Transmission of epi-alleles with MET1-dependent dense methylation in Arabidopsis thaliana

PLoS ONE

Volumn 9, Issue 8, 2014, Pages

  Watson, Michael ^a   Hawkes, Emily ^a   Meyer, Peter ^a  

^a UNIVERSITY OF LEEDS   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

DNA METHYLTRANSFERASE 1; PLANT DNA; UNTRANSLATED RNA; ARABIDOPSIS PROTEIN; DNA (CYTOSINE 5) METHYLTRANSFERASE; MET1 PROTEIN, ARABIDOPSIS;

ALLELE; ARABIDOPSIS THALIANA; ARTICLE; CONTROLLED STUDY; DINUCLEOTIDE REPEAT; DNA METHYLATION; DNA SEQUENCE; ECOTYPE; EPI ALLELE; GENE FUNCTION; GENE LOCUS; GENE NUMBER; GENE TRANSFER; GENETIC CORRELATION; GENETIC CROSS; NONHUMAN; ARABIDOPSIS; ENZYMOLOGY; GENE EXPRESSION REGULATION; GENE SILENCING; GENETICS; PHYSIOLOGY; PLANT GENE; PROMOTER REGION;

ALLELES; ARABIDOPSIS; ARABIDOPSIS PROTEINS; DNA (CYTOSINE-5-)-METHYLTRANSFERASE; DNA METHYLATION; GENE EXPRESSION REGULATION, PLANT; GENE SILENCING; GENES, PLANT; PROMOTER REGIONS, GENETIC;

EID: 84929938926     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0105338     Document Type: Article

References (43)

1. Huettel B, Kanno T, Daxinger L, Bucher E, van der Winden J, et al. (2007) RNA-directed DNA methylation mediated by DRD1 and Pol IVb: A versatile pathway for transcriptional gene silencing in plants. Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression 1769: 358.
2. Yao Y, Bilichak A, Golubov A, Kovalchuk I (2012) ddm1 plants are sensitive to methyl methane sulfonate and NaCl stresses and are deficient in DNA repair. Plant Cell Reports 31: 1549-1561.
3. Mirouze M, Lieberman-Lazarovich M, Aversano R, Bucher E, Nicolet J, et al. (2012) Loss of DNA methylation affects the recombination landscape in Arabidopsis. Proceedings of the National Academy of Sciences 109: 5880-5885.
4. Finnegan EJ, Peacock WJ, Dennis ES (1996) Reduced DNA methylation in Arabidopsis thaliana results in abnormal plant development. Proc Natl Acad Sci U S A 93: 8449-8454. (Pubitemid 26269578)
5. Kato M, Miura A, Bender J, Jacobsen SE, Kakutani T (2003) Role of CG and Non-CG Methylation in Immobilization of Transposons in Arabidopsis. Current Biology 13: 421.
6. Lopez-Maury L, Marguerat S, Bahler J (2008) Tuning gene expression to changing environments: from rapid responses to evolutionary adaptation. Nature Reviews Genetics 9: 583-593.
7. Becker C, Hagmann J, Muller J, Koenig D, Stegle O, et al. (2011) Spontaneous epigenetic variation in the Arabidopsis thaliana methylome. Nature 480: 245-249.
8. O'Malley RC, Ecker JR (2012) Epiallelic Variation in Arabidopsis thaliana. Cold Spring Harbor Symposia on Quantitative Biology 77: 135-145.
9. Lira-Medeiros CF, Parisod C, Fernandes RA, Mata CS, Cardoso MA, et al. (2010) Epigenetic Variation in Mangrove Plants Occurring in Contrasting Natural Environment. PLoS ONE 5: e10326.
10. Finnegan EJ (2002) Epialleles - a source of random variation in times of stress. Current Opinion in Plant Biology 5: 101-106.
11. Kou HP, Li Y, Song XX, Ou XF, Xing SC, et al. (2011) Heritable alteration in DNA methylation induced by nitrogen-deficiency stress accompanies enhanced tolerance by progenies to the stress in rice (Oryza sativa L.). Journal of Plant Physiology 168: 1685-1693.
12. Boyko A, Kathiria P, Zemp FJ, Yao Y, Pogribny I, et al. (2007) Transgenerational changes in the genome stability and methylation in pathogen-infected plants: (Virus-induced plant genome instability). Nucleic Acids Research 35: 1714-1725. (Pubitemid 46592888)
13. Kovarik A, Koukalová B, Bezdek M, Opatrn Z (1997) Hypermethylation of tobacco heterochromatic loci in response to osmotic stress. Theoretical and Applied Genetics 95: 301-306. (Pubitemid 27369654)
14. Matzke M, Kanno T, Daxinger L, Huettel B, Matzke AJM (2009) RNAmediated chromatin-based silencing in plants. Current Opinion in Cell Biology 21: 367-376.
15. Jackson JP, Lindroth AM, Cao X, Jacobsen SE (2002) Control of CpNpG DNA methylation by the KRYPTONITE histone H3 methyltransferase. Nature 416: 556.
16. Cao X, Aufsatz W, Zilberman D, Mette MF, Huang MS, et al. (2003) Role of the DRM and CMT3 Methyltransferases in RNA-Directed DNA Methylation. Current Biology 13: 2212-2217. (Pubitemid 38024949)
17. Cokus SJ, Feng S, Zhang X, Chen Z, Merriman B, et al. (2008) Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature 452: 215-219. (Pubitemid 351380251)
18. Schmitz RJ, Schultz MD, Urich MA, Nery JR, Pelizzola M, et al. (2013) Patterns of population epigenomic diversity. Nature 495: 193-198.
19. Greaves IK, Groszmann M, Wang A, Peacock WJ, Dennis ES (2014) Inheritance of Trans Chromosomal Methylation patterns from Arabidopsis F1 hybrids. Proceedings of the National Academy of Sciences 111: 2017-2022.
20. Mathieu O, Reinders J, Caikovski M, Smathajitt C, Paszkowski J (2007) Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation. Cell 130: 851-862. (Pubitemid 47334929)
21. Stroud H, Greenberg Maxim VC, Feng S, Bernatavichute Yana V, Jacobsen Steven E (2013) Comprehensive Analysis of Silencing Mutants Reveals Complex Regulation of the Arabidopsis Methylome. Cell 152: 352-364.
22. Rhee SY, Beavis W, Berardini TZ, Chen G, Dixon D, et al. (2003) The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community. Nucleic Acids Research 31: 224-228. (Pubitemid 36150370)
23. Manning K, Tor M, Poole M, Hong Y, Thompson AJ, et al. (2006) A naturally occurring epigenetic mutation in a gene encoding an SBP-box transcription factor inhibits tomato fruit ripening. Nat Genet 38: 948-952. (Pubitemid 44141665)
24. Kinoshita Y, Saze H, Kinoshita T, Miura A, Soppe WJJ, et al. (2007) Control of FWA gene silencing in Arabidopsis thaliana by SINE-related direct repeats. The Plant Journal 49: 38-45. (Pubitemid 44952696)
25. Miura K, Agetsuma M, Kitano H, Yoshimura A, Matsuoka M, et al. (2009) A metastable DWARF1 epigenetic mutant affecting plant stature in rice. Proceedings of the National Academy of Sciences 106: 11218-11223.
26. Silveira AB, Trontin C, Cortijo S, Barau J, Del Bem LEV, et al. (2013) Extensive Natural Epigenetic Variation at a De Novo Originated Gene PLoS Genet 9: e1003437.
27. You W, Tyczewska A, Spencer M, Daxinger L, Schmid M, et al. (2012) Atypical DNA methylation of genes encoding cysteine-rich peptides in Arabidopsis thaliana. BMC Plant Biology 12: 51.
28. Zemach A, Kim MY, Hsieh P-H, Coleman-Derr D, Eshed-Williams L, et al. (2013) The Arabidopsis Nucleosome Remodeler DDM1 Allows DNA Methyltransferases to Access H1-Containing Heterochromatin. Cell 153: 193-205.
29. Richards EJ (2006) Inherited epigenetic variation [mdash] revisiting soft inheritance. Nat Rev Genet 7: 395-401.
30. 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. (Pubitemid 29082948)
31. Teixeira FK, Heredia F, Sarazin A, Roudier F, Boccara M, et al. (2009) A Role for RNAi in the Selective Correction of DNA Methylation Defects. Science 323: 1600-1604.
32. Das OP, Messing J (1994) Variegated phenotype and developmental methylation changes of a maize allele originating from epimutation. Genetics 136: 1121-1141. (Pubitemid 24085659)
33. Cubas P, Vincent C, Coen E (1999) An epigenetic mutation responsible for natural variation in floral symmetry. Nature 401: 157-161. (Pubitemid 29436317)
34. Tariq M, Saze H, Probst AV, Lichota J, Habu Y, et al. (2003) Erasure of CpG methylation in Arabidopsis alters patterns of histone H3 methylation in heterochromatin. Proceedings of the National Academy of Sciences 100: 8823-8827. (Pubitemid 36899182)
35. Jullien PE, Mosquna A, Ingouff M, Sakata T, Ohad N, et al. (2008) Retinoblastoma and its binding partner MSI1 control imprinting in Arabidopsis. PLoS biology 6.
36. Saze H, Scheid OM, Paszkowski J (2003) Maintenance of CpG methylation is essential for epigenetic inheritance during plant gametogenesis. Nat Genet 34: 65-69. (Pubitemid 36548792)
37. Reinders J, Wulff BBH, Mirouze M, Marí-Ordóñez A, Dapp M, et al. (2009) Compromised stability of DNA methylation and transposon immobilization in mosaic Arabidopsis epigenomes. Genes & Development 23: 939-950.
38. Schmitz RJ, He Y, Valdés-López O, Khan SM, Joshi T, et al. (2013) Epigenome-wide inheritance of cytosine methylation variants in a recombinant inbred population. Genome Research 23: 1663-1674.
39. Vejlupkova Z, Fowler JE (2003) Maize DNA Preps for Undergraduate Students: A Robust Method for Pcr Genotyping. Maize Genetics Cooperation Newsletter: 24-25.
40. Stam M, de Bruin R, van Blokland R, van der Hoorn RA, Mol JN, et al. (2000) Distinct features of post-transcriptional gene silencing by antisense transgenes in single copy and inverted T-DNA repeat loci. Plant J 21: 27-42. (Pubitemid 30115695)
41. Dellaporta SL, Wood J, Hicks JB (1983) A plant DNA minipreparation: version II. Plant Molecular Biology Reporter 4: 19-21.
42. Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp Ser 41: 95-98.
43. Hetzl J, Foerster AM, Raidl G, Scheid OM (2007) CyMATE: a new tool for methylation analysis of plant genomic DNA after bisulphite sequencing. The Plant Journal 51: 526-536. (Pubitemid 47106545)