[1] Finnegan EJ, Genger RK, Peacock WJ, Dennis ES. 1998. DNA methylation in plants. Annual Review of Plant Physiology and Plant Molecular Biology 49:223−47 doi: 10.1146/annurev.arplant.49.1.223
[2] Zhang X, Yazaki J, Sundaresan A, Cokus S, Chan SWL, et al. 2006. Genome-wide high-resolution mapping and functional analysis of DNA methylation in Arabidopsis. Cell 126:1189−201 doi: 10.1016/j.cell.2006.08.003
[3] Grob S, Schmid MW, Grossniklaus U. 2014. Hi-C analysis in Arabidopsis identifies the KNOT, a structure with similarities to the flamenco locus of Drosophila. Molecular Cell 55:678−93 doi: 10.1016/j.molcel.2014.07.009
[4] Law JA, Jacobsen SE. 2010. Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nature Reviews Genetics 11:204−20 doi: 10.1038/nrg2719
[5] Zhang H, Lang Z, Zhu J. 2018. Dynamics and function of DNA methylation in plants. Nature Reviews Molecular Cell Biology 19:489−506 doi: 10.1038/s41580-018-0016-z
[6] Fujita N, Watanabe S, Ichimura T, Tsuruzoe S, Shinkai Y, et al. 2003. Methyl-CpG binding domain 1 (MBD1) interacts with the Suv39h1-HP1 heterochromatic complex for DNA methylation-based transcriptional repression. Journal of Biological Chemistry 278:24132−38 doi: 10.1074/jbc.M302283200
[7] Grafi G, Zemach A, Pitto L. 2007. Methyl-CpG-binding domain (MBD) proteins in plants. Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression 1769:287−94 doi: 10.1016/j.bbaexp.2007.02.004
[8] Potok ME, Wang Y, Xu L, Zhong Z, Liu W, et al. 2019. Arabidopsis SWR1-associated protein methyl-CpG-binding domain 9 is required for histone H2A.Z deposition. Nature Communications 10:3352 doi: 10.1038/s41467-019-11291-w
[9] Ehrlich KC. 1993. Characterization of DBPm, a plant protein that binds to DNA containing 5-methylcytosine. Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression 1172:108−16 doi: 10.1016/0167-4781(93)90276-j
[10] Springer NM, Kaeppler SM. 2005. Evolutionary divergence of monocot and dicot methyl-CpG-binding domain proteins. Plant Physiology 138:92−104 doi: 10.1104/pp.105.060566
[11] Parida AP, Raghuvanshi U, Pareek A, Singh V, Kumar R, et al. 2018. Genome-wide analysis of genes encoding MBD domain-containing proteins from tomato suggest their role in fruit development and abiotic stress responses. Molecular Biology Reports 45:2653−69 doi: 10.1007/s11033-018-4435-x
[12] Qian Y, Ren Q, Jiang L, Zhang J, Chen C, et al. 2020. Genome-wide analysis of maize MBD gene family and expression profiling under abiotic stress treatment at the seedling stage. Plant Biotechnology Reports 14:323−38 doi: 10.1007/s11816-020-00607-8
[13] Parida AP, Sharma A, Sharma AK. 2017. AtMBD6, a methyl CpG binding domain protein, maintains gene silencing in Arabidopsis by interacting with RNA binding proteins. Journal of Biosciences 42:57−68 doi: 10.1007/s12038-016-9658-1
[14] Lang Z, Lei M, Wang X, Tang K, Miki D, et al. 2015. The methyl-CpG-binding protein MBD7 facilitates active DNA demethylation to limit DNA hyper-methylation and transcriptional gene silencing. Molecular Cell 57:971−83 doi: 10.1016/j.molcel.2015.01.009
[15] Casati P, Stapleton AE, Blum JE, Walbot V. 2006. Genome-wide analysis of high-altitude maize and gene knockdown stocks implicates chromatin remodeling proteins in response to UV-B. The Plant Journal 46:613−27 doi: 10.1111/j.1365-313X.2006.02721.x
[16] Questa JI, Rius SP, Casadevall R, Casati P. 2016. ZmMBD101 is a DNA-binding protein that maintains Mutator elements chromatin in a repressive state in maize. Plant, Cell & Environment 39:174−84 doi: 10.1111/pce.12604
[17] Fang C, Chen W, Li C, Jian X, Li Y, et al. 2016. Methyl-CpG binding domain protein acts to regulate the repair of cyclobutane pyrimidine dimers on rice DNA. Scientific Reports 6:34569 doi: 10.1038/srep34569
[18] Zhou Y, Cao H, Yue C, Wang L, Hao X, et al. 2015. Changes of DNA methylation levels and patterns in tea plant (Camellia sinensis) during cold acclimation. Acta Agronomica Sinica 41:1047−55 doi: 10.3724/SP.J.1006.2015.01047
[19] Zhu C, Zhang S, Zhou C, Chen L, Fu H, et al. 2020. Genome-wide investigation and transcriptional analysis of cytosine-5 DNA methyltransferase and DNA demethylase gene families in tea plant (Camellia sinensis) under abiotic stress and withering processing. PeerJ 8:e8432 doi: 10.7717/peerj.8432
[20] Hao X, Yang Y, Yue C, Wang L, Horvath DP, et al. 2017. Comprehensive transcriptome analyses reveal differential gene expression profiles of Camellia sinensis axillary buds at para-, endo-, ecodormancy and bud flush stages. Front Plant Sci 8:553 doi: 10.3389/fpls.2017.00553
[21] Wang X, Feng H, Chang Y, Ma C, Wang L, et al. 2020. Population sequencing enhances understanding of tea plant evolution. Nature Communications 11:4447 doi: 10.1038/s41467-020-18228-8
[22] Thompson JD, Higgins DG, Gibson TJ. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research 22:4673−80 doi: 10.1093/nar/22.22.4673
[23] Chen C, Chen H, Zhang Y, Thomas HR, Frank MH, et al. 2020. TBtools: An integrative toolkit developed for interactive analyses of big biological data. Molecular Plant 13:1194−202 doi: 10.1016/j.molp.2020.06.009
[24] Hu B, Jin J, Guo A, Zhang H, Luo J, et al. 2015. GSDS 2.0: an upgraded gene feature visualization server. Bioinformatics 31:1296−97 doi: 10.1093/bioinformatics/btu817
[25] Wang Y, Qian W, Li N, Hao X, Wang L, et al. 2016. Metabolic changes of caffeine in tea plant (Camellia sinensis (L.) O. Kuntze) as defense response to colletotrichum fructicola. Journal of Agricultural and Food Chemistry 64:6685−93 doi: 10.1021/acs.jafc.6b02044
[26] Chen Y, Jie S, Yang C, Liu Z. 2017. Active and efficient Co-N/C catalysts derived from cobalt porphyrin for selective oxidation of alkylaromatics. Applied Surface Science 419:98−106 doi: 10.1016/j.apsusc.2017.04.246
[27] Hao X, Horvath DP, Chao WS, Yang Y, Wang X, et al. 2014. Identification and evaluation of reliable reference genes for quantitative real-time PCR analysis in tea plant (Camellia sinensis (L.) O. Kuntze). International Journal of Molecular Sciences 15:22155−72 doi: 10.3390/ijms151222155
[28] Livak KJ, Schmittgen TD. 2001. Analysis of relative gene expression data using real-time quantitative PCR and the 2−ΔΔCT method. Methods 25:402−8 doi: 10.1006/meth.2001.1262
[29] Zemach A, Grafi G. 2003. Characterization of Arabidopsis thaliana methyl-CpG-binding domain (MBD) proteins. The Plant Journal 34:565−72 doi: 10.1046/j.1365-313x.2003.01756.x
[30] Kumar R, Agarwal P, Tyagi AK, Sharma AK. 2012. Genome-wide investigation and expression analysis suggest diverse roles of auxin-responsive GH3 genes during development and response to different stimuli in tomato (Solanum lycopersicum). Molecular Genetics and Genomics 287:221−35 doi: 10.1007/s00438-011-0672-6
[31] Li Y, Deng H, Miao M, Li H, Huang S, et al. 2016. Tomato MBD5, a methyl CpG binding domain protein, physically interacting with UV-damaged DNA binding protein-1, functions in multiple processes. New Phytologist 210:208−26 doi: 10.1111/nph.13745
[32] Stangeland B, Maryann Rosenhave E, Winge P, Berg A, Amundsen SS, et al. 2009. AtMBD8 is involved in control of flowering time in the C24 ecotype of Arabidopsis thaliana. Physiologia Plantarum 136:110−26 doi: 10.1111/j.1399-3054.2009.01218.x
[33] Dowen RH, Pelizzola M, Schmitz RJ, Lister R, Dowen JM, et al. 2012. Widespread dynamic DNA methylation in response to biotic stress. PNAS 109:E2183−E2191 doi: 10.1073/pnas.1209329109
[34] Le TN, Schumann U, Smith NA, Tiwari S, Au PC, et al. 2014. DNA demethylases target promoter transposable elements to positively regulate stress responsive genes in Arabidopsis. Genome Biology 15:458 doi: 10.1186/s13059-014-0458-3
[35] Yu X, Zhang W, Zhang Y, Zhang X, Lang D, et al. 2019. The roles of methyl jasmonate to stress in plants. Functional Plant Biology 46:197−212 doi: 10.1071/fp18106
[36] Agius A, Kapoor A, Zhu J. 2006. Role of the Arabidopsis DNA glycosylase/lyase ROS1 in active DNA demethylation. PNAS 103:11796−801 doi: 10.1073/pnas.0603563103
[37] Yang R, Hong Y, Ren Z, Tang K, Zhang H, et al. 2019. A role for PICKLE in the regulation of cold and salt stress tolerance in Arabidopsis. Frontiers in Plant Science 10:900 doi: 10.3389/fpls.2019.00900
[38] Kwon CS, Lee D, Choi G, Chung WI. 2009. Histone occupancy-dependent and -independent removal of H3K27 trimethylation at cold-responsive genes in Arabidopsis. The Plant Journal 60:112−21 doi: 10.1111/j.1365-313X.2009.03938.x
[39] Kapazoglou A, Drosou V, Argiriou A, Tsaftaris AS. 2013. The study of a barley epigenetic regulator, HvDME, in seed development and under drought. BMC Plant Biology 13:172 doi: 10.1186/1471-2229-13-172
[40] Kawakatsu T, Nery JR, Castanon R, Ecker JR. 2017. Dynamic DNA methylation reconfiguration during seed development and germination. Genome Biology 18:171 doi: 10.1186/s13059-017-1251-x
[41] Yang H, Chang F, You C, Cui J, Zhu G, et al. 2015. Whole-genome DNA methylation patterns and complex associations with gene structure and expression during flower development in Arabidopsis. The Plant Journal 81:268−81 doi: 10.1111/tpj.12726
[42] Santamaría ME, Hasbún R, Valera MJ, Meijón M, Valledor L, et al. 2009. Acetylated H4 histone and genomic DNA methylation patterns during bud set and bud burst in Castanea sativa. Journal of Plant Physiology 166:1360−69 doi: 10.1016/j.jplph.2009.02.014
[43] Conde D, Le Gac AL, Perales M, Dervinis C, Kirst M, et al. 2017. Chilling-responsive DEMETER-LIKE DNA demethylase mediates in poplar bud break. Plant, Cell & Environment 40:2236−49 doi: 10.1111/pce.13019
[44] Yang Q, Yang B, Li J, Wang Y, Tao R, et al. 2020. ABA-responsive ABRE-BINDING FACTOR3 activates DAM3 expression to promote bud dormancy in Asian pear. Plant, Cell & Environment 43:1360−75 doi: 10.1111/pce.13744