Epigenetic transitions in plants not associated with changes in DNA or histone modification

Biochimica et Biophysica Acta - Gene Structure and Expression

Volumn 1769, Issue 5-6, 2007, Pages 393-398

  Nishimura, Taisuke ^a,b   Paszkowski, Jerzy ^a  

^a UNIVERSITY OF GENEVA   (Switzerland)

^b HOKKAIDO UNIVERSITY   (Japan)

Author keywords

BRU1 MGO3 TSK; Cytosine methylation; Epigenetic gene regulation; Histone modification; MOM1; RPA2

Indexed keywords

HISTONE; PLANT DNA; REPLICATION PROTEIN A; REPRESSOR OF SILENCING 1 PROTEIN; REPRESSOR PROTEIN; SMALL INTERFERING RNA; UNCLASSIFIED DRUG;

CHROMATIN; DNA METHYLATION; DNA MODIFICATION; EPIGENETICS; GENE CONTROL; GENE SILENCING; HERITABILITY; MUTATION; NONHUMAN; PLANT DEVELOPMENT; PRIORITY JOURNAL; REVIEW; X CHROMOSOME INACTIVATION;

ARABIDOPSIS; DNA METHYLATION; DNA, PLANT; EPIGENESIS, GENETIC; GENES, PLANT; HISTONES; PLANTS;

EID: 34249779220     PISSN: 01674781     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bbaexp.2007.03.002     Document Type: Review

References (55)

1. Tariq M. Paszkowski, DNA and histone methylation in plants. Trends Genet. 20 (2004) 244-251
2. Freitag M., and Selker E.U. Controlling DNA methylation: many roads to one modification. Curr. Opin. Genet. Dev. 15 (2005) 191-199
3. Bird A. DNA methylation patterns and epigenetic memory. Genes Dev. 16 (2002) 6-21
4. Margueron R., Trojer P., and Reinberg D. The key to development: interpreting the histone code?. Curr. Opin. Genet. Dev. 15 (2005) 163-176
5. Grunstein M. Histone acetylation in chromatin structure and transcription. Nature 389 (1997) 349-352
6. Fuchs J., Demidov D., Houben A., and Schubert I. Chromosomal histone modification patterns-From conservation to diversity. Trends Plant Sci. 11 (2006) 199-208
7. Mathieu O., Probst A.V., and Paszkowski J. Distinct regulation of histone H3 methylation at lysines 27 and 9 by CpG methylation in Arabidopsis. EMBO J. 24 (2005) 2783-2791
8. Zhang X.Y., Yazaki J., Sundaresan A., Cokus S., Chan S.W.L., Chen H.M., Henderson I.R., Shinn P., Pellegrini M., Jacobsen S.E., and Ecker J.R. Genome-wide high-resolution mapping and functional analysis of DNA methylation in Arabidopsis. Cell 126 (2006) 1189-1201
9. Zilberman D., Gehring M., Tran R.K., Ballinger T., and Henikoff S. Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. Nat. Genet. 39 (2006) 61-69
10. Saze H., Mittelsten Scheid O., and Paszkowski J. Maintenance of CpG methylation is essential for epigenetic inheritance during plant gametogenesis. Nat. Genet. 34 (2003) 65-69
11. Vongs A., Kakutani T., Martienssen R.A., and Richards E.J. Arabidopsis thaliana DNA methylation mutants. Science 260 (1993) 1926-1928
12. Kakutani T., Munakata K., Richards E.J., and Hirochika H. Meiotically and mitotically stable inheritance of DNA hypomethylation induced by ddm1 mutation of Arabidopsis thaliana. Genetics 151 (1999) 831-838
13. Kankel M.W., Ramsey D.E., Stokes T.L., Flowers S.K., Haag J.R., Jeddeloh J.A., Riddle N.C., Verbsky M.L., and Richards E.J. Arabidopsis MET1 cytosine methyltransferase mutants. Genetics 163 (2003) 1109-1122
14. Cao X.F., and 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. 99 (2002) 16491-16498
15. Chan S.W.L., Henderson I.R., Zhang X.Y., Shah G., Chien J.S.C., and Jacobsen S.E. RNAi, DRD1, and histone methylation actively target developmentally important non-CG DNA methylation in Arabidopsis. PLoS Genet. 2 (2006) e83
16. Matzke M., Aufsatz W., Kanno T., Daxinger L., Papp I., Mette A.F., and Matzke A.J.M. Genetic analysis of RNA-mediated transcriptional gene silencing. Biochim. Biophys. Acta N, Gene Struct. Expr. 1677 (2004) 129-141
17. Chan S.W.L., Henderson I.R., and Jacobsen S.E. Gardening the genome: DNA methylation in Arabidopsis thaliana. Nat. Rev., Genet. 6 (2005) 351-360
18. Volpe T.A., Kidner C., Hall I.M., Teng G., Grewal S.I.S., and Martienssen R.A. Regulation of heterochromatic silencing and histone H3 lysine-9 methylation by RNAi. Science 297 (2002) 1833-1837
19. Heard E. Delving into the diversity of facultative heterochromatin: the epigenetics of the inactive X chromosome. Curr. Opin. Genet. Dev. 15 (2005) 482-489
20. Sun B.K., Deaton A.M., and Lee J.T. A transient heterochromatic state in Xist preempts X inactivation choice without RNA stabilization. Mol. Cell 21 (2006) 617-628
21. Schneider R., Bannister A.J., Myers F.A., Thorne A.W., Crane-Robinson C., and Kouzarides T. Histone H3 lysine 4 methylation patterns in higher eukaryotic genes. Nat. Cell Biol. 6 (2004) 73-77
22. Bernstein B.E., Mikkelsen T.S., Xie X.H., Kamal M., Huebert D.J., Cuff J., Fry B., Meissner A., Wernig M., Plath K., Jaenisch R., Wagschal A., Feil R., Schreiber S.L., and Lander E.S. A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell 125 (2006) 315-326
23. Gendrel A.V., Lippman Z., Yordan C., Colot V., and Martienssen R.A. Dependence of heterochromatic histone H3 methylation patterns on the Arabidopsis gene DDM1. Science 297 (2002) 1871-1873
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., and Martienssen R. Role of transposable elements in heterochromatin and epigenetic control. Nature 430 (2004) 471-476
25. Habu Y., Mathieu O., Tariq M., Probst A., Smathajitt C., Zhu T., and Paszkowski J. Epigenetic regulation of transcription in intermediate heterochromatin. EMBO Rep. 7 (2006) 1279-1284
26. Amedeo P., Habu Y., Afsar K., Mittelsten Scheid O., and Paszkowski J. Disruption of the plant gene MOM releases transcriptional silencing of methylated genes. Nature 405 (2000) 203-206
27. Takeda S., Tadele Z., Hofmann I., Probst A.V., Angelis K.J., Kaya H., Araki T., Mengiste T., Mittelsten Scheid O., Shibahara K., Scheel D., and Paszkowski J. BRU1, a novel link between responses to DNA damage and epigenetic gene silencing in Arabidopsis. Genes Dev. 18 (2004) 782-793
28. Elmayan T., Proux F., and Vaucheret H. Arabidopsis RPA2: a genetic link among transcriptional gene silencing, DNA repair, and DNA replication. Curr. Biol. 15 (2005) 1919-1925
29. Kapoor A., Agarwal M., Andreucci A., Zheng X.W., Gong Z.Z., Hasegawa P.M., Bressan R.A., and Zhu J.K. Mutations in a conserved replication protein suppress transcriptional gene silencing in a DNA-methylation-independent manner in Arabidopsis. Curr. Biol. 15 (2005) 1912-1918
30. Xia R., Wang J.G., Liu C.Y., Wang Y., Wang Y.Q., Zhai J.X., Liu J., Hong X.H., Cao X.F., Zhu J.K., and Gong Z.Z. ROR1/RPA2A, a putative replication protein A2, functions in epigenetic gene silencing and in regulation of meristem development in Arabidopsis. Plant Cell 18 (2006) 85-103
31. Steimer A., Amedeo P., Afsar K., Fransz P., Mittelsten Scheid O., and Paszkowski J. Endogenous targets of transcriptional gene silencing in arabidopsis. Plant Cell 12 (2000) 1165-1178
32. Probst A.V., Fransz P.F., Paszkowski J., and Mittelsten Scheid O. Two means of transcriptional reactivation within heterochromatin. Plant J. 33 (2003) 743-749
33. Mittelsten Scheid O., Probst A.V., Afsar K., and Paszkowski J. Two regulatory levels of transcriptional gene silencing in Arabidopsis. Proc. Natl. Acad. Sci. U. S. A. 99 (2002) 13659-13662
34. Soppe W.J.J., Jasencakova Z., Houben A., Kakutani T., Meister A., Huang M.S., Jacobsen S.E., Schubert I., and Fransz P.F. DNA methylation controls histone H3 lysine 9 methylation and heterochromatin assembly in Arabidopsis. EMBO J. 21 (2002) 6549-6559
35. Fransz P., Soppe W., and Schubert I. Heterochromatin in interphase nuclei of Arabidopsis thaliana. Chromosome Res. 11 (2003) 227-240
36. Vaillant I., Schubert I., Tourmente S., and Mathieu O. MOM1 mediates DNA methylation-independent silencing of repetitive sequences in Arabidopsis. EMBO Rep. 7 (2006) 1273-1278
37. Mathieu O., Jasencakova Z., Vaillant I., Gendrel A.V., Colot V., Schubert I., and Tourmente S. Changes in 5S rDNA chromatin organization and transcription during heterochromatin establishment in Arabidopsis. Plant Cell 15 (2003) 2929-2939
38. Brzeski J., and Jerzmanowski A. Deficient in DNA methylation 1 (DDM1) defines a novel family of chromatin-remodeling factors. J. Biol. Chem. 278 (2003) 823-828
39. Tariq M., Habu Y., and Paszkowski J. Depletion of MOM1 in non-dividing cells of Arabidopsis plants releases transcriptional gene silencing. EMBO Rep. 3 (2002) 951-955
40. Ahmad K., and Henikoff S. Modulation of a transcription factor counteracts heterochromatic gene silencing in Drosophila. Cell 104 (2001) 839-847
41. Onodera Y., Haag J.R., Ream T., Nunes P.C., Pontes O., and Pikaard C.S. Plant nuclear RNA polymerase IV mediates siRNA and DNA methylation-dependent heterochromatin formation. Cell 120 (2005) 613-622
42. Guyomarc'h S., Vernoux T., Traas J., Zhou D.X., and Delarue M. MGOUN3, an Arabidopsis gene with tetratricopeptide-repeat-related motifs, regulates meristem cellular organization. J. Exp. Bot. 55 (2004) 673-684
43. Suzuki T., Inagaki S., Nakajima S., Akashi T., Ohto M., Kobayashi M., Seki M., Shinozaki K., Kato T., Tabata S., Nakamura K., and Morikami A. A novel Arabidopsis gene TONSOKU is required for proper cell arrangement in root and shoot apical meristems. Plant J. 38 (2004) 673-684
44. Guyomarc'h S., Benhamed M., Lemonnier G., Renou J.P., Zhou D.X., and Delarue M. MGOUN3: evidence for chromatin-mediated regulation of FLC expression. J. Exp. Bot. 57 (2006) 2111-2119
45. Sheldon C.C., Burn J.E., Perez P.P., Metzger J., Edwards J.A., Peacock W.J., and Dennis E.S. The FLF MADS box gene: a repressor of flowering in Arabidopsis regulated by vernalization and methylation. Plant Cell 11 (1999) 445-458
46. Bastow R., Mylne J.S., Lister C., Lippman Z., Martienssen R.A., and Dean C. Vernalization requires epigenetic silencing of FLC by histone methylation. Nature 427 (2004) 164-167
47. He Y.H., and Amasino R.M. Role of chromatin modification in flowering-time control. Trends Plant Sci. 10 (2005) 30-35
48. Suzuki T., Nakajima S., Inagaki S., Hirano-Nakakita M., Matsuoka K., Demura T., Fukuda H., Morikami A., and Nakamura K. TONSOKU is expressed in S phase of the cell cycle and its defect delays cell cycle progression in Arabidopsis. Plant Cell Physiol. 46 (2005) 736-742
49. Kaya H., Shibahara K., Taoka K., Iwabuchi M., Stillman B., and Araki T. FASCIATA genes for chromatin assembly factor-1 in Arabidopsis maintain the cellular organization of apical meristems. Cell 104 (2001) 131-142
50. Enomoto S., and Berman J. Chromatin assembly factor I contributes to the maintenance, but not the re-establishment, of silencing at the yeast silent mating loci. Genes Dev. 12 (1998) 219-232
51. Ono T., Kaya H., Takeda S., Abe M., Ogawa Y., Kato M., Kakutani T., Mittelsten Scheid O., Araki T., and Shibahara K. Chromatin assembly factor 1 ensures the stable maintenance of silent chromatin states in Arabidopsis. Genes Cells 11 (2006) 153-162
52. Suzuki T., Nakajima S., Morikami A., and Nakamura K. An Arabidopsis protein with a novel calcium-binding repeat sequence interacts with TONSOKU/MGOUN3/BRUSHY1 involved in meristem maintenance. Plant Cell Physiol. 46 (2005) 1452-1461
53. Gong Z., Morales-Ruiz T., Ariza R.R., Roldan-Arjona T., David L., and Zhu J.K. ROS1, a repressor of transcriptional gene silencing in Arabidopsis, encodes a DNA glycosylase/lyase. Cell 111 (2002) 803-814
54. Wold M.S. Replication protein A: A heterotrimeric, single-stranded DNA-binding protein required for eukaryotic DNA metabolism. Annu. Rev. Biochem. 66 (1997) 61-92
55. Polo S.E., Roche D., and Almouzni G. New histone incorporation marks sites of UV repair in human cells. Cell 127 (2006) 481-493