9.9
CiteScore
7.1
Impact Factor
Volume 52 Issue 2
Feb.  2025
Turn off MathJax
Article Contents
Article Navigation >  Journal of Genetics and Genomics  > 2025  >  52(2): 129-144

Epigenetic control of plant abiotic stress responses

doi: 10.1016/j.jgg.2024.09.008
  •  

    a. Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China;

  •  

    b. University of Chinese Academy of Sciences, Beijing 100049, China;

  •  

    c. Ministry of Education Key Laboratory of Plant Development and Environmental Adaption Biology, School of Life Sciences, Shandong University, Qingdao, Shandong 266237, China;

  •  

    d. Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Republic of Singapore

  • Received Date: 2024-08-15
  • Accepted Date: 2024-09-16
  • Rev Recd Date: 2024-09-14
    • Available Online: 2025-07-11
  • Publish Date: 2024-09-23
    Abstract
  • On top of genetic information, organisms have evolved complex and sophisticated epigenetic regulation to adjust gene expression in response to developmental and environmental signals. Key epigenetic mechanisms include DNA methylation, histone modifications and variants, chromatin remodeling, and chemical modifications of RNAs. Epigenetic control of environmental responses is particularly important for plants, which are sessile and unable to move away from adverse environments. Besides enabling plants to rapidly respond to environmental stresses, some stress-induced epigenetic changes can be maintained, providing plants with a pre-adapted state to recurring stresses. Understanding these epigenetic mechanisms offers valuable insights for developing crop varieties with enhanced stress tolerance. Here, we focus on abiotic stresses and summarize recent progress in characterizing stress-induced epigenetic changes and their regulatory mechanisms and roles in plant abiotic stress resistance.
    • FullText(HTML)
  • loading
    • References(230)
  • Amara, U., Hu, J., Park, S.J.,Kang, H., 2024. ECT12, an YTH-domain protein, is a potential mRNA m6A reader that affects abiotic stress responses by modulating mRNA stability in Arabidopsis. Plant Physiol. Biochem. 206, 108255.
    Amara, U., Shoaib, Y.,Kang, H., 2022. ALKBH9C, a potential RNA m6A demethylase, regulates the response of Arabidopsis to abiotic stresses and abscisic acid. Plant Cell Environ. 45, 3566-3581.
    Anderson, S.J., Kramer, M.C., Gosai, S.J., Yu, X., Vandivier, L.E., Nelson, A.D.L., Anderson, Z.D., Beilstein, M.A., Fray, R.G., Lyons, E., et al., 2018. N6-methyladenosine inhibits local ribonucleolytic cleavage to stabilize mRNAs in Arabidopsis. Cell Rep. 25, 1146-1157.
    Baek, D., Jiang, J., Chung, J.S., Wang, B., Chen, J., Xin, Z.,Shi, H., 2010. 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, 149-161.
    Barragan-Rosillo, A.C., Peralta-Alvarez, C.A., Ojeda-Rivera, J.O., Arzate-Mejia, R.G., Recillas-Targa, F.,Herrera-Estrella, L., 2021. Genome accessibility dynamics in response to phosphate limitation is controlled by the PHR1 family of transcription factors in Arabidopsis. Proc. Natl. Acad. Sci. U.S.A. 118, e2107558118.
    Bonev, B.,Cavalli, G., 2016. Organization and function of the 3D genome. Nat. Rev. Genet. 17, 661-678.
    Borg, M., Jiang, D.,Berger, F., 2021. Histone variants take center stage in shaping the epigenome. Curr. Opin. Plant Biol. 61, 101991.
    Brzezinka, K., Altmann, S.,Baurle, I., 2019. BRUSHY1/TONSOKU/MGOUN3 is required for heat stress memory. Plant Cell Environ. 42, 771-781.
    Brzezinka, K., Altmann, S., Czesnick, H., Nicolas, P., Gorka, M., Benke, E., Kabelitz, T., Jahne, F., Graf, A., Kappel, C., et al., 2016. Arabidopsis FORGETTER1 mediates stress-induced chromatin memory through nucleosome remodeling. Elife 5, e17061.
    Buszewicz, D., Archacki, R., Palusinski, A., Kotlinski, M., Fogtman, A., Iwanicka-Nowicka, R., Sosnowska, K., Kucinski, J., Pupel, P., Oledzki, J., et al., 2016. HD2C histone deacetylase and a SWI/SNF chromatin remodelling complex interact and both are involved in mediating the heat stress response in Arabidopsis. Plant Cell Environ. 39, 2108-2122.
    Cai, J., Hu, J., Xu, T.,Kang, H., 2024. FIONA1-mediated mRNA m6A methylation regulates the response of Arabidopsis to salt stress. Plant Cell Environ. 47, 900-912.
    Cappannini, A., Ray, A., Purta, E., Mukherjee, S., Boccaletto, P., Moafinejad, S.N., Lechner, A., Barchet, C., Klaholz, Bruno P., Stefaniak, F., et al., 2023. MODOMICS: a database of RNA modifications and related information. 2023 update. Nucleic Acids Res. 52, D239-D244.
    Cavrak, V.V., Lettner, N., Jamge, S., Kosarewicz, A., Bayer, L.M.,Mittelsten Scheid, O., 2014. How a retrotransposon exploits the plant's heat stress response for its activation. PLoS Genet. 10, e1004115.
    Charng, Y.Y., Liu, H.C., Liu, N.Y., Hsu, F.C.,Ko, S.S., 2006. Arabidopsis Hsa32, a novel heat shock protein, is essential for acquired thermotolerance during long recovery after acclimation. Plant Physiol. 140, 1297-1305.
    Chen, C.Y., Wu, K.,Schmidt, W., 2015. The histone deacetylase HDA19 controls root cell elongation and modulates a subset of phosphate starvation responses in Arabidopsis. Sci. Rep. 5, 15708.
    Chen, K., Du, K., Shi, Y., Yin, L., Shen, W.-H., Yu, Y., Liu, B.,Dong, A., 2021. H3K36 methyltransferase SDG708 enhances drought tolerance by promoting abscisic acid biosynthesis in rice. New Phytol. 230, 1967-1984.
    Cheng, Q., Wang, P., Wu, G., Wang, Y., Tan, J., Li, C., Zhang, X., Liu, S., Huang, S., Huang, T., et al., 2021. Coordination of m6A mRNA methylation and gene transcriptome in rice response to cadmium stress. Rice 14, 62.
    Cheng, X., Zhang, S., Tao, W., Zhang, X., Liu, J., Sun, J., Zhang, H., Pu, L., Huang, R.,Chen, T., 2018. INDETERMINATE SPIKELET1 recruits histone deacetylase and a transcriptional repression complex to regulate rice salt tolerance. Plant Physiol. 178, 824-837.
    Chinnusamy, V., Ohta, M., Kanrar, S., Lee, B.H., Hong, X., Agarwal, M.,Zhu, J.K., 2003. ICE1: a regulator of cold-induced transcriptome and freezing tolerance in Arabidopsis. Genes Dev. 17, 1043-1054.
    Chorostecki, U., Bologna, N.G.,Ariel, F., 2023. The plant noncoding transcriptome: a versatile environmental sensor. EMBO J. 42, e114400.
    Chu, S., Zhang, X., Yu, K., Lv, L., Sun, C., Liu, X., Zhang, J., Jiao, Y.,Zhang, D., 2020. Genome-wide analysis reveals dynamic epigenomic differences in soybean response to low-phosphorus stress. Int. J. Mol. Sci. 21, 6817.
    Chwialkowska, K., Nowakowska, U., Mroziewicz, A., Szarejko, I.,Kwasniewski, M., 2016. Water-deficiency conditions differently modulate the methylome of roots and leaves in barley (Hordeum vulgare L.). J. Exp. Bot. 67, 1109-1121.
    Clapier, C.R., Iwasa, J., Cairns, B.R.,Peterson, C.L., 2017. Mechanisms of action and regulation of ATP-dependent chromatin-remodelling complexes. Nat. Rev. Mol. Cell Biol. 18, 407-422.
    Coleman-Derr, D.,Zilberman, D., 2012. Deposition of histone variant H2A.Z within gene bodies regulates responsive genes. PLoS Genet.8, e1002988.
    Cong, W., Miao, Y., Xu, L., Zhang, Y., Yuan, C., Wang, J., Zhuang, T., Lin, X., Jiang, L., Wang, N., et al., 2019. Transgenerational memory of gene expression changes induced by heavy metal stress in rice (Oryza sativa L.). BMC Plant Biol. 19, 282.
    Crisp, P.A., Ganguly, D., Eichten, S.R., Borevitz, J.O.,Pogson, B.J., 2016. Reconsidering plant memory: intersections between stress recovery, RNA turnover, and epigenetics. Sci. Adv. 2, e1501340.
    Cui, X., Zheng, Y., Lu, Y., Issakidis-Bourguet, E.,Zhou, D.X., 2021. Metabolic control of histone demethylase activity involved in plant response to high temperature. Plant Physiol. 185, 1813-1828.
    Ding, Y., Avramova, Z.,Fromm, M., 2011. The Arabidopsis trithorax-like factor ATX1 functions in dehydration stress responses via ABA-dependent and ABA-independent pathways. Plant J. 66, 735-744.
    Ding, Y., Fromm, M.,Avramova, Z., 2012. Multiple exposures to drought 'train' transcriptional responses in Arabidopsis. Nat. Commun. 3, 740.
    Ding, Y., Shi, Y.,Yang, S., 2019. Advances and challenges in uncovering cold tolerance regulatory mechanisms in plants. New Phytol. 222, 1690-1704.
    Domb, K., Wang, N., Hummel, G.,Liu, C., 2022. Spatial features and functional implications of plant 3D genome organization. Annu. Rev. Plant Biol. 73, 173-200.
    Duan, H., Li, J., Zhu, Y., Jia, W., Wang, H., Jiang, L.,Zhou, Y., 2020. Responsive changes of DNA methylation in wheat (Triticum aestivum) under water deficit. Sci. Rep. 10, 7938.
    Fan, S.K., Ye, J.Y., Zhang, L.L., Chen, H.S., Zhang, H.H., Zhu, Y.X., Liu, X.X.,Jin, C.W., 2020. Inhibition of DNA demethylation enhances plant tolerance to cadmium toxicity by improving iron nutrition. Plant Cell Environ. 43, 275-291.
    Fan, W., Wang, L., Lei, Z., Li, H., Chu, J., Yan, M., Wang, Y., Wang, H., Yang, J.,Cho, J., 2023. m6A RNA demethylase AtALKBH9B promotes mobilization of a heat-activated long terminal repeat retrotransposon in Arabidopsis. Sci. Adv. 9, eadf3292.
    Feng, D., Wang, R., Sun, X., Liu, L.n., Liu, P., Tang, J., Zhang, C.,Liu, H., 2023. Heavy metal stress in plants: ways to alleviate with exogenous substances. Sci. Total Environ. 897, 165397.
    Feng, P., Sun, X., Liu, X., Li, Y., Sun, Q., Lu, H., Li, M., Ding, X.,Dong, Y., 2022. Epigenetic regulation of plant tolerance to salt stress by histone acetyltransferase GsMYST1 from wild soybean. Front. Plant Sci. 13, 860056.
    Feng, S.J., Liu, X.S., Tao, H., Tan, S.K., Chu, S.S., Oono, Y., Zhang, X.D., Chen, J.,Yang, Z.M., 2016a. Variation of DNA methylation patterns associated with gene expression in rice (Oryza sativa) exposed to cadmium. Plant Cell Environ. 39, 2629-2649.
    Feng, X.J., Li, J.R., Qi, S.L., Lin, Q.F., Jin, J.B.,Hua, X.J., 2016b. Light affects salt stress-induced transcriptional memory of P5CS1 in Arabidopsis. Proc. Natl. Acad. Sci. U.S.A. 113, E8335-E8343.
    Foroozani, M., Holder, D.H.,Deal, R.B., 2022. Histone variants in the specialization of plant chromatin. Annu. Rev. Plant Biol. 73, 149-172.
    Francis, B., Aravindakumar, C.T., Brewer, P.B.,Simon, S., 2023. Plant nutrient stress adaptation: a prospect for fertilizer limited agriculture. Environ. Exp. Bot. 213, 105431.
    Friedrich, T., Oberkofler, V., Trindade, I., Altmann, S., Brzezinka, K., Lamke, J., Gorka, M., Kappel, C., Sokolowska, E., Skirycz, A., et al., 2021. Heteromeric HSFA2/HSFA3 complexes drive transcriptional memory after heat stress in Arabidopsis. Nat. Commun. 12, 3426.
    Fu, Y.L., Zhang, G.B., Lv, X.F., Guan, Y., Yi, H.Y.,Gong, J.M., 2013. Arabidopsis histone methylase CAU1/PRMT5/SKB1 acts as an epigenetic suppressor of the calcium signaling gene CAS to mediate stomatal closure in response to extracellular calcium. Plant Cell 25, 2878-2891.
    Fu, Z.W., Li, J.H., Feng, Y.R., Yuan, X.,Lu, Y.T., 2021. The metabolite methylglyoxal-mediated gene expression is associated with histone methylglyoxalation. Nucleic Acids Res. 49, 1886-1899.
    Fursova, O.V., Pogorelko, G.V.,Tarasov, V.A., 2009. Identification of ICE2, a gene involved in cold acclimation which determines freezing tolerance in Arabidopsis thaliana. Gene 429, 98-103.
    Gallego-Bartolome, J., Gardiner, J., Liu, W., Papikian, A., Ghoshal, B., Kuo, H.Y., Zhao, J.M., Segal, D.J.,Jacobsen, S.E., 2018. Targeted DNA demethylation of the Arabidopsis genome using the human TET1 catalytic domain. Proc. Natl. Acad. Sci. U.S.A. 115, E2125-E2134.
    Gao, Z.,He, Y., 2023. Molecular epigenetic understanding of winter memory in Arabidopsis. Plant Physiol. 194, 1952-1961.
    Govindan, G., Sharma, B., Li, Y.-F., Armstrong, C.D., Merum, P., Rohila, J.S., Gregory, B.D.,Sunkar, R., 2022. mRNA N6-methyladenosine is critical for cold tolerance in Arabidopsis. Plant J. 111, 1052-1068.
    Guo, T., Wang, D., Fang, J., Zhao, J., Yuan, S., Xiao, L.,Li, X., 2019. Mutations in the rice OsCHR4 gene, encoding a CHD3 family chromatin remodeler, induce narrow and rolled leaves with increased cuticular wax. Int. J. Mol. Sci. 20, 2567.
    Guo, T., Yang, Z., Bao, R., Fu, X., Wang, N., Liu, C.,Ma, F., 2023a. The m6A reader MhYTP2 regulates the stability of its target mRNAs contributing to low nitrogen tolerance in apple (Malus domestica). Hortic. Res. 10.
    Guo, Y., Tan, Y., Qu, M., Hong, K., Zeng, L., Wang, L., Zhuang, C., Qian, Q., Hu, J.,Xiong, G., 2023b. OsWR2 recruits HDA704 to regulate the deacetylation of H4K8ac in the promoter of OsABI5 in response to drought stress. J. Integr. Plant Biol. 65, 1651-1669.
    Gupta, K.,Garg, R., 2023. Unravelling differential DNA methylation patterns in genotype dependent manner under salinity stress response in chickpea. Int. J. Mol. Sci. 24, 1863.
    Gutschker, S., Corral, J.M., Schmiedl, A., Ludewig, F., Koch, W., Fiedler-Wiechers, K., Czarnecki, O., Harms, K., Keller, I., Martins Rodrigues, C., et al., 2022. Multi-omics data integration reveals link between epigenetic modifications and gene expression in sugar beet (Beta vulgaris subsp. vulgaris) in response to cold. BMC Genom. 23, 144.
    Han, D., Chen, C., Xia, S., Liu, J., Shu, J., Nguyen, V., Lai, J., Cui, Y.,Yang, C., 2021. Chromatin-associated SUMOylation controls the transcriptional switch between plant development and heat stress responses. Plant Commun. 2, 100091.
    Han, X., Wang, J., Zhang, Y., Kong, Y., Dong, H., Feng, X., Li, T., Zhou, C., Yu, J., Xin, D., et al., 2023. Changes in the m6A RNA methylome accompany the promotion of soybean root growth by rhizobia under cadmium stress. J. Hazard Mater. 441, 129843.
    He, K., Cao, X.,Deng, X., 2021a. Histone methylation in epigenetic regulation and temperature responses. Curr. Opin. Plant Biol. 61, 102001.
    He, K., Mei, H., Zhu, J., Qiu, Q., Cao, X.,Deng, X., 2021b. The histone H3K27 demethylase REF6/JMJ12 promotes thermomorphogenesis in Arabidopsis. Natl. Sci. Rev. 9.
    Hilker, M., Schwachtje, J., Baier, M., Balazadeh, S., Baurle, I., Geiselhardt, S., Hincha, D.K., Kunze, R., Mueller-Roeber, B., Rillig, M.C., et al., 2016. Priming and memory of stress responses in organisms lacking a nervous system. Biol. Rev. Camb. Phil. Soc. 91, 1118-1133.
    Hossain, M.S., Kawakatsu, T., Kim, K.D., Zhang, N., Nguyen, C.T., Khan, S.M., Batek, J.M., Joshi, T., Schmutz, J., Grimwood, J., et al., 2017. Divergent cytosine DNA methylation patterns in single-cell, soybean root hairs. New Phytol. 214, 808-819.
    Hou, Y., Yan, Y.,Cao, X., 2022. Epigenetic regulation of thermomorphogenesis in Arabidopsis thaliana. aBIOTECH 3, 12-24.
    Hu, J., Cai, J., Park, S.J., Lee, K., Li, Y., Chen, Y., Yun, J.Y., Xu, T.,Kang, H., 2021. N6-methyladenosine mRNA methylation is important for salt stress tolerance in Arabidopsis. Plant J. 106, 1759-1775.
    Hu, Z., Song, N., Zheng, M., Liu, X., Liu, Z., Xing, J., Ma, J., Guo, W., Yao, Y., Peng, H., et al., 2015. Histone acetyltransferase GCN5 is essential for heat stress-responsive gene activation and thermotolerance in Arabidopsis. Plant J. 84, 1178-1191.
    Huang, S., Zhang, A., Jin, J.B., Zhao, B., Wang, T.J., Wu, Y., Wang, S., Liu, Y., Wang, J., Guo, P., et al., 2019. Arabidopsis histone H3K4 demethylase JMJ17 functions in dehydration stress response. New Phytol. 223, 1372-1387.
    Huang, Y., An, J., Sircar, S., Bergis, C., Lopes, C.D., He, X., Da Costa, B., Tan, F.Q., Bazin, J., Antunez-Sanchez, J., et al., 2023. HSFA1a modulates plant heat stress responses and alters the 3D chromatin organization of enhancer-promoter interactions. Nat. Commun. 14, 469.
    Huong, T.T., Ngoc, L.N.T.,Kang, H., 2020. Functional characterization of a putative RNA demethylase ALKBH6 in Arabidopsis growth and abiotic stress responses. Int. J. Mol. Sci. 21, 6707.
    Ito, H., Gaubert, H., Bucher, E., Mirouze, M., Vaillant, I.,Paszkowski, J., 2011. An siRNA pathway prevents transgenerational retrotransposition in plants subjected to stress. Nature 472, 115-119.
    Jegu, T., Veluchamy, A., Ramirez-Prado, J.S., Rizzi-Paillet, C., Perez, M., Lhomme, A., Latrasse, D., Coleno, E., Vicaire, S., Legras, S., et al., 2017. The Arabidopsis SWI/SNF protein BAF60 mediates seedling growth control by modulating DNA accessibility. Genome Biol. 18, 114.
    Jha, U.C., Nayyar, H., Jha, R., Khurshid, M., Zhou, M., Mantri, N.,Siddique, K.H.M., 2020. Long non-coding RNAs: emerging players regulating plant abiotic stress response and adaptation. BMC Plant Biol. 20, 466.
    Jiang, C., Mithani, A., Belfield, E.J., Mott, R., Hurst, L.D.,Harberd, N.P., 2014. Environmentally responsive genome-wide accumulation of de novo Arabidopsis thaliana mutations and epimutations. Genome Res. 24, 1821-1829.
    Jiang, D.,Berger, F., 2023. Variation is important: warranting chromatin function and dynamics by histone variants. Curr. Opin. Plant Biol. 75, 102408.
    Jiang, D., Gu, X.,He, Y., 2009. Establishment of the winter-annual growth habit via FRIGIDA-mediated histone methylation at FLOWERING LOCUS C in Arabidopsis. Plant Cell 21, 1733-1746.
    Jiang, D., Kong, N.C., Gu, X., Li, Z.,He, Y., 2011. Arabidopsis COMPASS-like complexes mediate histone H3 lysine-4 trimethylation to control floral transition and plant development. PLoS Genet. 7, e1001330.
    Jiang, P., Wang, S., Jiang, H., Cheng, B., Wu, K.,Ding, Y., 2018. The COMPASS-like complex promotes flowering and panicle branching in rice. Plant Physiol. 176, 2761-2771.
    Kakoulidou, I., Avramidou, E.V., Baranek, M., Brunel-Muguet, S., Farrona, S., Johannes, F., Kaiserli, E., Lieberman-Lazarovich, M., Martinelli, F., Mladenov, V., et al., 2021. Epigenetics for crop improvement in times of global change. Biology 10, 766.
    Kappel, C., Friedrich, T., Oberkofler, V., Jiang, L., Crawford, T., Lenhard, M.,Baurle, I., 2023. Genomic and epigenomic determinants of heat stress-induced transcriptional memory in Arabidopsis. Genome Biol. 24, 129.
    Kim, J.M., To, T.K., Ishida, J., Matsui, A., Kimura, H.,Seki, M., 2012. Transition of chromatin status during the process of recovery from drought stress in Arabidopsis thaliana. Plant Cell Physiol. 53, 847-856.
    Kim, J.M., To, T.K., Matsui, A., Tanoi, K., Kobayashi, N.I., Matsuda, F., Habu, Y., Ogawa, D., Sakamoto, T., Matsunaga, S., et al., 2017. Acetate-mediated novel survival strategy against drought in plants. Nat. Plants 3, 17097.
    Klemm, S.L., Shipony, Z.,Greenleaf, W.J., 2019. Chromatin accessibility and the regulatory epigenome. Nat. Rev. Genet. 20, 207-220.
    Korotko, U., Chwialkowska, K., Sanko-Sawczenko, I.,Kwasniewski, M., 2021. DNA demethylation in response to heat stress in Arabidopsis thaliana. Int. J. Mol. Sci. 22, 1555.
    Kotak, S., Larkindale, J., Lee, U., von Koskull-Doring, P., Vierling, E.,Scharf, K.D., 2007. Complexity of the heat stress response in plants. Curr. Opin. Plant Biol. 10, 310-316.
    Kou, S., Gu, Q., Duan, L., Liu, G., Yuan, P., Li, H., Wu, Z., Liu, W., Huang, P.,Liu, L., 2022. Genome-wide bisulphite sequencing uncovered the contribution of DNA methylation to rice short-term drought memory formation. J. Plant Growth Regul. 41, 2903-2917.
    Kumar, S., Beena, A.S., Awana, M.,Singh, A., 2017. Salt-induced tissue-specific cytosine methylation downregulates expression of HKT genes in contrasting wheat (Triticum aestivum L.) genotypes. DNA Cell Biol. 36, 283-294.
    Kumar, S.V.,Wigge, P.A., 2010. H2A.Z-containing nucleosomes mediate the thermosensory response in Arabidopsis. Cell 140, 136-147.
    Kwon, C.S., Lee, D., Choi, G.,Chung, W.I., 2009. Histone occupancy-dependent and -independent removal of H3K27 trimethylation at cold-responsive genes in Arabidopsis. Plant J. 60, 112-121.
    Lamke, J.,Baurle, I., 2017. Epigenetic and chromatin-based mechanisms in environmental stress adaptation and stress memory in plants. Genome Biol. 18, 124.
    Lamke, J., Brzezinka, K., Altmann, S.,Baurle, I., 2016. A hit-and-run heat shock factor governs sustained histone methylation and transcriptional stress memory. EMBO J. 35, 162-175.
    Lang, Z., Wang, Y., Tang, K., Tang, D., Datsenka, T., Cheng, J., Zhang, Y., Handa, A.K.,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.
    Lee, C.K., Shibata, Y., Rao, B., Strahl, B.D.,Lieb, J.D., 2004. Evidence for nucleosome depletion at active regulatory regions genome-wide. Nat. Genet. 36, 900-905.
    Lee, H.G.,Seo, P.J., 2019. MYB96 recruits the HDA15 protein to suppress negative regulators of ABA signaling in Arabidopsis. Nat. Commun. 10, 1713.
    Lee, H.J., Jung, J.H., Cortes Llorca, L., Kim, S.G., Lee, S., Baldwin, I.T.,Park, C.M., 2014. FCA mediates thermal adaptation of stem growth by attenuating auxin action in Arabidopsis. Nat. Commun. 5, 5473.
    Li, B., Yang, C., An, B., Wang, H., Albaqami, M., Abou-Elwafa, S.F., Xu, L.,Xu, Y., 2022a. Comparative transcriptomic and epigenetic analyses reveal conserved and divergent regulatory pathways in barley response to temperature stresses. Physiol. Plantarum 174, e13727.
    Li, B., Zhang, M., Sun, W., Yue, D., Ma, Y., Zhang, B., Duan, L., Wang, M., Lindsey, K., Nie, X., et al., 2023. N6-methyladenosine RNA modification regulates cotton drought response in a Ca2+ and ABA-dependent manner. Plant Biotechnol. J. 21, 1270-1285.
    Li, T., Zhang, R., Satheesh, V., Wang, P., Ma, G., Guo, J., An, G.-Y.,Lei, M., 2022b. The chromatin remodeler BRAHMA recruits HISTONE DEACETYLASE6 to regulate root growth inhibition in response to phosphate starvation in Arabidopsis. J. Integr. Plant Biol. 64, 2314-2326.
    Li, Y., Ma, H., Wu, Y., Ma, Y., Yang, J., Li, Y., Yue, D., Zhang, R., Kong, J., Lindsey, K., et al., 2024. Single-cell transcriptome atlas and regulatory dynamics in developing cotton anthers. Adv. Sci. 11, e2304017.
    Liang, Z., Zhang, Q., Ji, C., Hu, G., Zhang, P., Wang, Y., Yang, L.,Gu, X., 2021. Reorganization of the 3D chromatin architecture of rice genomes during heat stress. BMC Biol. 19, 53.
    Liao, H.S., Yang, C.C.,Hsieh, M.H., 2022. Nitrogen deficiency- and sucrose-induced anthocyanin biosynthesis is modulated by HISTONE DEACETYLASE15 in Arabidopsis. J. Exp. Bot. 73, 3726-3742.
    Lister, R., O'Malley, R.C., Tonti-Filippini, J., Gregory, B.D., Berry, C.C., Millar, A.H.,Ecker, J.R., 2008. Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133, 523-536.
    Liu, C., Lu, F., Cui, X.,Cao, X., 2010. Histone methylation in higher plants. Annu. Rev. Plant Biol. 61, 395-420.
    Liu, H.C., Lamke, J., Lin, S.Y., Hung, M.J., Liu, K.M., Charng, Y.Y.,Baurle, I., 2018a. Distinct heat shock factors and chromatin modifications mediate the organ-autonomous transcriptional memory of heat stress. Plant J. 95, 401-413.
    Liu, J., Feng, L., Gu, X., Deng, X., Qiu, Q., Li, Q., Zhang, Y., Wang, M., Deng, Y., Wang, E., et al., 2019a. An H3K27me3 demethylase-HSFA2 regulatory loop orchestrates transgenerational thermomemory in Arabidopsis. Cell Res. 29, 379-390.
    Liu, K., Chen, J., Sun, S., Chen, X., Zhao, X., Hu, Y., Qi, G., Li, X., Xu, B., Miao, J., et al., 2023. Histone deacetylase OsHDA706 increases salt tolerance via H4K5/K8 deacetylation of OsPP2C49 in rice. J. Integr. Plant Biol. 65, 1394-1407.
    Liu, S., de Jonge, J., Trejo-Arellano, M.S., Santos-Gonzalez, J., Kohler, C.,Hennig, L., 2021a. Role of H1 and DNA methylation in selective regulation of transposable elements during heat stress. New Phytol. 229, 2238-2250.
    Liu, X.S., Feng, S.J., Zhang, B.Q., Wang, M.Q., Cao, H.W., Rono, J.K., Chen, X.,Yang, Z.M., 2019b. OsZIP1 functions as a metal efflux transporter limiting excess zinc, copper and cadmium accumulation in rice. BMC Plant Biol. 19, 283.
    Liu, Y., Chen, X., Xue, S., Quan, T., Cui, D., Han, L., Cong, W., Li, M., Yun, D.J., Liu, B., et al., 2021b. SET DOMAIN GROUP 721 protein functions in saline-alkaline stress tolerance in the model rice variety kitaake. Plant Biotechnol. J. 19, 2576-2588.
    Liu, Y., Zhang, A., Yin, H., Meng, Q., Yu, X., Huang, S., Wang, J., Ahmad, R., Liu, B.,Xu, Z.Y., 2018b. Trithorax-group proteins ARABIDOPSIS TRITHORAX4 (ATX4) and ATX5 function in abscisic acid and dehydration stress responses. New Phytol. 217, 1582-1597.
    Lopez, M.E., Denoyes, B.,Bucher, E., 2024. Epigenomic and transcriptomic persistence of heat stress memory in strawberry (Fragaria vesca). BMC Plant Biol. 24, 405.
    Lu, L., Wei, W., Tao, J.J., Lu, X., Bian, X.H., Hu, Y., Cheng, T., Yin, C.C., Zhang, W.K., Chen, S.Y., et al., 2021. Nuclear factor Y subunit GmNFYA competes with GmHDA13 for interaction with GmFVE to positively regulate salt tolerance in soybean. Plant Biotechnol. J. 19, 2362-2379.
    Lu, X., Wang, X., Chen, X., Shu, N., Wang, J., Wang, D., Wang, S., Fan, W., Guo, L., Guo, X., et al., 2017. Single-base resolution methylomes of upland cotton (Gossypium hirsutum L.) reveal epigenome modifications in response to drought stress. BMC Genom. 18, 297.
    Luo, W., Tang, Y., Li, S., Zhang, L., Liu, Y., Zhang, R., Diao, X.,Yu, J., 2023. The m6A reader SiYTH1 enhances drought tolerance by affecting the messenger RNA stability of genes related to stomatal closure and reactive oxygen species scavenging in Setaria italica. J. Integr. Plant Biol. 65, 2569-2586.
    Ma, S., Tang, N., Li, X., Xie, Y., Xiang, D., Fu, J., Shen, J., Yang, J., Tu, H., Li, X., et al., 2019. Reversible histone H2B monoubiquitination fine-tunes abscisic acid signaling and drought response in rice. Mol. Plant 12, 263-277.
    Ma, T., Wang, S., Sun, C., Tian, J., Guo, H., Cui, S.,Zhao, H., 2023. Arabidopsis LFR, a SWI/SNF complex component, interacts with ICE1 and activates ICE1 and CBF3 expression in cold acclimation. Front. Plant Sci. 14, 1097158.
    Marmorstein, R.,Roth, S.Y., 2001. Histone acetyltransferases: function, structure, and catalysis. Curr. Opin. Genet. Dev. 11, 155-161.
    Marmorstein, R.,Zhou, M.M., 2014. Writers and readers of histone acetylation: structure, mechanism, and inhibition. Cold Spring Harbor Perspect. Biol. 6, a018762.
    Masclaux-Daubresse, C., Chen, Q.,Have, M., 2017. Regulation of nutrient recycling via autophagy. Curr. Opin. Plant Biol. 39, 8-17.
    Mehdi, S., Derkacheva, M., Ramstrom, M., Kralemann, L., Bergquist, J.,Hennig, L., 2015. The WD40 domain protein MSI1 functions in a histone deacetylase complex to fine-tune abscisic acid signaling. Plant Cell 28, 42-54.
    Miao, R., Zhang, Y., Liu, X., Yuan, Y., Zang, W., Li, Z., Yan, X., Pang, Q.,Zhang, A., 2024. Histone variant H2A.Z is required for plant salt response by regulating gene transcription. Plant Cell Environ. 47, 2691-2707.
    Millan-Zambrano, G., Burton, A., Bannister, A.J.,Schneider, R., 2022. Histone post-translational modifications - cause and consequence of genome function. Nat. Rev. Genet. 23, 563-580.
    Miryeganeh, M., Marletaz, F., Gavriouchkina, D.,Saze, H., 2022. De novo genome assembly and in natura epigenomics reveal salinity-induced DNA methylation in the mangrove tree Bruguiera gymnorhiza. New Phytol. 233, 2094-2110.
    Morgan, M.A.J.,Shilatifard, A., 2020. Reevaluating the roles of histone-modifying enzymes and their associated chromatin modifications in transcriptional regulation. Nat. Genet. 52, 1271-1281.
    Mozgova, I.,Hennig, L., 2015. The polycomb group protein regulatory network. Annu. Rev. Plant Biol. 66, 269-296.
    Mustilli, A.C., Merlot, S., Vavasseur, A., Fenzi, F.,Giraudat, J., 2002. Arabidopsis OST1 protein kinase mediates the regulation of stomatal aperture by abscisic acid and acts upstream of reactive oxygen species production. Plant Cell 14, 3089-3099.
    Naderi, S., Maali-Amiri, R., Sadeghi, L.,Hamidi, A., 2024. Physio-biochemical and DNA methylation analysis of the defense response network of wheat to drought stress. Plant Physiol. Biochem. 209, 108516.
    Niu, X., Chen, L., Kato, A.,Ito, H., 2022a. Regulatory mechanism of a heat-activated retrotransposon by DDR complex in Arabidopsis thaliana. Front. Plant Sci. 13, 1048957.
    Niu, Y., Bai, J., Liu, X., Zhang, H., Bao, J., Zhao, W., Hou, Y., Deng, X., Yang, C., Guo, L., et al., 2022b. HISTONE DEACETYLASE 9 transduces heat signal in plant cells. Proc. Natl. Acad. Sci. U.S.A. 119, e2206846119.
    Nozawa, K., Masuda, S., Saze, H., Ikeda, Y., Suzuki, T., Takagi, H., Tanaka, K., Ohama, N., Niu, X., Kato, A., et al., 2022. Epigenetic regulation of ecotype-specific expression of the heat-activated transposon ONSEN. Front. Plant Sci. 13, 899105.
    Oguz, M.C., Aycan, M., Oguz, E., Poyraz, I.,Yildiz, M., 2022. Drought stress tolerance in plants: interplay of molecular, biochemical and physiological responses in important development stages. Physiologia 2, 180-197.
    Pajoro, A., Severing, E., Angenent, G.C.,Immink, R.G.H., 2017. Histone H3 lysine 36 methylation affects temperature-induced alternative splicing and flowering in plants. Genome Biol. 18, 102.
    Pan, J., Zhang, H., Zhan, Z., Zhao, T.,Jiang, D., 2023. A REF6-dependent H3K27me3-depleted state facilitates gene activation during germination in Arabidopsis. J. Genet. Genomics 50, 178-191.
    Papikian, A., Liu, W., Gallego-Bartolome, J.,Jacobsen, S.E., 2019. Site-specific manipulation of Arabidopsis loci using CRISPR-Cas9 SunTag systems. Nat. Commun. 10, 729.
    Park, J., Lim, C.J., Shen, M., Park, H.J., Cha, J.Y., Iniesto, E., Rubio, V., Mengiste, T., Zhu, J.K., Bressan, R.A., et al., 2018. Epigenetic switch from repressive to permissive chromatin in response to cold stress. Proc. Natl. Acad. Sci. U.S.A. 115, E5400-E5409.
    Pearce, R.S., 2001. Plant freezing and damage. Ann. Bot. 87, 417-424.
    Pecinka, A., Dinh, H.Q., Baubec, T., Rosa, M., Lettner, N.,Mittelsten Scheid, O., 2010. Epigenetic regulation of repetitive elements is attenuated by prolonged heat stress in Arabidopsis. Plant Cell 22, 3118-3129.
    Penfield, S., 2008. Temperature perception and signal transduction in plants. New Phytol. 179, 615-628.
    Perrella, G., Baurle, I.,van Zanten, M., 2022. Epigenetic regulation of thermomorphogenesis and heat stress tolerance. New Phytol. 234, 1144-1160.
    Perrella, G., Fasano, C., Donald, N.A., Daddiego, L., Fang, W., Martignago, D., Carr, C., Conti, L., Herzyk, P.,Amtmann, A., 2024. Histone deacetylase complex 1 and histone 1 epigenetically moderate stress responsiveness of Arabidopsis thaliana seedlings. New Phytol. 241, 166-179.
    Pratx, L., Wendering, P., Kappel, C., Nikoloski, Z.,Baurle, I., 2023. Histone retention preserves epigenetic marks during heat stress-induced transcriptional memory in plants. EMBO J. 42, e113595.
    Probst, A.V., 2022. Deposition and eviction of histone variants define functional chromatin states in plants. Curr. Opin. Plant Biol. 69, 102266.
    Quint, M., Delker, C., Balasubramanian, S., Balcerowicz, M., Casal, J.J., Castroverde, C.D.M., Chen, M., Chen, X., De Smet, I., Fankhauser, C., et al., 2023. 25 years of thermomorphogenesis research: milestones and perspectives. Trends Plant Sci. 28, 1098-1100.
    Rajkumar, M.S., Shankar, R., Garg, R.,Jain, M., 2020. Bisulphite sequencing reveals dynamic DNA methylation under desiccation and salinity stresses in rice cultivars. Genomics 112, 3537-3548.
    Rajkumar, M.S., Tembhare, K., Garg, R.,Jain, M., 2024. Genome-wide mapping of DNase I hypersensitive sites revealed differential chromatin accessibility and regulatory DNA elements under drought stress in rice cultivars. Plant J. 119, 2063-2079.
    Roquis, D., Robertson, M., Yu, L., Thieme, M., Julkowska, M.,Bucher, E., 2021. Genomic impact of stress-induced transposable element mobility in Arabidopsis. Nucleic Acids Res. 49, 10431-10447.
    Roy, D., Paul, A., Roy, A., Ghosh, R., Ganguly, P.,Chaudhuri, S., 2014. Differential acetylation of histone H3 at the regulatory region of OsDREB1b promoter facilitates chromatin remodelling and transcription activation during cold stress. PLoS One 9, e100343.
    Sani, E., Herzyk, P., Perrella, G., Colot, V.,Amtmann, A., 2013. Hyperosmotic priming of Arabidopsis seedlings establishes a long-term somatic memory accompanied by specific changes of the epigenome. Genome Biol. 14, R59.
    Secco, D., Wang, C., Shou, H., Schultz, M.D., Chiarenza, S., Nussaume, L., Ecker, J.R., Whelan, J.,Lister, R., 2015. Stress induced gene expression drives transient DNA methylation changes at adjacent repetitive elements. Elife 4, e09343.
    Seleiman, M.F., Al-Suhaibani, N., Ali, N., Akmal, M., Alotaibi, M., Refay, Y., Dindaroglu, T., Abdul-Wajid, H.H.,Battaglia, M.L., 2021. Drought stress impacts on plants and different approaches to alleviate its adverse effects. Plants 10, 259.
    Shafiq, S., Zeb, Q., Ali, A., Sajjad, Y., Nazir, R., Widemann, E.,Liu, L., 2019. Lead, cadmium and zinc phytotoxicity alter DNA methylation levels to confer heavy metal tolerance in wheat. Int. J. Mol. Sci. 20, 4676.
    Shang, J.Y.,He, X.J., 2022. Chromatin-remodeling complexes: conserved and plant-specific subunits in Arabidopsis. J. Integr. Plant Biol. 64, 499-515.
    Sharma, M., Sharma, M., Jamsheer K, M.,Laxmi, A., 2022. A glucose-target of rapamycin signaling axis integrates environmental history of heat stress through maintenance of transcription-associated epigenetic memory in Arabidopsis. J. Exp. Bot. 73, 7083-7102.
    Shen, H., Zhou, Y., Liao, C., Xie, Q., Chen, G., Hu, Z.,Wu, T., 2024. The AlkB homolog SlALKBH10B negatively affects drought and salt tolerance in Solanum lycopersicum. Int. J. Mol. Sci. 25, 173.
    Shen, L., Ma, J., Li, P., Wu, Y.,Yu, H., 2023. Recent advances in the plant epitranscriptome. Genome Biol. 24, 43.
    Shen, X., De Jonge, J., Forsberg, S.K., Pettersson, M.E., Sheng, Z., Hennig, L.,Carlborg, O., 2014. Natural CMT2 variation is associated with genome-wide methylation changes and temperature seasonality. PLoS Genet. 10, e1004842.
    Shen, Y., Chi, Y., Lu, S., Lu, H.,Shi, L., 2022. Involvement of JMJ15 in the dynamic change of genome-wide H3K4me3 in response to salt stress. Front. Plant Sci. 13, 1009723.
    Shen, Y., Lei, T., Cui, X., Liu, X., Zhou, S., Zheng, Y., Guerard, F., Issakidis-Bourguet, E.,Zhou, D.X., 2019. Arabidopsis histone deacetylase HDA15 directly represses plant response to elevated ambient temperature. Plant J. 100, 991-1006.
    Shi, Y., Ding, Y.,Yang, S., 2018. Molecular regulation of CBF signaling in cold acclimation. Trends Plant Sci. 23, 623-637.
    Smith, A.P., Jain, A., Deal, R.B., Nagarajan, V.K., Poling, M.D., Raghothama, K.G.,Meagher, R.B., 2009. Histone H2A.Z regulates the expression of several classes of phosphate starvation response genes but not as a transcriptional activator. Plant Physiol. 152, 217-225.
    Song, Y., Jia, Z., Hou, Y., Ma, X., Li, L., Jin, X.,An, L., 2020. Roles of DNA methylation in cold priming in tartary buckwheat. Front. Plant Sci. 11, 608540.
    Song, Z.T., Zhang, L.L., Han, J.J., Zhou, M.,Liu, J.X., 2021. Histone H3K4 methyltransferases SDG25 and ATX1 maintain heat-stress gene expression during recovery in Arabidopsis. Plant J. 105, 1326-1338.
    Sun, L., Jing, Y., Liu, X., Li, Q., Xue, Z., Cheng, Z., Wang, D., He, H.,Qian, W., 2020a. Heat stress-induced transposon activation correlates with 3D chromatin organization rearrangement in Arabidopsis. Nat. Commun. 11, 1886.
    Sun, R.Z., Liu, J., Wang, Y.Y.,Deng, X., 2021. DNA methylation-mediated modulation of rapid desiccation tolerance acquisition and dehydration stress memory in the resurrection plant Boea hygrometrica. PLoS Genet. 17, e1009549.
    Sun, Y., Zhao, J., Li, X.,Li, Y., 2020b. E2 conjugases UBC1 and UBC2 regulate MYB42-mediated SOS pathway in response to salt stress in Arabidopsis. New Phytol. 227, 455-472.
    Sung, D.Y., Kaplan, F., Lee, K.J.,Guy, C.L., 2003. Acquired tolerance to temperature extremes. Trends Plant Sci. 8, 179-187.
    Svistoonoff, S., Creff, A., Reymond, M., Sigoillot-Claude, C., Ricaud, L., Blanchet, A., Nussaume, L.,Desnos, T., 2007. Root tip contact with low-phosphate media reprograms plant root architecture. Nat. Genet. 39, 792-796.
    Tang, J., Chen, S.,Jia, G., 2023. Detection, regulation, and functions of RNA N6-methyladenosine modification in plants. Plant Commun. 4, 100546.
    Tang, S., Yang, C., Wang, D., Deng, X., Cao, X.,Song, X., 2022a. Targeted DNA demethylation produces heritable epialleles in rice. Sci. China Life Sci. 65, 753-756.
    Tang, W.S., Zhong, L., Ding, Q.Q., Dou, Y.N., Li, W.W., Xu, Z.S., Zhou, Y.B., Chen, J., Chen, M.,Ma, Y.Z., 2022b. Histone deacetylase AtSRT2 regulates salt tolerance during seed germination via repression of vesicle-associated membrane protein 714 (VAMP714) in Arabidopsis. New Phytol. 234, 1278-1293.
    Tang, Y., Gao, C.C., Gao, Y., Yang, Y., Shi, B., Yu, J.L., Lyu, C., Sun, B.F., Wang, H.L., Xu, Y., et al., 2020. OsNSUN2-mediated 5-methylcytosine mRNA modification enhances rice adaptation to high temperature. Dev. Cell 53, 272-286.
    Tasset, C., Singh Yadav, A., Sureshkumar, S., Singh, R., van der Woude, L., Nekrasov, M., Tremethick, D., van Zanten, M.,Balasubramanian, S., 2018. POWERDRESS-mediated histone deacetylation is essential for thermomorphogenesis in Arabidopsis thaliana. PLoS Genet. 14, e1007280.
    Thurman, R.E., Rynes, E., Humbert, R., Vierstra, J., Maurano, M.T., Haugen, E., Sheffield, N.C., Stergachis, A.B., Wang, H., Vernot, B., et al., 2012. The accessible chromatin landscape of the human genome. Nature 489, 75-82.
    Tian, P., Lin, Z., Lin, D., Dong, S., Huang, J.,Huang, T., 2021. The pattern of DNA methylation alteration, and its association with the changes of gene expression and alternative splicing during phosphate starvation in tomato. Plant J. 108, 841-858.
    Tittel-Elmer, M., Bucher, E., Broger, L., Mathieu, O., Paszkowski, J.,Vaillant, I., 2010. Stress-induced activation of heterochromatic transcription. PLoS Genet. 6, e1001175.
    To, T.K., Nakaminami, K., Kim, J.M., Morosawa, T., Ishida, J., Tanaka, M., Yokoyama, S., Shinozaki, K.,Seki, M., 2011. Arabidopsis HDA6 is required for freezing tolerance. Biochem. Biophys. Res. Commun. 406, 414-419.
    Ueda, M., Matsui, A., Tanaka, M., Nakamura, T., Abe, T., Sako, K., Sasaki, T., Kim, J.M., Ito, A., Nishino, N., et al., 2017. The distinct roles of class I and II RPD3-like histone deacetylases in salinity stress response Plant Physiol. 175, 1760-1773.
    Ullah, F., Xu, Q., Zhao, Y.,Zhou, D.X., 2021. Histone deacetylase HDA710 controls salt tolerance by regulating ABA signaling in rice. J. Integr. Plant Biol. 63, 451-467.
    van der Woude, L.C., Perrella, G., Snoek, B.L., van Hoogdalem, M., Novak, O., van Verk, M.C., van Kooten, H.N., Zorn, L.E., Tonckens, R., Dongus, J.A., et al., 2019. HISTONE DEACETYLASE 9 stimulates auxin-dependent thermomorphogenesis in Arabidopsis thaliana by mediating H2A.Z depletion. Proc. Natl. Acad. Sci. U. S. A. 116, 25343-25354.
    Vandereyken, K., Sifrim, A., Thienpont, B.,Voet, T., 2023. Methods and applications for single-cell and spatial multi-omics. Nat. Rev. Genet. 24, 494-515.
    Vlachonasios, K.E., Thomashow, M.F.,Triezenberg, S.J., 2003. Disruption mutations of ADA2b and GCN5 transcriptional adaptor genes dramatically affect Arabidopsis growth, development, and gene expression. Plant Cell 15, 626-638.
    Wang, J., Nan, N., Li, N., Liu, Y., Wang, T.J., Hwang, I., Liu, B.,Xu, Z.Y., 2020. A DNA methylation reader-chaperone regulator-transcription factor complex activates OsHKT1;5 expression during salinity stress. Plant Cell 32, 3535-3558.
    Wang, L., Xue, M., Zhang, H., Ma, L.,Jiang, D., 2023a. TONSOKU is required for the maintenance of repressive chromatin modifications in Arabidopsis. Cell Rep. 42, 112738.
    Wang, M., Qin, L., Xie, C., Li, W., Yuan, J., Kong, L., Yu, W., Xia, G.,Liu, S., 2014. Induced and constitutive DNA methylation in a salinity-tolerant wheat introgression line. Plant Cell Physiol. 55, 1354-1365.
    Wang, N., Wang, Z., Tzourtzou, S., Wang, X., Bi, X., Leimeister, J., Xu, L., Sakamoto, T., Matsunaga, S., Schaller, A., et al., 2023b. The plant nuclear lamina disassembles to regulate genome folding in stress conditions. Nat. Plants 9, 1081-1093.
    Wang, Q., Liu, P., Jing, H., Zhou, X.F., Zhao, B., Li, Y.,Jin, J.B., 2021a. JMJ27-mediated histone H3K9 demethylation positively regulates drought-stress responses in Arabidopsis. New Phytol. 232, 221-236.
    Wang, Q., Xu, J., Pu, X., Lv, H., Liu, Y., Ma, H., Wu, F., Wang, Q., Feng, X., Liu, T., et al., 2021b. Maize DNA methylation in response to drought stress is involved in target gene expression and alternative splicing. Int. J. Mol. Sci. 22, 8285.
    Wang, T., Xing, J., Liu, Z., Zheng, M., Yao, Y., Hu, Z., Peng, H., Xin, M., Zhou, D.,Ni, Z., 2019. Histone acetyltransferase GCN5-mediated regulation of long non-coding RNA At4 contributes to phosphate starvation response in Arabidopsis. J. Exp. Bot. 70, 6337-6348.
    Wang, W., Huang, F., Qin, Q., Zhao, X., Li, Z.,Fu, B., 2015. Comparative analysis of DNA methylation changes in two rice genotypes under salt stress and subsequent recovery. Biochem. Biophys. Res. Commun. 465, 790-796.
    Wang, W., Qin, Q., Sun, F., Wang, Y., Xu, D., Li, Z.,Fu, B., 2016. Genome-wide differences in DNA methylation changes in two contrasting rice genotypes in response to drought conditions. Front. Plant Sci. 7, 1675.
    Wang, Y., Liu, Y., Qu, S., Liang, W., Sun, L., Ci, D., Ren, Z., Fan, L.-M.,Qian, W., 2022. Nitrogen starvation induces genome-wide activation of transposable elements in Arabidopsis. J. Integr. Plant Biol. 64, 2374-2384.
    Wang, Y., Wang, F., Lu, H., Lin, R., Liu, J., Liu, Y., Xu, J., Wu, Y., Wang, Z., Zhou, M., et al., 2023c. Rice chromatin protein OsHMGB1 is involved in phosphate homeostasis and plant growth by affecting chromatin accessibility. New Phytol. 240, 727-743.
    Wei, H., Wang, X., He, Y., Xu, H.,Wang, L., 2021. Clock component OsPRR73 positively regulates rice salt tolerance by modulating OsHKT2;1-mediated sodium homeostasis. EMBO J. 40, e105086.
    Wei, W., Lu, L., Bian, X.-H., Li, Q.-T., Han, J.-Q., Tao, J.-J., Yin, C.-C., Lai, Y.-C., Li, W., Bi, Y.-D., et al., 2023. Zinc-finger protein GmZF351 improves both salt and drought stress tolerance in soybean. J. Integr. Plant Biol. 65, 1636-1650.
    Wei, W., Tao, J.-J., Chen, H.-W., Li, Q.-T., Zhang, W.-K., Ma, B., Lin, Q., Zhang, J.-S.,Chen, S.-Y., 2017. A histone code reader and a transcriptional activator interact to regulate genes for salt tolerance. Plant Physiol. 175, 1304-1320.
    Weng, M., Yang, Y., Feng, H., Pan, Z., Shen, W.H., Zhu, Y.,Dong, A., 2014. Histone chaperone ASF1 is involved in gene transcription activation in response to heat stress in Arabidopsis thaliana. Plant Cell Environ. 37, 2128-2138.
    Wibowo, A., Becker, C., Marconi, G., Durr, J., Price, J., Hagmann, J., Papareddy, R., Putra, H., Kageyama, J., Becker, J., et al., 2016. Hyperosmotic stress memory in Arabidopsis is mediated by distinct epigenetically labile sites in the genome and is restricted in the male germline by DNA glycosylase activity. Elife 5, e13546.
    Wollmann, H., Stroud, H., Yelagandula, R., Tarutani, Y., Jiang, D., Jing, L., Jamge, B., Takeuchi, H., Holec, S., Nie, X., et al., 2017. The histone H3 variant H3.3 regulates gene body DNA methylation in Arabidopsis thaliana. Genome Biol. 18, 94.
    Wu, J., Liu, B.,Dong, A., 2024a. Interplay between histone variants and chaperones in plants. Curr. Opin. Plant Biol. 80, 102551.
    Wu, T., Pi, E.-X., Tsai, S.-N., Lam, H.-M., Sun, S.-M., Kwan, Y.W.,Ngai, S.-M., 2011. GmPHD5 acts as an important regulator for crosstalk between histone H3K4 di-methylation and H3K14 acetylation in response to salinity stress in soybean. BMC Plant Biol. 11, 178.
    Wu, X., Su, T., Zhang, S., Zhang, Y., Wong, C.E., Ma, J., Shao, Y., Hua, C., Shen, L.,Yu, H., 2024b. N6-methyladenosine-mediated feedback regulation of abscisic acid perception via phase-separated ECT8 condensates in Arabidopsis. Nat. Plants 10, 469-482.
    Wu, X., Xu, J., Meng, X., Fang, X., Xia, M., Zhang, J., Cao, S.,Fan, T., 2022. Linker histone variant HIS1-3 and WRKY1 oppositely regulate salt stress tolerance in Arabidopsis. Plant Physiol. 189, 1833-1847.
    Xiao, X., Zhang, J., Li, T., Fu, X., Satheesh, V., Niu, Q., Lang, Z., Zhu, J.K.,Lei, M., 2019. A group of SUVH methyl-DNA binding proteins regulate expression of the DNA demethylase ROS1 in Arabidopsis. J. Integr. Plant Biol. 61, 110-119.
    Xie, H., Sun, Y., Cheng, B., Xue, S., Cheng, D., Liu, L., Meng, L.,Qiang, S., 2018. Variation in ICE1 methylation primarily determines phenotypic variation in freezing tolerance in Arabidopsis thaliana. Plant Cell Physiol. 60, 152-165.
    Xu, J.M., Wang, Z.Q., Wang, J.Y., Li, P.F., Jin, J.F., Chen, W.W., Fan, W., Kochian, L.V., Zheng, S.J.,Yang, J.L., 2020. Low phosphate represses histone deacetylase complex1 to regulate root system architecture remodeling in Arabidopsis. New Phytol. 225, 1732-1745.
    Xue, M., Zhang, H., Zhao, F., Zhao, T., Li, H.,Jiang, D., 2021. The INO80 chromatin remodeling complex promotes thermomorphogenesis by connecting H2A.Z eviction and active transcription in Arabidopsis. Mol. Plant 14, 1799-1813.
    Yamaguchi, N., Matsubara, S., Yoshimizu, K., Seki, M., Hamada, K., Kamitani, M., Kurita, Y., Nomura, Y., Nagashima, K., Inagaki, S., et al., 2021. H3K27me3 demethylases alter HSP22 and HSP17.6C expression in response to recurring heat in Arabidopsis. Nat. Commun. 12, 3480.
    Yang, C., Shen, W., Yang, L., Sun, Y., Li, X., Lai, M., Wei, J., Wang, C., Xu, Y., Li, F., et al., 2020a. HY5-HDA9 module transcriptionally regulates plant autophagy in response to light-to-dark conversion and nitrogen starvation. Mol. Plant 13, 515-531.
    Yang, F., Sun, Y., Du, X., Chu, Z., Zhong, X.,Chen, X., 2023a. Plant-specific histone deacetylases associate with ARGONAUTE4 to promote heterochromatin stabilization and plant heat tolerance. New Phytol. 238, 252-269.
    Yang, J., Chang, Y., Qin, Y., Chen, D., Zhu, T., Peng, K., Wang, H., Tang, N., Li, X., Wang, Y., et al., 2020b. A lamin-like protein OsNMCP1 regulates drought resistance and root growth through chromatin accessibility modulation by interacting with a chromatin remodeller OsSWI3C in rice. New Phytol. 227, 65-83.
    Yang, J., Qu, X., Li, T., Gao, Y., Du, H., Zheng, L., Ji, M., Zhang, P., Zhang, Y., Hu, J., et al., 2023b. HY5-HDA9 orchestrates the transcription of HsfA2 to modulate salt stress response in Arabidopsis. J. Integr. Plant Biol. 65, 45-63.
    Yang, R., Hong, Y., Ren, Z., Tang, K., Zhang, H., Zhu, J.-K.,Zhao, C., 2019. A role for PICKLE in the regulation of cold and salt stress tolerance in Arabidopsis. Front. Plant Sci. 10, 900.
    Yang, Y.,Guo, Y., 2018. Elucidating the molecular mechanisms mediating plant salt-stress responses. New Phytol. 217, 523-539.
    Yong-Villalobos, L., Gonzalez-Morales, S.I., Wrobel, K., Gutierrez-Alanis, D., Cervantes-Perez, S.A., Hayano-Kanashiro, C., Oropeza-Aburto, A., Cruz-Ramirez, A., Martinez, O.,Herrera-Estrella, L., 2015. Methylome analysis reveals an important role for epigenetic changes in the regulation of the Arabidopsis response to phosphate starvation. Proc. Natl. Acad. Sci. U.S.A. 112, E7293-E7302.
    Yun, M., Wu, J., Workman, J.L.,Li, B., 2011. Readers of histone modifications. Cell Res. 21, 564-578.
    Zahraeifard, S., Foroozani, M., Sepehri, A., Oh, D.-H., Wang, G., Mangu, V., Chen, B., Baisakh, N., Dassanayake, M.,Smith, A.P., 2018. Rice H2A.Z negatively regulates genes responsive to nutrient starvation but promotes expression of key housekeeping genes. J. Exp. Bot. 69, 4907-4919.
    Zha, P., Jing, Y., Xu, G.,Lin, R., 2017. PICKLE chromatin-remodeling factor controls thermosensory hypocotyl growth of Arabidopsis. Plant Cell Environ. 40, 2426-2436.
    Zhan, J.,Meyers, B.C., 2023. Plant small RNAs: their biogenesis, regulatory roles, and functions. Annu. Rev. Plant Biol. 74, 21-51.
    Zhang, H., Jin, Z., Cui, F., Zhao, L., Zhang, X., Chen, J., Zhang, J., Li, Y., Li, Y., Niu, Y., et al., 2023. Epigenetic modifications regulate cultivar-specific root development and metabolic adaptation to nitrogen availability in wheat. Nat. Commun. 14, 8238.
    Zhang, H., Lang, Z.,Zhu, J.-K., 2018. Dynamics and function of DNA methylation in plants. Nat. Rev. Mol. Cell Biol. 19, 489-506.
    Zhang, H., Li, X., Song, R., Zhan, Z., Zhao, F., Li, Z.,Jiang, D., 2022. Cap-binding complex assists RNA polymerase II transcription in plant salt stress response. Plant Cell Environ. 45, 2780-2793.
    Zhang, H.,Zhu, J.K., 2024. Epigenetic gene regulation in plants and its potential applications in crop improvement. Nat. Rev. Mol. Cell Biol.
    Zhang, M., Zhang, X., Guo, L., Qi, T., Liu, G., Feng, J., Shahzad, K., Zhang, B., Li, X., Wang, H., et al., 2019. Single-base resolution methylome of cotton cytoplasmic male sterility system reveals epigenomic changes in response to high-temperature stress during anther development. J. Exp. Bot. 71, 951-969.
    Zhang, X., Yazaki, J., Sundaresan, A., Cokus, S., Chan, S.W., Chen, H., Henderson, I.R., Shinn, P., Pellegrini, M., Jacobsen, S.E., et al., 2006. Genome-wide high-resolution mapping and functional analysis of DNA methylation in Arabidopsis. Cell 126, 1189-1201.
    Zhao, F., Xue, M., Zhang, H., Li, H., Zhao, T.,Jiang, D., 2023. Coordinated histone variant H2A.Z eviction and H3.3 deposition control plant thermomorphogenesis. New Phytol. 238, 750-764.
    Zhao, F., Zhang, H., Zhao, T., Li, Z.,Jiang, D., 2021. The histone variant H3.3 promotes the active chromatin state to repress flowering in Arabidopsis. Plant Physiol. 186, 2051-2063.
    Zhao, P., Ma, B., Cai, C.,Xu, J., 2022. Transcriptome and methylome changes in two contrasting mungbean genotypes in response to drought stress. BMC Genom. 23, 80.
    Zhao, T., Zhan, Z.P.,Jiang, D.H., 2019. Histone modifications and their regulatory roles in plant development and environmental memory. J. Genet. Genomics 46, 467-476.
    Zhao, Y., Han, K.-J., Tian, Y.-T., Jia, K.-H., El-Kassaby, Y.A., Wu, Y., Liu, J., Si, H.-Y., Sun, Y.-H.,Li, Y., 2024. N6-methyladenosine mRNA methylation positively regulated the response of poplar to salt stress. Plant Cell Environ. 47, 1797-1812.
    Zheng, G., Dong, X., Wei, J., Liu, Z., Aslam, A., Cui, J., Li, H., Wang, Y., Tian, H.,Cao, X., 2022. Integrated methylome and transcriptome analysis unravel the cold tolerance mechanism in winter rapeseed(Brassica napus L.). BMC Plant Biol. 22, 414.
    Zheng, M., Lin, J., Liu, X., Chu, W., Li, J., Gao, Y., An, K., Song, W., Xin, M., Yao, Y., et al., 2021. Histone acetyltransferase TaHAG1 acts as a crucial regulator to strengthen salt tolerance of hexaploid wheat. Plant Physiol. 186, 1951-1969.
    Zheng, M., Liu, X., Lin, J., Liu, X., Wang, Z., Xin, M., Yao, Y., Peng, H., Zhou, D.-X., Ni, Z., et al., 2019a. Histone acetyltransferase GCN5 contributes to cell wall integrity and salt stress tolerance by altering the expression of cellulose synthesis genes. Plant J. 97, 587-602.
    Zheng, S., Hu, H., Ren, H., Yang, Z., Qiu, Q., Qi, W., Liu, X., Chen, X., Cui, X., Li, S., et al., 2019b. The Arabidopsis H3K27me3 demethylase JUMONJI 13 is a temperature and photoperiod dependent flowering repressor. Nat. Commun. 10, 1303.
    Zheng, X., Chen, L., Xia, H., Wei, H., Lou, Q., Li, M., Li, T.,Luo, L., 2017. Transgenerational epimutations induced by multi-generation drought imposition mediate rice plant's adaptation to drought condition. Sci. Rep. 7, 39843.
    Zheng, Y., Ding, Y., Sun, X., Xie, S., Wang, D., Liu, X., Su, L., Wei, W., Pan, L.,Zhou, D.-X., 2016. Histone deacetylase HDA9 negatively regulates salt and drought stress responsiveness in Arabidopsis. J. Exp. Bot. 67, 1703-1713.
    Zhou, S., Chen, Q., Sun, Y.,Li, Y., 2017. Histone H2B monoubiquitination regulates salt stress-induced microtubule depolymerization in Arabidopsis. Plant Cell Environ. 40, 1512-1530.
    • Relative Articles
    • Supplements(0)
    • Cited By
  • 加载中

Catalog

    通讯作者: 陈斌, bchen63@163.com
    • 1. 

      沈阳化工大学材料科学与工程学院 沈阳 110142

    1. 本站搜索
    2. 百度学术搜索
    3. 万方数据库搜索
    4. CNKI搜索
    Get Citation
    PDF

    Article Metrics

    Article views (2) PDF downloads (0) Cited by ()
    Proportional views
    Related

    Editorial Office

    Journal of Genetics and Genomics

    京ICP备09063187号-12

    No.1, West Beichen Road, Chaoyang District, Beijing 100101, P.R.China

    +86-10-64806528+86-10-64807786jgg@genetics.ac.cn

    Supported by: Beijing Renhe Information Technology Co. Ltd  

    /

    DownLoad:  Full-Size Img  PowerPoint
    Return
    Return