Epigenetic changes of Arabidopsis MET1 cytosine methyltransferase mutants under salt stress

References

• Arıkan B, Özden S, Turgut-Kara N. 2018. DNA methylation related gene expression and morphophysiological response to abiotic stresses in Arabidopsis thaliana. Environmental and Experimental Botany. 149:17–26.
   Web of Science ®Google Scholar
• Ashapkin VV, Kutueva LI, Vanyushin BF. 2002. The gene for domains rearranged methyltransferase (DRM2) in Arabidopsis thaliana plants is methylated at both cytosine and adenine residues. FEBS Lett. 532(3):367–372.
   PubMed Web of Science ®Google Scholar
• Baek D, Jiang J, Chung JS, Wang B, Chen J, Xin Z, Shi H. 2011. Regulated AtHKT1 gene expression by a distal enhancer element and DNA methylation in the promoter plays an important role in salt tolerance. Plant Cell Physiol. 52(1):149–161.
   PubMed Web of Science ®Google Scholar
• Bartee L, Bender J. 2001. Two Arabidopsis methylation-deficiency mutations confer only partial effects on a methylated endogenous gene family. Nucleic Acids Res. 29(10):2127–2134.
   PubMed Web of Science ®Google Scholar
• Berdasco M, Alcázar R, García-Ortiz MV, Ballestar E, Fernández AF, Roldán-Arjona T, Tiburcio AF, Altabella T, Buisine N, Quesneville H, et al. 2008. Promoter DNA hypermethylation and gene repression in undifferentiated Arabidopsis cells. PLoS One. 3(10):e3306.
   PubMed Web of Science ®Google Scholar
• Blevins T, Wang J, Pflieger D, Pontvianne F, Pikaard CS. 2017. Hybrid incompatibility caused by an epiallele. Proc Natl Acad Sci USA. 114(14):3702–3707.
   PubMed Web of Science ®Google Scholar
• Boyko A, Blevins T, Yao Y, Golubov A, Bilichak A, Ilnytskyy Y, Hollunder J, Meins F, Kovalchuk I. 2010. Transgenerational adaptation of Arabidopsis to stress requires DNA methylation and the function of Dicer-like proteins. PloS One. 5(3):e9514.
   PubMed Web of Science ®Google Scholar
• Brocklehurst S, Watson M, Carr IM, Out S, Heidmann I, Meyer P. 2018. Induction of epigenetic variation in Arabidopsis by over-expression of DNA methyltransferase1 (MET1). PloS One. 13(2):e0192170.
   PubMed Web of Science ®Google Scholar
• Carus S, Çakal Y. 2005. Yaprak Yüzeyinin Karaçam (Pinus nigra Arnold) ve Toros Sediri (Cedrus Libani A. Rich.) Fidanlarında Dip Çap ve Boy Artımı Üzerindeki Etkileri. Süleyman Demirel Üniversitesi Orman Fakültesi Dergisi 2(1302-7085):52–61.
   Google Scholar
• Chan SR, Blackburn EH. 2004. Telomeres and telomerase. Philos Trans R Soc Lond B Biol Sci. 359(1441):109–121.
   PubMed Web of Science ®Google Scholar
• Chinnusamy V, Zhu JK. 2009. RNA-directed DNA methylation and demethylation in plants. Sci China C Life Sci. 52(4):331–343.
   PubMedGoogle Scholar
• Cokus SJ, Feng S, Zhang X, Chen Z, Merriman B, Haudenschild CD, Pradhan S, Nelson SF, Pellegrini M, Jacobsen SE. 2008. Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature. 452(7184):215–219.
   PubMed Web of Science ®Google Scholar
• D’Amico-Willman KM, Anderson ES, Gradziel TM, Fresnedo-Ramírez J. 2021. Relative telomere length and telomerase reverse transcriptase (TERT) expressions are associated with age in almond (Prunus dulcis [Mill.] DA Webb). Plants. 10(2):189.
   Google Scholar
• Eckardt NA. 2006. Genetic and epigenetic regulation of embryogenesis. Plant Cell. 18(4):781–784.
   Web of Science ®Google Scholar
• FitzGerald J, Luo M, Chaudhury A, Berger F. 2008. DNA methylation causes predominant maternal controls of plant embryo growth. PloS One. 3(5):e2298.
   PubMed Web of Science ®Google Scholar
• Gao C, Deng M, Yang X, Yu W, Cai J, Shi Y, Zhu Z, Zhou T, Xue L, Cao F, et al. 2020. Genome-wide ıdentification and coexpression network analysis of DNA methylation pathway genes and their differentiated functions in Ginkgo biloba. L. Forests. 11(10):1076.
   Google Scholar
• Haag JR, Pikaard CS. 2011. Multisubunit RNA polymerases IV and V: purveyors of non-coding RNA for plant gene silencing. Nat Rev Mol Cell Biol. 12(8):483–492.
   PubMed Web of Science ®Google Scholar
• He L, Huang H, Bradai M, Zhao C, You Y, Ma J, Zhao L, Lozano-Durán R, Zhu J-K. 2022. DNA methylation-free Arabidopsis reveals crucial roles of DNA methylation in regulating gene expression and development. Nat Commun. 13(1):1–16.
   PubMed Web of Science ®Google Scholar
• Henderson IR, Jacobsen SE. 2007. Epigenetic inheritance in plants. Nature. 447(7143):418–424.
   PubMed Web of Science ®Google Scholar
• Houben JM, Moonen HJ, van Schooten FJ, Hageman GJ. 2008. Telomere length assessment: biomarker of chronic oxidative stress? Free Radic Biol Med. 44(3):235–246.
   PubMed Web of Science ®Google Scholar
• Huang C-F, Miki D, Tang K, Zhou H-R, Zheng Z, Chen W, Ma Z-Y, Yang L, Zhang H, Liu R, et al. 2013. A Pre-mRNA-splicing factor is required for RNA-directed DNA methylation in Arabidopsis. PLoS Genet. 9(9):e1003779.
   PubMed Web of Science ®Google Scholar
• Johnson LM, Bostick M, Zhang X, Kraft E, Henderson I, Callis J, Jacobsen SE. 2007. The SRA methyl-cytosine-binding domain links DNA and histone methylation. Curr Biol. 17(4):379–384.
   PubMed Web of Science ®Google Scholar
• Jullien PE, Katz A, Oliva M, Ohad N, Berger F. 2006. Polycomb group complexes self-regulate imprinting of the Polycomb group gene MEDEA in Arabidopsis. Curr Biol. 16(5):486–492.
   PubMed Web of Science ®Google Scholar
• Kinoshita T, Seki M. 2014. Epigenetic memory for stress response and adaptation in plants. Plant Cell Physiol. 55(11):1859–1863.
   PubMed Web of Science ®Google Scholar
• Law JA, Jacobsen SE. 2010. Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat Rev Genet. 11(3):204–220.
   PubMed Web of Science ®Google Scholar
• Li L, Wu W, Zhao Y, Zheng B. 2017. A reciprocal inhibition between ARID1 and MET1 in male and female gametes in Arabidopsis. J Integr Plant Biol. 59(9):657–668.
   PubMed Web of Science ®Google Scholar
• Lister R, O’Malley RC, Tonti-Filippini J, Gregory BD, Berry CC, Millar AH, Ecker JR. 2008. Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell. 133(3):523–536.
   PubMed Web of Science ®Google Scholar
• Liu B, Soundararajan P, Manivannan A. 2019. Mechanisms of silicon-mediated amelioration of salt stress in plants. Plants. 8(9):307.
   Google Scholar
• Livak KJ, Schmittgen TD. 2001. Analysis of relative gene expression data using real time quantitative PCR and the 2–ΔΔCT method. Methods. 25(4):402–408.
   PubMed Web of Science ®Google Scholar
• Molinier J, Ries G, Zipfel C, Hohn B. 2006. Transgeneration memory of stress in plants. Nature. 442(7106):1046–1049.
   PubMed Web of Science ®Google Scholar
• Murashige T, Skoog F. 1962. A revised medium for rapid growth and bioassays with tobacco tissue cultures. Physiol Plant. 15(3):473–497.
   Web of Science ®Google Scholar
• Naydenov M, Baev V, Apostolova E, Gospodinova N, Sablok G, Gozmanova M, Yahubyan G. 2015. High-temperature effect on genes engaged in DNA methylation and affected by DNA methylation in Arabidopsis. Plant Physiol Biochem. 87:102–108.
   PubMed Web of Science ®Google Scholar
• Ngara R, Ndimba BK. 2014. Understanding the complex nature of salinity and drought-stress response in cereals using proteomics Technologies. Proteomics. 14(4-5):611–621.
   PubMed Web of Science ®Google Scholar
• Ogrocká A, Sýkorová E, Fajkus J, Fojtová M. 2012. Developmental silencing of the AtTERT gene is associated with increased H3K27me3 loading and maintenance of its euchromatic environment. J Exp Bot. 63(11):4233–4241.
   PubMed Web of Science ®Google Scholar
• Papareddy RK, Páldi K, Smolka AD, Hüther P, Becker C, Nodine MD. 2021. Repression of chromomethylase 3 prevents epigenetic collateral damage in Arabidopsis. Elife. 10:e69396.
   PubMed Web of Science ®Google Scholar
• Peck S, Mittler R. 2020. Plant signaling in biotic and abiotic stress. J Exp Bot. 71(5):1649–1651.
   PubMed Web of Science ®Google Scholar
• Pettersen EF, Goddard TD, Huang CC, Meng EC, Couch GS, Croll TI, Morris JH, Ferrin TE. 2021. UCSF ChimeraX: structure visualization for researchers, educators, and developers. Protein Sci. 30(1):70–82.
   PubMed Web of Science ®Google Scholar
• Pontvianne F, Blevins T, Chandrasekhara C, Mozgová I, Hassel C, Pontes OMF, Tucker S, Mokros P, Muchová V, Fajkus J, et al. 2013. Subnuclear partitioning of rRNA genes between the nucleolus and nucleoplasm reflects alternative epiallelic states. Genes Dev. 27(14):1545–1550.,.
   PubMed Web of Science ®Google Scholar
• Rigal M, Becker C, Pélissier T, Pogorelcnik R, Devos J, Ikeda Y, Weigel D, Mathieu O. 2016. Epigenome confrontation triggers immediate reprogramming of DNA methylation and transposon silencing in Arabidopsis thaliana F1 epihybrids. Proc Natl Acad Sci USA. 113(14):E2083–E2092.
   PubMed Web of Science ®Google Scholar
• Sahu PP, Pandey G, Sharma N, Puranik S, Muthamilarasan M, Prasad M. 2013. Epigenetic mechanisms of plant stress responses and adaptation. Plant Cell Rep. 32(8):1151–1159.
   PubMed Web of Science ®Google Scholar
• Sáenz-Mata J, Jiménez-Bremont JF. 2012. HR4 gene is induced in the Arabidopsis-Trichoderma atroviride beneficial interaction. Int J Mol Sci. 13(7):9110–9128.
   PubMed Web of Science ®Google Scholar
• Saze H, Scheid OM, Paszkowski J. 2003. Maintenance of CpG methylation is essential for epigenetic inheritance during plant gametogenesis. Nat Genet. 34(1):65–69.
   PubMed Web of Science ®Google Scholar
• Shrivastava P, Kumar R. 2015. Soil salinity: a serious environmental issue and plant growth promoting bacteria as one of the tools for its alleviation. Saudi J Biol Sci. 22(2):123–131.
   PubMed Web of Science ®Google Scholar
• Sudan J, Raina M, Singh R. 2018. Plant epigenetic mechanisms: role in abiotic stress and their generational heritability. 3 Biotech. 8(3):172.
   PubMedGoogle Scholar
• Quadrana L, Colot V. 2016. Plant transgenerational epigenetics. Annu Rev Genet. 50:467–491.
   PubMed Web of Science ®Google Scholar
• Tellez-Plaza M, Tang W-Y, Shang Y, Umans JG, Francesconi KA, Goessler W, Ledesma M, Leon M, Laclaustra M, Pollak J, et al. 2014. Association of global DNA methylation and global DNA hydroxymethylation with metals and other exposures in human blood DNA samples. Environ Health Perspect. 122(9):946–954.
   PubMed Web of Science ®Google Scholar
• The Arabidopsis Information Resource (TAIR). 2021a. [accessed 2021 Jan 26]. https://www.arabidopsis.org/servlets/TairObject?id=94303&type=polyallele on www.arabidopsis.org
   Google Scholar
• The Arabidopsis Information Resource (TAIR). 2021b. [accessed 2021 Jan 26]. https://www.arabidopsis.org/servlets/TairObject?id=500447108&type=polyallele on www.arabidopsis.org.
   Google Scholar
• Von Zglinicki T. 2002. Oxidative stress shortens telomeres. Trends Biochem Sci. 27(7):339–344.
   PubMed Web of Science ®Google Scholar
• Wendte JM, Zhang Y, Ji L, Shi X, Hazarika RR, Shahryary Y, Johannes F, Schmitz RJ. 2019. Epimutations are associated with chromomethylase 3-induced de novo DNA methylation. Elife. 8:e47891.
   PubMed Web of Science ®Google Scholar
• Yang Y, Guo Y. 2018. Elucidating the molecular mechanisms mediating plant salt-stress responses. New Phytol. 217(2):523–539.
   PubMed Web of Science ®Google Scholar
• Yao Y, Bilichak A, Golubov A, Kovalchuk I. 2012. ddm1 plants are sensitive to methyl methanesulfonate and NaCl stresses and are deficient in DNA repair. Plant Cell Rep. 31(9):1549–1561.
   PubMed Web of Science ®Google Scholar
• Zangi M, Najjar MBB, Golalipour M, Aghdasi M. 2020. met1 DNA Methyltransferase controls TERT gene expression: a new insight to the role of telomerase in development. Cell J. 22(1):71–74.
   PubMed Web of Science ®Google Scholar
• Zhang H, Zhu JK. 2011. RNA-directed DNA methylation. Curr Opin Plant Biol. 14(2):142–147.
   PubMed Web of Science ®Google Scholar
• Zhong L, Xu YH, Wang JB. 2009. DNA-methylation changes induced by salt stress in wheat Triticum aestivum. Afr J Biotechnol. 8(22):6201–6207.
   Google Scholar
• Zhu JK. 2000. Genetic analysis of plant salt tolerance using Arabidopsis. Plant Physiol. 124(3):941–948.
   PubMed Web of Science ®Google Scholar