Endogenous targets of RNA-directed DNA methylation and Pol IV in Arabidopsis

EMBO Journal

Volumn 25, Issue 12, 2006, Pages 2828-2836

  Huettel, Bruno ^a   Kanno, Tatsuo ^a   Daxinger, Lucia ^a   Aufsatz, Werner ^a   Matzke, Antonius J M ^a   Matzke, Marjori ^a  

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

Author keywords

Chromatin; Histone methylation; Pol IV; RNA directed DNA methylation; Solo LTR

Indexed keywords

CYTOSINE; HISTONE; LYSINE; PROTEIN DRD1; PROTEIN SWI; RNA POLYMERASE; RNA POLYMERASE IVB; SPACER DNA; UNCLASSIFIED DRUG;

ARABIDOPSIS; ARTICLE; DNA METHYLATION; EPIGENETICS; EUCHROMATIN; GENE CONTROL; GENE REPRESSION; GENE SILENCING; HETEROCHROMATIN; LONG TERMINAL REPEAT; NONHUMAN; PRIORITY JOURNAL; PROTEIN MODIFICATION; RETROPOSON; TRANSCRIPTION REGULATION;

ARABIDOPSIS; ARABIDOPSIS PROTEINS; CHROMATIN IMMUNOPRECIPITATION; DNA METHYLATION; DNA POLYMERASE BETA; DNA-DIRECTED RNA POLYMERASES; DOWN-REGULATION; GENE EXPRESSION PROFILING; MODELS, GENETIC; MUTATION; RNA, PLANT; TERMINAL REPEAT SEQUENCES; UP-REGULATION;

ARABIDOPSIS;

EID: 33745561418     PISSN: 02614189     EISSN: 14602075     Source Type: Journal    
DOI: 10.1038/sj.emboj.7601150     Document Type: Article

References (36)

1. Aufsatz W, Mette MF, van der Winden J, Matzke AJM, Matzke M (2002) RNA-directed DNA methylation in Arabidopsis. Proc Natl Acad Sci USA 99: 16499-16506
2. Breyne P, Dreesen R, Cannoot B, Rombaut D, Vandepoele K, Rombauts S, Vanderhaeghen R, Inze D, Zabeau M (2003) Quantitative cDNA-AFLP analysis for genome-wide expression studies. Mol Genet Genomics 269: 173-179
3. Chan SW-L, Henderson IR, Jacobsen SE (2005) Gardening the genome: DNA methylation in Arabidopsis thaliana. Nat Rev Genet 6: 351-360
4. Cigan AM, Unger-Wallace E, Haug-Collet K (2005) Transcriptional gene silencing as a tool for uncovering gene function in maize. Plant J 43: 929-940
5. Dalmay T, Hamilton A, Rudd S, Angell S, Baulcombe DC (2000) An RNA-dependent RNA polymerase gene in Arabidopsis is required for posttranscriptional gene silencing mediated by a transgene but not by a virus. Cell 101: 543-553
6. Dennis K, Fan T, Geiman T, Yan Q, Muegge K (2001) Lsh, a member of the SNF2 family, is required for genome-wide methylation. Genes Dev 15: 2940-2944
7. Diatchenko L, Lau YF, Campbell AP, Chenchik A, Moqadam F, Huang B, Lukyanov S, Lukyanov K, Gurskaya N, Sverdlov ED, Siebert PD (1996) Suppression subtractive hybridization: a method for generating differentially regulated or tissue-specific cDNA probes and libraries. Proc Natl Acad Sci USA 93: 6025-6030
8. Fuchs J, Demidov D, Houben A, Schubert I (2006) Chromosomal histone modification patterns - from conservation to diversity. Trends Plant Sci 11: 199-208
9. Herr AJ, Jensen MB, Dalmay T, Baulcombe DC (2005) RNA polymerase IV directs silencing of endogenous DNA. Science 308: 118-120
10. Jeddeloh JA, Stokes TL, Richards EJ (1999) Maintenance of genomic methylation requires a SWI2/SNF2-like protein. Nat Genet 22: 94-97
11. Jones L, Ratcliff F, Baulcombe DC (2001) RNA-directed transcriptional gene silencing in plants can be inherited independently of the RNA trigger and requires Met 1 for maintenance. Curr Biol 11: 747-757
12. Jurka J, Kapitonov VV, Pavlicek A, Klonowski P, Kohany O, Walichiewicz J (2005) Repbase update, a database of eukaryotic repetitive elements. Cytogenet Genome Res 110: 462-467
13. Kanno T, Aufsatz W, Jaligot E, Mette MF, Matzke M, Matzke AJM (2005a) A SNF2-like protein facilitates dynamic control of DNA methylation. EMBO Rep 6: 649-655
14. Kanno T, Huettel B, Mette MF, Aufsatz W, Jaligot E, Daxinger L, Kreil DP, Matzke M, Matzke AJM (2005b) Atypical RNA polymerase subunits required for RNA-directed DNA methylation. Nat Genet 37: 761-765
15. Kanno T, Mette MF, Kreil DP, Aufsatz W, Matzke M, Matzke AJM (2004) Involvement of putative SNF2 chromatin remodelling protein DRD1 in RNA-directed DNA methylation. Curr Biol 14: 801-805
16. Kapoor A, Agius F, Zhu JK (2005) Preventing transcriptional gene silencing by active DNA demethylation. FEBS Lett 579: 5889-5898
17. Kashkush K, Feldman M, Levy AA (2003) Transcriptional activation of retrotransposons alters the expression of adjacent genes in wheat. Nat Genet 33: 102-106
18. Lippman Z, Gendrel AV, Black M, Vaughn MW, Dedhia N, McCombie WR, Lavine K, Mittal V, May B, Kasschau KD, Carrington JC, Doerge RW, Colot V, Martienssen R (2004) Role of transposable elements in heterochromatin and epigenetic control. Nature 430: 471-476
19. Lippman Z, May B, Yordan C, Singer T, Martienssen R (2003) Distinct mechanisms determine transposon inheritance and methylation via small interfering RNA and histone modification. PLoS Biol 1: 420-428
20. Lu C, Tej SS, Luo S, Haudenschild CD, Meyers BC, Green PJ (2005) Elucidation of the small RNA component of the transcriptome. Science 309: 1567-1569
21. Mathieu O, Bender J (2004) RNA-directed DNA methylation. J Cell Sci 117: 4881-4888
22. Matzke M, Aufsatz W, Kanno T, Daxinger L, Papp I, Mette MF, Matzke AJM (2004) Genetic analysis of RNA-mediated transcriptional gene silencing. Biochim Biophys Acta 1677: 129-141
23. Matzke MA, Birchler JA (2005) RNAi-mediated pathways in the nucleus. Nat Rev Genet 6: 24-35
24. Mette MF, Aufsatz W, van der Winden J, Matzke MA, Matzke AJM (2000) Transcriptional silencing and promoter methylation triggered by double-stranded RNA. EMBO J 19: 5194-5201
25. Mette MF, van der Winden J, Matzke MA, Matzke AJM (1999) Production of aberrant promoter transcripts contributes to methylation and silencing of unlinked homologous promoters in trans. EMBO J 18: 241-248
26. Morris KV (2005) siRNA-mediated transcriptional gene silencing: the potential mechanisms and a possible role in the histone code. Cell Mol Life Sci 62: 3057-3066
27. 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
28. Peterson-Burch BD, Nettleton D, Voytas DF (2004) Genomic neighbourhoods for Arabidopsis retrotransposons: a role for targeted integration in the distribution of the Metaviridae. Genome Biol 5: R78
29. Pontier D, Yahubyan G, Vega D, Bulski A, Saez-Vasquez J, Hakimi MA, Lerbs-Mache S, Colot V, Lagrange T (2005) Reinforcement of silencing at transposons and highly repeated sequences requires the concerted action of two distinct RNA polymerases IV in Arabidopsis. Genes Dev 19: 2030-2040
30. Sunkar R, Zhu JK (2004) Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis. Plant Cell 16: 2001-2019
31. Ting AH, Schuebel KE, Herman JG, Baylin SB (2005) Short double-stranded RNA induces transcriptional gene silencing in human cancer cells in the absence of DNA methylation. Nat Genet 37: 906-910
32. Tran R, Zilberman D, de Bustos C, Ditt RF, Henikoff JG, Lindroth AM, Delrow J, Boyle T, Kwong S, Bryson TD, Jacobsen SE, Henikoff S (2005) Chromatin and siRNA pathways cooperate to maintain DNA methylation of small transposable elements in Arabidopsis. Genome Biol 6: R90
33. Vongs A, Kakutani T, Martienssen RA, Richards EJ (1993) Arabidopsis thaliana DNA methylation mutants. Science 260: 1926-1928
34. Vos P, Hogers R, Bleeker M, Reijans M, van de Lee T, Hornes M, Frijters A, Pot J, Peleman J, Kuiper M, Zabeau M (1995) AFLP: a new technique for DNA fingerprinting. Nucl Acids Res 23: 4407-4414
35. Wassenegger M (2005) The role of the RNAi machinery in heterochromatin formation. Cell 122: 13-16
36. Weinberg MS, Villeneuve LM, Ehsani A, Aagaard L, Chen ZX, Riggs AD, Rossi JJ, Morris KV (2006) The antisense strand of small interfering RNAs directs histone methylation and transcriptional gene silencing in human cells. RNA 12: 256-262