Composition and formation of heterochromatin in Arabidopsis thaliana

Chromosome Research

Volumn 14, Issue 1, 2006, Pages 71-82

  Fransz, P ^a   Ten Hoopen, R ^a   Tessadori, F ^a  

^a UNIVERSITY OF AMSTERDAM   (Netherlands)

Author keywords

Arabidopsis; DNA methylation; Gene silencing; Heterochromatin

Indexed keywords

DNA; DNA METHYLTRANSFERASE; NUCLEAR PROTEIN; RNA; RNA DIRECTED RNA POLYMERASE; RNA POLYMERASE; SMALL INTERFERING RNA;

ANTIBODY LABELING; ARABIDOPSIS; CELL DIVISION; CELL NUCLEUS MEMBRANE; CHROMATIN ASSEMBLY AND DISASSEMBLY; CHROMOSOME SEGREGATION; CHROMOSOME STRUCTURE; CPG ISLAND; DEMETHYLATION; DNA METHYLATION; EPIGENETICS; GENE SILENCING; GENE TARGETING; GENOME ANALYSIS; HETEROCHROMATIN; INTERPHASE; INVERTED REPEAT; MOLECULAR GENETICS; MOLECULAR RECOGNITION; NEUROSPORA CRASSA; NONHUMAN; NUCLEOSOME; ORTHOLOGY; PRIORITY JOURNAL; PROTEIN FAMILY; PROTEIN PROTEIN INTERACTION; REVIEW; RNA DEGRADATION; SEQUENCE ANALYSIS; TANDEM REPEAT; TRANSGENE; TRANSPOSON;

ARABIDOPSIS; CELL NUCLEUS; CENTROMERE; CHROMOSOMES, PLANT; GENE SILENCING; HETEROCHROMATIN; PLANT PROTEINS; RECOMBINATION, GENETIC;

ARABIDOPSIS; ARABIDOPSIS THALIANA; NEUROSPORA CRASSA;

EID: 33644620812     PISSN: 09673849     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10577-005-1022-5     Document Type: Review

References (55)

1. Aufsatz W, Mette MF, van der Winden J, Matzke M, Matzke AJM (2002) HDA6, a putative histone deacetylase needed to enhance DNA methylation induced by double-stranded RNA. EMBO J 21: 6832-6841.
2. Aufsatz W, Mette M, Matzke A, Matzke M (2004) The role of MET1 in RNA-directed de-novo and maintenance methylation of CG dinucleotides. Plant Mol Biol 54: 793-804.
3. Bao N, Lye KW, Barton MK (2004) MicroRNA binding sites in Arabidopsis class III HD-ZIP mRNAs are required for methylation of the template chromosome. Dev Cell 7: 653-662.
4. Baumbusch LO, Thorstensen T, Krauss V 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. Nucl. Acids Res 29: 4319-4333.
5. Brzeski J, Jerzmanowski A (2004) Plant chromatin-epigenetics linked to ATP-dependent remodeling and architectural proteins. FEBS Lett 567: 15-19.
6. Chan SW-L, Zilberman D, Xie Z, Johansen LK, Carrington JC, Jacobsen SE (2004) RNA silencing genes control de novo DNA methylation. Science 303: 1336.
7. Finnegan EJ, Peacock WJ, Dennis ES (1996) Reduced DNA methylation in Arabidopsis thaliana results in abnormal plant development. Proc Natl Acad Sci USA 93: 8449-8454.
8. Fransz P, De Jong JH, Lysak M, Castiglione MR, Schubert I (2002) Interphase chromosomes in Arabidopsis are organized as well defined chromocentres from which euchromatin loops emanate. Proc Natl Acad Sci USA 99: 14584-14589.
9. Fransz P, Soppe W, Schubert I (2003) Heterochromatin in interphase nuclei of Arabidopsis thaliana. Chromosome Res 11: 227-240.
10. Gaudin V, Libault M, Pouteau S et al. (2001). Mutations in LIKE HETEROCHROMATIN PROTEIN 1 affect flowering time and plant architecture in Arabidopsis. Development 128: 4847-4858.
11. 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.
12. Hennig L, Taranto P, Walser M, Schonrock N, Gruissem W (2003) Arabidopsis MSI1 is required for epigenetic maintenance of reproductive development. Development 130: 2555-2565.
13. Herr AJ, Jensen MB, Dalmay T, Baulcombe DC (2005) RNA polymerase IV directs silencing of endogenous DNA. Science 308: 118-120.
14. Iida T, Suetake I, Tajima S et al. (2002) PCNA clamp facilitates action of DNA cytosine methyltransferase 1 on hemimethylated DNA. Genes Cells 7: 997-1007.
15. Jackson JP, Lindroth AM, Cao X, Jacobsen SE (2002) Control of CpNpG DNA methylation by the KRYPTONITE histone H3 methyltransferase. Nature 416: 556-560.
16. Jackson J, Johnson L, Jasencakova Z et al. (2004) Dimethylation of histone H3 lysine 9 is a critical mark for DNA methylation and gene silencing in Arabidopsis thaliana. Chromosoma 112: 308-315.
17. 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: 471-480.
18. Johnson L, Cao X, Jacobsen S (2002) Interplay between two epigenetic marks. DNA methylation and histone H3 lysine 9 methylation. Curr Biol 12: 1360-1367.
19. Kakutani T, Munakata, K., Richards EJ, Hirochika H (1999) Meiotically and mitotically stable inheritance of DNA hypomethylation induced by ddm1 mutation of Arabidopsis thaliana. Genetics 151: 831-838.
20. Kanno T, Mette MF, Kreil DP, Aufsatz W, Matzke M, Matzke AJM (2004). Involvement of putative SNF2 chromatin remodeling protein DRD1 in RNA-directed DNA methylation. Curr Biol 14: 801-805.
21. Kanno T, Aufsatz W, Jaligot E, Mette MF, Matzke M, Matzke AJ (2005a). A SNF2-like protein facilitates dynamic control of DNA methylation. EMBO Rep 6: 649-655.
22. Kanno T, Huettel B, Mette MF et al. (2005b) Atypical RNA polymerase subunits required for RNA-directed DNA methylation. Nat Genet 37: 761-765.
23. Kaya H, Shibahara KI, Taoka, KI, Iwabuchi M, Stillman B, Araki T (2001). FASCIATA genes for chromatin assembly factor-1 in arabidopsis maintain the cellular organization of apical meristems. Cell 104: 131-142.
24. Klochendler-Yeivin A, Muchardt C, Yaniv M (2002) SWI/SNF chromatin remodeling and cancer. Curr Opin Genet Dev 12: 73-79.
25. Lachner M, O'Carroll D, Rea S, Mechtler K, Jenuwein T (2001) Methylation of histone H3 lysine 9 creates a binding site for HP1 proteins. Nature 410: 116-120.
26. Lehnertz B, Ueda Y, Derijck AAHA et al. (2003) Suv39h-mediated histone H3 lysine 9 methylation directs DNA methylation to major satellite repeats at pericentric heterochromatin. Curr Biol 13: 1192-1200.
27. Libault M, Tessadori F, Germann S, Snijder B, Fransz P, Gaudin V (2005). The Arabidopsis LHP1 protein is a component of euchromatin. Planta DOI: 10.1007/s00425-005-0129-4.
28. Lindroth AM, Shultis D, Jasencakova Z et al. (2004). Dual histone H3 methylation marks at lysines 9 and 27 required for interaction with CHROMOMETHYLASE3. EMBO J 23: 4286-4296.
29. Lippman Z, Gendrel AV, Black M et al. (2004). Role of transposable elements in heterochromatin and epigenetic control. Nature 430: 471-476.
30. Liu J, He Y, Amasino R, Chen X (2004) siRNAs targeting an intronic transposon in the regulation of natural flowering behavior in Arabidopsis. Genes Dev 18: 2873-2878.
31. 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.
32. Mathieu O, Probst AV, Paszkowski J (2005) Distinct regulation of histone H3 methylation at lysines 27 and 9 by CpG methylation in Arabidopsis. EMBO J 24: 2783-2791.
33. Melquist S, Bender J (2004) An internal rearrangement in an Arabidopsis inverted repeat locus impairs DNA methylation triggered by the locus. Genetics 166: 437-448.
34. Mittelsten Scheid O, Probst AV, Afsar K, Paszkowski J (2002) Two regulatory levels of transcriptional gene silencing in Arabidopsis. Proc Natl Acad Sci USA 99: 13659-13662.
35. Nakahigashi K, Jasencakova Z, Schubert I, Goto K (2005) The Arabidopsis HETEROCHROMATIN PROTEIN1 homolog (TERMINAL FLOWER2) silences genes within euchromatic region but not genes positioned in heterochromatin. Plant Cell Physiol DOI: 10.1093/pcp/pci195.7
36. Naumann K, Fischer A, Hofmann I et al. (2005) Pivotal role of AtSUVH2 in heterochromatic histone methylation and gene silencing in Arabidopsis. EMBO J 24 1418-1429.
37. 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.
38. Peters AH, Kubicek S, Mechtler K et al. (2003) Partitioning and plasticity of repressive histone methylation states in mammalian chromatin. Mol Cell 12, 1577-1589.
39. Probst AV, Fransz PF, Paszkowski J, Mittelsten Scheid O (2003) Two means of transcriptional reactivation within heterochromatin. Plant J 33: 743-749.
40. Probst AV, Fagard M, Proux F 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: 1021-1034.
41. Quivy JP, Roche D, Kirschner D, Tagami H, Nakatani Y, Almouzni G (2004) A CAF-1 dependent pool of HP1 during heterochromatin duplication. EMBO J 23: 3516-3526.
42. Ramsahoye BH, Biniszkiewicz D, Lyko F, Clark V, Bird AP, Jaenisch R (2000) Non-CpG methylation is prevalent in embryonic stem cells and may be mediated by DNA methyltransferase 3a. PNAS 97: 5237-5242.
43. Rangwala SH, Richards EJ (2004) The value-added genome: building and maintaining genomic cytosine methylation landscapes. Curr Opin Genet Dev 14: 686-691.
44. Schotta G, Lachner M, Sarma K et al. (2004) A silencing pathway to induce H3-K9 and H4-K20 trimethylation at constitutive heterochromatin. Genes Dev 18: 1251-1262.
45. Soppe WJJ, Jacobsen SE, Alonso-Blanco C 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.
46. Soppe WJ, Jasencakova Z, Houben A et al. (2002) DNA methylation controls histone H3 lysine 9 methylation and heterochromatin assembly in Arabidopsis. EMBO J 21: 6549-6559.
47. Takeda S, Tadele Z, Hofmann I et al. (2004) BRU1, a novel link between responses to DNA damage and epigenetic gene silencing in Arabidopsis. Genes Dev 18: 782-793.
48. Tamaru H, Selker EU (2001) A histone H3 methyltransferase controls DNA methylation in Neurospora crassa. 414: 277-283.
49. Tariq M, Saze H, Probst AV, Lichota J Habu Y, Paszkowski J (2003) Erasure of CpG methylation in Arabidopsis alters patterns of histone H3 methylation in heterochromatin. Proc Natl Acad Sci USA 100: 8823-8827.
50. Tessadori F, van Driel R, Fransz P (2004) Cytogenetics as a tool to study gene regulation. Trends Plant Sci 9: 147-153.
51. The_Arabidopsis_Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408: 796-815.
52. Vaucheret H (2005) MicroRNA-dependent trans-acting siRNA production. Sci STKE 2005: pe43.
53. Xie Z, Johansen LK, Gustafson AM et al. (2004) Genetic and functional diversification of small RNA pathways in plants. PLoS Biology 2: e104.
54. Zemach A, Li Y, Wayburn B et al. (2005) DDM1 binds Arabidopsis methyl-CpG binding domain proteins and affects their subnuclear localization. Plant Cell 17: 1549-1558.
55. Zilberman D, Cao X, Jacobsen SE (2003) ARGONAUTE4 control of locus-specific siRNA accumulation and DNA and histone methylation. Science 299: 716-719.