Abstract
DNA methylation occurs mostly at the C5 position of dinucleotide symmetric CpG sites in genomic DNA. A balance is maintained in the plant genome between DNA methylation mediated by RNA-directed DNA methylation (RdDM) and DNA demethylation mediated by the DEMETER (DME) protein family and REPRESSOR OF SILENCING (ROS1). We used double-stranded RNA (dsRNA) silencing to suppress ROS1 protein expression in ‘Nanlin895’ (Populus deltoides × Populus euramericana ‘Nanlin895’). Leaves of WT and transformant poplars revealed more symmetric methylation on CpG sites than roots and stems. In addition, leaves of transformant poplars revealed more methylated CpG sites in both 5.8S rDNA and histone H3 compared to WT types via 0, 50 and 100 mM NaCl treatments. In asymmetric methylation sites, transformant poplars exhibited more methylated CpHpG and CpHpH contexts than WT poplars. On the other hand, hypermethylation induced by PtROS1-RNAi construct resulted in pleiotropic phenotypic changes in transgenic poplars. The percentage of wavy leaves was increased maximum by ~45% in transgenic poplars. Also, the number of leaves was increased by ~200 number in transformants. Furthermore, shooting (%) and rooting (%) was decreased in transgenic poplars versus WT.
Similar content being viewed by others
References
Agius F, Kapoor A, Zhu JK (2006) Role of the Arabidopsis DNA glycosylase/lyase ROS1 in active DNA demethylation. Proc Natl Acad Sci USA 103:11796–11801
Camargo RA, Barbosa GO, Possignolo IP, Peres LE, Lam E, Lima JE, Figueira A, Marques-Souza H (2016) RNA interference as a gene silencing tool to control Tuta absoluta in tomato (Solanum lycopersicum). PeerJ 4:e2673
Choi Y, Gehring M, Johnson L, Hannon M, Harada JJ, Goldberg RB, Jacobsen SE, Fischer RL (2002) DEMETER, a DNA glycosylase domain protein, is required for endosperm gene imprinting and seed viability in Arabidopsis. Cell 110:33–42
Dinh TT, Gao L, Liu X, Li D, Li S, Zhao Y, O'Leary M, Le B, Schmitz RJ, Manavella PA, Li S, Weigel D, Pontes O, Ecker JR, Chen X (2014) DNA topoisomerase 1alpha promotes transcriptional silencing of transposable elements through DNA methylation and histone lysine 9 dimethylation in Arabidopsis. PLoS Genet 10:e1004446
Feng S, Jacobsen SE, Reik W (2010) Epigenetic reprogramming in plant and animal development. Science 330:622–627
Furner IJ, Matzke M (2011) Methylation and demethylation of the Arabidopsis genome. Curr Opin Plant Biol 14:137–141
Gao Z, Liu HL, Daxinger L, Pontes O, He X, Qian W, Lin H, Xie M, Lorkovic ZJ, Zhang S, Miki D, Zhan X, Pontier D, Lagrange T, Jin H, Matzke AJ, Matzke M, Pikaard CS, Zhu JK (2010) An RNA polymerase II-and AGO4-associated protein acts in RNAdirected DNA methylation. Nature 465:106–109
Gehring M, Reik W, Henikoff S (2009) DNA demethylation by DNA repair. Trends Genet 25:82–90
Gong Z, Morales-Ruiz T, Ariza RR, Roldan-Arjona T, David L, Zhu JK (2002) ROS1, a repressor of transcriptional gene silencing in Arabidopsis, encodes a DNA glycosylase/lyase. Cell 111:803–814
Kapoor A, Agarwal M, Andreucci A, Zheng X, Gong Z, Hasegawa PM, Bressan RA, Zhu JK (2005) Mutations in a conserved replication protein suppress transcriptional gene silencing in a DNA-methylation-independent manner in Arabidopsis. Curr Biol 15:1912–1918
Lauria M, Rossi V (2011) Epigenetic control of gene regulation in plants. Biochim Biophys Acta 1809:369–378
Li Y, Tollefsbol TO (2011) DNA methylation detection: bisulfite genomic sequencing analysis Methods. Mol Biol 791:11–21
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
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 133:523–536
Mehrotra S, Goyal V (2014) Repetitive sequences in plant nuclear DNA: types, distribution, evolution and function. Genomics Proteomics Bioinformatics 12:164–171
Meng F, Li Y, Zang Z, Li N, Ran R, Cao Y, Li T, Zhou Q, Li W (2017) Expression of the double-stranded RNA of the soybean pod borer Leguminivora glycinivorella (Lepidoptera: Tortricidae) ribosomal protein P0 gene enhances the resistance of transgenic soybean plants. Pest Manag Sci 73:2447–2455
Movahedi A, Sun W, Zhang J, Wu X, Mousavi M, Mohammadi K, Yin T, Zhuge Q (2015a) RNA-directed DNA methylation in plants. Plant Cell Rep 34:1857–1862
Movahedi A, Zhang JX, Gao PH, Yang Y, Wang LK, Yin TM, Kadkhodaei S, Ebrahimi M, Qiang ZG (2015b) Expression of the chickpea CarNAC3 gene enhances salinity and drought tolerance in transgenic poplars. Plant Cell Tissue Organ Cult 120:141–154
Movahedi A, Zhang JX, Yin TM, Qiang ZG (2015c) Functional Analysis of Two Orthologous NAC Genes, CarNAC3, and CarNAC6 from Cicer arietinum, Involved in Abiotic Stresses in Poplar Plant. Plant Mol Biol Rep 33:1539–1551
Nakashima K, Ito Y, Yamaguchi-Shinozaki K (2009) Transcriptional regulatory networks in response to abiotic stresses in Arabidopsis and grasses. Plant Physiol 149:88–95
Omidvar V, Fellner M (2015) DNA methylation and transcriptomic changes in response to different lights and stresses in 7B-1 malesterile tomato. PLoS One 10:e0121864
Penterman J, Zilberman D, Huh JH, Ballinger T, Henikoff S, Fischer RL (2007) DNA demethylation in the Arabidopsis genome. Proc Natl Acad Sci USA 104:6752–6757
Questa JI, Fina JP, Casati P (2013) DDM1 and ROS1 have a role in UV-B induced-and oxidative DNA damage in A. thaliana. Front Plant Sci 420
Roudier F, Ahmed I, Berard C, Sarazin A, Mary-Huard T, Cortijo S, Bouyer D, Caillieux E, Duvernois-Berthet E, Al-Shikhley L, Giraut L, Despres B, Drevensek S, Barneche F, Derozier S, Brunaud V, Aubourg S, Schnittger A, Bowler C, Martin-Magniette ML, Robin S, Caboche M, Colot V (2011) Integrative epigenomic mapping defines four main chromatin states in Arabidopsis. EMBO J 30:1928–1938
Tariq M, Paszkowski J (2004) DNA and histone methylation in plants. Trends Genet 20:244–251
Vining KJ, Pomraning KR, Wilhelm LJ, Priest HD, Pellegrini M, Mockler TC, Freitag M, Strauss SH (2012) Dynamic DNA cytosine methylation in the Populus trichocarpa genome: tissuelevel variation and relationship to gene expression. BMC Genomics 13:27
Zhang J, Movahedi A, Wang X, Wu X, Yin T, Zhuge Q (2015) Molecular structure, chemical synthesis, and antibacterial activity of ABPdHC-cecropin A from drury (Hyphantria cunea) Peptides 68:197–204
Zhang X, Yazaki J, Sundaresan A, Cokus S, Chan SW, Chen H, Henderson IR, Shinn P, Pellegrini M, Jacobsen SE, Ecker JR (2006) Genome-wide high-resolution mapping and functional analysis of DNA methylation in Arabidopsis. Cell 126:1189–1201
Zhu J, Kapoor A, Sridhar VV, Agius F, Zhu JK (2007) The DNA glycosylase/lyase ROS1 functions in pruning DNA methylation patterns in Arabidopsis. Curr Biol 17:54–59
Zhu R, Shevchenko O, Ma C, Maury S, Freitag M, Strauss SH (2013) Poplars with a PtDDM1-RNAi transgene have reduced DNA methylation and show aberrant post-dormancy morphology. Planta 237:1483–1493
Author information
Authors and Affiliations
Corresponding author
Electronic supplementary material
Rights and permissions
About this article
Cite this article
Movahedi, A., Sang, M., Zhang, J. et al. Functional Analyses of PtROS1-RNAi in Poplars and Evaluation of Its Effect on DNA Methylation. J. Plant Biol. 61, 227–240 (2018). https://doi.org/10.1007/s12374-017-0410-7
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s12374-017-0410-7