Confining euchromatin/heterochromatin territory: Jumonji crosses the line

Genes and Development

Volumn 24, Issue 14, 2010, Pages 1465-1478

  Tamaru, Hisashi ^a  

^a GREGOR MENDEL INSTITUTE OF MOLECULAR PLANT BIOLOGY   (Austria)

Author keywords

5mC; Euchromatin heterochromatin; H3K9me; JmjC; Transcription

Indexed keywords

DNA METHYLATION MODULATOR 1; DNA METHYLATION MODULATOR 2; FUNGAL PROTEIN; HISTONE; INCREASE IN BONSAI METHYLATION 1 PROTEIN; JUMONJI C DOMAIN CONTAINING PROTEIN; NUCLEAR PROTEIN; PROTEIN EPE1; REGULATOR PROTEIN; REPETITIVE DNA; TRANSFER RNA; UNCLASSIFIED DRUG; VEGETABLE PROTEIN;

ARABIDOPSIS; CELL DIVISION; CELL FUNCTION; CHROMOSOME SEGREGATION; DNA BINDING; DNA METHYLATION; DNA SEQUENCE; EUCHROMATIN; FUNGAL GENOME; GENE MUTATION; GENE SILENCING; GENETIC TRANSCRIPTION; HETEROCHROMATIN; NEUROSPORA CRASSA; NONHUMAN; PLANT GENOME; PRIORITY JOURNAL; PROTEIN DOMAIN; REVIEW; SCHIZOSACCHAROMYCES POMBE; SIGNAL TRANSDUCTION;

ANIMALS; ARABIDOPSIS; EUCHROMATIN; HETEROCHROMATIN; HUMANS; NEUROSPORA CRASSA; NUCLEAR PROTEINS; PROTEIN STRUCTURE, TERTIARY; SCHIZOSACCHAROMYCES;

ARABIDOPSIS THALIANA; MAGNOLIOPHYTA; SCHIZOSACCHAROMYCES POMBE; SCHIZOSACCHAROMYCETACEAE;

EID: 77954838715     PISSN: 08909369     EISSN: 15495477     Source Type: Journal    
DOI: 10.1101/gad.1941010     Document Type: Review

References (160)

1. Aagaard L, Laible G, Selenko P, Schmid M, Dorn R, Schotta G, Kuhfittig S, Wolf A, Lebersorger A, Singh PB, et al. 1999. Functional mammalian homologues of the Drosophila PEV-modifier Su(var)3-9 encode centromere-associated proteins which complex with the heterochromatin component M31. EMBO J 18: 1923-1938.
2. Ayoub N, Noma K, Isaac S, Kahan T, Grewal SIS, Cohen A. 2003. A novel jmjC domain protein modulates heterochromatization in fission yeast. Mol Cell Biol 23: 4356-4370.
3. Baker WK. 1968. Position-effect variegation. Adv Genet 14: 133-169.
4. Bannister AJ, Zegerman P, Partridge JF, Miska EA, Thomas JO, Allshire RC, Kouzarides T. 2001. Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domain. Nature 410: 120-124.
5. Bartee L, Malagnac F, Bender J. 2001. Arabidopsis cmt3 chromomethylase mutations block non-CG methylation and silencing of an endogenous gene. Genes Dev 15: 1753-1758.
6. Bayne EH, Allshire RC. 2005. RNA-directed transcriptional gene silencing in mammals. Trends Genet 21: 370-373. (Pubitemid 40835719)
7. Blasco MA. 2007. The epigenetic regulation of mammalian telomeres. Nat Rev Genet 8: 299-309.
8. Buschhausen G, Wittig B, Graessmann M, Graessmann A. 1987. Chromatin structure is required to block transcription of the methylated herpes-simplex virus thymidine kinase gene. Proc Natl Acad Sci 84: 1177-1181.
9. Cam HP, Sugiyama T, Chen ES, Chen X, FitzGerald PC, Grewal SIS. 2005. Comprehensive analysis of heterochromatin- and RNAi-mediated epigenetic control of the fission yeast genome. Nat Genet 37: 809-819.
10. Cambareri EB, Jensen BC, Schabtach E, Selker EU. 1989. Repeat-induced G-C TO A-T mutations in Neurospora. Science 244: 1571-1575.
11. Cambareri EB, Foss HM, Rountree MR, Selker EU, Kinsey JA. 1996. Epigenetic control of a transposon-inactivated gene in Neurospora is dependent on DNA methylation. Genetics 143: 137-146.
12. Cao XF, Jacobsen SE. 2002a. Locus-specific control of asymmetric and CpNpG methylation by the DRM and CMT3 methyltransferase genes. Proc Natl Acad Sci 99: 16491-16498.
13. Cao XF, Jacobsen SE. 2002b. Role of the Arabidopsis DRM methyltransferases in de novo DNA methylation and gene silencing. Curr Biol 12: 1138-1144.
14. Chan SWL, Henderson IR, Jacobsen SE. 2005. Gardening the genome: DNA methylation in Arabidopsis thaliana. Nat Rev Genet 6: 351-360. (Pubitemid 40577179)
15. Chen ES, Zhang K, Nicolas E, Cam HP, Zofall M, Grewal SI. 2008. Cell cycle control of centromeric repeat transcription and heterochromatin assembly. Nature 451: 734-737.
16. Chicas A, Cogoni C, Macino G. 2004. RNAi-dependent and RNAi-independent mechanisms contribute to the silencing of RIPed sequences in Neurospora crassa. Nucleic Acids Res 32: 4237-4243.
17. Chicas A, Forrest EC, Sepich S, Cogoni C, Macino G. 2005. Small interfering RNAs that trigger posttranscriptional gene silencing are not required for the histone H3 Lys9 methylation necessary for transgenic tandem repeat stabilization in Neurospora crassa. Mol Cell Biol 25: 3793-3801.
18. Cogoni C. 2001. Homology-dependent gene silencing mechanisms in fungi. Annu Rev Microbiol 55: 381-406. (Pubitemid 32978111)
19. Cogoni C, Macino G. 1999a. Gene silencing in Neurospora crassa requires a protein homologous to RNA-dependent RNA polymerase. Nature 399: 166-169.
20. Cogoni C, Macino G. 1999b. Posttranscriptional gene silencing in Neurospora by a RecQ DNA helicase. Science 286: 2342-2344.
21. Cogoni C, Irelan JT, Schumacher M, Schmidhauser TJ, Selker EU, Macino G. 1996. Transgene silencing of the al-1 gene in vegetative cells of Neurospora is mediated by a cytoplasmic effector and does not depend on DNA-DNA interactions or DNA methylation. EMBO J 15: 3153-3163.
22. Cokus SJ, Feng SH, Zhang XY, Chen ZG, Merriman B, Haudenschild CD, Pradhan S, Nelson SF, Pellegrini M, Jacobsen SE. 2008. Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature 452: 215-219.
23. Daxinger L, Kanno T, Bucher E, van der Winden J, Naumann U, Matzke AJM, Matzke M. 2009. A stepwise pathway for biogenesis of 24-nt secondary siRNAs and spreading of DNA methylation. EMBO J 28: 48-57.
24. Djupedal I, Portoso M, Spahr H, Bonilla C, Gustafsson CM, Allshire RC, Ekwall K. 2005. RNA Pol II subunit Rpb7 promotes centromeric transcription and RNAi-directed chromatin silencing. Genes Dev 19: 2301-2306.
25. Eissenberg JC. 1989. Position effect variegation in Drosophila: Towards a genetics of chromatin assembly. Bioessays 11: 14-17.
26. Eissenberg JC, Reuter G. 2009. Cellular mechanism for targeting heterochromatin formation in Drosophila. Int Rev Cell Mol Biol 273: 1-47.
27. Eissenberg JC, James TC, Fosterhartnett DM, Hartnett T, Ngan V, Elgin SCR. 1990. Mutation in a heterochromatin-specific chromosomal protein is associated with suppression of position-effect variegation in Drosophila melanogaster. Proc Natl Acad Sci 87: 9923-9927. (Pubitemid 120016556)
28. Folco HD, Pidoux AL, Urano T, Allshire RC. 2008. Heterochromatin and RNAi are required to establish CENP-A chromatin at centromeres. Science 319: 94-97.
29. Foss HM, Roberts CJ, Claeys KM, Selker EU. 1993. Abnormal chromosome behavior in Neurospora mutants defective in DNA methylation. Science 262: 1737-1741.
30. Freitag M, Hickey PC, Khlafallah TK, Read ND, Selker EU. 2004a. HP1 is essential for DNA methylation in Neurospora. Mol Cell 13: 427-434.
31. Freitag M, Lee DW, Kothe GO, Pratt RJ, Aramayo R, Selker EU. 2004b. DNA methylation is independent of RNA interference in Neurospora. Science 304: 1939. (Pubitemid 38822180)
32. Fujita N, Watanabe S, Ichimura T, Tsuruzoe S, Shinkai Y, Tachibana M, Chiba T, Nakao M. 2003. Methyl-CpG binding domain 1 (MBD1) interacts with the Suv39h1-HP1 heterochromatic complex for DNA methylation-based transcriptional repression. J Biol Chem 278: 24132-24138.
33. Galagan JE, Selker EU. 2004. RIP: The evolutionary cost of genome defense. Trends Genet 20: 417-423.
34. Galagan JE, Calvo SE, Borkovich KA, Selker EU, Read ND, Jaffe D, FitzHugh W, Ma LJ, Smirnov S, Purcell S, et al. 2003. The genome sequence of the filamentous fungus Neurospora crassa. Nature 422: 859-868.
35. Gaszner M, Felsenfeld G. 2006. Insulators: Exploiting transcriptional and epigenetic mechanisms. Nat Rev Genet 7: 703-713. (Pubitemid 44260006)
36. 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: 1871-1873.
37. Grewal SI, Elgin SC. 2007. Transcription and RNA interference in the formation of heterochromatin. Nature 447: 399-406.
38. Grewal SIS, Jia ST. 2007. Heterochromatin revisited. Nat Rev Genet 8: 35-46.
39. Grewal SIS, Moazed D. 2003. Heterochromatin and epigenetic control of gene expression. Science 301: 798-802.
40. Grunstein M. 1998. Yeast heterochromatin: Regulation of its assembly and inheritance by histones. Cell 93: 325-328.
41. Hall IM, Shankaranarayana GD, Noma KI, Ayoub N, Cohen A, Grewal SIS. 2002. Establishment and maintenance of a heterochromatin domain. Science 297: 2232-2237.
42. Hall MC,Torres MP, Schroeder GK, Borchers CH. 2003. Mnd2 and Swm1 are core subunits of the Saccharomyces cerevisiae anaphase-promoting complex. J BiolChem 278: 16698-16705.
43. Henikoff S. 1990. Position-effect variegation after 60 years. Trends Genet 6: 422-426.
44. Hennig W. 1999. Heterochromatin. Chromosoma 108: 1-9.
45. Herr AJ, Jensen MB, Dalmay T, Baulcombe DC. 2005. RNA polymerase IV directs silencing of endogenous DNA. Science 308: 118-120.
46. Honda S, Selker EU. 2008. Direct interaction between DNA methyltransferase DIM-2 and HP1 is required for DNA methylation in Neurospora crassa. Mol Cell Biol 28: 6044-6055.
47. Honda S, Lewis ZA, Huarte M, Cho LY, David LL, Shi Y, Selker EU. 2010. The DMM complex prevents spreading of DNA methylation from transposons to nearby genes in Neurospora crassa. Genes Dev 24: 443-454.
48. Huang J, Sengupta R, Espejo AB, Lee MG, Dorsey JA, Richter M, Opravil S, Shiekhattar R, Bedford MT, Jenuwein T, et al. 2007. p53 is regulated by the lysine demethylase LSD1. Nature 449: 105-108.
49. Huang S, Li X, Yusufzai TM, Qiu Y, Felsenfeld G. 2007. USF1 recruits histone modification complexes and is critical for maintenance of a chromatin barrier. Mol Cell Biol 27: 7991-8002.
50. Huisinga KL, Brower-Toland B, Elgin SCR. 2006. The contradictory definitions of heterochromatin: Transcription and silencing. Chromosoma 115: 110-122.
51. Irelan JT, Selker EU. 1997. Cytosine methylation associated with repeat-induced point mutation causes epigenetic gene silencing in Neurospora crassa. Genetics 146: 509-523.
52. Isaac S, Walfridsson J, Zohar T, Lazar D, Kahan T, Ekwall K, Cohen A. 2007. Interaction of Epe1 with the heterochromatin assembly pathway in Schizosaccharomyces pombe. Genetics 175: 1549-1560.
53. Jackson JP, Lindroth AM, Cao XF, Jacobsen SE. 2002. Control of CpNpG DNA methylation by the KRYPTONITE histone H3 methyltransferase. Nature 416: 556-560.
54. Jacobsen SE, Sakai H, Finnegan EJ, Cao XF, Meyerowitz EM. 2000. Ectopic hypermethylation of flower-specific genes in Arabidopsis. Curr Biol 10: 179-186.
55. Jeddeloh JA, Stokes TL, Richards EJ. 1999. Maintenance of genomic methylation requires a SW12/SNF2-like protein. Nat Genet 22: 94-97.
56. Jenuwein T, Allis CD. 2001. Translating the histone code. Science 293: 1074-1080.
57. Jia ST, Noma K, Grewal SIS. 2004a. RNAi-independent heterochromatin nucleation by the stress-activated ATF/CREB family proteins. Science 304: 1971-1976.
58. Jia ST, Yamada T, Grewal SIS. 2004b. Heterochromatin regulates cell type-specific long-range chromatin interactions essential for directed recombination. Cell 119: 469-480.
59. Johnson LM, Bostick M, Zhang XY, Kraft E, Henderson I, Callis J, Jacobsen SE. 2007. The SRA methyl-cytosine-binding domain links DNA and histone methylation. Curr Biol 17: 379-384.
60. Kakutani T. 1997. Genetic characterization of late-flowering traits induced by DNA hypomethylation mutation in Arabidopsis thaliana. Plant J 12: 1447-1451. (Pubitemid 28042700)
61. Kakutani T, Jeddeloh JA, Flowers SK, Munakata K, Richards EJ. 1996. Developmental abnormalities and epimutations associated with DNA hypomethylation mutations. Proc Natl Acad Sci 93: 12406-12411.
62. Kanellopoulou C, Muljo SA, Kung AL, Ganesan S, Drapkin R, Jenuwein T, Livingston DM, Rajewsky K. 2005. Dicer-deficient mouse embryonic stem cells are defective in differentiation and centromeric silencing. Genes Dev 19: 489-501.
63. Kankel MW, Ramsey DE, Stokes TL, Flowers SK, Haag JR, Jeddeloh JA, Riddle NC, Verbsky ML, Richards EJ. 2003. Arabidopsis MET1 cytosine methyltransferase mutants. Genetics 163: 1109-1122.
64. Kanno T, Huettel B, Mette MF, Aufsatz W, Jaligot E, Daxinger L, Kreil DP, Matzke M, Matzke AJM. 2005. Atypical RNA polymerase subunits required for RNA-directed DNA methylation. Nat Genet 37: 761-765.
65. Kato H, Goto DB, Martienssen RA, Urano T, Furukawa K, Murakami Y. 2005. RNA polymerase II is required for RNAi-dependent heterochromatin assembly. Science 309: 467-469.
66. Keshet I, Liemanhurwitz J, Cedar H. 1986. DNA methylation affects the formation of active chromatin. Cell 44: 535-543. (Pubitemid 16083696)
67. Kinoshita T, Miura A, Choi YH, Kinoshita Y, Cao XF, Jacobsen SE, Fischer RL, Kakutani T. 2004. One-way control of FWA imprinting in Arabidopsis endosperm by DNA methylation. Science 303: 521-523. (Pubitemid 38120849)
68. Kloc A, Martienssen R. 2008. RNAi, heterochromatin and the cell cycle. Trends Genet 24: 511-517.
69. Kloc A, Zaratiegui M, Nora E, Martienssen R. 2008. RNA interference guides histone modification during the S phase of chromosomal replication. Curr Biol 18: 490-495.
70. Klose RJ, Kallin EM, Zhang Y. 2006a. JmjC-domain-containing proteins and histone demethylation. Nat Rev Genet 7: 715-727.
71. Klose RJ, Yamane K, Bae YJ, Zhang DZ, Erdjument-Bromage H, Tempst P, Wong JM, Zhang Y. 2006b. The transcriptional repressor JHDM3A demethylates trimethyl histone H3 lysine 9 and lysine 36. Nature 442: 312-316.
72. Kouzminova E, Selker EU. 2001. dim-2 encodes a DNA methyltransferase responsible for all known cytosine methylation in Neurospora. EMBO J 20: 4309-4323.
73. Lachner M, Jenuwein T. 2002. The many faces of histone lysine methylation. Curr Opin Cell Biol 14: 286-298.
74. Lachner M, O'Carroll N, Rea S, Mechtler K, Jenuwein T. 2001. Methylation of histone H3 lysine 9 creates a binding site for HP1 proteins. Nature 410: 116-120.
75. Lan F, Zaratiegui M, Villén J, Vaughn MW, Verdel A, Huarte M, Shi Y, Gygi SP, Moazed D, Martienssen RA, et al. 2007. S. pombe LSD1 homologs regulate heterochromatin propagation and euchromatic gene transcription. Mol Cell 26: 89-101.
76. Law JA, Jacobsen SE. 2010. Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat Rev Genet 11: 204-220.
77. Lehnertz B, Ueda Y, Derijck A, Braunschweig U, Perez-Burgos L, Kubicek S, Chen TP, Li E, Jenuwein T, Peters A. 2003. Suv39h-mediated histone H3 lysine 9 methylation directs DNA methylation to major satellite repeats at pericentric heterochromatin. Curr Biol 13: 1192-1200.
78. Lewis ZA, Honda S, Khlafallah TK, Jeffress JK, Freitag M, Mohn F, Schubeler D, Selker EU. 2009. Relics of repeat-induced point mutation direct heterochromatin formation in Neurospora crassa. Genome Res 19: 427-437.
79. Lindroth AM, Cao XF, Jackson JP, Zilberman D, McCallum CM, Henikoff S, Jacobsen SE. 2001. Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation. Science 292: 2077-2080.
80. Lindroth AM, Shultis D, Jasencakova Z, Fuchs J, Johnson L, Schubert D, Patnaik D, Pradhan S, Goodrich J, Schubert I, et al. 2004. Dual histone H3 methylation marks at lysines 9 and 27 required for interaction with CHROMOMETHYLASE3. EMBO J 23: 4146-4155.
81. Lippman Z, Martienssen R. 2004. The role of RNA interference in heterochromatic silencing. Nature 431: 364-370. (Pubitemid 39265677)
82. Lippman Z, Gendrel AV, Black M, Vaughn MW, Dedhia N, McCombie WR, Lavine K, Mittal V, May B, Kasschau KD, et al. 2004. Role of transposable elements in heterochromatin and epigenetic control. Nature 430: 471-476.
83. Lister R, O'Malley RC, Tonti-Filippini J, Gregory BD, Berry CC, Millar AH, Ecker JR. 2008. Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133: 523-536.
84. Litt MD, Simpson M, Gaszner M, Allis CD, Felsenfeld G. 2001. Correlation between histone lysine methylation and developmental changes at the chicken β-globin locus. Science 293: 2453-2455.
85. Luger K, Mader AW, Richmond RK, Sargent DF, Richmond TJ. 1997. Crystal structure of the nucleosome core particle at 2.8 angstrom resolution. Nature 389: 251-260.
86. MacPherson S, Larochelle M, Turcotte B. 2006. A fungal family of transcriptional regulators: The zinc cluster proteins. Microbiol Mol Biol Rev 70: 583-604.
87. Malagnac F, Bartee L, Bender J. 2002. An Arabidopsis SET domain protein required for maintenance but not establishment of DNA methylation. EMBO J 21: 6842-6852.
88. Margolin BS, Garrett-Engele PW, Stevens JN, Fritz DY, Garrett-Engele C, Metzenberg RL, Selker EU. 1998. A methylated Neurospora 5S rRNA pseudogene contains a transposable element inactivated by repeat-induced point mutation. Genetics 149: 1787-1797.
89. Martens JHA, O'Sullivan RJ, Braunschweig U, Opravil S, Radolf M, Steinlein P, Jenuwein T. 2005. The profile of repeat-associated histone lysine methylation states in the mouse epigenome. EMBO J 24: 800-812.
90. Martienssen RA. 2003. Maintenance of heterochromatin by RNA interference of tandem repeats. Nat Genet 35: 213-214.
91. Matzke MA, Birchler JA. 2005. RNAi-mediated pathways in the nucleus. Nat Rev Genet 6: 24-35.
92. May BP, Lippman ZB, Fang YD, Spector DL, Martienssen RA. 2005. Differential regulation of strand-specific transcripts from Arabidopsis centromeric satellite repeats. PLoS Genet 1: 705-714.
93. Metzger E, Wissmann M, Yin N, Müller JM, Schneider R, Peters AH, Günther T, Buettner R, Schüle R. 2005. LSD1 demethylates repressive histone marks to promote androgen-receptor-dependent transcription. Nature 437: 436-439.
94. Miao VPW, Freitag M, Selker EU. 2000. Short TpA-rich segments of the zeta-eta region induce DNA methylation in Neurospora crassa. J Mol Biol 300: 249-273.
95. Miura A, Yonebayashi S, Watanabe K, Toyama T, Shimada H, Kakutani T. 2001. Mobilization of transposons by a mutation abolishing full DNA methylation in Arabidopsis. Nature 411: 212-214.
96. Miura A, Nakamura M, Inagaki S, Kobayashi A, Saze H, Kakutani T. 2009. An Arabidopsis jmjC domain protein protects transcribed genes from DNA methylation at CHG sites. EMBO J 28: 1078-1086.
97. Morris KV, Chan SWL, Jacobsen SE, Looney DJ. 2004. Small interfering RNA-induced transcriptional gene silencing in human cells. Science 305: 1289-1292.
98. Motamedi MR, Verdel A, Colmenares SU, Gerber SA, Gygi SP, Moazed D. 2004. Two RNAi complexes, RITS and RDRC, physically interact and localize to noncoding centromeric RNAs. Cell 119: 789-802.
99. Nakayam J, Rice JC, Strahl BD, Allis CD, Grewal SIS. 2001. Role of histone H3 lysine 9 methylation in epigenetic control of heterochromatin assembly. Science 292: 110-113.
100. Noma K, Allis CD, Grewal SIS. 2001. Transitions in distinct histone H3 methylation patterns at the heterochromatin domain boundaries. Science 293: 1150-1155. (Pubitemid 32758098)
101. Noma K, Sugiyama T, Cam H, Verdel A, Zofall M, Jia ST, Moazed D, Grewal SIS. 2004. RITS acts in cis to promote RNA interference-mediated transcriptional and post-transcriptional silencing. Nat Genet 36: 1174-1180.
102. Noma KI, Cam HP, Maraia RJ, Grewal SIS. 2006. A role for TFIIIC transcription factor complex in genome organization. Cell 125: 859-872.
103. Onodera Y, Haag JR, Ream T, Nunes PC, Pontes O, Pikaard CS. 2005. Plant nuclear RNA polymerase IV mediates siRNA and DNA methylation-dependent heterochromatin formation. Cell 120: 613-622.
104. Ooi SKT, Qiu C, Bernstein E, Li KQ, Jia D, Yang Z, Erdjument-Bromage H, Tempst P, Lin SP, Allis CD, et al. 2007. DNMT3L connects unmethylated lysine 4 of histone H3 to de novo methylation of DNA. Nature 448: 714-717. (Pubitemid 47236857)
105. Peters A, O'Carroll D, Scherthan H, Mechtler K, Sauer S, Schofer C, Weipoltshammer K, Pagani M, Lachner M, Kohlmaier A, et al. 2001. Loss of the Suv39h histone methyltransferases impairs mammalian heterochromatin and genome stability. Cell 107: 323-337.
106. Pidoux AL, Allshire RC. 2005. The role of heterochromatin in centromere function. PhilosTrans R Soc B Biol Sci 360: 569-579.
107. Pontes O, Li CF, Nunes PC, Haag J, Ream T, Vitins A, Jacobsen SE, Pikaard CS. 2006. The Arabidopsis chromatin-modifying nuclear siRNA pathway involves a nucleolar RNA processing center. Cell 126: 79-92.
108. Rea S, Eisenhaber F, O'Carroll N, Strahl BD, Sun ZW, Schmid M, Opravil S, Mechtler K, Ponting CP, Allis CD, et al. 2000. Regulation of chromatin structure by site-specific histone H3 methyltransferases. Nature 406: 593-599.
109. Reeves R. 2001. Molecular biology of HMGA proteins: Hubs of nuclear function. Gene 277: 63-81. (Pubitemid 32972109)
110. Richards EJ, Elgin SC. 2002. Epigenetic codes for heterochromatin formation and silencing: Rounding up the usual suspects. Cell 108: 489-500.
111. Rountree MR, Selker EU. 1997. DNA methylation inhibits elongation but not initiation of transcription in Neurospora crassa. Genes Dev 11: 2383-2395.
112. Rudolph T, Yonezawa M, Lein S, Heidrich K, Kubicek S, Schäfer C, Phalke S, Walther M, Schmidt A, Jenuwein T, et al. 2007. Heterochromatin formation in Drosophila is initiated through active removal of H3K4 methylation by the LSD1 homolog SU(VAR)3-3. Mol Cell 26: 103-115.
113. Sarraf SA, Stancheva I. 2004. Methyl-CpG binding protein MBD1 couples histone H3 methylation at lysine 9 by SETDB1 to DNA replication and chromatin assembly. Mol Cell 15: 595-605.
114. Saze H, Kakutani T. 2007. Heritable epigenetic mutation of a transposon-flanked Arabidopsis gene due to lack of the chromatin-remodeling factor DDM1. EMBO J 26: 3641-3652.
115. Saze H, Shiraishi A, Miura A, Kakutani T. 2008. Control of genic DNA methylation by a jmjC domain-containing protein in Arabidopsis thaliana. Science 319: 462-465.
116. Schoeftner S, Blasco MA. 2009. A 'higher order' of telomere regulation: Telomere heterochromatin and telomeric RNAs. EMBO J 28: 2323-2336.
117. Schofield CJ, Ratcliffe PJ. 2005. Signalling hypoxia by HIF hydroxylases. Biochem Biophys Res Commun 338: 617-626.
118. Schotta G, Ebert A, Krauss V, Fischer A, Hoffmann J, Rea S, Jenuwein T, Dorn R, Reuter G. 2002. Central role of Drosophila SU(VAR)3-9 in histone H3-K9 methylation and heterochromatic gene silencing. EMBO J 21: 1121-1131.
119. Schotta G, Ebert A, Dorn R, Reuter G. 2003. Position-effect variegation and the genetic dissection of chromatin regulation in Drosophila. Semin Cell Dev Biol 14: 67-75.
120. Schueler MG, Sullivan BA. 2006. Structural and functional dynamics of human centromeric chromatin. Annu Rev Genomics Hum Genet 7: 301-313. (Pubitemid 44627932)
121. Selker EU. 1990. Premeiotic instability of repeated sequences in Neurospora-crassa. Annu Rev Genet 24: 579-613.
122. Selker EU. 2004. Genome defense and DNA methylation in Neurospora. Cold Spring Harb Symp Quant Biol 69: 119-124.
123. Selker EU, Fritz DY, Singer MJ. 1993. dense nonsymmetrical DNA methylation resulting from repeat-induced point mutation in Neurospora. Science 262: 1724-1728.
124. Selker EU, Freitag M, Kothe GO, Margolin BS, Rountree MR, Allis CD, Tamaru H. 2002. Induction and maintenance of nonsymmetrical DNA methylation in Neurospora. Proc Natl Acad Sci 99: 16485-16490.
125. Selker EU, Tountas NA, Cross SH, Margolin BS, Murphy JG, Bird AP, Freitag M. 2003. The methylated component of the Neurospora crassa genome. Nature 422: 893-897. (Pubitemid 36520041)
126. Singer MJ, Marcotte BA, Selker EU. 1995. DNA methylation associated with repeat-induced point mutation in Neurospora-crassa. Mol Cell Biol 15: 5586-5597.
127. 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.
128. Slotkin RK, Martienssen R. 2007. Transposable elements and the epigenetic regulation of the genome. Nat Rev Genet 8: 272-285.
129. Soppe WJJ, Jacobsen SE, Alonso-Blanco C, Jackson JP, Kakutani T, Koornneef M, Peeters AJM. 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.
130. Sugiyama T, Cam H, Verdel A, Moazed D, Grewal SIS. 2005. RNA-dependent RNA polymerase is an essential component of a self-enforcing loop coupling heterochromatin assembly to siRNA production. Proc Natl Acad Sci 102: 152-157.
131. Sugiyama T, Cam HP, Sugiyama R, Noma K, Zofall M, Kobayashi R, Grewal SIS. 2007. SHREC, an effector complex for heterochromatic transcriptional silencing. Cell 128: 491-504.
132. Sun FL, Haynes K, Simpson CL, Lee SD, Collins L, Wuller J, Eissenberg JC, Elgin SCR. 2004. Cis-acting determinants of heterochromatin formation on Drosophila melanogaster chromosome four. Mol Cell Biol 24: 8210-8220. (Pubitemid 39167468)
133. Suzuki MM, Bird A. 2008. DNA methylation landscapes: Provocative insights from epigenomics. Nat Rev Genet 9: 465-476. (Pubitemid 351693975)
134. Takeuchi T, Yamazaki Y, Katohfukui Y, Tsuchiya R, Kondo S, Motoyama J, Higashinakagawa T. 1995. Gene trap capture of a novel mouse gene, jumonji, required for neural-tube formation. Genes Dev 9: 1211-1222.
135. Takeuchi T, Watanabe Y, Takano-Shimizu T, Kondo S. 2006. Roles of jumonji and jumonji family genes in chromatin regulation and development. Dev Dyn 235: 2449-2459.
136. Talbert PB, Henikoff S. 2006. Spreading of silent chromatin: Inaction at a distance. Nat Rev Genet 7: 793-803.
137. Tamaru H, Selker EU. 2001. A histone H3 methyltransferase controls DNA methylation in Neurospora crassa. Nature 414: 277-283.
138. Tamaru H, Selker EU. 2003. Synthesis of signals for de novo DNA methylation in Neurospora crassa. Mol Cell Biol 23: 2379-2394. (Pubitemid 36351020)
139. Tamaru H, Zhang X, McMillen D, Singh PB, Nakayama J, Grewal SI, Allis CD, Cheng XD, Selker EU. 2003. Trimethylated lysine 9 of histone H3 is a mark for DNA methylation in Neurospora crassa. Nat Genet 34: 75-79. (Pubitemid 36548794)
140. Thon G, Bjerling P, Bunner CM, Verhein-Hansen J. 2002. Expression-state boundaries in the mating-type region of fission yeast. Genetics 161: 611-622.
141. Trewick SC, McLaughlin PJ, Allshire RC. 2005. Methylation: Lost in hydroxylation? EMBO Rep 6: 315-320.
142. Trewick SC, Minc E, Antonelli R, Urano T, Allshire RC. 2007. The JmjC domain protein Epe1 prevents unregulated assembly and disassembly of heterochromatin. EMBO J 26: 4670-4682.
143. Tschiersch B, Hofmann A, Krauss V, Dorn R, Korge G, Reuter G. 1994. 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 13: 3822-3831.
144. Tsukada Y, Fang J, Erdjument-Bromage H, Warren ME, Borchers CH, Tempst P, Zhang Y. 2006. Histone demethylation by a family of JmjC domain-containing proteins. Nature 439: 811-816. (Pubitemid 43255695)
145. Tsukahara S, Kobayashi A, Kawabe A, Mathieu O, Miura A, Kakutani T. 2009. Bursts of retrotransposition reproduced in Arabidopsis. Nature 461: 423-426.
146. Ufano S, San-Segundo P, del Rey F, de Aldana CRV. 1999. SWM1, a developmentally regulated gene, is required for spore wall assembly in Saccharomyces cerevisiae. Mol Cell Biol 19: 2118-2129.
147. Verdel A, Jia ST, Gerber S, Sugiyama T, Gygi S, Grewal SIS, Moazed D. 2004. RNAi-mediated targeting of heterochromatin by the RITS complex. Science 303: 672-676.
148. Volpe TA, Kidner C, Hall IM, Teng G, Grewal SIS, Martienssen RA. 2002. Regulation of heterochromatic silencing and histone H3 lysine-9 methylation by RNAi. Science 297: 1833-1837.
149. Vongs A, Kakutani T, Martienssen RA, Richards EJ. 1993. Arabidopsis-thaliana DNA methylation mutants. Science 260: 1926-1928.
150. Wassenegger M. 2000. RNA-directed DNA methylation. Plant Mol Biol 43: 203-220.
151. Wassenegger M, Heimes S, Riedel L, Sanger HL. 1994. RNA-directed de-novo methylation of genomic sequences in plants. Cell 76: 567-576.
152. Xie ZX, Johansen LK, Gustafson AM, Kasschau KD, Lellis AD, Zilberman D, Jacobsen SE, Carrington JC. 2004. Genetic and functional diversification of small RNA pathways in plants. PLoS Biol 2: 642-652.
153. Yamada T, Fischle W, Sugiyama T, Allis CD, Grewal SIS. 2005. The nucleation and maintenance of heterochromatin by a histone deacetylase in fission yeast. Mol Cell 20: 173-185.
154. Yoon HJ, Feoktistova A, Wolfe BA, Jennings JL, Link AJ, Gould KL. 2002. Proteomics analysis identifies new components of the fission and budding yeast anaphase-promoting complexes. Curr Biol 12: 2048-2054.
155. Zhang XY, Yazaki J, Sundaresan A, Cokus S, Chan SWL, Chen HM, Henderson IR, Shinn P, Pellegrini M, Jacobsen SE, et al. 2006. Genome-wide high-resolution mapping and functional analysis of DNA methylation in Arabidopsis. Cell 126: 1189-1201.
156. Zhang K, Mosch K, Fischle W, Grewal SIS. 2008. Roles of the Clr4 methyltransferase complex in nucleation, spreading and maintenance of heterochromatin. Nat Struct Mol Biol 15: 381-388.
157. Zilberman D, Cao XF, Jacobsen SE. 2003. ARGONAUTE4 control of locus-specific siRNA accumulation and DNA and histone methylation. Science 299: 716-719.
158. Zilberman D, Cao XF, Johansen LK, Xie ZX, Carrington JC, Jacobsen SE. 2004. Role of arabidopsis ARGONAUTE4 in RNA-directed DNA methylation triggered by inverted repeats. Curr Biol 14: 1214-1220.
159. Zilberman D, Gehring M, Tran RK, Ballinger T, Henikoff S. 2007. Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. Nat Genet 39: 61-69.
160. Zofall M, Grewal SIS. 2006. Swi6/HP1 recruits a JmjC domain protein to facilitate transcription of heterochromatic repeats. Mol Cell 22: 681-692. (Pubitemid 43817605)