Unlocking the Arabidopsis epigenome

Epigenetics

Volumn 4, Issue 8, 2009, Pages 557-563

  Reinders, Jon ^a   Paszkowski, Jerzy ^a  

^a UNIVERSITY OF GENEVA   (Switzerland)

Author keywords

DDM1; Epialleles; Epigenetics; EpiRILS; MET1; RNA directed DNA methylation (RdDM)

Indexed keywords

DNA METHYLTRANSFERASE; SMALL INTERFERING RNA;

ALLELE; ARABIDOPSIS; CHROMATIN; DNA METHYLATION; EPIGENETICS; GENETIC STABILITY; GENETIC VARIABILITY; INBRED STRAIN; NONHUMAN; PLANT GENOME; REVIEW;

ARABIDOPSIS; ARABIDOPSIS THALIANA; MAMMALIA;

EID: 74549137524     PISSN: 15592294     EISSN: 15592308     Source Type: Journal    
DOI: 10.4161/epi.4.8.10347     Document Type: Review

References (59)

1. Finnegan EJ. The Role of DNA methylation in Plant Development. In: Russo V, Martienssen R, Riggs A, eds. Epigenetic Mechanisms of Gene Regulation. Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Press 1996; 127-40.
2. Ronemus MJ, Galbiati M, Ticknor C, Chen J, Dellaporta SL. Demethylation-induced developmental pleiotropy in Arabidopsis. Science 1996; 273:654-7.
3. Bird A. DNA methylation patterns and epigenetic memory. Genes Dev 2002; 16:6-21.
4. Reik W. Stability and flexibility of epigenetic gene regulation in mammalian development. 2007; 447:425-32.
5. Teixeira FK, Heredia F, Sarazin A, Roudier F, Boccara M, Ciaudo C, et al. A Role for RNAi in the Selective Correction of DNA Methylation Defects. Science 2009; 323:1600-4.
6. Reinders J, Wulff BB, Mirouze M, Mari-Ordonez A, Dapp M, Rozhon W, et al. Compromised stability of DNA methylation and transposon immobilization in mosaic Arabidopsis epigenomes. Genes Dev 2009; 23:939-50.
7. Johannes F, Porcher E, Teixeira FK, Saliba-Colombani V, Simon M, Agier N, et al. Assessing the impact of transgenerational epigenetic variation on complex traits. PLoS Genet 2009; 5:1000530.
8. Bestor TH. The DNA methyltransferases of mammals. Hum Mol Genet 2000; 9:2395-402.
9. Goll M, Bestor T. Eukaryotic cytosine methyltransferases. Annu Rev Biochem 2005; 74:481-514.
10. Li E, Bestor TH, Jaenisch R. Targeted mutation of the DNA methyltransferase gene results in embryonic lethality. Cell 1992; 69:915-26.
11. Li E, Beard C, Forster AC, Bestor TH, Jaenisch R. DNA methylation, genomic imprinting, and mammalian development. Cold Spring Harb Symp Quant Biol 1993; 58:297-305.
12. Kankel MW, Ramsey DE, Stokes TL, Flowers SK, Haag JR, Jeddeloh JA, et al. Arabidopsis MET1 Cytosine Methyltransferase Mutants. Genetics 2003; 163:1109-22.
13. Saze H, Mittelsten Scheid O, Paszkowski J. Maintenance of CpG methylation is essential for epigenetic inheritance during plant gametogenesis. Nat Genet 2003; 34:65-9.
14. Jeddeloh JA, Bender J, Richards EJ. The DNA methylation locus DDM1 is required for maintenance of gene silencing in Arabidopsis. Genes Dev 1998; 12:1714-25.
15. Jeddeloh JA, Stokes TL, Richards EJ. Maintenance of genomic methylation requires a SWI2/SNF2-like protein. Nat Genet 1999; 22:94-7.
16. Brzeski J, Jerzmanowski A. Deficient in DNA methylation 1 (DDM1) defines a novel family of chromatin remodeling factors. J Biol Chem 2003; 278:823-8.
17. Dennis K, Fan T, Geiman T, Yan Q, Muegge K. Lsh, a member of the SNF2 family, is required for genome-wide methylation. Genes Dev 2001; 15:2940-4.
18. Vongs A, Kakutani T, Martienssen R, Richards E. Arabidopsis thaliana DNA methylation mutants. Science 1993; 260:1926-8.
19. Kakutani T, Jeddeloh JA, Flowers SK, Munakata K, Richards EJ. Developmental abnormalities and epimutations associated with DNA hypomethylation mutations. Proc Natl Acad Sci USA 1996; 93:12406-11.
20. Mittelsten Scheid O, Afsar K, Paszkowski J. Release of epigenetic gene silencing by trans-acting mutations in Arabidopsis. Proc Natl Acad Sci USA 1998; 95:632-7.
21. Finnegan EJ, Peacock WJ, Dennis ES. Reduced DNA methylation in Arabidopsis thaliana results in abnormal plant development. Proc Natl Acad Sci USA 1996; 93:8449-54.
22. Kakutani T, Munakata K, Richards EJ, Hirochika H. Meiotically and mitotically stable inheritance of DNA hypomethylation induced by ddm1 mutation of Arabidopsis thaliana. Genetics 1999; 151:831-8.
23. Soppe WJ, Jasencakova Z, Houben A, Kakutani T, Meister A, Huang MS, et al. DNA methylation controls histone H3 lysine 9 methylation and heterochromatin assembly in Arabidopsis. EMBO J 2002; 21:6549-59.
24. Tariq M, Saze H, Probst AV, Lichota J, Habu Y, Paszkowski J. Erasure of CpG methylation in Arabidopsis alters patterns of histone H3 methylation in heterochromatin. Proc Natl Acad Sci USA 2003; 100:8823-7.
25. Lippman Z, Gendrel AV, Black M, Vaughn MW, Dedhia N, McCombie WR, et al. Role of transposable elements in heterochromatin and epigenetic control. Nature 2004; 430:471-6.
26. Johnson LM, Cao X, Jacobsen SE. Interplay between two epigenetic marks: DNA methylation and histone H3 lysine 9 methylation. Curr Biol 2002.
27. Yan Q, Huang J, Fan T, Zhu H, Muegge K. Lsh, a modulator of CpG methylation, is crucial for normal histone methylation. EMBO J 2003; 22:5154-62.
28. Mathieu O, Probst A, Paszkowski J. Distinct regulation of histone H3 methylation at lysines 27 and 9 by CpG methylation in Arabidopsis. EMBO J 2005; 24:783-91.
29. Mathieu O, Reinders J, Caikovski M, Smathajitt C, Paszkowski J. Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation. Cell 2007; 130:851-62.
30. Soppe WJ, Jacobsen SE, Alonso-Blanco C, Jackson JP, Kakutani T, Koornneef M, Peeters AJ. 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.
31. Jacobsen SE, Meyerowitz EM. Hypermethylated SUPERMAN epigenetic alleles in arabidopsis. Science 1997; 277:1100-3.
32. Stokes TL, Kunkel BN, Richards EJ. Epigenetic variation in Arabidopsis disease resistance. Genes Dev 2002; 16:171-82.
33. 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; 26:3641-52.
34. Richards EJ. Quantitative epigenetics: DNA sequence variation need not apply. Genes Dev 2009; 23:1601-5.
35. Huettel B, Kanno T, Daxinger L, Aufsatz W, Matzke AJ, Matzke M. Endogenous targets of RNA-directed DNA methylation and Pol IV in Arabidopsis. EMBO J 2006; 25:2828-36.
36. Pikaard CS, Haag JR, Ream T, Wierzbicki AT. Roles of RNA polymerase IV in gene silencing. Trends Plant Sci 2008; 13:390-7.
37. Zilberman D, Cao X, Johansen LK, Xie Z, Carrington JC, Jacobsen SE. Role of Arabidopsis ARGONAUTE4 in RNA-directed DNA methylation triggered by inverted repeats. Curr Biol 2004; 14:1214-20.
38. Chan SW, Zilberman D, Xie Z, Johansen LK, Carrington JC, Jacobsen SE. RNA silencing genes control de novo DNA methylation. Science 2004; 303:1336.
39. Herr AJ, Jensen MB, Dalmay T, Baulcombe DC. RNA polymerase IV directs silencing of endogenous DNA. Science 2005; 308:118-20.
40. Kanno T, Huettel B, Mette MF, Aufsatz W, Jaligot E, Daxinger L, et al. Atypical RNA polymerase subunits required for RNA-directed DNA methylation. Nat Genet 2005; 37:761-5.
41. Onodera Y, Haag JR, Ream T, Nunes PC, Pontes O, Pikaard CS. Plant nuclear RNA polymerase IV mediates siRNA and DNA methylation-dependent heterochromatin formation. Cell 2005; 120:613-22.
42. Chapman EJ, Carrington JC. Specialization and evolution of endogenous small RNA pathways. Nat Rev Genet 2007; 8:884-96.
43. Matzke M, Kanno T, Daxinger L, Huettel B, Matzke AJ. RNA-mediated chromatin-based silencing in plants. Curr Opin Cell Biol 2009; 21:367-76.
44. Huettel B, Kanno T, Daxinger L, Bucher E, van der Winden J, Matzke AJ, Matzke M. RNA-directed DNA methylation mediated by DRD1 and Pol IVb: a versatile pathway for transcriptional gene silencing in plants. Biochim Biophys Acta 2007; 1769:358-74.
45. Kanno T, Bucher E, Daxinger L, Huettel B, Bohmdorfer G, Gregor W, et al. A structural-maintenance-of-chromosomes hinge domain-containing protein is required for RNA-directed DNA methylation. Nat Genet 2008; 40:670-5.
46. Li CF, Pontes O, El-Shami M, Henderson IR, Bernatavichute YV, Chan SW, et al. An ARGONAUTE4-containing nuclear processing center colocalized with Cajal bodies in Arabidopsis thaliana. Cell 2006; 126:93-106.
47. El-Shami M, Pontier D, Lahmy S, Braun L, Picart C, Vega D, et al. Reiterated WG/GW motifs form functionally and evolutionarily conserved ARGONAUTE-binding platforms in RNAi-related components. Genes Dev 2007; 21:2539-44.
48. Wierzbicki AT, Haag JR, Pikaard CS. Noncoding transcription by RNA polymerase Pol IVb/Pol V mediates transcriptional silencing of overlapping and adjacent genes. Cell 2008; 135:635-48.
49. Wierzbicki AT, Ream TS, Haag JR, Pikaard CS. RNA polymerase V transcription guides ARGONAUTE4 to chromatin. Nat Genet 2009; 41:630-4.
50. Cokus SJ, Feng S, Zhang X, Chen Z, Merriman B, Haudenschild CD, et al. Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature 2008; 452:215-9.
51. Lister R, O'Malley RC, Tonti-Filippini J, Gregory BD, Berry CC, Millar AH, Ecker JR. Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 2008; 133:523-36.
52. Bartee L, Bender J. Two Arabidopsis methylation-deficiency mutations confer only partial effects on a methylated endogenous gene family. Nucleic Acids Res 2001; 29:2127-34.
53. Jackson JP, Lindroth AM, Cao X, Jacobsen SE. Control of CpNpG DNA methylation by the KRYPTONITE histone H3 methyltransferase. Nature 2002; 416:556-60.
54. Malagnac F, Bartee L, Bender J. An Arabidopsis SET domain protein required for maintenance but not establishment of DNA methylation. EMBO J 2002; 21:6842-52.
55. Johnson LM, Bostick M, Zhang X, Kraft E, Henderson I, Callis J, Jacobsen SE. The SRA methyl-cytosine-binding domain links DNA and histone methylation. Curr Biol 2007; 17:379-84.
56. Chandler V, Alleman M. Paramutation: Epigenetic Instructions Passed Across Generations. Genetics 2008; 178:1839-44.
57. Mosher RA, Melnyk CW, Kelly KA, Dunn RM, Studholme DJ, Baulcombe DC. Uniparental expression of PolIV-dependent siRNAs in developing endosperm of Arabidopsis. Nature 2009; 460:283-6.
58. Mosher RA, Schwach F, Studholme D, Baulcombe DC. PolIVb influences RNA-directed DNA methylation independently of its role in siRNA biogenesis. Proc Natl Acad Sci USA 2008; 105:3145-50.
59. Zheng X, Pontes O, Zhu J, Miki D, Zhang F, Li W-X, et al. ROS3 is an RNA-binding protein required for DNA demethylation in Arabidopsis. Nature 2008; 455:1259-62.