liang MZ, et al. 2008. A genome-wide transcription analysis reveals a close correlation of promoter INDEL polymorphism and heterotic gene expression in rice hybrids. Mol. Plant 1:720-31.
140. Zhang X. 2008. The epigenetic landscape of plants. Science 320:489-92. (Pubitemid 351590632)
141. Zhang X, Bernatavichute YV, Cokus S, Pellegrini M, Jacobsen SE. 2009. Genome-wide analysis of mono-, di- and trimethylation of histone H3 lysine 4 in Arabidopsis thaliana. Genome Biol. 10:R62.
142. Zhang X, Clarenz O, Cokus S, Bernatavichute YV, PellegriniM, et al. 2007. Whole-genome analysis of histone H3 lysine 27 trimethylation in Arabidopsis. PLoS Biol. 5:e129.
143. Zhang X, Shiu SH, Cal A, Borevitz JO. 2008. Global analysis of genetic, epigenetic and transcriptional polymorphisms in Arabidopsis thaliana using whole genome tiling arrays. PLoS Genet. 4:e1000032.
144. ZhangX,Yazaki J, SundaresanA,Cokus S, ChanSW,et al. 2006. Genome-wide high-resolution mapping and functional analysis of DNA methylation in Arabidopsis. Cell 126:1189-201. (Pubitemid 44380289)
145. Zhou J, Wang X, He K, Charron JB, Elling AA, Deng XW. 2010. Genome-wide profiling of histone H3 lysine 9 acetylation and dimethylation in Arabidopsis reveals correlation between multiple histone marks and gene expression. Plant Mol. Biol. 72:585-95.
146. Zhu JK. 2008. Epigenome sequencing comes of age. Cell 133:395-97.
147. ZilbermanD,Gehring M, Tran RK, Ballinger T,Henikoff S. 2007. Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. Nat. Genet. 39:61-69. (Pubitemid 46026502)
148. Zilberman D, Henikoff S. 2007. Genome-wide analysis of DNA methylation patterns. Development 134:3959-65 (Pubitemid 350269413)