Biology of chromatin dynamics

Annual Review of Plant Biology

Volumn 56, Issue , 2005, Pages 327-351

  Hsieh, Tzung Fu ^a   Fischer, Robert L ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Chromatin remodeling; DNA methylation; Epigenetic inheritance; Histone modification; RNA interference

Indexed keywords

HISTONE;

CHEMISTRY; CHROMATIN; DNA METHYLATION; GENETIC EPIGENESIS; GENETICS; METABOLISM; PHYSIOLOGY; REVIEW; RNA INTERFERENCE;

CHROMATIN; DNA METHYLATION; EPIGENESIS, GENETIC; HISTONES; RNA INTERFERENCE;

EID: 20444365864     PISSN: 15435008     EISSN: None     Source Type: Book Series    
DOI: 10.1146/annurev.arplant.56.032604.144118     Document Type: Review

References (201)

1. Aalfs JD, Kingston RE. 2000. What does 'chromatin remodeling' mean? Trends Biochem. Sci. 25:548-55
2. Ahmad K, Henikoff S. 2002. The histone variant H3.3 marks active chromatin by replication-independent nucleosome assembly. Mol. Cell 9:1191-200
3. Allfrey VG, Faulkner R, Mirsky AE. 1964. Acetylation and methylation of histones and their possible role in the regulation of RNA synthesis. Proc. Natl. Acad. Sci. USA 51:786-94
4. Alvarez-Venegas R, Avramova Z. 2002. SET-domain proteins of the Su(var)3-9, E(z) and trithorax families. Gene 285:25-37
5. Alvarez-Venegas R, Pien S, Sadder M, Witmer X, Grossniklaus U, Avramova Z. 2003. ATX-1, an Arabidopsis homolog of trithorax, activates flower homeotic genes. Curr. Biol. 13:627-37
6. Amedeo P, Habu Y, Afsar K, Scheid OM, Paszkowski J. 2000. Disruption of the plant gene MOM releases transcriptional silencing of methylated genes. Nature 405:203-6
7. Aufsatz W, Mette MF, van der Winden J, Matzke M, Matzke AJ. 2002. HDA6, a putative histone deacetylase needed to enhance DNA methylation induced by double-stranded RNA. EMBO J. 21:6832-41
8. Bartee L, Malagnac F, Bender J. 2001. Arabidopsis cmt3 chromomethylase mutations block non-CG methylation and silencing of an endogenous gene. Genes Dev. 15:1753-58
9. Bartolomei MS, Tilghman SM. 1997. Genomic imprinting in mammals. Annu. Rev. Genet. 31:493-525
10. Bastow R, Mylne JS, Lister C, Lippman Z, Martienssen RA, Dean C. 2004. Vernalization requires epigenetic silencing of FLC by histone methylation. Nature 427:164-67
11. Baumbusch LO, Thorstensen T, Krauss V, Fischer A, Naumann K, et al. 2001. The Arabidopsis thaliana genome contains at least 29 active genes encoding SET domain proteins that can be assigned to four evolutionarily conserved classes. Nucleic Acids Res. 29:4319-33
12. Beisel C, Imhof A, Greene J, Kremmer E, Sauer F. 2002. Histone methylation by the Drosophila epigenetic transcriptional regulator Ash1. Nature 419:857-62
13. Bender J. 2004. DNA methylation and epigenetics. Annu. Rev. Plant. Biol. 55:41-68
14. Berg A, Meza TJ, Mahic M, Thorstensen T, Kristiansen K, Aalen RB. 2003. Ten members of the Arabidopsis gene family encoding methyl-CpG-binding domain proteins are transcriptionally active and at least one, AtMBD11, is crucial for normal development. Nucleic Acids Res. 31:5291-304
15. Berger F, Gaudin V. 2003. Chromatin dynamics and Arabidopsis development. Chromosome Res. 11:277-304
16. Bernstein E, Caudy AA, Hammond SM, Hannon GJ. 2001. Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature 409:363-66
17. Bertrand C, Bergounioux C, Domenichini S, Delarue M, Zhou DX. 2003. Arabidopsis histone acetyltransferase AtGCN5 regulates the floral meristem activity through the WUSCHEL/AGAMOUS pathway. J. Biol. Chem. 278:28246-51
18. 17a. Bestor TH. 2000. The DNA methyltransferases of mammals. Hum. Mol. Genet. 9:2395-402
19. Bhat RA, Riehl M, Santandrea G, Velasco R, Slocombe S, et al. 2003. Alteration of GCN5 levels in maize reveals dynamic responses to manipulating histone acetylation. Plant J. 33:455-69
20. Bird A. 2002. DNA methylation patterns and epigenetic memory. Genes Dev. 16:6-21
21. Bird AP, Wolffe AP. 1999. Methylation-induced repression-belts, braces, and chromatin. Cell 99:451-54
22. Bordoli L, Husser S, Luthi U, Netsch M, Osmani H, Eckner R. 2001. Functional analysis of the p300 acetyltransferase domain: the PHD finger of p300 but not of CBP is dispensable for enzymatic activity. Nucleic Acids Res. 29:4462-71
23. Bordoli L, Netsch M, Luthi U, Lutz W, Eckner R. 2001. Plant orthologs of p300/CBP: conservation of a core domain in metazoan p300/CBP acetyltransferase-related proteins. Nucleic Acids Res. 29:589-97
24. Bork P, Koonin EV. 1993. An expanding family of helicases within the 'DEAD/H' superfamily. Nucleic Acids Res. 21:751-52
25. Boutanaev AM, Kalmykova AI, Shevelyov YY, Nurminsky DI. 2002. Large clusters of coexpressed genes in the Drosophila genome. Nature 420:666-69
26. Brink RA. 1956. A genetic change associated with the R locus in maize which is directed and potentially reversible. Genetics 41:872-89
27. Britten RJ, Davidson EH. 1969. Gene regulation for higher cells: a theory. Science 165:349-57
28. Brock HW, van Lohuizen M. 2001. The Polycomb group-no longer an exclusive club? Curr. Opin. Genet. Dev. 11:175-81
29. Brownell JE, Zhou J, Ranalli T, Kobayashi R, Edmondson DG, et al. 1996. Tetrahymena histone acetyltransferase A: a homolog to yeast Gcn5p linking histone acetylation to gene activation. Cell 84:843-51
30. Brzeski J, Jerzmanowski A. 2003. Deficient in DNA methylation 1 (DDM1) defines a novel family of chromatin-remodeling factors. J. Biol. Chem. 278:823-28
31. Brzeski J, Podstolski W, Olczak K, Jerzmanowski A. 1999. Identification and analysis of the Arabidopsis thaliana BSH gene, a member of the SNF5 gene family. Nucleic Acids Res. 27:2393-99
32. Byrd KN, Shearn A. 2003. ASH1, a Drosophila trithorax group protein, is required for methylation of lysine 4 residues on histone H3. Proc. Natl. Acad. Sci. USA 100:11535-40
33. Cao R, Zhang Y. 2004. The functions of E(Z)/EZH2-mediated methylation of lysine 27 in histone H3. Curr. Opin. Genet. Dev. 14:155-64
34. Cao X, Aufsatz W, Zilberman D, Mette MF, Huang MS, et al. 2003. Role of the DRM and CMT3 methyltransferases in RNA-directed DNA methylation. Curr. Biol. 13:2212-17
35. Cao X, Jacobsen SE. 2002. Locus-specific control of asymmetric and CpNpG methylation by the DRM and CMT3 methyltransferase genes. Proc. Natl. Acad. Sci. USA 99(Suppl. 4): 16491-98
36. Cao X, Jacobsen SE. 2002. Role of the Arabidopsis DRM methyltransferases in de novo DNA methylation and gene silencing. Curr. Biol. 12:1138-44
37. 35a. Cao X, Springer NM, Muszynski MG, Phillips RL, Kaeppler S, Jacobsen SE. 2000. Conserved plant genes with similarity to mammalian de novo DNA methyltransferases. Proc. Natl. Acad. Sci. USA 97:4979-84
38. Carrington JC, Ambros V. 2003. Role of microRNAs in plant and animal development. Science 301:336-38
39. Chan SW, Zilberman D, Xie Z, Johansen LK, Carrington JC, Jacobsen SE. 2004. RNA silencing genes control de novo DNA methylation. Science 303:1336
40. Chandler VL, Eggleston WB, Dorweiler JE. 2000. Paramutation in maize. Plant Mol. Biol. 43:121-45
41. Chandler VL, Stam M. 2004. Chromatin conversations: mechanisms and implications of paramutation. Nat. Rev. Genet. 5:532-44
42. 39a. Chanvivattana Y, Bishopp A, Schubert D, Stock C, Moon YH. 2004. Interaction of Polycomb-group proteins controlling flowering in Arabidopsis. Development 131:5263-76
43. Chen X. 2004. A microRNA as a translational repressor of APETALA2 in Arabidopsis flower development. Science 303:2022-25
44. 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
45. 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
46. 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
47. Cunliffe VT. 2003. Memory by modification: the influence of chromatin structure on gene expression during vertebrate development. Gene 305:141-50
48. Della Vedova CB, Cone KC. 2004. Paramutation: the chromatin connection. Plant Cell 16:1358-64
49. Deuring R, Fanti L, Armstrong JA, Sarte M, Papoulas O, et al. 2000. The ISWI chromatin-remodeling protein is required for gene expression and the maintenance of higher order chromatin structure in vivo. Mol. Cell 5:355-65
50. Eshed Y, Baum SF, Bowman JL. 1999. Distinct mechanisms promote polarity establishment in carpels of Arabidopsis. Cell 99:199-209
51. Farrona S, Hurtado L, Bowman JL, Reyes JC. 2004. The Arabidopsis thaliana SNF2 homolog AtBRM controls shoot development and flowering. Development 131:4965-75
52. Feng Q, Wang H, Ng HH, Erdjument-Bromage H, Tempst P, et al. 2002. Methylation of H3-lysine 79 is mediated by a new family of HMTases without a SET domain. Curr. Biol. 12:1052-58
53. Ferguson-Smith AC, Surani MA. 2001. Imprinting and the epigenetic asymmetry between parental genomes. Science 293:1086-89
54. 50a. Finnegan EJ, Dennis ES. 1993. Isolation and identification by sequence homology of a putative cytosine methyltransferase from Arabidopsis thaliana. Nucleic Acids Res. 21:2383-88
55. Finnegan EJ, Peacock WJ, Dennis ES. 2000. DNA methylation, a key regulator of plant development and other processes. Curr. Opin. Genet. Dev. 10:217-23
56. Finnegan EJ, Sheldon CC, Jardinaud F, Peacock WJ, Dennis ES. 2004. A cluster of Arabidopsis genes with a coordinate response to an environmental stimulus. Curr. Biol. 14:911-16
57. Fire A, Xu S, Montgomery MK, Kostas SA, Driver SE, Mello CC. 1998. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391:806-11
58. Fischle W, Wang Y, Allis CD. 2003. Histone and chromatin cross-talk. Curr. Opin. Cell. Biol. 15:172-83
59. Francis NJ, Kingston RE. 2001. Mechanisms of transcriptional memory. Nat. Rev. Mol. Cell. Biol. 2:409-21
60. Fransz PF, de Jong JH. 2002. Chromatin dynamics in plants. Curr. Opin. Plant Biol. 5:560-67
61. Furner IJ, Sheikh MA, Collett CE. 1998. Gene silencing and homology-dependent gene silencing in Arabidopsis: genetic modifiers and DNA methylation. Genetics 149:651-62
62. Gavin IM, Simpson RT. 1997. Interplay of yeast global transcriptional regulators Ssn6p-Tup1p and Swi-Snf and their effect on chromatin structure. EMBO J. 16:6263-71
63. Gendall AR, Levy YY, Wilson A, Dean C. 2001. The VERNALIZATION 2 gene mediates the epigenetic regulation of vernalization in Arabidopsis. Cell 107:525-35
64. Gendrel AV, Lippman Z, Yordan C, Colot V, Martienssen RA. 2002. Dependence of heterochromatic histone H3 methylation patterns on the Arabidopsis gene DDM1. Science 297:1871-73
65. Geng F, Cao Y, Laurent BC. 2001. Essential roles of Snf5p in Snf-Swi chromatin remodeling in vivo. Mol. Cell. Biol. 21:4311-20
66. Gong Z, Morales-Ruiz T, Ariza RR, Roldan-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
67. Goodrich J, Puangsomlee P, Martin M, Long D, Meyerowitz EM, Coupland G. 1997. A Polycomb-group gene regulates homeotic gene expression in Arabidopsis. Nature 386:44-51
68. Grewal SI, Elgin SC. 2002. Heterochromatin: new possibilities for the inheritance of structure. Curr. Opin. Genet. Dev. 12:178-87
69. Grewal SI, Moazed D. 2003. Heterochromatin and epigenetic control of gene expression. Science 301:798-802
70. Guitton AE, Page DR, Chambrier P, Lionnet C, Faure JE, 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 131:2971-81
71. Hall IM, Noma K, Grewal SI. 2003. RNA interference machinery regulates chromosome dynamics during mitosis and meiosis in fission yeast. Proc. Natl. Acad. Sci. USA 100:193-98
72. Hall IM, Shankaranarayana GD, Noma K, Ayoub N, Cohen A, Grewal SI. 2002. Establishment and maintenance of a heterochromatin domain. Science 297:2232-37
73. Hamilton A, Voinnet O, Chappell L, Baulcombe D. 2002. Two classes of short interfering RNA in RNA silencing. EMBO J. 21:4671-79
74. Hammond SM, Bernstein E, Beach D, Hannon GJ. 2000. An RNA-directed nuclease mediates post-transcriptional gene silencing in Drosophila cells. Nature 404:293-96
75. Hayes JJ, Hansen JC. 2001. Nucleosomes and the chromatin fiber. Curr. Opin. Genet. Dev. 11:124-29
76. Heitz E. 1928. Das heterochromatin der Moose. Jehrb. Wiss. Botanik 69:762-818
77. Henderson IR, Shindo C, Dean C. 2003. The need for winter in the switch to flowering. Amu. Rev. Genet. 37:371-92
78. Henikoff S, Comai L. 1998. A DNA methyltransferase homolog with a chromodomain exists in multiple polymorphic forms in Arabidopsis. Genetics 149:307-18
79. Henikoff S, Furuyama T, Ahmad K. 2004. Histone variants, nucleosome assembly and epigenetic inheritance. Trends Genet. 20:320-26
80. Herman H, Lu M, Anggraini M, Sikora A, Chang Y, et al. 2003. Trans allele methylation and paramutation-like effects in mice. Nat. Genet. 34:199-202
81. Hirochika H, Okamoto H, Kakutani T. 2000. Silencing of retrotransposons in arabidopsis and reactivation by the ddm1 mutation. Plant Cell 12:357-69
82. Hsieh TF, Hakim O, Ohad N, Fischer RL. 2003. From flour to flower: how Polycomb group proteins influence multiple aspects of plant development. Trends Plant Sci. 8:439-45
83. Iizuka M, Smith MM. 2003. Functional consequences of histone modifications. Curr. Opin. Genet. Dev. 13:154-60
84. Ito T, Bulger M, Pazin MJ, Kobayashi R, Kadonaga JT. 1997. ACF, an ISWI-containing and ATP-utilizing chromatin assembly and remodeling factor. Cell 90:145-55
85. Jackson JP, Lindroth AM, Cao X, Jacobsen S. 2002. Control of CpNpG DNA methylation by the KRYPTONITE histone H3 methyltransferase. Nature 416:556-60
86. Jackson JP, Lindroth AM, Cao X, Jacobsen SE. 2002. Control of CpNpG DNA methylation by the KRYPTONITE histone H3 methyltransferase. Nature 416:556-60
87. Jasencakova Z, Soppe WJ, Meister A, Gernand D, Turner BM, Schubert I. 2003. Histone modifications in Arabidopsis - high methylation of H3 lysine 9 is dispensable for constitutive heterochromatin. Plant J. 33:471-80
88. Jeddeloh JA, Bender J, Richards EJ. 1998. The DNA methylation locus DDM1 is required for maintenance of gene silencing in Arabidopsis. Genes Dev. 12:1714-25
89. Jeddeloh JA, Stokes TL, Richards EJ. 1999. Maintenance of genomic methylation requires a SWI2/SNF2-like protein. Nat. Genet. 22:94-97
90. Jenuwein T, Allis CD. 2001. Translating the histone code. Science 293:1074-80
91. Kadosh D, Struhl K. 1998. Targeted recruitment of the Sin3-Rpd3 histone deacetylase complex generates a highly localized domain of repressed chromatin in vivo. Mol. Cell. Biol. 18:5121-27
92. Kanno T, Mette MF, Kreil DP, Aufsatz W, Matzke M, Matzke AJ. 2004. Involvement of putative SNF2 chromatin remodeling protein DRD1 in RNA-directed DNA methylation. Curr. Biol. 14:801-5
93. Katz A, Oliva M, Mosquna A, Hakim O, Ohad N. 2004. FIE and CURLY LEAF polycomb proteins interact in the regulation of homeobox gene expression during sporophyte development. Plant J. 37:707-19
94. Kaufman PD, Kobayashi R, Stillman B. 1997. Ultraviolet radiation sensitivity and reduction of telomeric silencing in Saccharomyces cerevisiae cells lacking chromatin assembly factor-I. Genes Dev. 11:345-57
95. Kawasaki H, Taira K. 2004. Induction of DNA methylation and gene silencing by short interfering RNAs in human cells. Nature 431:211-17
96. Kingston RE, Narlikar GJ. 1999. ATP-dependent remodeling and acetylation as regulators of chromatin fluidity. Genes Dev. 13:2339-52
97. Kinoshita T, Harada JJ, Goldberg RB, Fischer RL. 2001. Polycomb repression of flowering during early plant development. Proc. Natl. Acad. Sci. USA 98:14156-61
98. 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
99. Kinoshita T, Yadegari R, Harada JJ, Goldberg RB, Fischer RL. 1999. Imprinting of the MEDEA polycomb gene in the Arabidopsis endosperm. Plant Cell 11:1945-52
100. Kohler C, Hennig L, Bouveret R, Gheyselinck J, Grossniklaus U, Gruissem W. 2003. Arabidopsis MSI1 is a component of the MEA/FIE Polycomb group complex and required for seed development. EMBO J. 22:4804-14
101. Kohler C, Hennig L, Spillane C, Pien S, Gruissem W, Grossniklaus U. 2003. The Polycomb-group protein MEDEA regulates seed development by controlling expression of the MADS-box gene PHERES1. Genes Dev. 17:1540-53
102. Kolle D, Brosch G, Lechner T, Pipal A, Helliger W, et al. 1999. Different types of maize histone deacetylases are distinguished by a highly complex substrate and site specificity. Biochemistry 38:6769-73
103. Kuo MH, vom Baur E, Struhl K, Allis CD. 2000. Gcn4 activator targets Gcn5 histone acetyltransferase to specific promoters independently of transcription. Mol. Cell 6:1309-20
104. Kurdistani SK, Grunstein M. 2003. Histone acetylation and deacetylation in yeast. Nat. Rev. Mol. Cell. Biol. 4:276-84
105. Langst G, Becker PB. 2004. Nucleosome remodeling: one mechanism, many phenomena? Biochim. Biophys. Acta 1677:58-63
106. Lawrence RJ, Earley K, Pontes O, Silva M, Chen ZJ, et al. 2004. A concerted DNA methylation/histone methylation switch regulates rRNA gene dosage control and nucleolar dominance. Mol. Cell 13:599-609
107. Lechner T, Lusser A, Pipal A, Brosch G, Loidl A, et al. 2000. RPD3-type histone deacetylases in maize embryos. Biochemistry 39:1683-92
108. Lercher MJ, Urrutia AO, Hurst LD. 2002. Clustering of housekeeping genes provides a unified model of gene order in the human genome. Nat. Genet. 31:180-83
109. Levy YY, Mesnage S, Mylne JS, Gendall AR, Dean C. 2002. Multiple roles of Arabidopsis VRN1 in vernalization and flowering time control. Science 297:243-46
110. Lindroth AM, Cao X, Jackson JP, Zilberman D, McCallum CM, et al. 2001. Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation. Science 292:2077-80
111. Lippraan ZL, Gendrel AV, Black M, Vaughn MW, Dedhia N, et al. 2004. Role of transposable elements in heterochroraatin and epigenetic control. Nature 430:471-76
112. Llave C, Xie Z, Kasschau KD, Carrington JC. 2002. Cleavage of Scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA. Science 297:2053-56
113. Loidl P. 2004. A plant dialect of the histone language. Trends Plant Sci. 9:84-90
114. Lunyak VV, Burgess R, Prefontaine GG, Nelson C, Sze SH, et al. 2002. Corepressor-dependent silencing of chromosomal regions encoding neuronal genes. Science 298:1747-52
115. Lusser A, Brosch G, Loidl A, Haas H, Loidl P. 1997. Identification of maize histone deacetylase HD2 as an acidic nucleolar phosphoprotein. Science 277:88-91
116. Lusser A, Kadonaga JT. 2003. Chromatin remodeling by ATP-dependent molecular machines. Bioessays 25:1192-200
117. Malagnac F, Bartee L, Bender J. 2002. An Arabidopsis SET domain protein required for maintenance but not establishment of DNA methylation. EMBO J. 21:6842-52
118. Martens JA, Winston F. 2003. Recent advances in understanding chromatin remodeling by Swi/Snf complexes. Curr. Opin. Genet. Dev. 13:136-42
119. Martienssen RA, Colot V. 2001. DNA methylation and epigenetic inheritance in plants and filamentous fungi. Science 293:1070-74
120. Matzke M, Matzke AJ, Kooter JM. 2001. RNA: guiding gene silencing. Science 293:1080-83
121. McKittrick E, Gafken PR, Ahmad K, Henikoff S. 2004. Histone H3.3 is enriched in covalent modifications associated with active chromatin. Proc. Natl. Acad. Sci. USA 101:1525-30
122. Mette MF, Aufsatz W, van der Winden J, Matzke MA, Matzke AJ. 2000. Transcriptional silencing and promoter methylation triggered by double-stranded RNA. EMBO J. 19:5194-201
123. Milne TA, Briggs SD, Brock HW, Martin ME, Gibbs D, et al. 2002. MLL targets SET domain methyltransferase activity to Hox gene promoters. Mol. Cell 10:1107-17
124. Monson EK, de Bruin D, Zakian VA. 1997. The yeast Cac1 protein is required for the stable inheritance of transcriptionally repressed chromatin at telomeres. Proc. Natl. Acad. Sci. USA 94:13081-86
125. Morris KV, Chan SW, Jacobsen SE, Looney DJ. 2004. Small interfering RNA-induced transcriptional gene silencing in human cells. Science 305:1289-92
126. Murfett J, Wang XJ, Hagen G, Guilfoyle TJ. 2001. Identification of Arabidopsis histone deacetylase HDA6 mutants that affect transgene expression. Plant Cell 13:1047-61
127. Nakamura T, Mori T, Tada S, Krajewski W, Rozovskaia T, et al. 2002. ALL-1 is a histone methyltransferase that assembles a supercomplex of proteins involved in transcriptional regulation. Mol. Cell 10:1119-28
128. Nakayama J, Rice JC, Strahl BD, Allis CD, Grewal SI. 2001. Role of histone H3 lysine 9 methylation in epigenetic control of heterochromatin assembly. Science 292:110-13
129. Noh YS, Amasino RM. 2003. PIE1, an ISWI family gene, is required for FLC activation and floral repression in Arabidopsis. Plant Cell 15:1671-82
130. Ogas J, Cheng JC, Sung ZR, Somerville C. 1997. Cellular differentiation regulated by gibberellin in the Arabidopsis thaliana pickle mutant. Science 277:91-94
131. Ogas J, Kaufmann S, Henderson J, Somerville C. 1999. PICKLE is a CHD3 chromatin-remodeling factor that regulates the transition from embryonic to vegetative development in Arabidopsis. Proc. Natl. Acad. Sci. USA 96:13839-44
132. Ogryzko VV. 2001. Mammalian histone acetyltransferases and their complexes. Cell. Mol. Life Sci. 58:683-92
133. Okano M, Bell DW, Haber DA, Li E. 1999. DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development. Cell 99:247-57
134. Olsen PH, Ambros V. 1999. The lin-4 regulatory RNA controls developmental timing in Caenorhabditis elegans by blocking LIN-14 protein synthesis after the initiation of translation. Dev. Biol. 216:671-80
135. Osley MA. 1991. The regulation of histone synthesis in the cell cycle. Annu. Rev. Biochem. 60:827-61
136. Pal-Bhadra M, Leibovitch BA, Gandhi SG, Rao M, Bhadra U, et al. 2004. Heterochromatic silencing and HP1 localization in Drosophila are dependent on the RNAi machinery. Science 303:669-72
137. Pal-Bhadra M, Bhadra U, Birchler JA. 2002. RNAi related mechanisms affect both transcriptional and posttranscriptional transgene silencing in Drosophila. Mol. Cell 9:315-27
138. Palatnik JF, Allen E, Wu X, Schommer C, Schwab R, et al. 2003. Control of leaf morphogenesis by microRNAs. Nature 425:257-63
139. Pandey R, Muller A, Napoli CA, Selinger DA, Pikaard CS, et al. 2002. Analysis of histone acetyltransferase and histone deacetylase families of Arabidopsis thaliana suggests functional diversification of chromatin modification among multicellular eukaryotes. Nucleic Acids Res. 30:5036-55
140. Papa CM, Springer NM, Muszynski MG, Meeley R, Kaeppler SM. 2001. Maize chromomethylase Zea methyltransferase2 is required for CpNpG methylation. Plant Cell 13:1919-28
141. Partridge JF, Scott KS, Bannister AJ, Kouzarides T, Allshire RC. 2002. cis-acting DNA from fission yeast centromeres mediates histone H3 methylation and recruitment of silencing factors and cohesin to an ectopic site. Curr. Biol. 12:1652-60
142. Phelan ML, Sif S, Narlikar GJ, Kingston RE. 1999. Reconstitution of a core chromatin remodeling complex from SWI/SNF subunits. Mol. Cell 3:247-53
143. Probst AV, Fagard M, Proux F, Mourrain P, Boutet S, et al. 2004. Arabidopsis histone deacetylase HDA6 is required for maintenance of transcriptional gene silencing and determines nuclear organization of rDNA repeats. Plant Cell 16:1021-34
144. Rea S, Eisenhaber F, O'Carroll D, Strahl BD, Sun ZW, et al. 2000. Regulation of chromatin structure by site-specific histone H3 methyltransferases. Nature 406:593-59
145. Reik W, Walter J. 2001. Genomic imprinting: parental influence on the genome. Nat. Rev. Genet. 2:21-32
146. Reyes JC, Grossniklaus U. 2003. Diverse functions of Polycomb group proteins during plant development. Semin. Cell. Dev. Biol. 14:77-84
147. Reyes JC, Hennig L, Gruissem W. 2002. Chromatin-remodeling and memory factors. New regulators of plant development. Plant Physiol. 130:1090-101
148. Rice JC, Briggs SD, Ueberheide B, Barber CM, Shabanowitz J, et al. 2003. Histone methyltransferases direct different degrees of methylation to define distinct chromatin domains. Mol. Cell 12:1591-98
149. Roth SY, Denu JM, Allis CD. 2001. Histone acetyltransferases. Annu. Rev. Biochem. 70:81-120
150. Santisteban MS, Kalashnikova T, Smith MM. 2000. Histone H2A.Z regulates transcription and is partially redundant with nucleosome remodeling complexes. Cell 103:411-22
151. Santos-Rosa H, Schneider R, Bannister AJ, Sherriff J, Bernstein BE, et al. 2002. Active genes are tri-methylated at K4 of histone H3. Nature 419:407-11
152. Sarnowski TJ, Swiezewski S, Pawlikowska K, Kaczanowski S, Jerzmanowski A. 2002. AtSWI3B, an Arabidopsis homolog of SWI3, a core subunit of yeast Swi/Snf chromatin remodeling complex, interacts with FCA, a regulator of flowering time. Nucleic Acids Res. 30:3412-21
153. Schramke V, Allshire R. 2003. Hairpin RNAs and retrotransposon LTRs effect RNAi and chromatin-based gene silencing. Science 301:1069-74
154. Sijen T, Vijn I, Rebocho A, van Blokland R, Roelofs D, et al. 2001. Transcriptional and posttranscriptional gene silencing are mechanistically related. Curr. Biol. 11:436-40
155. Sims RJ 3rd, Nishioka K, Reinberg D. 2003. Histone lysine methylation: a signature for chromatin function. Trends Genet. 19:629-39
156. Singer T, Yordan C, Martienssen RA. 2001. Robertson's mutator transposons in A. thaliana are regulated by the chromatin-remodeling gene decrease in DNA methylation (DDM1). Genes Dev. 15:591-602
157. Smith MM. 2002. Histone variants and nucleosome deposition pathways. Mol. Cell 9:1158-60
158. Soppe WJ, Jacobsen SE, Alonso-Blanco C, Jackson KJ, Kakutani T, et al. 2000. The late flowering phenotype of fwa mutants is caused by gain-of-function epigenetic alleles of a homeodomain gene. Mol. Cell 6:791-802
159. Springer NM, Napoli CA, Selinger DA, Pandey R, Cone KC, et al. 2003. Comparative analysis of SET domain proteins in maize and Arabidopsis reveals multiple duplications preceding the divergence of monocots and dicots. Plant Physiol. 132:907-25
160. Stam M, Belele C, Dorweiler JE, Chandler VL. 2002. Differential chromatin structure within a tandem array 100 kb upstream of the maize b1 locus is associated with paramutation. Genes Dev. 16:1906-18
161. Stam M, Belele C, Ramakrishna W, Dorweiler JE, Bennetzen JL, Chandler VL. 2002. The regulatory regions required for B′ paramutation and expression are located far upstream of the maize b1 transcribed sequences. Genetics 162:917-30
162. Stockinger EJ, Mao Y, Regier MK, Triezenberg SJ, Thomashow MF. 2001. Transcriptional adaptor and histone acetyltransferase proteins in Arabidopsis and their interactions with CBF1, a transcriptional activator involved in cold-regulated gene expression. Nucleic Acids Res. 29:1524-33
163. Strahl BD, Allis CD. 2000. The language of covalent histone modifications. Nature 403:41-45
164. Sun FL, Cuaycong MH, Elgin SC. 2001. Long-range nucleosome ordering is associated with gene silencing in Drosophila melanogaster pericentric heterochromatin. Mol. Cell. Biol. 21:2867-79
165. 160a. Sung S, Amasino RM. 2005. Remembering winter: toward a molecular understanding of vernalization. Annu. Rev. Plant. Biol. 56:491-508
166. Sung S, Amasino RM. 2004. Vernalization and epigenetics: how plants remember winter. Curr. Opin. Plant Biol. 7:4-10
167. Sung S, Amasino RM. 2004. Vernalization in Arabidopsis thaliana is mediated by the PHD finger protein VIN3. Nature 427:159-64
168. Tagami H, Ray-Gallet D, Almouzni G, Nakatani Y. 2004. Histone H3.1 and H3.3 complexes mediate nucleosome assembly pathways dependent or independent of DNA synthesis. Cell 116:51-61
169. Tamaru H, Selker EU. 2001. A histone H3 methyltransferase controls DNA methylation in Neurospora crassa. Nature 414:277-83
170. Tamaru H, Zhang X, McMillen D, Singh PB, Nakayama J, et al. 2003. Trimethylated lysine 9 of histone H3 is a mark for DNA methylation in Neurospora crassa. Nat. Genet. 34:75-79
171. Tariq M, Paszkowski J. 2004. DNA and histone methylation in plants. Trends Genet. 20:244-51
172. Taunton J, Hassig CA, Schreiber SL. 1996. A mammalian histone deacetylase related to the yeast transcriptional regulator Rpd3p. Science 272:408-11
173. Tian L, Fong MP, Wang JJ, Wei NE, Jiang H, et al. 2004. Reversible histone acetylation and deacetylation mediate genome-wide, promoter-dependent, and locus-specific changes in gene expression during plant development. Genetics In press
174. Tian L, Wang J, Fong MP, Chen M, Cao H, et al. 2003. Genetic control of developmental changes induced by disruption of Arabidopsis histone deacetylase 1 (AtHD1) expression. Genetics 165:399-409
175. Turner BM. 2002. Cellular memory and the histone code. Cell 111:285-91
176. Verdel A, Jia S, Gerber S, Sugiyama T, Gygi S, et al. 2004. RNAi-mediated targeting of heterochromatin by the RITS complex. Science 303:672-76
177. Vielle-Calzada JP, Thomas J, Spillane C, Coluccio A, Hoeppner MA, Grossniklaus U. 1999. Maintenance of genomic imprinting at the Arabidopsis medea locus requires zygotic DDM1 activity. Genes Dev. 13:2971-82
178. Vlachonasios KE, Thomashow MF, Triezenberg SJ. 2003. Disruption mutations of ADA2b and GCN5 transcriptional adaptor genes dramatically affect Arabidopsis growth, development, and gene expression. Plant Cell 15:626-38
179. Volpe T, Schramke V, Hamilton GL, White SA, Teng G, et al. 2003. RNA interference is required for normal centromere function in fission yeast. Chromosome Res. 11:137-46
180. Volpe TA, Kidner C, Hall IM, Teng G, Grewal SI, Martienssen RA. 2002. Regulation of heterochromatic silencing and histone H3 lysine-9 methylation by RNAi. Science 297:1833-37
181. Wagner D, Meyerowitz EM. 2002. SPLAYED, a novel SWI/SNF ATPase homolog, controls reproductive development in Arabidopsis. Curr. Biol. 12:85-94
182. Wassenegger M, Heimes S, Riedel L, Sanger HL. 1994. RNA-directed de novo methylation of genomic sequences in plants. Cell 76:567-76
183. Waterborg JH. 1993. Dynamic methylation of alfalfa histone H3. J. Biol. Chem. 268:4918-21
184. Waterborg JH. 1993. Histone synthesis and turnover in alfalfa. Fast loss of highly acetylated replacement histone variant H3.2. J. Biol. Chem. 268:4912-17
185. Weitzman JB. 2002. Transcriptional territories in the genome. J. Biol. 1:2
186. 180a. Winston F, Carlson M. 1992. Yeast SNF/SWI transcriptional activators and the SPT/SIN chromatin connection. Trends Genet. 8:387-91
187. Wolffe AP. 1998. Chromatin: Structure and Function. London: Academic
188. Wu K, Malik K, Tian L, Brown D, Miki B. 2000. Functional analysis of a RPD3 histone deacetylase homologue in Arabidopsis thaliana. Plant Mol. Biol. 44:167-76
189. Wu K, Tian L, Malik K, Brown D, Miki B. 2000. Functional analysis of HD2 histone deacetylase homologues in Arabidopsis thaliana. Plant J. 22:19-27
190. Wu L, Winston F. 1997. Evidence that Snf-Swi controls chromatin structure over both the TATA and UAS regions of the SUC2 promoter in Saccharomyces cerevisiae. Nucleic Acids Res. 25:4230-34
191. Xiao W, Gehring M, Choi Y, Margossian L, Pu H, et al. 2003. Imprinting of the MEA Polycomb gene is controlled by antagonism between MET1 methyltransferase and DME glycosylase. Dev. Cell 5:891-901
192. Xie Z, Johansen LK, Gustafson AM, Kasschaul KD, Lellis AD, et al. 2004. Genetic and functional diversification of small RNA pathways in plants. PLoS Biol. 2:E104
193. Xin Z, Allis CD, Wagstaff J. 2001. Parent-specific complementary patterns of histone H3 lysine 9 and H3 lysine 4 methylation at the Prader-Willi syndrome imprinting center. Am. J. Hum. Genet. 69:1389-94
194. Yoshida N, Yanai Y, Chen L, Kato Y, Hiratsuka J, et al. 2001. EMBRYONIC FLOWER2, a novel polycomb group protein homolog, mediates shoot development and flowering in Arabidopsis. Plant Cell 13:2471-81
195. Zemach A, Grafi G. 2003. Characterization of Arabidopsis thaliana methyl-CpG-binding domain (MBD) proteins. Plant J. 34:565-72
196. Zhou C, Labbe H, Sridha S, Wang L, Tian L, et al. 2004. Expression and function of HD2-type histone deacetylases in Arabidopsis development. Plant J. 38:715-24
197. Zhou C, Miki B, Wu K. 2003. CHB2, a member of the SWI3 gene family, is a global regulator in Arabidopsis. Plant Mol. Biol. 52:1125-34
198. Zilberman D, Cao X, Jacobsen SE. 2003. ARGONAUTE4 control of locus-specific siRNA accumulation and DNA and histone methylation. Science 299:716-19
199. He Y, Michaels SD, Amasino RM. 2003. Regulation of flowering time by histone acetylation in Arabidopsis. Science 302:1751-54
200. Kohler C, Page DR, Gagliardini V, Grossniklaus U. 2005. The Arabidopsis thaliana MEDEA Polycomb group protein controls expression of PHERES1 by parental imprinting. Nat. Genet. 37:28-30
201. Shi Y, Lan F, Matson C, Mulligan P, Whetstine JR, et al. 2004. Histone demethylation mediated by the nuclear amine oxidase homolog LSD1. Cell 119:941-53