1. SchuettengruberB, ChourroutD, VervoortM, LeblancB, CavalliG (2007) Genome regulation by polycomb and trithorax proteins. Cell 128: 735–745.
2. SchwartzYB, PirrottaV (2008) Polycomb complexes and epigenetic states. Curr Opin Cell Biol 20: 266–273.
3. De LuciaF, CrevillenP, JonesAM, GrebT, DeanC (2008) A PHD-polycomb repressive complex 2 triggers the epigenetic silencing of FLC during vernalization. Proc Natl Acad Sci U S A 105: 16831–16836.
4. GoodrichJ, PuangsomleeP, MartinM, LongD, MeyerowitzEM, et al. (1997) A Polycomb-group gene regulates homeotic gene expression in Arabidopsis. Nature 386: 44–51.
5. GrossniklausU, Vielle-CalzadaJP, HoeppnerMA, GaglianoWB (1998) Maternal control of embryogenesis by MEDEA, a polycomb group gene in Arabidopsis. Science 280: 446–450.
6. OhadN, YadegariR, MargossianL, HannonM, MichaeliD, et al. (1999) Mutations in FIE, a WD polycomb group gene, allow endosperm development without fertilization. Plant Cell 11: 407–416.
7. LuoM, BilodeauP, KoltunowA, DennisES, PeacockWJ, et al. (1999) Genes controlling fertilization-independent seed development in Arabidopsis thaliana. Proc Natl Acad Sci U S A 96: 296–301.
8. KohlerC, HennigL, BouveretR, GheyselinckJ, GrossniklausU, et al. (2003a) Arabidopsis MSI1 is a component of the MEA/FIE Polycomb group complex and required for seed development. EMBO J 22: 4804–4814.
9. KohlerC, HennigL, SpillaneC, PienS, GruissemW, et al. (2003b) The Polycomb-group protein MEDEA regulates seed development by controlling expression of the MADS-box gene PHERES1. Genes Dev 17: 1540–1553.
10. HuhJH, BauerMJ, HsiehTF, FischerRL (2008) Cellular programming of plant gene imprinting. Cell 132: 735–744.
11. ChanvivattanaY, BishoppA, SchubertD, StockC, MoonYH, et al. (2004) Interaction of Polycomb-group proteins controlling flowering in Arabidopsis. Development 131: 5263–5276.
12. LuoM, BilodeauP, DennisES, PeacockWJ, ChaudhuryA (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.
13. KatzA, OlivaM, MosqunaA, HakimO, OhadN (2004) FIE and CURLY LEAF polycomb proteins interact in the regulation of homeobox gene expression during sporophyte development. Plant J 37: 707–719.
14. WoodCC, RobertsonM, TannerG, PeacockWJ, DennisES, et al. (2006) The Arabidopsis thaliana vernalization response requires a polycomb-like protein complex that also includes VERNALIZATION INSENSITIVE 3. Proc Natl Acad Sci U S A 103: 14631–14636.
15. SpillaneC, MacDougallC, StockC, KohlerC, Vielle-CalzadaJP, et al. (2000) Interaction of the Arabidopsis polycomb group proteins FIE and MEA mediates their common phenotypes. Curr Biol 10: 1535–1538.
16. YadegariR, KinoshitaT, LotanO, CohenG, KatzA, 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: 2367–2382.
17. WangD, TysonMD, JacksonSS, YadegariR (2006) Partially redundant functions of two SET-domain polycomb-group proteins in controlling initiation of seed development in Arabidopsis. Proc Natl Acad Sci U S A 103: 13244–13249.
18. YoshidaN, YanaiY, ChenL, KatoY, HiratsukaJ, et al. (2001) EMBRYONIC FLOWER2, a novel polycomb group protein homolog, mediates shoot development and flowering in Arabidopsis. Plant Cell 13: 2471–2481.
19. JiangH, WongWH (2008) SeqMap: mapping massive amount of oligonucleotides to the genome. Bioinformatics 24: 2395–2396.
20. SchonrockN, BouveretR, LeroyO, BorghiL, KohlerC, et al. (2006) Polycomb-group proteins repress the floral activator AGL19 in the FLC-independent vernalization pathway. Genes Dev 20: 1667–1678.
21. GendallAR, LevyYY, WilsonA, DeanC (2001) The VERNALIZATION 2 gene mediates the epigenetic regulation of vernalization in Arabidopsis. Cell 107: 525–535.
22. SungS, AmasinoRM (2004) Vernalization in Arabidopsis thaliana is mediated by the PHD finger protein VIN3. Nature 427: 159–164.
23. AngelA, SongJ, DeanC, HowardM (2011) A Polycomb-based switch underlying quantitative epigenetic memory. Nature 476: 105–108.
24. NowackMK, ShirzadiR, DissmeyerN, DolfA, EndlE, et al. (2007) Bypassing genomic imprinting allows seed development. Nature 447: 312–315.
25. GehringM, ChoiY, FischerRL (2004) Imprinting and seed development. Plant Cell 16 Suppl: S203–213.
26. GuittonAE, PageDR, ChambrierP, LionnetC, FaureJE, et al. (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.
27. ChaudhuryAM, MingL, MillerC, CraigS, DennisES, et al. (1997) Fertilization-independent seed development in Arabidopsis thaliana. Proc Natl Acad Sci U S A 94: 4223–4228.
28. KiyosueT, OhadN, YadegariR, HannonM, DinnenyJ, et al. (1999) Control of fertilization-independent endosperm development by the MEDEA polycomb gene in Arabidopsis. Proc Natl Acad Sci U S A 96: 4186–4191.
29. XiaoW, GehringM, ChoiY, MargossianL, PuH, et al. (2003) Imprinting of the MEA Polycomb gene is controlled by antagonism between MET1 methyltransferase and DME glycosylase. Dev Cell 5: 891–901.
30. LeroyO, HennigL, BreuningerH, LauxT, KohlerC (2007) Polycomb group proteins function in the female gametophyte to determine seed development in plants. Development 134: 3639–3648.
31. KinoshitaT, YadegariR, HaradaJJ, GoldbergRB, FischerRL (1999) Imprinting of the MEDEA polycomb gene in the Arabidopsis endosperm. Plant Cell 11: 1945–1952.
32. JullienPE, KatzA, OlivaM, OhadN, BergerF (2006a) Polycomb group complexes self-regulate imprinting of the Polycomb group gene MEDEA in Arabidopsis. Curr Biol 16: 486–492.
33. JullienPE, KinoshitaT, OhadN, BergerF (2006b) Maintenance of DNA methylation during the Arabidopsis life cycle is essential for parental imprinting. Plant Cell 18: 1360–1372.
34. BouyerD, RoudierF, HeeseM, AndersenED, GeyD, et al. (2011) Polycomb repressive complex 2 controls the embryo-to-seedling phase transition. PLoS Genet 7: e1002014 doi:10.1371/journal.pgen.1002014.
35. RoszakP, KohlerC (2011) Polycomb group proteins are required to couple seed coat initiation to fertilization. Proc Natl Acad Sci U S A 108: 20826–20831.
36. DanilevskayaON, HermonP, HantkeS, MuszynskiMG, KolliparaK, et al. (2003) Duplicated fie genes in maize: expression pattern and imprinting suggest distinct functions. Plant Cell 15: 425–438.
37. Gutierrez-MarcosJF, CostaLM, Dal PraM, ScholtenS, KranzE, et al. (2006) Epigenetic asymmetry of imprinted genes in plant gametes. Nat Genet 38: 876–878.
38. HermonP, SrilunchangKO, ZouJ, DresselhausT, DanilevskayaON (2007) Activation of the imprinted Polycomb Group Fie1 gene in maize endosperm requires demethylation of the maternal allele. Plant Mol Biol 64: 387–395.
39. SpringerNM, DanilevskayaON, HermonP, HelentjarisTG, PhillipsRL, et al. (2002) Sequence relationships, conserved domains, and expression patterns for maize homologs of the polycomb group genes E(z), esc, and E(Pc). Plant Physiol 128: 1332–1345.
40. HaunWJ, Laoueille-DupratS, O'Connell MJ, SpillaneC, GrossniklausU, et al. (2007) Genomic imprinting, methylation and molecular evolution of maize Enhancer of zeste (Mez) homologs. Plant J 49: 325–337.
41. KapazoglouA, TondelliA, PapaefthimiouD, AmpatzidouH, FranciaE, et al. (2010) Epigenetic chromatin modifiers in barley: IV. The study of barley polycomb group (PcG) genes during seed development and in response to external ABA. BMC Plant Biol 10: 73.
42. LuoM, PlattenD, ChaudhuryA, PeacockWJ, DennisES (2009) Expression, imprinting, and evolution of rice homologs of the polycomb group genes. Mol Plant 2: 711–723.
43. LiangYK, WangY, ZhangY, LiSG, LuXC, et al. (2003) OsSET1, a novel SET-domain-containing gene from rice. J Exp Bot 54: 1995–1996.
44. ThakurJK, MalikMR, BhattV, ReddyMK, SoporySK, et al. (2003) 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 314: 1–13.
45. LuoM, TaylorJM, SpriggsA, ZhangH, WuX, et al. (2011) A genome-wide survey of imprinted genes in rice seeds reveals imprinting primarily occurs in the endosperm. PLoS Genet 7: e1002125 doi:10.1371/journal.pgen.1002125.
46. RodriguesJC, LuoM, BergerF, KoltunowAM (2010) Polycomb group gene function in sexual and asexual seed development in angiosperms. Sex Plant Reprod 23: 123–133.
47. SpillaneC, SchmidKJ, Laoueille-DupratS, PienS, Escobar-RestrepoJM, et al. (2007) Positive darwinian selection at the imprinted MEDEA locus in plants. Nature 448: 349–352.
48. RodriguesJC, TuckerMR, JohnsonSD, HrmovaM, KoltunowAM (2008) Sexual and apomictic seed formation in Hieracium requires the plant polycomb-group gene FERTILIZATION INDEPENDENT ENDOSPERM. Plant Cell 20: 2372–2386.
49. RigautG, ShevchenkoA, RutzB, WilmM, MannM, et al. (1999) A generic protein purification method for protein complex characterization and proteome exploration. Nat Biotechnol 17: 1030–1032.
50. PuigO, CasparyF, RigautG, RutzB, BouveretE, et al. (2001) The tandem affinity purification (TAP) method: a general procedure of protein complex purification. Methods 24: 218–229.
51. RohilaJS, ChenM, CernyR, FrommME (2004) Improved tandem affinity purification tag and methods for isolation of protein heterocomplexes from plants. Plant J 38: 172–181.
52. RubioV, ShenY, SaijoY, LiuY, GusmaroliG, et al. (2005) An alternative tandem affinity purification strategy applied to Arabidopsis protein complex isolation. Plant J 41: 767–778.
53. RohilaJS, ChenM, ChenS, ChenJ, CernyR, et al. (2006) Protein-protein interactions of tandem affinity purification-tagged protein kinases in rice. Plant J 46: 1–13.
54. Van LeeneJ, StalsH, EeckhoutD, PersiauG, Van De SlijkeE, et al. (2007) A tandem affinity purification-based technology platform to study the cell cycle interactome in Arabidopsis thaliana. Mol Cell Proteomics 6: 1226–1238.
55. BrownAP, AffleckV, FawcettT, SlabasAR (2006) Tandem affinity purification tagging of fatty acid biosynthetic enzymes in Synechocystis sp. PCC6803 and Arabidopsis thaliana. J Exp Bot 57: 1563–1571.
56. RivasS, RomeisT, JonesJD (2002) The Cf-9 disease resistance protein is present in an approximately 420-kilodalton heteromultimeric membrane-associated complex at one molecule per complex. Plant Cell 14: 689–702.
57. AbeM, FujiwaraM, KurotaniK, YokoiS, ShimamotoK (2008) Identification of dynamin as an interactor of rice GIGANTEA by tandem affinity purification (TAP). Plant Cell Physiol 49: 420–432.
58. ChittetiBR, TanF, MujahidH, MageeBG, BridgesSM, et al. (2008) Comparative analysis of proteome differential regulation during cell dedifferentiation in Arabidopsis. Proteomics 8: 4303–4316.
59. TanF, LiG, ChittetiBR, PengZ (2007) Proteome and phosphoproteome analysis of chromatin associated proteins in rice (Oryza sativa). Proteomics 7: 4511–4527.
60. TanF, ZhangK, MujahidH, VermaDP, PengZ (2010) Differential histone modification and protein expression associated with cell wall removal and regeneration in rice (Oryza sativa). J Proteome Res 10: 551–563.
61. TieF, StrattonCA, KurzhalsRL, HartePJ (2007) The N terminus of Drosophila ESC binds directly to histone H3 and is required for E(Z)-dependent trimethylation of H3 lysine 27. Mol Cell Biol 27: 2014–2026.
62. VerreaultA, KaufmanPD, KobayashiR, StillmanB (1998) Nucleosomal DNA regulates the core-histone-binding subunit of the human Hat1 acetyltransferase. Curr Biol 8: 96–108.
63. VermaakD, WadePA, JonesPL, ShiYB, WolffeAP (1999) Functional analysis of the SIN3-histone deacetylase RPD3-RbAp48-histone H4 connection in the Xenopus oocyte. Mol Cell Biol 19: 5847–5860.
64. JoungJK, RammEI, PaboCO (2000) A bacterial two-hybrid selection system for studying protein-DNA and protein-protein interactions. Proc Natl Acad Sci U S A 97: 7382–7387.
65. CaoR, WangL, WangH, XiaL, Erdjument-BromageH, et al. (2002) Role of histone H3 lysine 27 methylation in Polycomb-group silencing. Science 298: 1039–1043.
66. CzerminB, MelfiR, McCabeD, SeitzV, ImhofA, et al. (2002) Drosophila enhancer of Zeste/ESC complexes have a histone H3 methyltransferase activity that marks chromosomal Polycomb sites. Cell 111: 185–196.
67. KuzmichevA, NishiokaK, Erdjument-BromageH, TempstP, ReinbergD (2002) Histone methyltransferase activity associated with a human multiprotein complex containing the Enhancer of Zeste protein. Genes Dev 16: 2893–2905.
68. MullerJ, HartCM, FrancisNJ, VargasML, SenguptaA, et al. (2002) Histone methyltransferase activity of a Drosophila Polycomb group repressor complex. Cell 111: 197–208.
69. OhdanT, FranciscoPBJr, SawadaT, HiroseT, TeraoT, et al. (2005) Expression profiling of genes involved in starch synthesis in sink and source organs of rice. J Exp Bot 56: 3229–3244.
70. GirouxMJ, BoyerC, FeixG, HannahLC (1994) Coordinated Transcriptional Regulation of Storage Product Genes in the Maize Endosperm. Plant Physiol 106: 713–722.
71. SheKC, KusanoH, KoizumiK, YamakawaH, HakataM, et al. (2010) A novel factor FLOURY ENDOSPERM2 is involved in regulation of rice grain size and starch quality. Plant Cell 22: 3280–3294.
72. LiG, NallamilliBR, TanF, PengZ (2008) Removal of high-abundance proteins for nuclear subproteome studies in rice (Oryza sativa) endosperm. Electrophoresis 29: 604–617.
73. MaloneBM, TanF, BridgesSM, PengZ (2011) Comparison of four ChIP-Seq analytical algorithms using rice endosperm H3K27 trimethylation profiling data. PLoS ONE 6: e25260 doi:10.1371/journal.pone.0025260.
74. EgelhoferTA, MinodaA, KlugmanS, LeeK, Kolasinska-ZwierzP, et al. (2011) An assessment of histone-modification antibody quality. Nat Struct Mol Biol 18: 91–93.
75. KondouY, NakazawaM, KawashimaM, IchikawaT, YoshizumiT, et al. (2008) Retarded growth of EMBRYO1, a new basic helix-loop-helix protein, expression in endosperm to control embryo growth. Plant Physiol 147: 1924–1935.
76. YangS, JohnstonN, TalidehE, MitchellS, JeffreeC, et al. (2008) The endosperm-specific ZHOUPI gene of Arabidopsis thaliana regulates endosperm breakdown and embryonic epidermal development. Development 135: 3501–3509.
77. SwiezewskiS, LiuF, MagusinA, DeanC (2009) Cold-induced silencing by long antisense transcripts of an Arabidopsis Polycomb target. Nature 462: 799–802.
78. HeoJB, SungS (2011) Vernalization-mediated epigenetic silencing by a long intronic noncoding RNA. Science 331: 76–79.
79. BastowR, MylneJS, ListerC, LippmanZ, MartienssenRA, et al. (2004) Vernalization requires epigenetic silencing of FLC by histone methylation. Nature 427: 164–167.
80. GehringM, HuhJH, HsiehTF, PentermanJ, ChoiY, et al. (2006) DEMETER DNA glycosylase establishes MEDEA polycomb gene self-imprinting by allele-specific demethylation. Cell 124: 495–506.
81. ZhangJ, NallamilliBR, MujahidH, PengZ (2010) OsMADS6 plays an essential role in endosperm nutrient accumulation and is subject to epigenetic regulation in rice (Oryza sativa). Plant J 64: 604–617.
82. WuC, LiX, YuanW, ChenG, KilianA, et al. (2003) Development of enhancer trap lines for functional analysis of the rice genome. Plant J 35: 418–427.
83. MikiD, ShimamotoK (2004) Simple RNAi vectors for stable and transient suppression of gene function in rice. Plant Cell Physiol 45: 490–495.
84. LiJ, MoazedD, GygiSP (2002) Association of the histone methyltransferase Set2 with RNA polymerase II plays a role in transcription elongation. J Biol Chem 277: 49383–49388.
85. ChittetiBR, PengZ (2007) Proteome and phosphoproteome dynamic change during cell dedifferentiation in Arabidopsis. Proteomics 7: 1473–1500.
86. LivakKJ, SchmittgenTD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods 25: 402–408.
87. ChhunT, AyaK, AsanoK, YamamotoE, MorinakaY, et al. (2007) Gibberellin regulates pollen viability and pollen tube growth in rice. Plant Cell 19: 3876–3888.
88. GendrelAV, LippmanZ, MartienssenR, ColotV (2005) Profiling histone modification patterns in plants using genomic tiling microarrays. Nat Methods 2: 213–218.
89. JiangH, WongWH (2008) SeqMap: mapping massive amount of oligonucleotides to the genome. Bioinformatics 24: 2395–2396.
90. OuyangS, ZhuW, HamiltonJ, LinH, CampbellM, et al. (2007) The TIGR Rice Genome Annotation Resource: improvements and new features. Nucleic Acids Res 35: D883–887.
91. FejesAP, RobertsonG, BilenkyM, VarholR, BainbridgeM, et al. (2008) FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology. Bioinformatics 24: 1729–1730.