Functional roles of histone modification, chromatin remodeling and microRNAs in arabidopsis flower development

International Review of Cell and Molecular Biology

Volumn 305, Issue , 2013, Pages 115-161

  Gan, Eng Seng ^a   Huang, Jiangbo ^a   Ito, Toshiro ^a  

^a NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

Author keywords

Arabidopsis flower development; Cell memory; Chromatin remodeling; Floral stem cells; Histone acetylation; Histone methylation; MicroRNAs; Organ identity

Indexed keywords

DNA GLYCOSYLTRANSFERASE; GIBBERELLIN; HISTONE METHYLTRANSFERASE; MADS DOMAIN PROTEIN; METHYLTRANSFERASE; MICRORNA; RNA POLYMERASE II; SMALL INTERFERING RNA;

ANTHER; ARABIDOPSIS; ARTICLE; CHROMATIN ASSEMBLY AND DISASSEMBLY; DNA METHYLATION; DNA SEQUENCE; FLOWER DEVELOPMENT; GAMETOGENESIS; GENE ACTIVATION; GENE CONTROL; GENE EXPRESSION; GENE EXPRESSION REGULATION; GENOMIC INSTABILITY; GERMINATION; HETEROCHROMATIN; HISTONE ACETYLATION; HISTONE METHYLATION; HISTONE MODIFICATION; HISTONE PHOSPHORYLATION; HISTONE UBIQUITINATION; MERISTEM; NONHUMAN; OVULE; OXIDATION; PLANT GENETICS; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN PROCESSING; RNA PROCESSING; ROLE PLAYING; SEED DEVELOPMENT; SUMOYLATION; TRANSCRIPTION INITIATION; VERNALIZATION;

ARABIDOPSIS; MAGNOLIOPHYTA;

ARABIDOPSIS FLOWER DEVELOPMENT; CELL MEMORY; CHROMATIN REMODELING; FLORAL STEM CELLS; HISTONE ACETYLATION; HISTONE METHYLATION; MICRORNAS; ORGAN IDENTITY;

ARABIDOPSIS; CHROMATIN; CHROMATIN ASSEMBLY AND DISASSEMBLY; FLOWERS; HISTONES; MICRORNAS; MODELS, BIOLOGICAL;

EID: 84880806371     PISSN: 19376448     EISSN: None     Source Type: Book Series    
DOI: 10.1016/B978-0-12-407695-2.00003-2     Document Type: Chapter

References (240)

1. Achard P., Herr A., Baulcombe D.C., Harberd N.P. Modulation of floral development by a gibberellin-regulated microRNA. Development 2004, 131:3357-3365.
2. Agger K., Cloos P.A., Christensen J., Pasini D., Rose S., Rappsilber J., Issaeva I., Canaani E., Salcini A.E., Helin K. UTX and JMJD3 are histone H3K27 demethylases involved in HOX gene regulation and development. Nature 2007, 449:731-734.
3. Aida M., Ishida T., Fukaki H., Fujisawa H., Tasaka M. Genes involved in organ separation in Arabidopsis: an analysis of the cup-shaped cotyledon mutant. Plant Cell 1997, 9:841-857.
4. Allen E., Xie Z., Gustafson A.M., Carrington J.C. microRNA-directed phasing during trans-acting siRNA biogenesis in plants. Cell 2005, 121:207-221.
5. Allen R.S., Li J., Stahle M.I., Dubroue A., Gubler F., Millar A.A. Genetic analysis reveals functional redundancy and the major target genes of the Arabidopsis miR159 family. Proc. Natl. Acad. Sci. USA 2007, 104:16371-16376.
6. Alvarez-Buylla E.R., Azpeitia E., Barrio R., Benitez M., Padilla-Longoria P. From ABC genes to regulatory networks, epigenetic landscapes and flower morphogenesis: making biological sense of theoretical approaches. Semin. Cell Dev. Biol. 2010, 21:108-117.
7. Alvarez-Venegas R., Pien S., Sadder M., Witmer X., Grossniklaus U., Avramova Z. ATX-1, an Arabidopsis homolog of trithorax, activates flower homeotic genes. Curr. Biol. 2003, 13:627-637.
8. Aufsatz W., Mette M.F., van der Winden J., Matzke M., Matzke A.J. HDA6, a putative histone deacetylase needed to enhance DNA methylation induced by double-stranded RNA. EMBO J. 2002, 21:6832-6841.
9. Aukerman M.J., Sakai H. Regulation of flowering time and floral organ identity by a MicroRNA and its APETALA2-like target genes. Plant Cell 2003, 15:2730-2741.
10. Ausin I., Alonso-Blanco C., Jarillo J.A., Ruiz-Garcia L., Martinez-Zapater J.M. Regulation of flowering time by FVE, a retinoblastoma-associated protein. Nat. Genet. 2004, 36:162-166.
11. Baker C.C., Sieber P., Wellmer F., Meyerowitz E.M. The early extra petals1 mutant uncovers a role for microRNA miR164c in regulating petal number in Arabidopsis. Curr. Biol. 2005, 15:303-315.
12. Bartee L., Malagnac F., Bender J. Arabidopsis cmt3 chromomethylase mutations block non-CG methylation and silencing of an endogenous gene. Genes Dev. 2001, 15:1753-1758.
13. Bartel D.P. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 2004, 116:281-297.
14. Berger S.L., Kouzarides T., Shiekhattar R., Shilatifard A. An operational definition of epigenetics. Genes Dev. 2009, 23:781-783.
15. Berger N., Dubreucq B., Roudier F., Dubos C., Lepiniec L. Transcriptional regulation of Arabidopsis LEAFY COTYLEDON2 involves RLE, a cis-element that regulates trimethylation of histone H3 at lysine-27. Plant Cell 2011, 23:4065-4078.
16. Bernatavichute Y.V., Zhang X., Cokus S., Pellegrini M., Jacobsen S.E. Genome-wide association of histone H3 lysine nine methylation with CHG DNA methylation in Arabidopsis thaliana. PLoS One 2008, 3:e3156.
17. Berr A., Xu L., Gao J., Cognat V., Steinmetz A., Dong A., Shen W.H. SET DOMAIN GROUP25 encodes a histone methyltransferase and is involved in FLOWERING LOCUS C activation and repression of flowering. Plant Physiol. 2009, 151:1476-1485.
18. Berr A., McCallum E.J., Menard R., Meyer D., Fuchs J., Dong A., Shen W.H. Arabidopsis SET DOMAIN GROUP2 is required for H3K4 trimethylation and is crucial for both sporophyte and gametophyte development. Plant Cell 2010, 22:3232-3248.
19. Bertrand C., Bergounioux C., Domenichini S., Delarue M., Zhou D.X. Arabidopsis histone acetyltransferase AtGCN5 regulates the floral meristem activity through the WUSCHEL/AGAMOUS pathway. J. Biol. Chem. 2003, 278:28246-28251.
20. Bezhani S., Winter C., Hershman S., Wagner J.D., Kennedy J.F., Kwon C.S., Pfluger J., Su Y., Wagner D. Unique, shared, and redundant roles for the Arabidopsis SWI/SNF chromatin remodeling ATPases BRAHMA and SPLAYED. Plant Cell 2007, 19:403-416.
21. Birnbaum K., Jung J.W., Wang J.Y., Lambert G.M., Hirst J.A., Galbraith D.W., Benfey P.N. Cell type-specific expression profiling in plants via cell sorting of protoplasts from fluorescent reporter lines. Nat. Methods 2005, 2:615-619.
22. Blazquez M.A., Ahn J.H., Weigel D. A thermosensory pathway controlling flowering time in Arabidopsis thaliana. Nat. Genet. 2003, 33:168-171.
23. Bollman K.M., Aukerman M.J., Park M.Y., Hunter C., Berardini T.Z., Poethig R.S. HASTY, the Arabidopsis ortholog of exportin 5/MSN5, regulates phase change and morphogenesis. Development 2003, 130:1493-1504.
24. Bonnet E., Wuyts J., Rouze P., Van de Peer Y. Detection of 91 potential conserved plant microRNAs in Arabidopsis thaliana and Oryza sativa identifies important target genes. Proc. Natl. Acad. Sci. USA 2004, 101:11511-11516.
25. Borsani O., Zhu J., Verslues P.E., Sunkar R., Zhu J.K. Endogenous siRNAs derived from a pair of natural cis-antisense transcripts regulate salt tolerance in Arabidopsis. Cell 2005, 123:1279-1291.
26. Bouyer D., Roudier F., Heese M., Andersen E.D., Gey D., Nowack M.K., Goodrich J., Renou J.P., Grini P.E., Colot V., Schnittger A. Polycomb repressive complex 2 controls the embryo-to-seedling phase transition. PLoS Genet. 2011, 7:e1002014.
27. Bowman J.L., Smyth D.R., Meyerowitz E.M. Genes directing flower development in Arabidopsis. Plant Cell 1989, 1:37-52.
28. Bowman J.L., Smyth D.R., Meyerowitz E.M. Genetic interactions among floral homeotic genes of Arabidopsis. Development 1991, 112:1-20.
29. Bratzel F., López-Torrejón G., Koch M., Del Pozo J.C., Calonje M. Keeping Cell Identity in Arabidopsis Requires PRC1 RING-Finger Homologs that Catalyze H2A Monoubiquitination. Curr. Biol. 2010, 20:1853-1859.
30. Buzas D.M., Tamada Y., Kurata T. FLC: a hidden polycomb response element shows up in silence. Plant Cell Physiol. 2012, 53:785-793.
31. Cao X., Jacobsen S.E. Role of the arabidopsis DRM methyltransferases in de novo DNA methylation and gene silencing. Curr. Biol. 2002, 12:1138-1144.
32. Cao Y., Dai Y., Cui S., Ma L. Histone H2B monoubiquitination in the chromatin of FLOWERING LOCUS C regulates flowering time in Arabidopsis. Plant Cell 2008, 20:2586-2602.
33. Cardon G.H., Hohmann S., Nettesheim K., Saedler H., Huijser P. Functional analysis of the Arabidopsis thaliana SBP-box gene SPL3: a novel gene involved in the floral transition. Plant J. 1997, 12:367-377.
34. Carles C.C., Fletcher J.C. The SAND domain protein ULTRAPETALA1 acts as a trithorax group factor to regulate cell fate in plants. Genes Dev. 2009, 23:2723-2728.
35. Cartagena J.A., Matsunaga S., Seki M., Kurihara D., Yokoyama M., Shinozaki K., Fujimoto S., Azumi Y., Uchiyama S., Fukui K. The Arabidopsis SDG4 contributes to the regulation of pollen tube growth by methylation of histone H3 lysines 4 and 36 in mature pollen. Dev. Biol. 2008, 315:355-368.
36. Cazzonelli C.I., Cuttriss A.J., Cossetto S.B., Pye W., Crisp P., Whelan J., Finnegan E.J., Turnbull C., Pogson B.J. Regulation of carotenoid composition and shoot branching in Arabidopsis by a chromatin modifying histone methyltransferase, SDG8. Plant Cell 2009, 21:39-53.
37. Chanvivattana Y., Bishopp A., Schubert D., Stock C., Moon Y.H., Sung Z.R., Goodrich J. Interaction of Polycomb-group proteins controlling flowering in Arabidopsis. Development 2004, 131:5263-5276.
38. Chen X. A microRNA as a translational repressor of APETALA2 in Arabidopsis flower development. Science 2004, 303:2022-2025.
39. Chen X., Liu J., Cheng Y., Jia D. HEN1 functions pleiotropically in Arabidopsis development and acts in C function in the flower. Development 2002, 129:1085-1094.
40. Cho H.J., Kim J.J., Lee J.H., Kim W., Jung J.H., Park C.M., Ahn J.H. SHORT VEGETATIVE PHASE (SVP) protein negatively regulates miR172 transcription via direct binding to the pri-miR172a promoter in Arabidopsis. FEBS Lett. 2012, 586:2332-2337.
41. 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.
42. Coen E.S., Meyerowitz E.M. The war of the whorls: genetic interactions controlling flower development. Nature 1991, 353:31-37.
43. Crawford B.C., Nath U., Carpenter R., Coen E.S. CINCINNATA controls both cell differentiation and growth in petal lobes and leaves of Antirrhinum. Plant Physiol. 2004, 135:244-253.
44. Davie J.R., Chadee D.N. Regulation and regulatory parameters of histone modifications. J. Cell. Biochem. 1998, 30-31(Suppl.):203-213.
45. Deal R.B., Henikoff S. A simple method for gene expression and chromatin profiling of individual cell types within a tissue. Dev. Cell 2010, 18:1030-1040.
46. Dennis E.S., Peacock W.J. Epigenetic regulation of flowering. Curr. Opin. Plant Biol. 2007, 10:520-527.
47. Dyson M.H., Rose S., Mahadevan L.C. Acetyllysine-binding and function of bromodomain-containing proteins in chromatin. Front. Biosci. 2001, 6:D853-D865.
48. Ebbs M.L., Bender J. Locus-specific control of DNA methylation by the Arabidopsis SUVH5 histone methyltransferase. Plant Cell 2006, 18:1166-1176.
49. Ebbs M.L., Bartee L., Bender J. H3 lysine 9 methylation is maintained on a transcribed inverted repeat by combined action of SUVH6 and SUVH4 methyltransferases. Mol. Cell Biol. 2005, 25:10507-10515.
50. Efroni I., Blum E., Goldshmidt A., Eshed Y. A protracted and dynamic maturation schedule underlies Arabidopsis leaf development. Plant Cell 2008, 20:2293-2306.
51. Fahlgren N., Montgomery T.A., Howell M.D., Allen E., Dvorak S.K., Alexander A.L., Carrington J.C. Regulation of AUXIN RESPONSE FACTOR3 by TAS3 ta-siRNA affects developmental timing and patterning in Arabidopsis. Curr. Biol. 2006, 16:939-944.
52. Fahrner J.A., Baylin S.B. Heterochromatin: stable and unstable invasions at home and abroad. Genes Dev. 2003, 17:1805-1812.
53. Fan D., Dai Y., Wang X., Wang Z., He H., Yang H., Cao Y., Deng X.W., Ma L. IBM1, a JmjC domain-containing histone demethylase, is involved in the regulation of RNA-directed DNA methylation through the epigenetic control of RDR2 and DCL3 expression in Arabidopsis. Nucleic Acids Res. 2012, 40:8905-8916.
54. Feng S., Jacobsen S.E. Epigenetic modifications in plants: an evolutionary perspective. Curr. Opin. Plant Biol. 2011, 14:179-186.
55. Finnegan E.J., Peacock W.J., Dennis E.S. Reduced DNA methylation in Arabidopsis thaliana results in abnormal plant development. Proc. Natl. Acad. Sci. USA 1996, 93:8449-8454.
56. Franks R.G., Wang C., Levin J.Z., Liu Z. SEUSS, a member of a novel family of plant regulatory proteins, represses floral homeotic gene expression with LEUNIG. Development 2002, 129:253-263.
57. Fuks F. DNA methylation and histone modifications: teaming up to silence genes. Curr. Opin. Genet. Dev. 2005, 15:490-495.
58. Furner I.J., Matzke M. Methylation and demethylation of the Arabidopsis genome. Curr. Opin. Plant Biol. 2011, 14:137-141.
59. Gandikota M., Birkenbihl R.P., Hohmann S., Cardon G.H., Saedler H., Huijser P. The miRNA156/157 recognition element in the 3' UTR of the Arabidopsis SBP box gene SPL3 prevents early flowering by translational inhibition in seedlings. Plant J. 2007, 49:683-693.
60. Gocal G.F., Sheldon C.C., Gubler F., Moritz T., Bagnall D.J., MacMillan C.P., Li S.F., Parish R.W., Dennis E.S., Weigel D., King R.W. GAMYB-like genes, flowering, and gibberellin signaling in Arabidopsis. Plant Physiol. 2001, 127:1682-1693.
61. Gonzalez D., Bowen A.J., Carroll T.S., Conlan R.S. The transcription corepressor LEUNIG interacts with the histone deacetylase HDA19 and mediator components MED14 (SWP) and CDK8 (HEN3) to repress transcription. Mol. Cell Biol. 2007, 27:5306-5315.
62. Goodrich J., Puangsomlee P., Martin M., Long D., Meyerowitz E.M., Coupland G. A Polycomb-group gene regulates homeotic gene expression in Arabidopsis. Nature 1997, 386:44-51.
63. Greb T., Mylne J.S., Crevillen P., Geraldo N., An H., Gendall A.R., Dean C. The PHD finger protein VRN5 functions in the epigenetic silencing of Arabidopsis FLC. Curr. Biol. 2007, 17:73-78.
64. Grini P.E., Thorstensen T., Alm V., Vizcay-Barrena G., Windju S.S., Jorstad T.S., Wilson Z.A., Aalen R.B. The ASH1 HOMOLOG 2 (ASHH2) histone H3 methyltransferase is required for ovule and anther development in Arabidopsis. PLoS One 2009, 4:e7817.
65. Gu X., Jiang D., Yang W., Jacob Y., Michaels S.D., He Y. Arabidopsis homologs of retinoblastoma-associated protein 46/48 associate with a histone deacetylase to act redundantly in chromatin silencing. PLoS Genet. 2011, 7:e1002366.
66. Han M.H., Goud S., Song L., Fedoroff N. The Arabidopsis double-stranded RNA-binding protein HYL1 plays a role in microRNA-mediated gene regulation. Proc. Natl. Acad. Sci. USA 2004, 101:1093-1098.
67. Hansen J.C., Tse C., Wolffe A.P. Structure and function of the core histone N-termini: more than meets the eye. Biochemistry 1998, 37:17637-17641.
68. He Y. Control of the transition to flowering by chromatin modifications. Mol. Plant 2009, 2:554-564.
69. Hennig L., Bouveret R., Gruissem W. MSI1-like proteins: an escort service for chromatin assembly and remodeling complexes. Trends Cell Biol. 2005, 15:295-302.
70. Hiraguri A., Itoh R., Kondo N., Nomura Y., Aizawa D., Murai Y., Koiwa H., Seki M., Shinozaki K., Fukuhara T. Specific interactions between Dicer-like proteins and HYL1/DRB-family dsRNA-binding proteins in Arabidopsis thaliana. Plant Mol. Biol. 2005, 57:173-188.
71. Hong E.H., Jeong Y.M., Ryu J.Y., Amasino R.M., Noh B., Noh Y.S. Temporal and spatial expression patterns of nine Arabidopsis genes encoding Jumonji C-domain proteins. Mol. Cells 2009, 27:481-490.
72. Hunter C., Willmann M.R., Wu G., Yoshikawa M., de la Luz Gutierrez-Nava M., Poethig S.R. Trans-acting siRNA-mediated repression of ETTIN and ARF4 regulates heteroblasty in Arabidopsis. Development 2006, 133:2973-2981.
73. Hurtado L., Farrona S., Reyes J.C. The putative SWI/SNF complex subunit BRAHMA activates flower homeotic genes in Arabidopsis thaliana. Plant Mol. Biol. 2006, 62:291-304.
74. Inagaki S., Miura-Kamio A., Nakamura Y., Lu F., Cui X., Cao X., Kimura H., Saze H., Kakutani T. Autocatalytic differentiation of epigenetic modifications within the Arabidopsis genome. EMBO J. 2010, 29:3496-3506.
75. Ito T. Coordination of flower development by homeotic master regulators. Curr. Opin. Plant Biol. 2011, 14:53-59.
76. Jackson J.P., Lindroth A.M., Cao X., Jacobsen S.E. Control of CpNpG DNA methylation by the KRYPTONITE histone H3 methyltransferase. Nature 2002, 416:556-560.
77. Jackson J.P., Johnson L., Jasencakova Z., Zhang X., PerezBurgos L., Singh P.B., Cheng X., Schubert I., Jenuwein T., Jacobsen S.E. Dimethylation of histone H3 lysine 9 is a critical mark for DNA methylation and gene silencing in Arabidopsis thaliana. Chromosoma 2004, 112:308-315.
78. Jacob Y., Stroud H., Leblanc C., Feng S., Zhuo L., Caro E., Hassel C., Gutierrez C., Michaels S.D., Jacobsen S.E. Regulation of heterochromatic DNA replication by histone H3 lysine 27 methyltransferases. Nature 2010, 466:987-991.
79. Jacobsen S.E., Meyerowitz E.M. Hypermethylated SUPERMAN epigenetic alleles in arabidopsis. Science 1997, 277:1100-1103.
80. Jacobsen S.E., Running M.P., Meyerowitz E.M. Disruption of an RNA helicase/RNAse III gene in Arabidopsis causes unregulated cell division in floral meristems. Development 1999, 126:5231-5243.
81. Jacobsen S.E., Sakai H., Finnegan E.J., Cao X., Meyerowitz E.M. Ectopic hypermethylation of flower-specific genes in Arabidopsis. Curr. Biol. 2000, 10:179-186.
82. Jarillo J.A., Pineiro M. Timing is everything in plant development. The central role of floral repressors. Plant Sci. 2011, 181:364-378.
83. Jarillo J.A., Pineiro M., Cubas P., Martinez-Zapater J.M. Chromatin remodeling in plant development. Int. J. Dev. Biol. 2009, 53:1581-1596.
84. Jenuwein T., Allis C.D. Translating the histone code. Science 2001, 293:1074-1080.
85. Ji L., Liu X., Yan J., Wang W., Yumul R.E., Kim Y.J., Dinh T.T., Liu J., Cui X., Zheng B., Agarwal M., Liu C., Cao X., Tang G., Chen X. ARGONAUTE10 and ARGONAUTE1 regulate the termination of floral stem cells through two microRNAs in Arabidopsis. PLoS Genet. 2011, 7:e1001358.
86. Jiang D., Yang W., He Y., Amasino R.M. Arabidopsis relatives of the human lysine-specific Demethylase1 repress the expression of FWA and FLOWERING LOCUS C and thus promote the floral transition. Plant Cell 2007, 19:2975-2987.
87. Jones R.S., Gelbart W.M. The Drosophila Polycomb-group gene Enhancer of zeste contains a region with sequence similarity to trithorax. Mol. Cell Biol. 1993, 13:6357-6366.
88. Jung J.H., Park C.M. MIR166/165 genes exhibit dynamic expression patterns in regulating shoot apical meristem and floral development in Arabidopsis. Planta 2007, 225:1327-1338.
89. Jung J.H., Seo Y.H., Seo P.J., Reyes J.L., Yun J., Chua N.H., Park C.M. The GIGANTEA-regulated microRNA172 mediates photoperiodic flowering independent of CONSTANS in Arabidopsis. Plant Cell 2007, 19:2736-2748.
90. Jung J.H., Seo P.J., Ahn J.H., Park C.M. Arabidopsis RNA-binding protein FCA regulates microRNA172 processing in thermosensory flowering. J. Biol. Chem. 2012, 287:16007-16016.
91. Kakutani T., Jeddeloh J.A., Flowers S.K., Munakata K., Richards E.J. Developmental abnormalities and epimutations associated with DNA hypomethylation mutations. Proc. Natl. Acad. Sci. USA 1996, 93:12406-12411.
92. Kankel M.W., Ramsey D.E., Stokes T.L., Flowers S.K., Haag J.R., Jeddeloh J.A., Riddle N.C., Verbsky M.L., Richards E.J. Arabidopsis MET1 cytosine methyltransferase mutants. Genetics 2003, 163:1109-1122.
93. Katiyar-Agarwal S., Morgan R., Dahlbeck D., Borsani O., Villegas A., Zhu J.K., Staskawicz B.J., Jin H. A pathogen-inducible endogenous siRNA in plant immunity. Proc. Natl. Acad. Sci. USA 2006, 103:18002-18007.
94. Katz A., Oliva M., Mosquna A., Hakim O., Ohad N. FIE and CURLY LEAF polycomb proteins interact in the regulation of homeobox gene expression during sporophyte development. Plant J. 2004, 37:707-719.
95. Kaya H., Shibahara K.I., Taoka K.I., Iwabuchi M., Stillman B., Araki T. FASCIATA genes for chromatin assembly factor-1 in arabidopsis maintain the cellular organization of apical meristems. Cell 2001, 104:131-142.
96. Khvorova A., Reynolds A., Jayasena S.D. Functional siRNAs and miRNAs exhibit strand bias. Cell 2003, 115:209-216.
97. Kidner C.A., Martienssen R.A. Spatially restricted microRNA directs leaf polarity through ARGONAUTE1. Nature 2004, 428:81-84.
98. Kim J., Jung J.H., Reyes J.L., Kim Y.S., Kim S.Y., Chung K.S., Kim J.A., Lee M., Lee Y., Narry Kim V., Chua N.H., Park C.M. microRNA-directed cleavage of ATHB15 mRNA regulates vascular development in Arabidopsis inflorescence stems. Plant J. 2005, 42:84-94.
99. Kim S.Y., He Y., Jacob Y., Noh Y.S., Michaels S., Amasino R. Establishment of the vernalization-responsive, winter-annual habit in Arabidopsis requires a putative histone H3 methyl transferase. Plant Cell 2005, 17:3301-3310.
100. Kim S., Soltis P.S., Wall K., Soltis D.E. Phylogeny and domain evolution in the APETALA2-like gene family. Mol. Biol. Evol. 2006, 23:107-120.
101. Kinoshita T., Harada J.J., Goldberg R.B., Fischer R.L. Polycomb repression of flowering during early plant development. Proc. Natl. Acad. Sci. USA 2001, 98:14156-14161.
102. Kotake T., Takada S., Nakahigashi K., Ohto M., Goto K. Arabidopsis TERMINAL FLOWER 2 gene encodes a heterochromatin protein 1 homolog and represses both FLOWERING LOCUS T to regulate flowering time and several floral homeotic genes. Plant Cell Physiol. 2003, 44:555-564.
103. Krogan N.T., Hogan K., Long J.A. APETALA2 negatively regulates multiple floral organ identity genes in Arabidopsis by recruiting the co-repressor TOPLESS and the histone deacetylase HDA19. Development 2012, 139:4180-4190.
104. Kurihara Y., Watanabe Y. Arabidopsis micro-RNA biogenesis through Dicer-like 1 protein functions. Proc. Natl. Acad. Sci. USA 2004, 101:12753-12758.
105. Kurihara Y., Takashi Y., Watanabe Y. The interaction between DCL1 and HYL1 is important for efficient and precise processing of pri-miRNA in plant microRNA biogenesis. RNA 2006, 12:206-212.
106. Kwon C.S., Chen C., Wagner D. WUSCHEL is a primary target for transcriptional regulation by SPLAYED in dynamic control of stem cell fate in Arabidopsis. Genes Dev. 2005, 19:992-1003.
107. Lafos M., Kroll P., Hohenstatt M.L., Thorpe F.L., Clarenz O., Schubert D. Dynamic regulation of H3K27 trimethylation during Arabidopsis differentiation. PLoS Genet. 2011, 7:e1002040.
108. Lee R.C., Feinbaum R.L., Ambros V. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 1993, 75:843-854.
109. Lee H., Yoo S.J., Lee J.H., Kim W., Yoo S.K., Fitzgerald H., Carrington J.C., Ahn J.H. Genetic framework for flowering-time regulation by ambient temperature-responsive miRNAs in Arabidopsis. Nucleic Acids Res. 2010, 38:3081-3093.
110. Lee J.S., Smith E., Shilatifard A. The language of histone crosstalk. Cell 2010, 142:682-685.
111. Li H., Luan S. The cyclophilin AtCYP71 interacts with CAF-1 and LHP1 and functions in multiple chromatin remodeling processes. Mol. Plant 2011, 4:748-758.
112. Li H., He Z., Lu G., Lee S.C., Alonso J., Ecker J.R., Luan S. A WD40 domain cyclophilin interacts with histone H3 and functions in gene repression and organogenesis in Arabidopsis. Plant Cell 2007, 19:2403-2416.
113. Li W., Wang Z., Li J., Yang H., Cui S., Wang X., Ma L. Overexpression of AtBMI1C, a polycomb group protein gene, accelerates flowering in Arabidopsis. PLoS One 2011, 6:e21364.
114. Lindroth A.M., Cao X., Jackson J.P., Zilberman D., McCallum C.M., Henikoff S., Jacobsen S.E. Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation. Science 2001, 292:2077-2080.
115. Lippman Z., May B., Yordan C., Singer T., Martienssen R. Distinct mechanisms determine transposon inheritance and methylation via small interfering RNA and histone modification. PLoS Biol. 2003, 1:E67.
116. Liu Z., Meyerowitz E.M. LEUNIG regulates AGAMOUS expression in Arabidopsis flowers. Development 1995, 121:975-991.
117. Liu C., Thong Z., Yu H. Coming into bloom: the specification of floral meristems. Development 2009, 136:3379-3391.
118. Liu Q., Yao X., Pi L., Wang H., Cui X., Huang H. The ARGONAUTE10 gene modulates shoot apical meristem maintenance and establishment of leaf polarity by repressing miR165/166 in Arabidopsis. Plant J. 2009, 58:27-40.
119. Liu C., Lu F., Cui X., Cao X. Histone methylation in higher plants. Annu. Rev. Plant Biol. 2010, 61:395-420.
120. Lobbes D., Rallapalli G., Schmidt D.D., Martin C., Clarke J. SERRATE: a new player on the plant microRNA scene. EMBO Rep. 2006, 7:1052-1058.
121. Long J.A., Moan E.I., Medford J.I., Barton M.K. A member of the KNOTTED class of homeodomain proteins encoded by the STM gene of Arabidopsis. Nature 1996, 379:66-69.
122. Lu C., Fedoroff N. A mutation in the Arabidopsis HYL1 gene encoding a dsRNA binding protein affects responses to abscisic acid, auxin, and cytokinin. Plant Cell 2000, 12:2351-2366.
123. Lu F., Li G., Cui X., Liu C., Wang X.J., Cao X. Comparative analysis of JmjC domain-containing proteins reveals the potential histone demethylases in Arabidopsis and rice. J. Integr. Plant Biol. 2008, 50:886-896.
124. Lu F., Cui X., Zhang S., Liu C., Cao X. JMJ14 is an H3K4 demethylase regulating flowering time in Arabidopsis. Cell Res. 2010, 20:387-390.
125. Lu F., Cui X., Zhang S., Jenuwein T., Cao X. Arabidopsis REF6 is a histone H3 lysine 27 demethylase. Nat. Genet. 2011, 43:715-719.
126. Luo D., Carpenter R., Vincent C., Copsey L., Coen E. Origin of floral asymmetry in Antirrhinum. Nature 1996, 383:794-799.
127. Luo D., Carpenter R., Copsey L., Vincent C., Clark J., Coen E. Control of organ asymmetry in flowers of Antirrhinum. Cell 1999, 99:367-376.
128. Ma J.B., Ye K., Patel D.J. Structural basis for overhang-specific small interfering RNA recognition by the PAZ domain. Nature 2004, 429:318-322.
129. Ma J.B., Yuan Y.R., Meister G., Pei Y., Tuschl T., Patel D.J. Structural basis for 5'-end-specific recognition of guide RNA by the A. fulgidus Piwi protein. Nature 2005, 434:666-670.
130. Mallory A.C., Dugas D.V., Bartel D.P., Bartel B. MicroRNA regulation of NAC-domain targets is required for proper formation and separation of adjacent embryonic, vegetative, and floral organs. Curr. Biol. 2004, 14:1035-1046.
131. Mateos J.L., Bologna N.G., Chorostecki U., Palatnik J.F. Identification of microRNA processing determinants by random mutagenesis of Arabidopsis MIR172a precursor. Curr. Biol. 2010, 20:49-54.
132. Mathieu O., Probst A.V., Paszkowski J. Distinct regulation of histone H3 methylation at lysines 27 and 9 by CpG methylation in Arabidopsis. EMBO J. 2005, 24:2783-2791.
133. Mathieu J., Yant L.J., Murdter F., Kuttner F., Schmid M. Repression of flowering by the miR172 target SMZ. PLoS Biol. 2009, 7:e1000148.
134. Millar A.A., Gubler F. The Arabidopsis GAMYB-like genes, MYB33 and MYB65, are microRNA-regulated genes that redundantly facilitate anther development. Plant Cell 2005, 17:705-721.
135. Miura A., Nakamura M., Inagaki S., Kobayashi A., Saze H., Kakutani T. An Arabidopsis jmjC domain protein protects transcribed genes from DNA methylation at CHG sites. EMBO J. 2009, 28:1078-1086.
136. Murfett J., Wang X.J., Hagen G., Guilfoyle T.J. Identification of Arabidopsis histone deacetylase HDA6 mutants that affect transgene expression. Plant Cell 2001, 13:1047-1061.
137. Nag A., King S., Jack T. miR319a targeting of TCP4 is critical for petal growth and development in Arabidopsis. Proc. Natl. Acad. Sci. USA 2009, 106:22534-22539.
138. Nagpal P., Ellis C.M., Weber H., Ploense S.E., Barkawi L.S., Guilfoyle T.J., Hagen G., Alonso J.M., Cohen J.D., Farmer E.E., Ecker J.R., Reed J.W. Auxin response factors ARF6 and ARF8 promote jasmonic acid production and flower maturation. Development 2005, 132:4107-4118.
139. Nath U., Crawford B.C., Carpenter R., Coen E. Genetic control of surface curvature. Science 2003, 299:1404-1407.
140. Naumann K., Fischer A., Hofmann I., Krauss V., Phalke S., Irmler K., Hause G., Aurich A.C., Dorn R., Jenuwein T., Reuter G. Pivotal role of AtSUVH2 in heterochromatic histone methylation and gene silencing in Arabidopsis. EMBO J. 2005, 24:1418-1429.
141. Ng K.H., Yu H., Ito T. AGAMOUS controls GIANT KILLER, a multifunctional chromatin modifier in reproductive organ patterning and differentiation. PLoS Biol. 2009, 7:e1000251.
142. Nikovics K., Blein T., Peaucelle A., Ishida T., Morin H., Aida M., Laufs P. The balance between the MIR164A and CUC2 genes controls leaf margin serration in Arabidopsis. Plant Cell 2006, 18:2929-2945.
143. Ogas J., Kaufmann S., Henderson J., Somerville C. PICKLE is a CHD3 chromatin-remodeling factor that regulates the transition from embryonic to vegetative development in Arabidopsis. Proc. Natl. Acad. Sci. USA 1999, 96:13839-13844.
144. Ori N., Eshed Y., Chuck G., Bowman J.L., Hake S. Mechanisms that control knox gene expression in the Arabidopsis shoot. Development 2000, 127:5523-5532.
145. Palatnik J.F., Allen E., Wu X., Schommer C., Schwab R., Carrington J.C., Weigel D. Control of leaf morphogenesis by microRNAs. Nature 2003, 425:257-263.
146. Palatnik J.F., Wollmann H., Schommer C., Schwab R., Boisbouvier J., Rodriguez R., Warthmann N., Allen E., Dezulian T., Huson D., Carrington J.C., Weigel D. Sequence and expression differences underlie functional specialization of Arabidopsis microRNAs miR159 and miR319. Dev. Cell 2007, 13:115-125.
147. Parcy F., Nilsson O., Busch M.A., Lee I., Weigel D. A genetic framework for floral patterning. Nature 1998, 395:561-566.
148. Park W., Li J., Song R., Messing J., Chen X. CARPEL FACTORY, a Dicer homolog, and HEN1, a novel protein, act in microRNA metabolism in Arabidopsis thaliana. Curr. Biol. 2002, 12:1484-1495.
149. Park M.Y., Wu G., Gonzalez-Sulser A., Vaucheret H., Poethig R.S. Nuclear processing and export of microRNAs in Arabidopsis. Proc. Natl. Acad. Sci. USA 2005, 102:3691-3696.
150. Parker J.S., Roe S.M., Barford D. Crystal structure of a PIWI protein suggests mechanisms for siRNA recognition and slicer activity. EMBO J. 2004, 23:4727-4737.
151. Parker J.S., Roe S.M., Barford D. Structural insights into mRNA recognition from a PIWI domain-siRNA guide complex. Nature 2005, 434:663-666.
152. Peaucelle A., Morin H., Traas J., Laufs P. Plants expressing a miR164-resistant CUC2 gene reveal the importance of post-meristematic maintenance of phyllotaxy in Arabidopsis. Development 2007, 134:1045-1050.
153. Peragine A., Yoshikawa M., Wu G., Albrecht H.L., Poethig R.S. SGS3 and SGS2/SDE1/RDR6 are required for juvenile development and the production of trans-acting siRNAs in Arabidopsis. Genes Dev. 2004, 18:2368-2379.
154. Pien S., Grossniklaus U. Polycomb group and trithorax group proteins in Arabidopsis. Biochim. Biophys. Acta 2007, 1769:375-382.
155. Pien S., Fleury D., Mylne J.S., Crevillen P., Inze D., Avramova Z., Dean C., Grossniklaus U. ARABIDOPSIS TRITHORAX1 dynamically regulates FLOWERING LOCUS C activation via histone 3 lysine 4 trimethylation. Plant Cell 2008, 20:580-588.
156. Probst A.V., Fagard M., Proux F., Mourrain P., Boutet S., Earley K., Lawrence R.J., Pikaard C.S., Murfett J., Furner I., Vaucheret H., Mittelsten Scheid O. Arabidopsis histone deacetylase HDA6 is required for maintenance of transcriptional gene silencing and determines nuclear organization of rDNA repeats. Plant Cell 2004, 16:1021-1034.
157. Rajagopalan R., Vaucheret H., Trejo J., Bartel D.P. A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana. Genes Dev. 2006, 20:3407-3425.
158. Ray A., Lang J.D., Golden T., Ray S. SHORT INTEGUMENT (SIN1), a gene required for ovule development in Arabidopsis, also controls flowering time. Development 1996, 122:2631-2638.
159. Reeves P.H., Ellis C.M., Ploense S.E., Wu M.F., Yadav V., Tholl D., Chetelat A., Haupt I., Kennerley B.J., Hodgens C., Farmer E.E., Nagpal P., Reed J.W. A regulatory network for coordinated flower maturation. PLoS Genet. 2012, 8:e1002506.
160. Reinhart B.J., Weinstein E.G., Rhoades M.W., Bartel B., Bartel D.P. MicroRNAs in plants. Genes Dev. 2002, 16:1616-1626.
161. Remington D.L., Vision T.J., Guilfoyle T.J., Reed J.W. Contrasting modes of diversification in the Aux/IAA and ARF gene families. Plant Physiol. 2004, 135:1738-1752.
162. Reyes J.C., Hennig L., Gruissem W. Chromatin-remodeling and memory factors. New regulators of plant development. Plant Physiol. 2002, 130:1090-1101.
163. Richards E.J., Elgin S.C. Epigenetic codes for heterochromatin formation and silencing: rounding up the usual suspects. Cell 2002, 108:489-500.
164. Rigal M., Kevei Z., Pelissier T., Mathieu O. DNA methylation in an intron of the IBM1 histone demethylase gene stabilizes chromatin modification patterns. EMBO J. 2012, 31:2981-2993.
165. Sablowski R. Flowering and determinacy in Arabidopsis. J. Exp. Bot. 2007, 58:899-907.
166. Sakai H., Medrano L.J., Meyerowitz E.M. Role of SUPERMAN in maintaining Arabidopsis floral whorl boundaries. Nature 1995, 378:199-203.
167. Saleh A., Alvarez-Venegas R., Yilmaz M., Le O., Hou G., Sadder M., Al-Abdallat A., Xia Y., Lu G., Ladunga I., Avramova Z. The highly similar Arabidopsis homologs of trithorax ATX1 and ATX2 encode proteins with divergent biochemical functions. Plant Cell 2008, 20:568-579.
168. Saze H., Shiraishi A., Miura A., Kakutani T. Control of genic DNA methylation by a jmjC domain-containing protein in Arabidopsis thaliana. Science 2008, 319:462-465.
169. Schmid M., Uhlenhaut N.H., Godard F., Demar M., Bressan R., Weigel D., Lohmann J.U. Dissection of floral induction pathways using global expression analysis. Development 2003, 130:6001-6012.
170. Schubert D., Clarenz O., Goodrich J. Epigenetic control of plant development by Polycomb-group proteins. Curr. Opin. Plant Biol. 2005, 8:553-561.
171. Schubert D., Primavesi L., Bishopp A., Roberts G., Doonan J., Jenuwein T., Goodrich J. Silencing by plant Polycomb-group genes requires dispersed trimethylation of histone H3 at lysine 27. EMBO J. 2006, 25:4638-4649.
172. Schwab R., Palatnik J.F., Riester M., Schommer C., Schmid M., Weigel D. Specific effects of microRNAs on the plant transcriptome. Dev. Cell 2005, 8:517-527.
173. Schwartz Y.B., Pirrotta V. Polycomb complexes and epigenetic states. Curr. Opin. Cell Biol. 2008, 20:266-273.
174. Schwarz D.S., Hutvagner G., Du T., Xu Z., Aronin N., Zamore P.D. Asymmetry in the assembly of the RNAi enzyme complex. Cell 2003, 115:199-208.
175. Shi Y., Lan F., Matson C., Mulligan P., Whetstine J.R., Cole P.A., Casero R.A. Histone demethylation mediated by the nuclear amine oxidase homolog LSD1. Cell 2004, 119:941-953.
176. Shigyo M., Hasebe M., Ito M. Molecular evolution of the AP2 subfamily. Gene 2006, 366:256-265.
177. Sieber P., Wellmer F., Gheyselinck J., Riechmann J.L., Meyerowitz E.M. Redundancy and specialization among plant microRNAs: role of the MIR164 family in developmental robustness. Development 2007, 134:1051-1060.
178. Sieburth L.E., Running M.P., Meyerowitz E.M. Genetic separation of third and fourth whorl functions of AGAMOUS. Plant Cell 1995, 7:1249-1258.
179. Song J.J., Smith S.K., Hannon G.J., Joshua-Tor L. Crystal structure of Argonaute and its implications for RISC slicer activity. Science 2004, 305:1434-1437.
180. Song L., Axtell M.J., Fedoroff N.V. RNA secondary structural determinants of miRNA precursor processing in Arabidopsis. Curr. Biol. 2010, 20:37-41.
181. Soppe W.J., Bentsink L., Koornneef M. The early-flowering mutant efs is involved in the autonomous promotion pathway of Arabidopsis thaliana. Development 1999, 126:4763-4770.
182. Soppe W.J., Jacobsen S.E., Alonso-Blanco C., Jackson J.P., Kakutani T., Koornneef M., Peeters A.J. The late flowering phenotype of fwa mutants is caused by gain-of-function epigenetic alleles of a homeodomain gene. Mol. Cell 2000, 6:791-802.
183. Spedaletti V., Polticelli F., Capodaglio V., Schinina M.E., Stano P., Federico R., Tavladoraki P. Characterization of a lysine-specific histone demethylase from Arabidopsis thaliana. Biochemistry 2008, 47:4936-4947.
184. Sridhar V.V., Surendrarao A., Gonzalez D., Conlan R.S., Liu Z. Transcriptional repression of target genes by LEUNIG and SEUSS, two interacting regulatory proteins for Arabidopsis flower development. Proc. Natl. Acad. Sci. USA 2004, 101:11494-11499.
185. Srikanth A., Schmid M. Regulation of flowering time: all roads lead to Rome. Cell. Mol. Life Sci. 2011, 68:2013-2037.
186. Stassen M.J., Bailey D., Nelson S., Chinwalla V., Harte P.J. The Drosophila trithorax proteins contain a novel variant of the nuclear receptor type DNA binding domain and an ancient conserved motif found in other chromosomal proteins. Mech. Dev. 1995, 52:209-223.
187. Strahl B.D., Allis C.D. The language of covalent histone modifications. Nature 2000, 403:41-45.
188. 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.
189. Sun B., Xu Y., Ng K.H., Ito T. A timing mechanism for stem cell maintenance and differentiation in the Arabidopsis floral meristem. Genes Dev. 2009, 23:1791-1804.
190. Sung S., Amasino R.M. Vernalization in Arabidopsis thaliana is mediated by the PHD finger protein VIN3. Nature 2004, 427:159-164.
191. Sung Z.R., Belachew A., Shunong B., Bertrand-Garcia R. EMF, an Arabidopsis Gene Required for Vegetative Shoot Development. Science 1992, 258:1645-1647.
192. Swiezewski S., Crevillen P., Liu F., Ecker J.R., Jerzmanowski A., Dean C. Small RNA-mediated chromatin silencing directed to the 3' region of the Arabidopsis gene encoding the developmental regulator, FLC. Proc. Natl. Acad. Sci. USA 2007, 104:3633-3638.
193. Takada S., Hibara K., Ishida T., Tasaka M. The CUP-SHAPED COTYLEDON1 gene of Arabidopsis regulates shoot apical meristem formation. Development 2001, 128:1127-1135.
194. Tamada Y., Yun J.Y., Woo S.C., Amasino R.M. ARABIDOPSIS TRITHORAX-RELATED7 is required for methylation of lysine 4 of histone H3 and for transcriptional activation of FLOWERING LOCUS C. Plant Cell 2009, 21:3257-3269.
195. Tanaka M., Kikuchi A., Kamada H. The Arabidopsis histone deacetylases HDA6 and HDA19 contribute to the repression of embryonic properties after germination. Plant Physiol. 2008, 146:149-161.
196. Tang G., Reinhart B.J., Bartel D.P., Zamore P.D. A biochemical framework for RNA silencing in plants. Genes Dev. 2003, 17:49-63.
197. Thorstensen T., Fischer A., Sandvik S.V., Johnsen S.S., Grini P.E., Reuter G., Aalen R.B. The Arabidopsis SUVR4 protein is a nucleolar histone methyltransferase with preference for monomethylated H3K9. Nucleic Acids Res. 2006, 34:5461-5470.
198. Thorstensen T., Grini P.E., Mercy I.S., Alm V., Erdal S., Aasland R., Aalen R.B. The Arabidopsis SET-domain protein ASHR3 is involved in stamen development and interacts with the bHLH transcription factor ABORTED MICROSPORES (AMS). Plant Mol. Biol. 2008, 66:47-59.
199. Thorstensen T., Grini P.E., Aalen R.B. SET domain proteins in plant development. Biochim. Biophys. Acta 2011, 1809:407-420.
200. Tian L., Chen Z.J. Blocking histone deacetylation in Arabidopsis induces pleiotropic effects on plant gene regulation and development. Proc. Natl. Acad. Sci. USA 2001, 98:200-205.
201. Tian L., Wang J., Fong M.P., Chen M., Cao H., Gelvin S.B., Chen Z.J. Genetic control of developmental changes induced by disruption of Arabidopsis histone deacetylase 1 (AtHD1) expression. Genetics 2003, 165:399-409.
202. To T.K., Kim J.M., Matsui A., Kurihara Y., Morosawa T., Ishida J., Tanaka M., Endo T., Kakutani T., Toyoda T., Kimura H., Yokoyama S., Shinozaki K., Seki M. Arabidopsis HDA6 regulates locus-directed heterochromatin silencing in cooperation with MET1. PLoS Genet. 2011, 7:e1002055.
203. Tschiersch B., Hofmann A., Krauss V., Dorn R., Korge G., Reuter G. The protein encoded by the Drosophila position-effect variegation suppressor gene Su(var)3-9 combines domains of antagonistic regulators of homeotic gene complexes. EMBO J. 1994, 13:3822-3831.
204. Tsukada Y., Fang J., Erdjument-Bromage H., Warren M.E., Borchers C.H., Tempst P., Zhang Y. Histone demethylation by a family of JmjC domain-containing proteins. Nature 2006, 439:811-816.
205. Varga-Weisz P. ATP-dependent chromatin remodeling factors: nucleosome shufflers with many missions. Oncogene 2001, 20:3076-3085.
206. Vazquez F., Vaucheret H., Rajagopalan R., Lepers C., Gasciolli V., Mallory A.C., Hilbert J.L., Bartel D.P., Crete P. Endogenous trans-acting siRNAs regulate the accumulation of Arabidopsis mRNAs. Mol. Cell 2004, 16:69-79.
207. Vermaak D., Ahmad K., Henikoff S. Maintenance of chromatin states: an open-and-shut case. Curr. Opin. Cell Biol. 2003, 15:266-274.
208. Wang J.W., Schwab R., Czech B., Mica E., Weigel D. Dual effects of miR156-targeted SPL genes and CYP78A5/KLUH on plastochron length and organ size in Arabidopsis thaliana. Plant Cell 2008, 20:1231-1243.
209. Wellmer F., Riechmann J.L., Alves-Ferreira M., Meyerowitz E.M. Genome-wide analysis of spatial gene expression in Arabidopsis flowers. Plant Cell 2004, 16:1314-1326.
210. Werner S., Wollmann H., Schneeberger K., Weigel D. Structure determinants for accurate processing of miR172a in Arabidopsis thaliana. Curr. Biol. 2010, 20:42-48.
211. Williams L., Carles C.C., Osmont K.S., Fletcher J.C. A database analysis method identifies an endogenous trans-acting short-interfering RNA that targets the Arabidopsis ARF2, ARF3, and ARF4 genes. Proc. Natl. Acad. Sci. USA 2005, 102:9703-9708.
212. Williams L., Grigg S.P., Xie M., Christensen S., Fletcher J.C. Regulation of Arabidopsis shoot apical meristem and lateral organ formation by microRNA miR166g and its AtHD-ZIP target genes. Development 2005, 132:3657-3668.
213. Wu G., Poethig R.S. Temporal regulation of shoot development in Arabidopsis thaliana by miR156 and its target SPL3. Development 2006, 133:3539-3547.
214. Wu M.F., Tian Q., Reed J.W. Arabidopsis microRNA167 controls patterns of ARF6 and ARF8 expression, and regulates both female and male reproduction. Development 2006, 133:4211-4218.
215. Wu G., Park M.Y., Conway S.R., Wang J.W., Weigel D., Poethig R.S. The sequential action of miR156 and miR172 regulates developmental timing in Arabidopsis. Cell 2009, 138:750-759.
216. Wu M.F., Sang Y., Bezhani S., Yamaguchi N., Han S.K., Li Z., Su Y., Slewinski T.L., Wagner D. SWI2/SNF2 chromatin remodeling ATPases overcome polycomb repression and control floral organ identity with the LEAFY and SEPALLATA3 transcription factors. Proc. Natl. Acad. Sci. USA 2012, 109:3576-3581.
217. Wurschum T., Gross-Hardt R., Laux T. APETALA2 regulates the stem cell niche in the Arabidopsis shoot meristem. Plant Cell 2006, 18:295-307.
218. Xiao W., Gehring M., Choi Y., Margossian L., Pu H., Harada J.J., Goldberg R.B., Pennell R.I., Fischer R.L. Imprinting of the MEA Polycomb gene is controlled by antagonism between MET1 methyltransferase and DME glycosylase. Dev. Cell 2003, 5:891-901.
219. Xu L., Zhao Z., Dong A., Soubigou-Taconnat L., Renou J.P., Steinmetz A., Shen W.H. Di- and tri- but not monomethylation on histone H3 lysine 36 marks active transcription of genes involved in flowering time regulation and other processes in Arabidopsis thaliana. Mol. Cell Biol. 2008, 28:1348-1360.
220. Xu Y., Wang Y., Stroud H., Gu X., Sun B., Gan E.-S., Ng K.-H., Jacobsen S., He Y., Ito T. An Arabidopsis Matrix Protein Silences Transposons and Transposon-Containing Floral Repressors through Direct Interaction with Retinoblastoma-Associated Proteins. Curr. Biol. 2013, 23(4):345-350.
221. Yadav R.K., Girke T., Pasala S., Xie M., Reddy G.V. Gene expression map of the Arabidopsis shoot apical meristem stem cell niche. Proc. Natl. Acad. Sci. USA 2009, 106:4941-4946.
222. Yang C.H., Chen L.J., Sung Z.R. Genetic regulation of shoot development in Arabidopsis: role of the EMF genes. Dev. Biol. 1995, 169:421-435.
223. Yang L., Liu Z., Lu F., Dong A., Huang H. SERRATE is a novel nuclear regulator in primary microRNA processing in Arabidopsis. Plant J. 2006, 47:841-850.
224. Yang Z., Ebright Y.W., Yu B., Chen X. HEN1 recognizes 21-24 nt small RNA duplexes and deposits a methyl group onto the 2' OH of the 3' terminal nucleotide. Nucleic Acids Res. 2006, 34:667-675.
225. Yang W., Jiang D., Jiang J., He Y. A plant-specific histone H3 lysine 4 demethylase represses the floral transition in Arabidopsis. Plant J. 2010, 62:663-673.
226. Yang H., Han Z., Cao Y., Fan D., Li H., Mo H., Feng Y., Liu L., Wang Z., Yue Y., Cui S., Chen S., Chai J., Ma L. A companion cell-dominant and developmentally regulated H3K4 demethylase controls flowering time in Arabidopsis via the repression of FLC expression. PLoS Genet. 2012, 8:e1002664.
227. Yang H., Mo H., Fan D., Cao Y., Cui S., Ma L. Overexpression of a histone H3K4 demethylase, JMJ15, accelerates flowering time in Arabidopsis. Plant Cell Rep. 2012, 31:1297-1308.
228. Yant L., Mathieu J., Dinh T.T., Ott F., Lanz C., Wollmann H., Chen X., Schmid M. Orchestration of the floral transition and floral development in Arabidopsis by the bifunctional transcription factor APETALA2. Plant Cell 2010, 22:2156-2170.
229. Yoshikawa M., Peragine A., Park M.Y., Poethig R.S. A pathway for the biogenesis of trans-acting siRNAs in Arabidopsis. Genes Dev. 2005, 19:2164-2175.
230. Yu B., Yang Z., Li J., Minakhina S., Yang M., Padgett R.W., Steward R., Chen X. Methylation as a crucial step in plant microRNA biogenesis. Science 2005, 307:932-935.
231. Yu C.W., Liu X., Luo M., Chen C., Lin X., Tian G., Lu Q., Cui Y., Wu K. HISTONE DEACETYLASE6 interacts with FLOWERING LOCUS D and regulates flowering in Arabidopsis. Plant Physiol. 2011, 156:173-184.
232. Zhang H., Zhu J.K. RNA-directed DNA methylation. Curr. Opin. Plant Biol. 2011, 14:142-147.
233. Zhang X., Yazaki J., Sundaresan A., Cokus S., Chan S.W., Chen H., Henderson I.R., Shinn P., Pellegrini M., Jacobsen S.E., Ecker J.R. Genome-wide high-resolution mapping and functional analysis of DNA methylation in arabidopsis. Cell 2006, 126:1189-1201.
234. 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.
235. Zhao Z., Yu Y., Meyer D., Wu C., Shen W.H. Prevention of early flowering by expression of FLOWERING LOCUS C requires methylation of histone H3 K36. Nat. Cell Biol. 2005, 7:1256-1260.
236. Zhao L., Kim Y., Dinh T.T., Chen X. miR172 regulates stem cell fate and defines the inner boundary of APETALA3 and PISTILLATA expression domain in Arabidopsis floral meristems. Plant J. 2007, 51:840-849.
237. Zheng B., Chen X. Dynamics of histone H3 lysine 27 trimethylation in plant development. Curr. Opin. Plant Biol. 2011, 14:123-129.
238. Zhou G.K., Kubo M., Zhong R., Demura T., Ye Z.H. Overexpression of miR165 affects apical meristem formation, organ polarity establishment and vascular development in Arabidopsis. Plant Cell Physiol. 2007, 48:391-404.
239. Zhu H., Hu F., Wang R., Zhou X., Sze S.H., Liou L.W., Barefoot A., Dickman M., Zhang X. Arabidopsis Argonaute10 specifically sequesters miR166/165 to regulate shoot apical meristem development. Cell 2011, 145:242-256.
240. Zilberman D., Gehring M., Tran R.K., Ballinger T., Henikoff S. Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. Nat. Genet. 2007, 39:61-69.