1 |
Zilberman, D., Gehring, M., Tran, R.K., Ballinger, T., and Henikoff, S. (2007). Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. Nat. Genet. 39, 61-69.
DOI
|
2 |
Lang, Z., Wang, Y., Tang, K., Tang, D., Datsenka, T., Cheng, J., Zhang, Y., Handa, A.K., and Zhu, J.K. (2017). Critical roles of DNA demethylation in the activation of ripening-induced genes and inhibition of ripening-repressed genes in tomato fruit. Proc. Natl. Acad. Sci. U. S. A. 114, E4511-E4519.
|
3 |
Langmead, B. and Salzberg, S.L. (2012). Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357-359.
DOI
|
4 |
Lee, K., Park, O.S., and Seo, P.J. (2017). Arabidopsis ATXR2 deposits H3K36me3 at the promoters of LBD genes to facilitate cellular dedifferentiation. Sci. Signal. 10, eaan0316.
DOI
|
5 |
Zubko, E., Gentry, M., Kunova, A., and Meyer, P. (2012). De novo DNA methylation activity of METHYLTRANSFERASE 1 (MET1) partially restores body methylation in Arabidopsis thaliana. Plant J. 71, 1029-1037.
DOI
|
6 |
Ingouff, M., Selles, B., Michaud, C., Vu, T.M., Berger, F., Schorn, A.J., Autran, D., Van Durme, M., Nowack, M.K., Martienssen, R.A., et al. (2017). Live-cell analysis of DNA methylation during sexual reproduction in Arabidopsis reveals context and sex-specific dynamics controlled by noncanonical RdDM. Genes Dev. 31, 72-83.
DOI
|
7 |
Ishihara, H., Sugimoto, K., Tarr, P.T., Temman, H., Kadokura, S., Inui, Y., Sakamoto, T., Sasaki, T., Aida, M., Suzuki, T., et al. (2019). Primed histone demethylation regulates shoot regenerative competency. Nat. Commun. 10, 1786.
DOI
|
8 |
Ito, T., Nishio, H., Tarutani, Y., Emura, N., Honjo, M.N., Toyoda, A., Fujiyama, A., Kakutani, T., and Kudoh, H. (2019). Seasonal stability and dynamics of DNA methylation in plants in a natural environment. Genes 10, 544.
DOI
|
9 |
Johnson, L.M., Bostick, M., Zhang, X., Kraft, E., Henderson, I., Callis, J., and Jacobsen, S.E. (2007). The SRA methyl-cytosine-binding domain links DNA and histone methylation. Curr. Biol. 17, 379-384.
DOI
|
10 |
Kareem, A., Durgaprasad, K., Sugimoto, K., Du, Y., Pulianmackal, A.J., Trivedi, Z.B., Abhayadev, P.V., Pinon, V., Meyerowitz, E.M., Scheres, B., et al. (2015). PLETHORA genes control regeneration by a two-step mechanism. Curr. Biol. 25, 1017-1030.
DOI
|
11 |
Ramirez, F., Dundar, F., Diehl, S., Gruning, B.A., and Manke, T. (2014). deepTools: a flexible platform for exploring deep-sequencing data. Nucleic Acids Res. 42(Web Server issue), W187-W191.
DOI
|
12 |
Lee, K. and Seo, P.J. (2018). Dynamic epigenetic changes during plant regeneration. Trends Plant Sci. 23, 235-247.
DOI
|
13 |
Shim, S., Lee, H.G., Park, O.S., Shin, H., Lee, K., Lee, H., Huh, J.H., and Seo, P.J. (2021). Dynamic changes in DNA methylation occur in TE regions and affect cell proliferation during leaf-to-callus transition in Arabidopsis. Epigenetics 2021 Jan 15 [Epub]. https://doi.org/10.1080/15592294.2021.1872927
DOI
|
14 |
Quinlan, A.R. and Hall, I.M. (2010). BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841-842.
DOI
|
15 |
Skoog, F. and Miller, C.O. (1957). Chemical regulation of growth and organ formation in plant tissues cultured in vitro. Symp. Soc. Exp. Biol. 11, 118-130.
|
16 |
Kim, M.J., Lee, H.J., Choi, M.Y., Kang, S.S., Kim, Y.S., Shin, J.K., and Choi, W.S. (2021). UHRF1 induces methylation of the TXNIP promoter and downregulates gene expression in cervical cancer. Mol. Cells 44, 146-159.
DOI
|
17 |
Lin, C., Yang, H., Guo, H., Mockler, T., Chen, J., and Cashmore, A.R. (1998). Enhancement of blue-light sensitivity of Arabidopsis seedlings by a blue light receptor cryptochrome 2. Proc. Natl. Acad. Sci. U. S. A. 95, 2686-2690.
DOI
|
18 |
Koornneef, M., Hanhart, C.J., and van der Veen, J.H. (1991). A genetic and physiological analysis of late flowering mutants in Arabidopsis thaliana. Mol. Gen. Genet. 229, 57-66.
DOI
|
19 |
Koornneef, M., Rolff, E., and Spruit, C.J.P. (1980). Genetic control of light-inhibited hypocotyl elongation in Arabidopsis thaliana (L.) Heynh. Z. Pflanzenphysiol. 100, 147-160.
DOI
|
20 |
Gaillochet, C. and Lohmann, J.U. (2015). The never-ending story: from pluripotency to plant developmental plasticity. Development 142, 2237-2249.
DOI
|
21 |
Cao, X. and Jacobsen, S.E. (2002b). Locus-specific control of asymmetric and CpNpG methylation by the DRM and CMT3 methyltransferase genes. Proc. Natl. Acad. Sci. U. S. A. 99(Suppl 4), 16491-16498.
DOI
|
22 |
Chen, M., Ha, M., Lackey, E., Wang, J., and Chen, Z.J. (2008). RNAi of met1 reduces DNA methylation and induces genome-specific changes in gene expression and centromeric small RNA accumulation in Arabidopsis allopolyploids. Genetics 178, 1845-1858.
DOI
|
23 |
Dubrovsky, J.G., Doerner, P.W., Colon-Carmona, A., and Rost, T.L. (2000). Pericycle cell proliferation and lateral root initiation in Arabidopsis. Plant Physiol. 124, 1648-1657.
DOI
|
24 |
Fan, M., Xu, C., Xu, K., and Hu, Y. (2012). LATERAL ORGAN BOUNDARIES DOMAIN transcription factors direct callus formation in Arabidopsis regeneration. Cell Res. 22, 1169-1180.
DOI
|
25 |
Fujita, N., Watanabe, S., Ichimura, T., Ohkuma, Y., Chiba, T., Saya, H., and Nakao, M. (2003). MCAF mediates MBD1-dependent transcriptional repression. Mol. Cell. Biol. 23, 2834-2843.
DOI
|
26 |
Stassen, J.H.M., Lopez, A., Jain, R., Pascual-Pardo, D., Luna, E., Smith, L.M., and Ton, J. (2018). The relationship between transgenerational acquired resistance and global DNA methylation in Arabidopsis. Sci. Rep. 8, 14761.
DOI
|
27 |
Sugimoto, K., Jiao, Y., and Meyerowitz, E.M. (2010). Arabidopsis regeneration from multiple tissues occurs via a root development pathway. Dev. Cell 18, 463-471.
DOI
|
28 |
Liu, J., Sheng, L., Xu, Y., Li, J., Yang, Z., Huang, H., and Xu, L. (2014). WOX11 and 12 are involved in the first-step cell fate transition during de novo root organogenesis in Arabidopsis. Plant Cell 26, 1081-1093.
DOI
|
29 |
Penterman, J., Zilberman, D., Huh, J.H., Ballinger, T., Henikoff, S., and Fischer, R.L. (2007). DNA demethylation in the Arabidopsis genome. Proc. Natl. Acad. Sci. U. S. A. 104, 6752-6757.
DOI
|
30 |
Saze, H., Scheid, O., and Paszkowski, J. (2003). Maintenance of CpG methylation is essential for epigenetic inheritance during plant gametogenesis. Nat. Genet. 34, 65-69.
DOI
|
31 |
Usadel, B., Poree, F., Nagel, A., Lohse, M., Czedik-Eysenberg, A., and Stitt, M. (2009). A guide to using MapMan to visualize and compare Omics data in plants: a case study in the crop species, Maize. Plant Cell Environ. 32, 1211-1129.
DOI
|
32 |
Waterfield, M., Khan, I.S., Cortez, J.T., Fan, U., Metzger, T., Greer, A., Fasano, K., Martinez-Llordella, M., Pollack, J.L., Erle, D.J., et al. (2014). The transcriptional regulator Aire co-opts the repressive ATF7ip-MBD1 complex for induction of immune tolerance. Nat. Immunol. 15, 258-265.
DOI
|
33 |
Smallwood, S.A., Lee, H.J., Angermueller, C., Krueger, F., Saadeh, H., Peat, J., Andrews, S.R., Stegle, O., Reik, W., and Kelsey, G. (2014). Single-cell genome-wide bisulfite sequencing for assessing epigenetic heterogeneity. Nat. Methods 11, 817-820.
DOI
|
34 |
Ikeuchi, M., Ogawa, Y., Iwase, A., and Sugimoto, K. (2016). Plant regeneration: cellular origins and molecular mechanisms. Development 143, 1442-1451.
DOI
|
35 |
Kim, J., Yang, W., Forner, J., Lohmann, J.U., Noh, B., and Noh, Y. (2018). Epigenetic reprogramming by histone acetyltransferase HAG1/AtGCN5 is required for pluripotency acquisition in Arabidopsis. EMBO J. 37, e98726.
|
36 |
Fukushige, S., Kondo, E., Gu, Z., Suzuki, H., and Horii, A. (2006). RET finger protein enhances MBD2- and MBD4-dependent transcriptional repression. Biochem. Biophys. Res. Commun. 351, 85-92.
DOI
|
37 |
Gangappa, S.N. and Botto, J.F. (2016). The multifaceted roles of HY5 in plant growth and development. Mol. Plant 9, 1353-1365.
DOI
|
38 |
Gaspar, J.M. and Hart, R.P. (2017). DMRfinder: efficiently identifying differentially methylated regions from MethylC-seq data. BMC Bioinformatics 18, 528.
DOI
|
39 |
He, C., Chen, X., Huang, H., and Xu, L. (2012). Reprogramming of H3K27me3 is critical for acquisition of pluripotency from cultured Arabidopsis tissues. PLoS Genet. 8, e1002911.
DOI
|
40 |
Krueger, F. and Andrews, S.R. (2011). Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics 27, 1571-1572.
DOI
|
41 |
Lee, K., Park, O.S., and Seo, P.J. (2016). RNA-seq analysis of the Arabidopsis transcriptome in pluripotent calli. Mol. Cells 39, 484-494.
DOI
|
42 |
Obayashi, T., Aoki, Y., Tadaka, S., Kagaya, Y., and Kinoshita, K. (2018). ATTED-II in 2018: a plant coexpression database based on investigation of the statistical property of the mutual rank index. Plant Cell Physiol. 59, e3.
DOI
|
43 |
Nameth, B., Dinka, S.J., Chatfield, S.P., Morris, A., English, J., Lewis, D., Oro, R., and Raizada, M.N. (2013). The shoot regeneration capacity of excised Arabidopsis cotyledons is established during the initial hours after injury and is modulated by a complex genetic network of light signalling. Plant Cell Environ. 36, 68-86.
DOI
|
44 |
Li, W., Liu, H., Cheng, Z.J., Su, Y.H., Han, H.N., Zhang, Y., and Zhang, X.S. (2011). DNA methylation and histone modifications regulate de novo shoot regeneration in Arabidopsis by modulating WUSCHEL expression and auxin signaling. PLoS Genet. 7, e1002243.
DOI
|
45 |
Liang, L., Chang, Y., Lu, J., Wu, X., Liu, Q., Zhang, W., Su, X., and Zhang, B. (2019). Global methylomic and transcriptomic analyses reveal the broad participation of DNA methylation in daily gene expression regulation of Populus trichocarpa. Front. Plant Sci. 10, 243.
DOI
|
46 |
Liu, H., Zhang, H., Dong, Y.X., Hao, Y.J., and Zhang, X.S. (2018). DNA METHYLTRANSFERASE1-mediated shoot regeneration is regulated by cytokinin-induced cell cycle in Arabidopsis. New Phytol. 217, 219-232.
DOI
|
47 |
Atta, R., Laurens, L., Boucheron-Dubuisson, E., Guivarc'h, A., Carnero, E., Giraudat-Pautot, V., Rech, P., and Chriqui, D. (2009). Pluripotency of Arabidopsis xylem pericycle underlies shoot regeneration from root and hypocotyl explants grown in vitro. Plant J. 57, 626-644.
DOI
|
48 |
Vandenbussche, F., Habricot, Y., Condiff, A.S., Maldiney, R., Straeten, D.V.D., and Ahmad, M. (2007). HY5 is a point of convergence between cryptochrome and cytokinin signalling pathways in Arabidopsis thaliana. Plant J. 49, 428-441.
DOI
|
49 |
Jeddeloh, J.A., Bender, J., and Richards, E.J. (1998). The DNA methylation locus DDM1 is required for maintenance of gene silencing in Arabidopsis. Genes Dev. 12, 1714-1725.
DOI
|
50 |
Liu, Z.W., Zhou, J.X., Huang, H.W., Li, Y.Q., Shao, C.R., Li, L., Cai, T., Chen, S., and He, X.J. (2016). Two components of the RNA-directed DNA methylation pathway associate with MORC6 and silence loci targeted by MORC6 in Arabidopsis. PLoS Genet. 12, e1006026.
DOI
|
51 |
Ortega-Galisteo, A.P., Morales-Ruiz, T., Ariza, R.R., and Roldan-Arjona, T. (2008). Arabidopsis DEMETER-LIKE proteins DML2 and DML3 are required for appropriate distribution of DNA methylation marks. Plant Mol. Biol. 67, 671-681.
DOI
|
52 |
Zemach, A. and Grafi, G. (2003). Characterization of Arabidopsis thaliana methyl-CpG-binding domain (MBD) proteins. Plant J. 34, 565-572.
DOI
|
53 |
Bartee, L., Malagnac, F., and Bender, J. (2001). Arabidopsis cmt3 chromomethylase mutations block non-CG methylation and silencing of an endogenous gene. Genes Dev. 15, 1753-1758.
DOI
|
54 |
Bhatia, H., Khemka, N., Jain, M., and Garg, R. (2018). Genome-wide bisulphite-sequencing reveals organ-specific methylation patterns in chickpea. Sci. Rep. 8, 9704.
DOI
|
55 |
Brackertz, M., Boeke, J., Zhang, R., and Renkawitz, R. (2002). Two highly related p66 proteins comprise a new family of potent transcriptional repressors interacting with MBD2 and MBD3. J. Biol. Chem. 277, 40958-40966.
DOI
|
56 |
Yoo, H., Park, K., Lee, J., Lee, S., and Choi, Y. (2021). An optimized method for the construction of a DNA methylome from small quantities of tissue or purified DNA from Arabidopsis embryo. Mol. Cells 44, 602-612.
DOI
|
57 |
Yu, X., Liu, H., Klejnot, J., and Lin, C. (2010). The cryptochrome blue light receptors. Arabidopsis Book 8, e0135.
DOI
|
58 |
Zhang, T.Q., Lian, H., Zhou, C.M., Xu, L., Jiao, Y., and Wang, J.W. (2017). A two-step model for de novo activation of WUSCHEL during plant shoot regeneration. Plant Cell 29, 1073-1087.
DOI
|
59 |
Lindroth, A.M., Cao, X., Jackson, J.P., Zilberman, D., McCallum, C.M., Henikoff, S., and Jacobsen, S.E. (2001). Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation. Science 292, 2077-2080.
DOI
|
60 |
Meng, W.J., Cheng, Z.J., Sang, Y.L., Zhang, M.M., Rong, X.F., Wang, Z.W., Tang, Y.Y., and Zhang, X.S. (2017). Type-B ARABIDOPSIS RESPONSE REGULATORs specify the shoot stem cell niche by dual regulation of WUSCHEL. Plant Cell 29, 1357-1372.
DOI
|
61 |
Zhou, M., Sng, N.J., LeFrois, C.E., Paul, A.L., and Ferl, R.J. (2019). Epigenomics in an extraterrestrial environment: organ-specific alteration of DNA methylation and gene expression elicited by spaceflight in Arabidopsis thaliana. BMC Genomics 20, 205.
DOI
|
62 |
Harris, C.J., Scheibe, M., Wongpalee, S.P., Liu, W., Cornett, E.M., Vaughan, R.M., Li, X., Chen, W., Xue, Y., Zhong, Z., et al. (2018). A DNA methylation reader complex that enhances gene transcription. Science 362, 1182-1186.
DOI
|
63 |
Chen, X., Schonberger, B., Menz, J., and Ludewig, U. (2018). Plasticity of DNA methylation and gene expression under zinc deficiency in Arabidopsis roots. Plant Cell Physiol. 59, 1790-1802.
DOI
|
64 |
Feng, Z., Zhu, J., Du, X., and Cui, X. (2012). Effects of three auxin-inducible LBD members on lateral root formation in Arabidopsis thaliana. Planta 236, 1227-1237.
DOI
|
65 |
Baubec, T., Ivanek, R., Lienert, F., and Schubeler, D. (2013). Methylation-dependent and -independent genomic targeting principles of the MBD protein family. Cell 153, 480-492.
DOI
|
66 |
Cao, X. and Jacobsen, S.E. (2002a). Role of the Arabidopsis DRM methyltransferases in de novo DNA methylation and gene silencing. Curr. Biol. 12, 1138-1144.
DOI
|