Molecules and Cells

Korean Society for Molecular and Cellular Biology (한국분자세포생물학회)
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MET1-Dependent DNA Methylation Represses Light Signaling and Influences Plant Regeneration in Arabidopsis

  • Shim, Sangrea (Department of Chemistry, Seoul National University) ;
  • Lee, Hong Gil (Plant Genomics and Breeding Institute, Seoul National University) ;
  • Seo, Pil Joon (Department of Chemistry, Seoul National University)
  • Received : 2021.06.18
  • Accepted : 2021.08.24
  • Published : 2021.10.31
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Abstract

Plant somatic cells can be reprogrammed into a pluripotent cell mass, called callus, which can be subsequently used for de novo shoot regeneration through a two-step in vitro tissue culture method. MET1-dependent CG methylation has been implicated in plant regeneration in Arabidopsis, because the met1-3 mutant exhibits increased shoot regeneration compared with the wild-type. To understand the role of MET1 in de novo shoot regeneration, we compared the genome-wide DNA methylomes and transcriptomes of wildtype and met1-3 callus and leaf. The CG methylation patterns were largely unchanged during leaf-to-callus transition, suggesting that the altered regeneration phenotype of met1-3 was caused by the constitutively hypomethylated genes, independent of the tissue type. In particular, MET1-dependent CG methylation was observed at the blue light receptor genes, CRYPTOCHROME 1 (CRY1) and CRY2, which reduced their expression. Coexpression network analysis revealed that the CRY1 gene was closely linked to cytokinin signaling genes. Consistently, functional enrichment analysis of differentially expressed genes in met1-3 showed that gene ontology terms related to light and hormone signaling were overrepresented. Overall, our findings indicate that MET1-dependent repression of light and cytokinin signaling influences plant regeneration capacity and shoot identity establishment.

Keywords

Acknowledgement

This work was supported by the Basic Science Research (NRF-2019R1I1A1A01061376 to S.S.; NRF-2019R1A2C2006915 to P.J.S.) and Basic Research Laboratory (NRF-2020R1A4A2002901 to P.J.S.) programs provided by the National Research Foundation of Korea, by the National Research Foundation of Korea, and by the Creative-Pioneering Researchers Program through Seoul National University (0409-20200281 to P.J.S.).

References

  1. 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. https://doi.org/10.1111/j.1365-313X.2008.03715.x
  2. 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. https://doi.org/10.1101/gad.905701
  3. 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. https://doi.org/10.1016/j.cell.2013.03.011
  4. 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. https://doi.org/10.1038/s41598-018-27979-w
  5. 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. https://doi.org/10.1074/jbc.M207467200
  6. 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. https://doi.org/10.1016/S0960-9822(02)00925-9
  7. 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. https://doi.org/10.1073/pnas.162371599
  8. 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. https://doi.org/10.1534/genetics.107.086272
  9. 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. https://doi.org/10.1093/pcp/pcy100
  10. 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. https://doi.org/10.1104/pp.124.4.1648
  11. 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. https://doi.org/10.1038/cr.2012.63
  12. 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. https://doi.org/10.1007/s00425-012-1673-3
  13. 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. https://doi.org/10.1128/MCB.23.8.2834-2843.2003
  14. 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. https://doi.org/10.1016/j.bbrc.2006.10.005
  15. Gaillochet, C. and Lohmann, J.U. (2015). The never-ending story: from pluripotency to plant developmental plasticity. Development 142, 2237-2249. https://doi.org/10.1242/dev.117614
  16. Gangappa, S.N. and Botto, J.F. (2016). The multifaceted roles of HY5 in plant growth and development. Mol. Plant 9, 1353-1365. https://doi.org/10.1016/j.molp.2016.07.002
  17. Gaspar, J.M. and Hart, R.P. (2017). DMRfinder: efficiently identifying differentially methylated regions from MethylC-seq data. BMC Bioinformatics 18, 528. https://doi.org/10.1186/s12859-017-1909-0
  18. 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. https://doi.org/10.1126/science.aar7854
  19. 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. https://doi.org/10.1371/journal.pgen.1002911
  20. Ikeuchi, M., Ogawa, Y., Iwase, A., and Sugimoto, K. (2016). Plant regeneration: cellular origins and molecular mechanisms. Development 143, 1442-1451. https://doi.org/10.1242/dev.134668
  21. 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. https://doi.org/10.1101/gad.289397.116
  22. 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. https://doi.org/10.1038/s41467-019-09386-5
  23. 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. https://doi.org/10.3390/genes10070544
  24. 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. https://doi.org/10.1101/gad.12.11.1714
  25. 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. https://doi.org/10.1016/j.cub.2007.01.009
  26. 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. https://doi.org/10.1016/j.cub.2015.02.022
  27. 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.
  28. 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. https://doi.org/10.14348/molcells.2021.0001
  29. 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. https://doi.org/10.1007/BF00264213
  30. 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. https://doi.org/10.1016/S0044-328X(80)80208-X
  31. Krueger, F. and Andrews, S.R. (2011). Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics 27, 1571-1572. https://doi.org/10.1093/bioinformatics/btr167
  32. 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.
  33. Langmead, B. and Salzberg, S.L. (2012). Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357-359. https://doi.org/10.1038/nmeth.1923
  34. 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. https://doi.org/10.14348/MOLCELLS.2016.0049
  35. 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. https://doi.org/10.1126/scisignal.aan0316
  36. Lee, K. and Seo, P.J. (2018). Dynamic epigenetic changes during plant regeneration. Trends Plant Sci. 23, 235-247. https://doi.org/10.1016/j.tplants.2017.11.009
  37. 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. https://doi.org/10.1371/journal.pgen.1002243
  38. 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. https://doi.org/10.3389/fpls.2019.00243
  39. 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. https://doi.org/10.1073/pnas.95.5.2686
  40. 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. https://doi.org/10.1126/science.1059745
  41. 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. https://doi.org/10.1111/nph.14814
  42. 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. https://doi.org/10.1105/tpc.114.122887
  43. 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. https://doi.org/10.1371/journal.pgen.1006026
  44. 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. https://doi.org/10.1105/tpc.16.00640
  45. 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. https://doi.org/10.1111/j.1365-3040.2012.02554.x
  46. 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. https://doi.org/10.1093/pcp/pcx191
  47. 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. https://doi.org/10.1007/s11103-008-9346-0
  48. 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. https://doi.org/10.1073/pnas.0701861104
  49. Quinlan, A.R. and Hall, I.M. (2010). BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841-842. https://doi.org/10.1093/bioinformatics/btq033
  50. 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. https://doi.org/10.1093/nar/gku365
  51. 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. https://doi.org/10.1038/ng1138
  52. 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
  53. 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.
  54. 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. https://doi.org/10.1038/nmeth.3035
  55. 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. https://doi.org/10.1038/s41598-018-32448-5
  56. 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. https://doi.org/10.1016/j.devcel.2010.02.004
  57. 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. https://doi.org/10.1111/j.1365-3040.2009.01978.x
  58. 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. https://doi.org/10.1111/j.1365-313X.2006.02973.x
  59. 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. https://doi.org/10.1038/ni.2820
  60. 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. https://doi.org/10.14348/molcells.2021.0084
  61. Yu, X., Liu, H., Klejnot, J., and Lin, C. (2010). The cryptochrome blue light receptors. Arabidopsis Book 8, e0135. https://doi.org/10.1199/tab.0135
  62. Zemach, A. and Grafi, G. (2003). Characterization of Arabidopsis thaliana methyl-CpG-binding domain (MBD) proteins. Plant J. 34, 565-572. https://doi.org/10.1046/j.1365-313X.2003.01756.x
  63. 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. https://doi.org/10.1105/tpc.16.00863
  64. 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. https://doi.org/10.1186/s12864-019-5554-z
  65. 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. https://doi.org/10.1038/ng1929
  66. 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. https://doi.org/10.1111/j.1365-313X.2012.05051.x