Epigenetic control of gene regulation in plants

Biochimica et Biophysica Acta - Gene Regulatory Mechanisms

Volumn 1809, Issue 8, 2011, Pages 369-378

  Lauria, Massimiliano ^a   Rossi, Vincenzo ^b  

^a CNR Consiglio Nazionale delle Ricerche   (Italy)

^b ISTITUTO NAZIONALE DELLA NUTRIZIONE   (Italy)

Author keywords

Chromatin; Epigenetics; Gene regulation; Transcription factor; Transposable element

Indexed keywords

CYTOSINE; HISTONE;

CARBOXY TERMINAL SEQUENCE; CHROMATIN; DNA BINDING; DNA HYBRIDIZATION; DNA REPLICATION; EPIGENETICS; GENE CONTROL; GENETIC ANALYSIS; GENETIC ASSOCIATION; GENETIC TRANSCRIPTION; METHYLATION; NONHUMAN; NUCLEOSOME; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEIN PROCESSING; REVIEW; TRANSPOSON;

CHROMATIN; CYTOSINE; DNA METHYLATION; DNA TRANSPOSABLE ELEMENTS; DNA, PLANT; EPIGENESIS, GENETIC; GENE EXPRESSION REGULATION, PLANT; GENOME-WIDE ASSOCIATION STUDY; HISTONES; MODELS, GENETIC; NUCLEOSOMES; PLANT PROTEINS; PLANTS; PROTEIN PROCESSING, POST-TRANSLATIONAL; TRANSCRIPTION FACTORS; TRANSCRIPTION, GENETIC;

EUKARYOTA;

EID: 79961207189     PISSN: 18749399     EISSN: 18764320     Source Type: Journal    
DOI: 10.1016/j.bbagrm.2011.03.002     Document Type: Review

References (121)

1. Jacob F., Monod J. Genetic regulatory mechanisms in the synthesis of proteins. J. Mol. Biol. 1961, 3:318-356.
2. Englesberg E., Irr J., Power J., Lee N. Positive control of enzyme synthesis by gene C in the l-arabinose system. J. Bacteriol. 1965, 90:946-957.
3. Gilbert W., Muller-Hill B. Isolation of the lac repressor. Proc. Natl Acad. Sci. U.S.A. 1966, 56:1891-1898.
4. Ptashne M. Isolation of the lambda phage repressor. Proc. Natl Acad. Sci. U.S.A. 1967, 57:306-313.
5. Yilmaz A., Grotewold E. Components and mechanisms of regulation of gene expression. Methods Mol. Biol. 2010, 674:23-32.
6. Kornberg R.D. Chromatin structure: a repeating unit of histones and DNA. Science 1974, 184:868-871.
7. Luger K., Mader A.W., Richmond R.K., Sargent D.F., Richmond T.J. Crystal structure of the nucleosome core particle at 2.8? resolution. Nature 1997, 389:251-260.
8. Lorch Y., LaPointe J.W., Kornberg R.D. Nucleosomes inhibit the initiation of transcription but allow chain elongation with displacement of histones. Cell 1987, 49:203-210.
9. Han M., Grunstein M. Nucleosome loss activates yeast downstream promoters in vivo. Cell 1988, 55:1137-1145.
10. Cote J., Quinn J., Workman J.L., Peterson C.L. Stimulation of GAL4 derivative binding to nucleosomal DNA by the yeast SWI/SNF complex. Science 1994, 265:53-60.
11. Imbalzano A.N., Kwon H., Green M.R., Kingston R.E. Facilitated binding of TATA-binding protein to nucleosomal DNA. Nature 1994, 370:481-485.
12. Kwon H., Imbalzano A.N., Khavari P.A., Kingston R.E., Green M.R. Nucleosome disruption and enhancement of activator binding by a human SWI/SNF complex. Nature 1994, 370:477-481.
13. Brownell J.E., Zhou J., Ranalli T., Kobayashi R., Edmondson D.G., Roth S.Y., Allis C.D. Tetrahymena histone acetyltransferase A: a homolog to yeast Gcn5p linking histone acetylation to gene activation. Cell 1996, 84:843-851.
14. Taunton J., Hassig C.A., Schreiber S.L. A mammalian histone deacetylase related to the yeast transcriptional regulator Rpd3p. Science 1996, 272:408-411.
15. Jones P.A., Taylor S.M. Cellular differentiation, cytidine analogs, and DNA methylation. Cell 1980, 20:85-93.
16. Jones P.L., Veenstra G.C.J., Wade P.A., Vermaak D., Kaas S.U., Landsberger N., Strouboulis J., Wolffe A.P. Methylated DNA and MeCP2 recruit histone deacetylase to repress transcription. Nat. Genet. 1998, 19:187-191.
17. Nan X., Ng H.-H., Johnson C.A., Laherty C.D., Turner B.M., Eisenman R.N., Bird A. Transcriptional repression by the methyl-CpG-binding protein MeCP2 involves a histone deacetylase complex. Nature 1998, 393:386-389.
18. Struhl K. Fundamentally different logic of gene regulation in eukaryotes and prokaryotes. Cell 1999, 98:1-4.
19. Bonasio R., Tu S., Reinberg D. Molecular signals of epigenetic states. Science 2010, 330:612-616.
20. Saze H., Kakutani T. Differentiation and epigenetic modifications between transposons and genes. Curr. Opin. Plant Biol. 2011, 14:81-87.
21. Goldberg A.D., Allis C.D., Bernstein E. Epigenetics: a landscape takes shape. Cell 2007, 128:635-638.
22. Law J.A., Jacobsen S.E. Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat. Rev. Genet. 2010, 11:204-220.
23. Zemach A., Grafi G. Methyl-CpG-binding domain proteins in plants: interpreters of DNA methylation. Trends Plant Sci. 2007, 12:80-85.
24. Lippman Z., Gendrel A.V., Black M., Vaughn M.W., Dedhia N., McCombie W.R., Lavine K., Mittal V., May B., Kasschau K.D., Carrington J.C., Doerge R.W., Colot V., Martienssen R.A. Role of transposable elements in heterochromatin and epigenetic control. Nature 2004, 430:471-476.
25. Vaughn M.W., Tanurdzic M., Lippman Z., Jiang H., Carrasquillo R., Rabinowicz P.D., Dedhia N., McCombie W.R., Ager N., Bulski A., Colot V., Doerge R.W., Martienssen R.A. Epigenetic natural variation in Arabidopsis thaliana. PLoS Biol. 2007, 5:e174.
26. Li X., Wang X., He K., Ma Y., Su N., He H., Stolc V., Tongprasit W., Jin W., Jiang J., Terzaghi W., Li S., Deng X.W. High-resolution mapping of epigenetic modifications of the rice genome uncovers interplay between DNA methylation, histone methylation and gene expression. Plant Cell 2008, 20:259-276.
27. Wang X., Elling A.A., Li X., Li N., Peng Z., He G., Sun H., Qi Y., Liu X.S., Deng X.W. Genome-wide and organ-specific landscapes of epigenetic modifications and their relationships to mRNA and small RNA transcriptomes in maize. Plant Cell 2009, 21:1053-1069.
28. 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.
29. 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.
30. Cokus S.J., Feng S., Zhang X., Chen Z., Merriman B., Haudenschild C.D., Pradhan S., Nelson S.F., Pellegrini M., Jacobsen S.E. Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature 2008, 452:215-219.
31. Lister R., O'Malley R.C., Tonti-Filippini J., Gregory B.D., Berry C.C., Millar A.H., Ecker J.R. Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 2008, 133:523-536.
32. Feng S., Cokus S.J., Zhang X., Chen P.Y., Bostick M., Goll M.G., Hetzel J., Jain J., Strauss S.H., Halpern M.E., Ukomadu C., Sadler K.C., Pellegrini M., Jacobsen S.E. Conservation and divergence of plant and animal methylation patterning. Proc. Natl Acad. Sci. U.S.A. 2010, 107:8689-8694.
33. Zemach A., McDaniel I.E., Silva P., Zilberman D. Genome-wide evolutionary analysis of eukaryotic DNA methylation. Science 2010, 328:916-919.
34. Gehring M., Bubb K.L., Henikoff S. Extensive demethylation of repetitive elements during seed development underlines gene imprinting. Science 2009, 324:1447-1451.
35. Hsieh T.-F., Ibarra C.A., Silva P., Zemach A., Eshed-Williams L., Fischer R.L., Zilberman D. Genome-wide demethylation of Arabidopsis endosperm. Science 2009, 324:1451-1454.
36. Zemach A., Kim M.Y., Silva P., Rodrigues J.A., Dotson B., Brooks M.D., Zilberman D. Local DNA hypomethylation activates genes in rice endosperm. Proc. Natl Acad. Sci. U.S.A. 2010, 106:18729-18734.
37. Tran R.K., Henikoff J.G., Zilberman D., Ditt R.F., Jacobsen S.E., Henikoff S. DNA methylation profiling identifies CG methylation clusters in Arabidopsis genes. Curr. Biol. 2005, 15:154-159.
38. Chodavarapu R.K., Feng S., Bernatavichute Y.V., Chen P.Y., Stroud H., Yu Y., Hetzel J., Kuo F., Kim J., Cokus S., Casero D., Bernal M., Huijser P., Kramer U., Merchant S.S., Zhang X., Jacobsen S.E., Pellegrini M. Relationship between nucleosome positioning and DNA methylation. Nature 2010, 466:388-392.
39. Clapier C.R., Cairns B.R. The biology of chromatin remodeling complexes. Annu. Rev. Biochem. 2009, 78:273-304.
40. Kusch T., Workman J.L. Histone variants and complexes involved in their exchange. Subcell. Biochem. 2007, 41:91-109.
41. Henikoff S. Epigenetic profiling of histone variants. Epigenomics Part II 2009, 101-118. A.C. Ferguson-Smith, J.M. Greally, R.A. Martienssen (Eds.).
42. Zhang X., Leroy 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.
43. Oh S., Park S., van Nocker S. Genic and global functions for Paf1C in chromatin modification and gene expression in Arabidopsis. PLoS Genet. 2008, 4:e1000077.
44. Zilberman D., Coleman-Derr D., Ballinger T., Henikoff S. Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks. Nature 2008, 456:125-129.
45. Kouzarides T. Chromatin modifications and their functions. Cell 2007, 128:693-705.
46. Li B., Carey M., Workman J.L. The role of chromatin during transcription. Cell 2007, 128:707-709.
47. Strahl B.D., Allis C.D. The language of covalent histone modifications. Nature 2000, 403:41-45.
48. Berger S.L. The complex language of chromatin regulation during transcription. Nature 2007, 447:407-412.
49. Charron J.-B.F., He H., Elling A.A., Deng X.W. Dynamic landscapes of four histone modifications during deetiolation in Arabidopsis. Plant Cell 2009, 21:3732-3748.
50. Zhou J., Wang X., He K., Charron J.-B.F., Elling A.A., Deng X.W. 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. 2010, 72:585-595.
51. Tanurdzic M., Vaughn M.W., Jiang H., Lee T.-J., Slotkin R.K., Sosinski B., Thompson W.F., Doerge R.W., Martienssen R.A. Epigenomic consequences of immortalized plant cell suspension culture. PLoS Biol. 2008, 6:2880-2895.
52. Zhang X., Bernatavichute Y.V., Cokus S., Pellegrini M., Jacobsen S.E. Genome-wide analysis of mono-, di- and trimethylation of histone H3 lysine 4 in Arabidopsis thaliana. Genome Biol. 2009, 10:R62.
53. Turck F., Roudier F., Farrona S., Martin-Magniette M.L., Guillaume E., Buisine N., Gagnot S., Martienssen R.A., Coupland G., Colot V. Arabidopsis TFL2/LHP1 specifically associates with genes marked by trimethylation of histone H3 lysine 27. PLoS Genet. 2007, 3:e86.
54. Wang Z., Zhang C., Rosenfeld J.A., Schones D.E., Barski A., Cuddapah S., Cui K., Roh T.-Y., Peng W., Zhang M.Q., Zhao K. Combinatorial patterns of histone acetylations and methylations in the human genome. Nat. Genet. 2008, 7:897-903.
55. Talbot D.R., Adang M.J., Slightom J.L., Hall T.C. Size and organization of a multigene family encoding phaseolin, the major seed storage protein of Phaseolus vulgaris L. Mol. Genet. Genom. 1984, 198:42-49.
56. Li G., Chandrasekharan M.B., Wolffe A.P., Hall T.C. Chromatin structure and phaseolin gene regulation. Plant Mol. Biol. 2001, 46:121-129.
57. Frisch D.A., van der Geest A.H.M., Dias K., Hall T.C. Chromosomal integration is required for spatial regulation of expression from the beta-phaseolin promoter. Plant J. 1995, 7:503-512.
58. Li G., Chandler S.P., Wolffe A.P., Hall T.C. Architectural specificity in chromatin structure at the TATA box in vivo: nucleosome displacement upon beta-phaseolin gene activation. Proc. Natl Acad. Sci. U.S.A. 1998, 95:4772-4777.
59. Li G., Bishop K.J., Chandrasekharan M.B., Hall T.C. beta-Phaseolin gene activation is a two-step process: PvALF facilitated chromatin modification followed by abscisic acid mediated gene activation. Proc. Natl Acad. Sci. U.S.A. 1999, 96:7104-7109.
60. Ng D.W., Chandrasekharan M.B., Hall T.C. Ordered histone modifications are associated with transcriptional poising and activation of the phaseolin promoter. Plant Cell 2006, 18:119-132.
61. Schmidt R.J., Burr F.A., Burr B. Transposon tagging and molecular analysis of the maize regulatory locus opaque-2. Science 1987, 238:960-963.
62. Motto M., Balconi C., Hartings H., Lauria M., Rossi V. Improvement of quality-related traits in maize grain: gene identification and exploitation. Maydica 2009, 54:321-342.
63. Rossi V., Motto M., Pellegrini L. Analysis of the methylation pattern of the maize opaque-2 (O2) promoter and in vitro binding studies indicate that the O2 bZIP protein and other endosperm factors can bind to methylated target sequences. J. Biol. Chem. 1997, 272:13758-13765.
64. Sturaro M., Viotti A. Methylation of the Opaque2 box in zein genes is parent dependent and affects O2 DNA binding activity, in vitro. Plant Mol. Biol. 2001, 46:549-560.
65. Bhat R.A., Borst J.W., Riehl M., Thompson R.D. Interaction of maize Opaque-2 and the transcriptional co-activators GCN5 and ADA2, in the modulation of transcriptional activity. Plant Mol. Biol. 2004, 55:239-252.
66. Locatelli S., Piatti P., Motto M., Rossi V. Chromatin and DNA modifications in the Opaque2-mediated regulation of gene transcription during maize endosperm development. Plant Cell 2009, 21:1410-1427.
67. Crevillen P., Dean C. Regulation of the flower repressor gene FLC: the complexity of transcription in a chromatin context. Curr. Opin. Plant Biol. 2011, 14:38-44.
68. Jiang D., Gu X., He Y. Establishment of a winter-annual growth via FRIGIDA-mediated histone methylation at FLOWERING LOCUS C in Arabidopsis. Plant Cell 2009, 21:1733-1746.
69. He Y., Doyle M.R., Amasino R.M. PAF1-complex-mediated histone methylation of FLOWERING LOCUS C chromatin is required for the vernalization-responsive, winter-annual habit in Arabidopsis. Genes Dev. 2004, 18:2774-2784.
70. Deal R.B., Topp C.N., McKinney E.C., Meagher R.B. Repression of flowering in Arabidopsis requires activation of FLOWERING LOCUS C expression by the histone variant H2A.Z. Plant Cell 2007, 19:74-83.
71. 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.
72. Lolas I.B., Himanen K., Gronlund J.T., Lynggaard C., Houben A., Melzer M., Van Lijsebettens M., Grasser K.D. The transcript elongation factor FACT affects Arabidopsis vegetative and reproductive development and genetically interacts with HUB1/2. Plant J. 2010, 61:686-697.
73. He Y. Control of the transition to flowering by chromatin modifications. Mol. Plant 2009, 2:554-564.
74. Kim D.-H., Doyle M.R., Sung S., Amasino R.M. Vernalization: winter and the timing of flowering in plants. Annu. Rev. Cell Dev. Biol. 2009, 25:277-299.
75. De Lucia F., Crevillen P., Jones A.M., Greb T., Dean C. A PHD-Polycomb repressive complex 2 triggers the epigenetic silencing of FLC during vernalization. Proc. Natl Acad. Sci. U.S.A. 2008, 105:16831-16836.
76. Bastow R., Mylne J.S., Lister C., Lippman Z., Martienssen R.A., Dean C. Vernalization requires epigenetic silencing of FLC by histone methylation. Nature 2004, 427:164-167.
77. Sung S., Amasino R.M. Vernalization in Arabidopsis thaliana is mediated by the PHD finger protein VIN3. Nature 2004, 427:159-164.
78. Zhang X., Germann S., Blus J.B., Khorasanizadeh S., Gaudin V., Jacobsen S.E. The Arabidopsis LHP1 protein colocalizes with histone H3 Lys27 trimethylation. Nat. Struct. Mol. Biol. 2007, 14:869-871.
79. Marquardt S., Boss P.K., Hatfield J., Dean C. Additional targets of the Arabidopsis autonomous pathway members, FCA and FY. J. Exp. Bot. 2006, 57:3379-3386.
80. 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.
81. Ko J.-H., Mitina I., Tamada Y., Hyun Y., Choi Y., Amasino R.M., Noh B., Noh Y.-S. Growth habit determination by the balance of histone methylation activities in Arabidopsis. EMBO J. 2010, 29:3208-3215.
82. Hornyik C., Terzi L.C., Simpson G.G. The spen family protein FPA controls alternative cleavage and polyadenylation of RNA. Dev. Cell 2010, 18:203-213.
83. Liu F., Marquardt S., Lister C., Swiezewski S., Dean C. Targeted 3? processing of antisense transcripts triggers Arabidopsis FLC chromatin silencing. Science 2010, 327:94-97.
84. Liu F., Quesada V., Crevillen P., Baurle I., Swiezewski S., Dean C. The Arabidopsis RNA-binding protein FCA requires a lysine-specific demethylase 1 homolog to down-regulate FLC. Mol. Cell 2007, 28:398-407.
85. Swiezewski S., Liu F., Magusin A., Dean C. Cold-induced silencing by long antisense transcripts of an Arabidopsis Polycomb target. Nature 2009, 462:799-802.
86. Heo J.B., Sung S. Vernalization-mediated epigenetic silencing by a long intronic noncoding RNA. Science 2011, 331:76-79.
87. De Lucia F., Dean C. Long antisense transcripts and chromatin regulation. Curr. Opin. Plant Biol. 2010, 10.1016/j.pbi.2010.11.006.
88. Kaufmann K., Pajoro A., Agenent G.C. Regulation of transcription in plants: mechanisms controlling developmental switches. Nat. Rev. Genet. 2010, 11:830-842.
89. 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.
90. Luo C., Durgin B.G., Watanabe N., Lam E. Defining the functional network of epigenetic regulators in Arabidopsis thaliana. Mol. Plant 2009, 4:661-674.
91. Slotkin R.K., Martienssen R. Transposable elements and the epigenetic regulation of the genome. Nat. Rev. Genet. 2007, 8:272-285.
92. Lisch D. Epigenetic regulation of transposable elements in plants. Annu. Rev. Plant Biol. 2009, 60:43-66.
93. Matzke M., Kanno T., Daxinger L., Huettel B., Matzke A.J. RNA-mediated chromatin-basedsilencinginplants. Curr. Opin Cell Biol. 2009, 21:367-376.
94. SanMiguel P., Tikhonov A., Jin Y.K., Motchoulskaia N., Zakharov D., Melake-Berhan A., Springer P.S., Edwards K.J., Lee M., Avramova Z., Bennetzen J.L. Nested retrotransposons in the intergenic regions of the maize genome. Science 1996, 1:765-768.
95. Wei F., Stein J.C., Liang C., Zhang J., Fulton R.S., Baucom R.S., De Paoli E., Zhou S., Yang L., Han Y., Pasternak S., Narechania A., Zhang L., Yeh C.-T., Ying K., Nagel D.H., Collura K., Kudrna D., Currie J., Lin J., Kim H., Angelova A., Scara G., Wissotski M., Golser W., Courtney L., Kruchowski S., Graves T.A., Rock S.M., Adams S., Fulton L.A., Fronick C., Courtney W., Kramer M., Spiegel L., Nascimento L., Kalyanaraman A., Chaparro C., Deragon J.-M., San Miguel P., Jiang N., Wessler S.R., Green P.J., Yu Y., Schwartz D.C., Meyers B.C., Bennetzen J.L., Martienssen R.A., McCombie W.R., Aluru S., Clifton S.W., Schnable P.S., Ware D., Wilson R.K., Wing R.A. Detailed analysis of a contiguous 22-Mb region of the maize genome. PLoS Genet. 2009, 5:e1000728.
96. Gaszner M., Felsenfeld G. Insulators: exploiting transcriptional and epigenetic mechanisms. Nat. Rev. Genet. 2006, 7:703-713.
97. Stam M., Belele C., Dorweiler J.E., Chandler V.L. Differential chromatin structure within a tandem array 100kb upstream of the maize b1 locus is associated with paramutation. Genes Dev. 2002, 16:1906-1918.
98. Walker E.L., Panavas T. Structural features and methylation patterns associated with paramutation at the r1 locus of Zea mays. Genetics 2001, 159:1201-1215.
99. Sidorenko L.V., Chandler V.L. RNA dependent RNA polymerase is required for enhancer mediated transcriptional silencing associated with paramutation at the maize p1 gene. Genetics 2008, 180:1983-1993.
100. Miura K., Agetsuma M., Kitano H., Yoshimura A., Matsuoka M., Jacobsen S.E., Ashikari M. A metastable DWARF1 epigenetic mutant affecting plant stature in rice. Proc. Natl Acad. Sci. U.S.A. 2009, 106:11218-11223.
101. Banks J.A., Masson P., Fedoroff N. Molecular mechanisms in the developmental regulation of the maize suppressor-mutator transposable element. Genes Dev. 1988, 2:1364-1380.
102. Martienssen R., Baron A. Coordinate suppression of mutations caused by Robertson's mutator transposons in maize. Genetics 1994, 136:1157-1170.
103. Kalisz S., Purugganan M.D. Epialleles via DNA methylation: consequences for plant evolution. Trends Ecol. Evol. 2004, 19:309-314.
104. 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.
105. Kinoshita T., Miura A., Choi Y., Kinoshita Y., Cao X., Jacobsen S.E., Fischer R.L., Kakutani T. One-way control of FWA imprinting in Arabidopsis endosperm by DNA methylation. Science 2004, 303:521-523.
106. Chan S.W., Zhang X., Bernatavichute Y.V., Jacobsen S.E. Two-step recruitment of RNA-directed DNA methylation to tandem repeats. PLoS Biol. 2006, 4:e363.
107. Fujimoto R., Kinoshita Y., Kawabe A., Kinoshita T., Takashima K., Nordborg M., Nasrallah M.E., Shimizu K.K., Kudoh H., Kakutani T. Evolution and control of imprinted FWA genes in the genus Arabidopsis. PLoS Genet. 2008, 4:e1000048.
108. Cao X., Jacobsen S.E. Locus-specific control of asymmetric and CpNpG methylation by the DRM and CMT3 methyltransferase genes. Proc. Natl Acad. Sci. U.S.A. 2002, 99:16491-16498.
109. Castro A., Bernis C., Vigneron S., Labbe J.C., Lorca T. The anaphase-promoting complex: a key factor in the regulation of cell cycle. Oncogene 2005, 24:314-325.
110. Saze H., Kakutani T. Heritable epigenetic mutation of a transposon-flanked Arabidopsis gene due to lack of the chromatin-remodeling factor DDM1. EMBO J. 2007, 26:3641-3652.
111. 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.
112. Lister R., Pelizzola M., Dowen R.H., Hawkins R.D., Hon G., Tonti-Filippini J., Nery J.R., Lee L., Ye Z., Ngo Q.M., Edsall L., Antosiewicz-Bourget J., Stewart R., Ruotti V., Harvey-Millar A., Thomson J.A., Ren B., Ecker J.R. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 2009, 19:315-322.
113. Loidl P. A plant dialect of the histone language. Trends Plant Sci. 2004, 9:84-90.
114. Lachner M., Sengupta R., Schotta G., Jenuwein T. Trilogies of histone lysine methylation as epigenetic landmarks of the eukaryotic genome. Cold Spring Harb. Symp. Quant. Biol. 2004, 69:209-218.
115. Guenther M.G., Levine S.S., Boyer L.A., Jaenisch R., Young R.A. A chromatin landmark and transcription initiation at most promoters in human cells. Cell 2007, 130:77-88.
116. Bernstein B.E., Mikkelsen T.S., Xie X., Kamal M., Huebert D.J., Cuff J., Fry B., Meissner A., Wernig M., Plath K., Jaenisch R., Wagschal A., Feil R., Schreiber S.L., Lander E.S. A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell 2006, 125:315-326.
117. Pauler F.M., Sloane M.A., Huang R., Regha K., Koerner M.V., Tamir I., Sommer A., Aszodi A., Jenuwein T., Barlow D.P. H3K27me3 forms BLOCs over silent genes and intergenic regions and specifies a histone banding pattern on a mouse autosomal chromosome. Genome Res. 2009, 19:221-233.
118. 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.
119. Deal R.B., Henikoff J.G., Henikoff S. Genome-wide kinetics of the nucleosome turnover determined by metabolic labeling of histones. Science 2010, 328:1161-1164.
120. Schwartz S., Ast G. Chromatin density and splicing destiny: on the cross-talk between chromatin structure and splicing. EMBO J. 2010, 29:1629-1636.
121. Faulkner G.J., Kimura Y., Daub C.O., Wani S., Plessy C., Irvine K.M., Schroder K., Cloonan N., Steptoe A.L., Lassmann T., Waki K., Hornig N., Arakawa T., Takahashi H., Kawai J., Forrest A.R.R., Suzuki H., Hayashizaki Y., Hume D.A., Orlando V., Grimmond S.M., Carninci P. The regulated retrotransposon transcriptome of mammalian cells. Nat. Genet. 2009, 41:563-571.