High-temperature effect on genes engaged in DNA methylation and affected by DNA methylation in Arabidopsis

Plant Physiology and Biochemistry

Volumn 87, Issue , 2015, Pages 102-108

  Naydenov, Mladen ^a   Baev, Vesselin ^a   Apostolova, Elena ^a   Gospodinova, Nadezhda ^a   Sablok, Gaurav ^b   Gozmanova, Mariyana ^a   Yahubyan, Galina ^a  

^a UNIVERSITY OF PLOVDIV   (Bulgaria)

^b RESEARCH AND INNOVATION CENTRE   (Italy)

Author keywords

DNA methylation; Gene expression; Heat stress; PolIV; PolV

Indexed keywords

ARABIDOPSIS;

ARABIDOPSIS PROTEIN; DNA (CYTOSINE 5) METHYLTRANSFERASE; DNA DIRECTED RNA POLYMERASE; PLANT DNA;

ARABIDOPSIS; DNA METHYLATION; GENETICS; HEAT; HEAT SHOCK RESPONSE; METABOLISM; MUTATION; PHYSIOLOGY;

ARABIDOPSIS; ARABIDOPSIS PROTEINS; DNA METHYLATION; DNA, PLANT; DNA-CYTOSINE METHYLASES; DNA-DIRECTED RNA POLYMERASES; HEAT-SHOCK RESPONSE; HOT TEMPERATURE; MUTATION;

EID: 84922754801     PISSN: 09819428     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.plaphy.2014.12.022     Document Type: Article

References (54)

1. Baev V., Naydenov M., Apostolova E., Ivanova D., Doncheva S., Minkov I., Yahubyan G. Identification of RNA-dependent DNA-methylation regulated promoters in Arabidopsis. Plant Physiol. Biochem. 2010, 48:393-400.
2. Bartee L., Bender J. Two Arabidopsis methylation-deficiency mutations confer only partial effects on a methylated endogenous gene family. Nucleic Acids Res. 2001, 29:2127-2134.
3. Baurle I., Dean C. Differential interactions of the autonomous pathway RRM proteins and chromatin regulators in the silencing of Arabidopsis targets. PLoS One 2008, 3:e2733.
4. Bestor T.H., Verdine G.L. DNA methyltransferases. Curr. Opin. Cell. Biol. 1994, 6:380-389.
5. Bilichak A., Ilnystkyy Y., Hollunder J., Kovalchuk I. The progeny of Arabidopsis thaliana plants exposed to salt exhibit changes in DNA methylation, histone modifications and gene expression. PLoS One 2012, 7:e30515.
6. Boyko A., Blevins T., Yao Y., Golubov A., Bilichak A., Ilnytskyy Y., Hollunder J., Meins F., Kovalchuk I. Transgenerational adaptation of Arabidopsis to stress requires DNA methylation and the function of Dicer-like proteins. PLoS One 2010, 5:e9514.
7. Cao X., 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. 2002, 99(Suppl.4):16491-16498.
8. Cao X., Jacobsen S.E. Role of the arabidopsis DRM methyltransferases in de novo DNA methylation and gene silencing. Curr. Biol. 2002, 12:1138-1144.
9. Cao X., Springer N.M., Muszynski M.G., Phillips R.L., Kaeppler S., Jacobsen S.E. Conserved plant genes with similarity to mammalian de novo DNA methyltransferases. Proc. Natl. Acad. Sci. U. S. A. 2000, 97:4979-4984.
10. Cavrak V.V., Lettner N., Jamge S., Kosarewicz A., Bayer L.M., Mittelsten Scheid O. How a retrotransposon exploits the plant's heat stress response for its activation. PLoS Genet. 2014, 10:e1004115.
11. Chan S.W., Henderson I.R., Jacobsen S.E. Gardening the genome: DNA methylation in Arabidopsis thaliana. Nat. Rev. Genet. 2005, 6:351-360.
12. Choi Y., Gehring M., Johnson L., Hannon M., Harada J.J., Goldberg R.B., Jacobsen S.E., Fischer R.L. DEMETER, a DNA glycosylase domain protein, is required for endosperm gene imprinting and seed viability in arabidopsis. Cell 2002, 110:33-42.
13. Cokus S.J., Feng S., Zhang X., Chen Z., Merriman B., Haudenschild C.D., Pradhan S., Nelson S.F., Pellegrini M., Jacobsen S.E. Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature 2008, 452:215-219.
14. Czechowski T., Stitt M., Altmann T., Udvardi M.K., Scheible W.R. Genome-wide identification and testing of superior reference genes for transcript normalization in Arabidopsis. Plant Physiol. 2005, 139:5-17.
15. Denoux C., Galletti R., Mammarella N., Gopalan S., Werck D., De Lorenzo G., Ferrari S., Ausubel F.M., Dewdney J. Activation of defense response pathways by OGs and Flg22 elicitors in Arabidopsis seedlings. Mol. Plant 2008, 1:423-445.
16. Douet J., Tutois S., Tourmente S. APol V-mediated silencing, independent of RNA-directed DNA methylation, applies to 5S rDNA. PLoS Genet. 2009, 5:e1000690.
17. Dowen R.H., Pelizzola M., Schmitz R.J., Lister R., Dowen J.M., Nery J.R., Dixon J.E., Ecker J.R. Widespread dynamic DNA methylation in response to biotic stress. Proc. Natl. Acad. Sci. U. S. A. 2012, 109:E2183-E2191.
18. Dyachenko O.V., Zakharchenko N.S., Shevchuk T.V., Bohnert H.J., Cushman J.C., Buryanov Y.I. Effect of hypermethylation of CCWGG sequences in DNA of Mesembryanthemum crystallinum plants on their adaptation to salt stress. Biochem. (Mosc) 2006, 71:461-465.
19. Feng S., Cokus S.J., Zhang X., Chen P.Y., Bostick M., Goll M.G., Hetzel J., Jain J., Strauss S.H., Halpern M.E., Ukomadu C., Sadler K.C., Pradhan S., Pellegrini M., Jacobsen S.E. Conservation and divergence of methylation patterning in plants and animals. Proc. Natl. Acad. Sci. U. S. A. 2010, 107:8689-8694.
20. Finnegan E.J., Peacock W.J., Dennis E.S. Reduced DNA methylation in Arabidopsis thaliana results in abnormal plant development. Proc. Natl. Acad. Sci. U. S. A. 1996, 93:8449-8454.
21. Grandbastien M.A. Stress activation and genomic impact of plant retrotransposons. J.Soc. Biol. 2004, 198:425-432.
22. Haag J.R., Pikaard C.S. Multisubunit RNA polymerases IV and V: purveyors of non-coding RNA for plant gene silencing. Nat. Rev. Mol. Cell. Biol. 2011, 12:483-492.
23. Hamilton A., Voinnet O., Chappell L., Baulcombe D. Two classes of short interfering RNA in RNA silencing. EMBO J. 2002, 21:4671-4679.
24. Hashida S.N., Uchiyama T., Martin C., Kishima Y., Sano Y., Mikami T. The temperature-dependent change in methylation of the Antirrhinum transposon Tam3 is controlled by the activity of its transposase. Plant Cell. 2006, 18:104-118.
25. Henikoff S., Comai L. ADNA methyltransferase homolog with a chromodomain exists in multiple polymorphic forms in Arabidopsis. Genetics 1998, 149:307-318.
26. Huettel B., Kanno T., Daxinger L., Aufsatz W., Matzke A.J., Matzke M. Endogenous targets of RNA-directed DNA methylation and Pol IV in Arabidopsis. EMBO J. 2006, 25:2828-2836.
27. Huettel B., Kanno T., Daxinger L., Bucher E., van der Winden J., Matzke A.J., 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, 1769:358-374.
28. Ito H., Gaubert H., Bucher E., Mirouze M., Vaillant I., Paszkowski J. An siRNA pathway prevents transgenerational retrotransposition in plants subjected to stress. Nature 2011, 472:115-119.
29. Kanno T., Huettel B., Mette M.F., Aufsatz W., Jaligot E., Daxinger L., Kreil D.P., Matzke M., Matzke A.J. Atypical RNA polymerase subunits required for RNA-directed DNA methylation. Nat. Genet. 2005, 37:761-765.
30. Kashkush K., Feldman M., Levy A.A. Transcriptional activation of retrotransposons alters the expression of adjacent genes in wheat. Nat. Genet. 2003, 33:102-106.
31. Kinoshita T., Miura A., Choi Y., Kinoshita Y., Cao X., Jacobsen S.E., Fischer R.L., Kakutani T. One-way control of FWA imprinting in Arabidopsis endosperm by DNA methylation. Science 2004, 303:521-523.
32. Kishimoto N., Sakai H., Jackson J., Jacobsen S.E., Meyerowitz E.M., Dennis E.S., Finnegan E.J. Site specificity of the Arabidopsis METI DNA methyltransferase demonstrated through hypermethylation of the superman locus. Plant Mol. Biol. 2001, 46:171-183.
33. Lang-Mladek C., Popova O., Kiok K., Berlinger M., Rakic B., Aufsatz W., Jonak C., Hauser M.T., Luschnig C. Transgenerational inheritance and resetting of stress-induced loss of epigenetic gene silencing in Arabidopsis. Mol. Plant 2010, 3:594-602.
34. Laurent L., Wong E., Li G., Huynh T., Tsirigos A., Ong C.T., Low H.M., Kin Sung K.W., Rigoutsos I., Loring J., Wei C.L. Dynamic changes in the human methylome during differentiation. Genome Res. 2010, 20:320-331.
35. Law J.A., Jacobsen S.E. Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat. Rev. Genet. 2010, 11:204-220.
36. Lindroth A.M., Cao X., Jackson J.P., Zilberman D., McCallum C.M., Henikoff S., Jacobsen S.E. Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation. Science 2001, 292:2077-2080.
37. Lister R., O'Malley R.C., Tonti-Filippini J., Gregory B.D., Berry C.C., Millar A.H., Ecker J.R. Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 2008, 133:523-536.
38. Matsunaga W., Kobayashi A., Kato A., Ito H. The effects of heat induction and the siRNA biogenesis pathway on the transgenerational transposition of ONSEN, a copia-like retrotransposon in Arabidopsis thaliana. Plant Cell. Physiol. 2012, 53:824-833.
39. McCallum C.M., Comai L., Greene E.A., Henikoff S. Targeted screening for induced mutations. Nat. Biotechnol. 2000, 18:455-457.
40. Ou X., Zhang Y., Xu C., Lin X., Zang Q., Zhuang T., Jiang L., von Wettstein D., Liu B. Transgenerational inheritance of modified DNA methylation patterns and enhanced tolerance induced by heavy metal stress in rice (Oryza sativa L.). PLoS One 2012, 7:e41143.
41. Pontes O., Costa-Nunes P., Vithayathil P., Pikaard C.S. RNA polymerase V functions in Arabidopsis interphase heterochromatin organization independently of the 24-nt siRNA-directed DNA methylation pathway. Mol. Plant 2009, 2:700-710.
42. Pontes O., Li C.F., Costa Nunes P., Haag J., Ream T., Vitins A., Jacobsen S.E., Pikaard C.S. The Arabidopsis chromatin-modifying nuclear siRNA pathway involves a nucleolar RNA processing center. Cell 2006, 126:79-92.
43. Pontier D., Yahubyan G., Vega D., Bulski A., Saez-Vasquez J., Hakimi M.A., Lerbs-Mache S., Colot V., Lagrange T. Reinforcement of silencing at transposons and highly repeated sequences requires the concerted action of two distinct RNA polymerases IV in Arabidopsis. Genes. Dev. 2005, 19:2030-2040.
44. Popova O., Dinh H., Aufsatz W., Jonak C. The RdDM pathway is required for basal heat tolerance in Arabidopsis. Mol. Plant 2013, 6:396-410.
45. Smith L.M., Pontes O., Searle I., Yelina N., Yousafzai F.K., Herr A.J., Pikaard C.S., Baulcombe D.C. An SNF2 protein associated with nuclear RNA silencing and the spread of a silencing signal between cells in Arabidopsis. Plant Cell. 2007, 19:1507-1521.
46. Steward N., Ito M., Yamaguchi Y., Koizumi N., Sano H. Periodic DNA methylation in maize nucleosomes and demethylation by environmental stress. J.Biol. Chem. 2002, 277:37741-37746.
47. Steward N., Kusano T., Sano H. Expression of ZmMET1, a gene encoding a DNA methyltransferase from maize, is associated not only with DNA replication in actively proliferating cells, but also with altered DNA methylation status in cold-stressed quiescent cells. Nucleic Acids Res. 2000, 28:3250-3259.
48. Tittel-Elmer M., Bucher E., Broger L., Mathieu O., Paszkowski J., Vaillant I. Stress-induced activation of heterochromatic transcription. PLoS Genet. 2010, 6:e1001175.
49. Tran R.K., Henikoff J.G., Zilberman D., Ditt R.F., Jacobsen S.E., Henikoff S. DNA methylation profiling identifies CG methylation clusters in Arabidopsis genes. Curr. Biol. 2005, 15:154-159.
50. Xie Z., Johansen L.K., Gustafson A.M., Kasschau K.D., Lellis A.D., Zilberman D., Jacobsen S.E., Carrington J.C. Genetic and functional diversification of small RNA pathways in plants. PLoS Biol. 2004, 2:E104.
51. Zeller G., Henz S.R., Widmer C.K., Sachsenberg T., Ratsch G., Weigel D., Laubinger S. Stress-induced changes in the Arabidopsis thaliana transcriptome analyzed using whole-genome tiling arrays. Plant J. 2009, 58:1068-1082.
52. Zemach A., McDaniel I.E., Silva P., Zilberman D. Genome-wide evolutionary analysis of eukaryotic DNA methylation. Science 2010, 328:916-919.
53. Zhang X., Yazaki J., Sundaresan A., Cokus S., Chan S.W., Chen H., Henderson I.R., Shinn P., Pellegrini M., Jacobsen S.E., Ecker J.R. Genome-wide high-resolution mapping and functional analysis of DNA methylation in arabidopsis. Cell 2006, 126:1189-1201.
54. Zilberman D., Gehring M., Tran R.K., Ballinger T., Henikoff S. Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. Nat. Genet. 2007, 39:61-69.