Dynamic regulatory mechanisms of histone methylation in plant development and environmental adaptation

Rina Sa , Xinyue Fan , Hongmei Sun

Horticulture Research ›› 2026, Vol. 13 ›› Issue (5) : 47

PDF (2411KB)
Horticulture Research ›› 2026, Vol. 13 ›› Issue (5) :47 DOI: 10.1093/hr/uhag047
Review Article
research-article
Dynamic regulatory mechanisms of histone methylation in plant development and environmental adaptation
Author information +
History +
PDF (2411KB)

Abstract

Histone modification is an important part of epigenetic research and plays a significant role in maintaining the stability of eukaryotic genomes, regulating gene expression, and chromatin remodeling. Histone methylation is one of the most complex modification forms in epigenetic regulation, which can occur on specific lysine or arginine residues at the tail of histones. Its biological function depends on the degree of methylation (me/me2/me3). Histone methylation involves multiple links, such as ‘writer’, ‘reader’, and ‘eraser’ enzymes, and can activate or inhibit gene transcription by recruiting various downstream effector proteins. As molecular biology techniques have advanced, significant progress has been made in fundamental research on histone methylations in plants, and researchers have gained insights into its complex multilevel regulatory mechanisms. This review systematically summarizes recent advances in the roles of histone methylation in regulating plant dormancy and germination, flowering and senescence, as well as stress responses, and proposes a cross-regulatory model integrating histone methylation with multiple signaling pathways. These insights provide a theoretical foundation for the application of epigenetic breeding strategies in horticultural crops, with the goal of enhancing stress tolerance and yield.

Cite this article

Download citation ▾
Rina Sa, Xinyue Fan, Hongmei Sun. Dynamic regulatory mechanisms of histone methylation in plant development and environmental adaptation. Horticulture Research, 2026, 13 (5) : 47 DOI:10.1093/hr/uhag047

登录浏览全文

4963

注册一个新账户 忘记密码

Acknowledgements

This work was financed by the National Natural Science Foundation of China (grant number 32372741, 32302589), Liaoning Province Germplasm Innovation Grain Storage Technology Special Plan (2023JH1/10200010), and the earmarked fund for CARS (CARS-23).

Author contributions

R.S.: Writing-original draft and drawing; X.F.: Writing-review & editing; H.S.: Conceptualization, Writing-review & editing, Supervision, and Funding acquisition. All the authors read and approved the final version of the paper.

Conflicts of interest statement

The authors declare no conflicts of interest in the submission of this manuscript.

References

[1]

Su LY, Li SS, Liu H. et al. The origin, evolution, and functional divergence of the Dicer-like (DCL) and Argonaute (AGO) gene families in plants . Epigenetics Insights. 2024; 17: e003

[2]

Yu X, Yu H, Lu Y. et al. Genetic and epigenetic variations underlying flavonoid divergence in Beihua and Sijihua honeysuckles. Epigenetics Insights . 2024; 17: e002

[3]

Jenuwein T, Allis CD . Translating the histone code. Science. 2001; 293: 1074-80

[4]

Barré-Villeneuve C, Azevedo-Favory J . R-methylation in plants: a key regulator of plant development and response to the environment. Int J Mol Sci . 2024; 25: 9937

[5]

Kennison JA . The polycomb and trithorax group proteins of Drosophila: trans-regulators of homeotic gene function . Annu Rev Genet. 1995; 29: 289-303

[6]

Goodrich J, Puangsomlee P, Martin M. et al. A polycomb-group gene regulates homeotic gene expression in Arabidopsis. Nature. 1997; 386: 44-51

[7]

Zhang LS, Ma CR, Ji Q. et al. Genome-wide identification, classification and expression analyses of SET domain gene family in Arabidopsis and rice. Yi Chuan. 2009; 31: 186-98

[8]

Springer NM, Napoli CA, Selinger DA. et al. Comparative analysis of SET domain proteins in maize and Arabidopsis reveals multiple duplications preceding the divergence of monocots and dicots. Plant Physiol. 2003; 132: 907-25

[9]

Zhang LS, Ma H . Complex evolutionary history and diverse domain organization of SET proteins suggest divergent regulatory interactions. New Phytol. 2012; 195: 248-63

[10]

Liu C, Lu F, Cui X. et al. Histone methylation in higher plants. Annu Rev Plant Biol . 2010; 61: 395-420

[11]

Berger SL . The complex language of chromatin regulation during transcription. Nature. 2007; 447: 407-12

[12]

ZBu, YYu, ZLi. et al. Regulation of Arabidopsis flowering by the histone mark readers MRG1/2 via interaction with constans to modulate FT expression . PLoS Genet. 2014; 10: e1004617

[13]

Jiang D, Kong NC, Gu X. et al. Arabidopsis compass-like complexes mediate histone H3 lysine-4 trimethylation to control floral transition and plant development. PLoS Genet. 2011; 7: e1001330

[14]

Pien S, Fleury D, Mylne JS. et al. Arabidopsistrithorax1 dynamically regulates flowering locus C activation via histone 3 lysine 4 trimethylation. Plant Cell. 2008; 20: 580-8

[15]

Chen LQ, Luo JH, Cui ZH. et al. ATX3, ATX4, and ATX5 encode putative H3K4 methyltransferases and are critical for plant development . Plant Physiol. 2017; 174: 1795-806

[16]

Berr A, McCallum EJ, Ménard R. et al. Arabidopsis set domain group2 is required for H3K4 trimethylation and is crucial for both sporophyte and gametophyte development. Plant Cell. 2010; 22: 3232-48

[17]

Guo L, Yu Y, Law JA. et al. Set domain group2 is the major histone H3 lysine 4 trimethyltransferase in Arabidopsis. Proc Natl Acad Sci USA . 2010; 107: 18557

[18]

Tamada Y, Yun JY, Woo SC. et al. Arabidopsis trithorax-related7 is required for methylation of lysine 4 of histone H3 and for transcriptional activation of flowering locus C. Plant Cell. 2009; 21: 3257-69

[19]

Cartagena JA, Matsunaga S, Seki M. et al. The Arabidopsis SDG4 contributes to the regulation of pollen tube growth by methylation of histone H3 lysines 4 and 36 in mature pollen . Dev Biol. 2008; 315: 355-68

[20]

Berr A, Shafiq S, Pinon V. et al. The trxG family histone methyltransferase set domain group 26 promotes flowering via a distinctive genetic pathway. Plant J. 2015; 81: 316-28

[21]

Xu L, Zhao Z, Dong A. et al. Di- and tri- but not monomethylation on histone H3 lysine 36 marks active transcription of genes involved in flowering time regulation and other processes in Arabidopsis thaliana . Mol Cell Biol. 2008; 28: 1348-60

[22]

Liu Y, Chen X, Xue S. et al. Set domain group 721 protein functions in saline-alkaline stress tolerance in the model rice variety Kitaake. Plant Biotechnol J. 2021; 19: 2576-88

[23]

Rea S, Eisenhaber F, O’Carroll D. et al. Regulation of chromatin structure by site-specific histone H3 methyltransferases. Nature. 2000; 406: 593-9

[24]

Jackson JP, Lindroth AM, Cao X. et al. Control of CpNpG DNA methylation by the Kryptonite histone H3 methyltransferase. Nature. 2002; 416: 556-60

[25]

Jackson JP, Johnson L, Jasencakova Z. et al. Dimethylation of histone H3 lysine 9 is a critical mark for DNA methylation and gene silencing in Arabidopsis thaliana . Chromosoma. 2004; 112: 308-15

[26]

Ding Y, Wang X, Su L. et al. SDG714, a histone H3K9 methyltransferase, is involved in Tos17 DNA methylation and transposition in rice. Plant Cell. 2007; 19: 9-22

[27]

Ebbs M, Bender J . Locus-specific control of DNA methylation by the Arabidopsis SUVH5 histone methyltransferase . Plant Cell. 2006; 18: 1166-76

[28]

Hennig L, Derkacheva M . Diversity of polycomb group complexes in plants: same rules, different players? Trends Genet. 2009; 25: 414-23

[29]

Jacob Y, Bergamin E, Donoghue MTA. et al. Selective methylation of histone H3 variant H3.1 regulates heterochromatin replication. Science. 2014; 343: 1249-53

[30]

Zhang X, Germann S, Blus BJ. et al. The Arabidopsis LHP1 protein colocalizes with histone H3 Lys27 trimethylation . Nat Struct Mol Biol. 2007; 14: 869-71

[31]

Luo M, Bilodeau P, Koltunow A. et al. Genes controlling fertilization-independent seed development in Arabidopsis thaliana . Proc Natl Acad Sci USA. 1999; 96: 296-301

[32]

Gendall AR, Levy YY, Wilson A. et al. The vernalization 2 gene mediates the epigenetic regulation of vernalization in Arabidopsis . Cell. 2001; 107: 525-35

[33]

Yoshida N, Yanai Y, Chen L. et al. Embryonic flower2, a novel polycomb group protein homolog, mediates shoot development and flowering in Arabidopsis . Plant Cell. 2001; 13: 2471-81

[34]

Ohad N, Yadegari R, Margossian L. et al. Mutations in FIE, a WD polycomb group gene, allow endosperm development without fertilization. Plant Cell. 1999; 11: 407-16

[35]

Ach RA, Taranto P, Gruissem W . A conserved family of WD-40 proteins binds to the retinoblastoma protein in both plants and animals. Plant Cell . 1997; 9: 1595-606

[36]

Liu DD, Zhou LJ, Fang MJ. et al. Polycomb-group protein SlMSI1 represses the expression of fruit-ripening genes to prolong shelf life in tomato. Sci Rep . 2016; 6: 31806

[37]

Jacob Y, Feng S, LeBlanc CA. et al. ATXR5 and ATXR6 are H3K27 monomethyltransferases required for chromatin structure and gene silencing. Nat Struct Mol Biol. 2009; 16: 763-8

[38]

De la Paz M, Gutierrez C . Arabidopsis ORC1 is a PHD-containing H3K4me3 effector that regulates transcription . Proc Natl Acad Sci USA. 2009; 106: 2065-70

[39]

Liang X, Lei M, Li F. et al. Family-wide characterization of histone binding abilities of PHD domains of AL proteins in Arabidopsis thaliana . Protein J. 2018; 37: 531-8

[40]

Pena PV, Davrazou F, Shi X. et al. Molecular mechanism of histone H3K4me3 recognition by plant homeodomain of ING2. Nature. 2006; 442: 100-3

[41]

Lee WY, Lee D, Chung WI. et al. Arabidopsis ING and Alfin1-like protein families localize to the nucleus and bind to H3K4me3/2 via plant homeodomain fingers. Plant J. 2009; 58: 511-24

[42]

Lu F, Li G, Cui X. et al. Comparative analysis of JmjC domain-containing proteins reveals the potential histone demethylases in Arabidopsis and rice. J Integr Plant Biol. 2008; 50: 886-96

[43]

Tan LM, Liu R, Gu BW. et al. Dual recognition of H3K4me3 and DNA by the ISWI component ARID5 regulates the floral transition in Arabidopsis. Plant Cell. 2020; 32: 2178-95

[44]

Du J, Zhong X, Bernatavichute YV. et al. Dual binding of chromomethylase domains to H3K9me2-containing nucleosomes directs DNA methylation in plants. Cell. 2012; 151: 167-80

[45]

Berry S, Rosa S, Howard M. et al. Disruption of an RNA-binding hinge region abolishes LHP1-mediated epigenetic repression. Genes Dev . 2017; 31: 2115-20

[46]

Liang Q, Deng H, Li Y. et al. Like heterochromatin protein 1b represses fruit ripening via regulating the H3K27me3 levels in ripening-related genes in tomato. New Phytol. 2020; 227: 485-97

[47]

Li Z, Fu X, Wang Y. et al. Polycomb-mediated gene silencing by the BAH-EMF1 complex in plants. Nat Genet. 2018; 50: 1254-61

[48]

Qian F, Zhao QY, Zhang TN. et al. A histone H3K27me3 reader cooperates with a family of PHD finger-containing proteins to regulate flowering time in Arabidopsis . J Integr Plant Biol. 2021; 63: 787-802

[49]

Law JA, Du J, Hale CJ. et al. Polymerase IV occupancy at RNA-directed DNA methylation sites requires SHH1. Nature. 2013; 498: 385-9

[50]

Coursey T, Milutinovic M, Regedanz E. et al. Arabidopsis histone reader EMSY LIKE 1 binds H3K36 and suppresses geminivirus infection. J Virol. 2018; 92: e00219-8

[51]

Miura A, Nakamura M, Inagaki S. et al. An Arabidopsis jmjC domain protein protects transcribed genes from DNA methylation at CHG sites. EMBO J. 2009; 28: 1078-86

[52]

Saze H, Shiraishi A, Miura A. et al. Control of genic DNA methylation by a jmjC domain-containing protein in Arabidopsis thaliana. Science. 2008; 319: 462-5

[53]

Cui X, Lu F, Qiu Q. et al. REF6 recognizes a specific DNA sequence to demethylate H3K27me3 and regulate organ boundary formation in Arabidopsis. Nature Genet. 2016; 48: 694-9

[54]

Noh B, Lee SH, Kim HJ. et al. Divergent roles of a pair of homologous jumonji/zinc-finger-class transcription factor proteins in the regulation of Arabidopsis flowering time . Plant Cell. 2004; 16: 2601-13

[55]

Tsukada Y, Fang J, Erdjument-Bromage H. et al. Histone demethylation by a family of JmjC domain-containing proteins. Nature. 2006; 439: 811-6

[56]

Klose RJ, Zhang Y . Regulation of histone methylation by demethylimination and demethylation. Nat Rev Mol Cell Biol. 2007; 8: 307-18

[57]

Shi Y, Lan F, Matson C. et al. Histone demethylation mediated by the nuclear amine oxidase homolog LSD1. Cell . 2004; 119: 941-53

[58]

Jiang D, Yang W, He Y. et al. Arabidopsis relatives of the human lysine-specific demethylase1 repress the expression of FWA and FLOWERING LOCUS C and thus promote the floral transition. Plant Cell. 2007; 19: 2975-87

[59]

Spedaletti V, Polticelli F, Capodaglio V. et al. Characterization of a lysine-specific histone demethylase from Arabidopsis thaliana . Biochemistry. 2008; 47: 4936-47

[60]

Wei X, Li Y, Zhu X. et al. The GATA transcription factor TaGATA1 recruits demethylase TaELF6-A1 and enhances seed dormancy in wheat by directly regulating TaABI5. J Integr Plant Biol. 2023; 65: 1262-76

[61]

Alonso-Blanco C, Bentsink L, Hanhart CJ. et al. Analysis of natural allelic variation at seed dormancy loci of Arabidopsis thaliana . Genetics. 2003; 164: 711-29

[62]

Zheng J, Chen F, Wang Z. et al. A novel role for histone methyltransferase KYP/SUVH4 in the control of Arabidopsis primary seed dormancy. New Phytol. 2012; 193: 605-16

[63]

Zhou Y, Yang P, Zhang F. et al. Histone deacetylase HDA19 interacts with histone methyltransferase SUVH5 to regulate seed dormancy in Arabidopsis . Plant Biol. 2020; 22: 1062-71

[64]

Chen N, Wang H, Abdelmageed H. et al. HSI2/VAL1 and HSL1/VAL2 function redundantly to repress DOG1 expression in Arabidopsis seeds and seedlings . New Phytol. 2020; 227: 840-56

[65]

Monfared MM, Simon MK, Meister RJ. et al. Overlapping and antagonistic activities of BASIC PENTACYSTEINE genes affect a range of developmental processes in Arabidopsis . Plant J. 2011; 66: 1020-31

[66]

Li JR, Pan W, Liang J. et al. BASIC PENTACYSTEINE2 fine-tunes corm dormancy release in Gladiolus. Plant Physiol . 2023; 191: 2489-505

[67]

Pan W, Li J, Du Y. et al. Epigenetic silencing of callose synthase by VIL1 promotes bud-growth transition in lily bulbs. Nat Plants. 2023; 9: 1451-67

[68]

Molitor AM, Bu Z, Yu Y. et al. Arabidopsis AL PHD-PRC1 complexes promote seed germination through H3K4me3-to-H3K27me3 chromatin state switch in repression of seed developmental genes. PLoS Genet. 2014; 10: e1004091

[69]

Wu R, Wang T, Richardson AC. et al. Histone modification and activation by SOC1-like and drought stress-related transcription factors may regulate AcSVP2 expression during kiwifruit winter dormancy. Plant Sci. 2019; 281: 242-50

[70]

Leida C , Conesa A , Llácer G . et al. Histone modifications and expression of DAM6 gene in peach are modulated during bud dormancy release in a cultivar-dependent manner. New Phytol. 2012; 193: 67-80

[71]

Saito T, Bai S, Imai T. et al. Histone modification and signalling cascade of the dormancy-associated MADS-box gene, PpMADS13-1, in Japanese pear (Pyrus pyrifolia) during endodormancy . Plant Cell Environ. 2015; 38: 1157-66

[72]

Zhao Z, Yu Y, Meyer D. et al. Prevention of early flowering by expression of FLOWERING LOCUS C requires methylation of histone H3K36. Nat Cell Biol. 2005; 7: 1256-60

[73]

Guo Z, Li Z, Liu Y. et al. MRG1/2 histone methylation readers and HD2C histone deacetylase associate in repression of the florigen gene FT to set a proper flowering time in response to day-length changes. New Phytol. 2020; 227: 1453-66

[74]

Turck F, Fornara F, Coupland G . Regulation and identity of florigen: FLOWERING LOCUS T moves center stage. Annu Rev Plant Biol. 2008; 59: 573-94

[75]

Sung S, Amasino RM . Vernalization in Arabidopsis thaliana is mediated by the PHD finger protein VIN3. Nature. 2004; 427: 159-64

[76]

Hou X, Zhou J, Liu C. et al. Nuclear factor Y-mediated H3K27me3 demethylation of the SOC1 locus orchestrates flowering responses of Arabidopsis . Nat Commun. 2014; 5: 4601

[77]

Ye R, Wang M, Du H. et al. Glucose-driven TOR-FIE-PRC2 signalling controls plant development. Nature. 2022; 609: 986-93

[78]

De Lucia F, Crevillen P, Jones AM. et al. A PHD-polycomb repressive complex 2 triggers the epigenetic silencing of FLC during vernalization. Proc Natl Acad Sci USA. 2008; 105: 16831-6

[79]

Yang HC, Berry S, Olsson TSG. et al. Distinct phases of polycomb silencing to hold epigenetic memory of cold in Arabidopsis . Science. 2017; 357: 1142-5

[80]

Zhu P, Lister C, Dean C . Cold-induced Arabidopsis FRIGIDA nuclear condensates for FLC repression. Nature. 2021; 599: 657-61

[81]

Feng S, Jiang X, Wang R. et al. Histone H3K4 methyltransferase DcATX1 promotes ethylene induced petal senescence in carnation. Plant Physiol. 2023; 192: 546-64

[82]

Ay N, Irmler K, Fischer A. et al. Epigenetic programming via histone methylation at WRKY53 controls leaf senescence in Arabidopsis thaliana . Plant J. 2009; 58: 333-46

[83]

Brusslan JA, Rus Alvarez-Canterbury AM, Nair NU. et al. Genome-wide evaluation of histone methylation changes associated with leaf senescence in Arabidopsis . PLoS One. 2012; 7: e33151

[84]

Brusslan JA, Bonora G, Rus-Canterbury AM. et al. A genome-wide chronological study of gene expression and two histone modifications, H3K4me3 and H3K9ac, during developmental leaf senescence. Plant Physiol. 2015; 168: 1246-61

[85]

Liu P, Zhang S, Zhou B. et al. The histone H3K4 demethylase JMJ16 represses leaf senescence in Arabidopsis . Plant Cell. 2019; 31: 430-43

[86]

Wang X, Gao J, Gao S. et al. The H3K27me3 demethylase REF6 promotes leaf senescence through directly activating major senescence regulatory and functional genes in Arabidopsis. PLoS Genet. 2019; 15: e1008068

[87]

Kim JM, To TK, Ishida J. et al. Transition of chromatin status during the process of recovery from drought stress in Arabidopsis thaliana . Plant Cell Physiol. 2012; 53: 847-56

[88]

Ding Y, Avramova Z, Fromm M . The Arabidopsis trithorax-like factor ATX1 functions in dehydration stress responses via ABA-dependent and ABA-independent pathways. Plant J. 2011; 66: 735-44

[89]

Liu Y, Zhang A, Yin H. et al. Trithorax-group proteins ARABIDOPSIS TRITHORAX4 (ATX4) and ATX5 function in abscisic acid and dehydration stress responses. New Phytol. 2018; 217: 1582-97

[90]

Wang Z, Zhang Y, Kang Z. et al. Improvement of wheat drought tolerance through editing of TaATX4 by CRISPR/Cas9. J Genet Genomics. 2023; 50: 913-6

[91]

Zhang B, Wang Z, Dai X. et al. A COMPASS histone H3K4 trimethyltransferase pentamer transactivates drought tolerance and growth/biomass production in Populus trichocarpa . New Phytol. 2024; 241: 1950-72

[92]

Wang Q, Liu P, Jing H. et al. JMJ27-mediated histone H3K9 demethylation positively regulates drought-stress responses in Arabidopsis . New Phytol. 2021; 232: 221-36

[93]

Wang X, Yu Z, Xu H. et al. An H3K9me2 demethylase encoded by Jumonji C domain-containing DT2 regulates drought tolerance in rice. Plant Physiol. 2025; 198: kiaf280

[94]

Wu J, Ichihashi Y, Suzuki T. et al. Abscisic acid-dependent histone demethylation during post germination growth arrest in Arabidopsis. Plant Cell Environ . 2019; 42: 2198-214

[95]

Wei W, Lu L, Bian XH. et al. Zinc-finger protein GmZF351 improves both salt and drought stress tolerance in soybean. J Integr Plant Biol. 2023; 65: 1636-50

[96]

Zhao W, Wang X, Zhang Q. et al. H3K36 demethylase JMJ710 negatively regulates drought tolerance by suppressing MYB48-1 expression in rice. Plant Physiol. 2022; 189: 1050-64

[97]

Song Y, He J, Guo J. et al. The chromatin remodeller MdRAD5B enhances drought tolerance by coupling MdLHP1-mediated H3K27me3 in apple. Plant Biotechnol J. 2024; 22: 617-34

[98]

Peng Y, Zhu H, Wang Y. et al. Revisiting the role of light signaling in plant responses to salt stress. Hortic Res. 2024; 12: uhae262

[99]

Yung WS, Wang Q, Huang M. et al. Priming-induced alterations in histone modifications modulate transcriptional responses in soybean under salt stress. Plant J. 2022; 109: 1575-90

[100]

Bastola DR, Pethe VV, Winicov I . Alfin1, a novel zinc-finger protein in alfalfa roots that binds to promoter elements in the salt-inducible MsPRP2 gene . Plant Mol Biol. 1998; 38: 1123-35

[101]

Wei W, Huang J, Hao YJ. et al. Soybean GmPHD-type transcription regulators improve stress tolerance in transgenic Arabidopsis plants. PLoS One. 2009; 4: e7209

[102]

Wu T, Pi EX, Tsai SN. et al. 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. 2011; 11: 178

[103]

Wei W, Tao JJ, Chen HW. et al. A histone code reader and a transcriptional activator interact to regulate genes for salt tolerance. Plant Physiol. 2017; 175: 1304-20

[104]

Paul A, Dasgupta P, Roy D. et al. Comparative analysis of histone modifications and DNA methylation at OsBZ8 locus under salinity stress in IR64 and Nonabokra rice varieties. Plant Mol Biol. 2017; 95: 63-88

[105]

Sani E, Herzyk P, Perrella G. et al. Hyperosmotic priming of Arabidopsis seedlings establishes a long-term somatic memory accompanied by specific changes of the epigenome. Genome Biol. 2013; 14: R59

[106]

Han B, Xu W, Ahmed N. et al. Changes and associations of genomic transcription and histone methylation with salt stress in castor bean. Plant Cell Physiol. 2020; 61: 1120-33

[107]

Pajoro A, Severing E, Angenent GC. et al. Histone H3 lysine 36 methylation affects temperature-induced alternative splicing and flowering in plants. Genome Biol. 2017; 18: 102

[108]

Song Z, Zhang L, Han J. et al. Histone H3K4 methyltransferases SDG25 and ATX1 maintain heat-stress gene expression during recovery in Arabidopsis . Plant J. 2021; 105: 1326-38

[109]

Lämke J, Brzezinka K, Altmann S. et al. A hit-and-run heat shock factor governs sustained histone methylation and transcriptional stress memory. EMBO J. 2016; 35: 162-75

[110]

Cui X, Zheng Y, Lu Y. et al. Metabolic control of histone demethylase activity involved in plant response to high temperature. Plant Physiol . 2021; 185: 1813-28

[111]

Chai J, Gu X, Song P. et al. Histone demethylase JMJ713 interaction with JMJ708 modulating H3K36me2, enhances rice heat tolerance through promoting hydrogen peroxide scavenging. Plant Physiol Biochem. 2024; 217: 109284

[112]

Yamaguchi N, Matsubara S, Yoshimizu K. et al. H3K27me3 demethylases alter HSP22 and HSP17.6C expression in response to recurring heat in Arabidopsis . Nat Commun. 2021; 12: 3480

[113]

Zeng Z, Zhang W, Marand AP. et al. Cold stress induces enhanced chromatin accessibility and bivalent histone modifications H3K4me3 and H3K27me3 of active genes in potato. Genome Biol . 2019; 20: 123

[114]

Kwon CS, Lee D, Choi G. et al. Histone occupancy-dependent and -independent removal of H3K27 trimethylation at cold-responsive genes in Arabidopsis . Plant J. 2009; 60: 112-21

[115]

Luo Y, Wang Y, Li X. et al. Transcription factor DgMYB recruits H3K4me3 methylase to DgPEROXIDASE to enhance chrysanthemum cold tolerance. Plant Physiol. 2024; 194: 1104-19

[116]

Gu T, Han Y, Huang R. et al. Identification and characterization of histone lysine methylation modifiers in Fragaria vesca . Sci Rep. 2016; 6: 23581

[117]

Di Q, Zhou M, Li Y. et al. RESPIRATORY BURST OXIDASE HOMOLOG 5.1 regulates H3K4me3 deposition and transcription after cold priming in cucumber. Plant Physiol. 2025; 197: kiae461

[118]

Kim J, Bordiya Y, Kathare PK. et al. Phytochrome B triggers light-dependent chromatin remodelling through the PRC2-associated PHD finger protein VIL1. Nat Plants. 2021; 7: 1213-9

[119]

Yan Y, Zhu J, Qiu Q. et al. The Arabidopsis demethylase REF6 physically interacts with phyB to promote hypocotyl elongation under red light. Proc Natl Acad Sci USA. 2025; 122: e2417253122

[120]

Wang P, Zhang H, Yin Y. et al. Differential epigenetic regulation by blue and UV-A light reveals the key role of CsSDG36-mediated H3K4 methylation in leaf development and secondary metabolism in Camellia sinensis . Genome Biol. 2025; 26: 150

[121]

Fan D, Wang X, Liu T. et al. Epigenetic regulation of high light-induced anthocyanin biosynthesis by histone demethylase IBM1 in Arabidopsis. New Phytol. 2024; 242: 2570-85

[122]

Wang W, Kim J, Sung HS . COP1 controls light-dependent chromatin remodeling. Proc Natl Acad Sci USA . 2024; 121: e2312853121-1

[123]

Luo X, Li X, Chen Z. et al. A pair of readers of histone H3K4 methylation recruit polycomb repressive complex 2 to regulate photoperiodic flowering. Nat Commun. 2025; 16: 9376

[124]

Gu D, Wang Y, Zhao M. et al. Phytochrome B stabilizes the KNOX transcription factor BP/KNAT1 to promote light-initiated seed germination in Arabidopsis thaliana. Plant Commun . 2025; 6: 101517

[125]

Sharma M, Banday ZZ, Shukla BN. et al. Glucose-regulated HLP1 acts as a key molecule in governing thermomemory. Plant Physiol . 2019; 180: 1081-100

[126]

Sharma M, Sharma M, Jamsheer KM. et al. 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. 2022; 73: 7083-102

[127]

Dong Y, Uslu VV, Berr A. et al. TOR represses stress responses through global regulation of H3K27 trimethylation in plants. J Exp Bot. 2023; 74: 1420-31

[128]

Dong Y, Oubassou EZ, Hoffmann E. et al. Target of rapamycin (TOR) regulates CURLY LEAF (CLF) translation in response to environmental stimuli. bioRxiv. 2024. https://doi.org/10.1101/2024.06.28.601127

[129]

Shi M, Wang C, Wang P. et al. Role of methylation in vernalization and photoperiod pathway: a potential flowering regulator? Hortic Res. 2023; 10: uhad174

[130]

Lu J, Jiang Z, Chen J. et al. SET DOMAIN GROUP 711-mediated H3K27me3 methylation of cytokinin metabolism genes regulates organ size in rice. Plant Physiol. 2024; 194: 2069-85

[131]

Lee S, Fu F, Xu S. et al. Global regulation of plant immunity by histone lysine methyl transferases. Plant Cell . 2016; 28: 1640-61

[132]

Cheng K, Xu Y, Yang C. et al. Histone tales: lysine methylation, a protagonist in Arabidopsis development. J Exp Botn. 2020; 71: 793-807

[133]

Oberkofler V, Bäurle I . Inducible epigenome editing probes for the role of histone H3K4 methylation in Arabidopsis heat stress memory. Plant Physiol. 2022; 189: 703-14

[134]

Lin G, Zhou Y, Li M. et al. Histone 3 lysine 36 to methionine mutations stably interact with and sequester SDG8 in Arabidopsis thaliana. Sci China Life Sci. 2018; 61: 225-34

[135]

Fal K, Berr A, Le Masson M. et al. Lysine 27 of histone H3.3 is a fine modulator of developmental gene expression and stands as an epigenetic checkpoint for lignin biosynthesis in Arabidopsis. New Phytol. 2023; 238: 1085-100

[136]

Xue M, Ma L, Li X. et al. Single amino acid mutations in histone H3.3 illuminate the functional significance of H3K4 methylation in plants. Nat Commun. 2025; 16: 4408

[137]

Yihan D, Uslu VV, Berr A. et al. TOR represses stress responses through global regulation of H3K27me3 in plants. J Exp Botn. 2023; 74: 1420-31

[138]

Liu N, Fromm M, Avramova Z. et al. H3K27me3 and H3K4me3 chromatin environment at super-induced dehydration stress memory genes of Arabidopsis thaliana . Mol Plant. 2014; 7: 502-13

[139]

Qian S, Lv X, Scheid R. et al. Dual recognition of H3K4me3 and H3K27me3 by a plant histone reader SHL. Nat Commun . 2018; 9: 2425

[140]

Wang H, Yin C, Zhang G. et al. Cold-induced deposition of bivalent H3K4me3-H3K27me3 modification and nucleosome depletion in Arabidopsis. Plant J. 2024; 118: 549-64

[141]

Zhao F, Liu Y, Su X. et al. Molecular basis for histone H3“K4me3-K9me3/2” methylation pattern readout by Spindlin1. J Biol Chem . 2020; 295: 16877-87

[142]

Pan Q, Guo S, Ding J. et al. Dynamic histone modification signatures coordinate developmental programs in strawberry fruit ripening. Hortic Res. 2024; 11: uhae158

[143]

Li Z, Jiang G, Liu X. et al. Histone demethylase SlJMJ6 promotes fruit ripening by removing H3K27 methylation of ripening-related genes in tomato. New Phytol. 2020; 227: 1138-56

[144]

Ding X, Liu X, Jiang G. et al. SlJMJ7 orchestrates tomato fruit ripening via crosstalk between H3K4me3 and DML2-mediated DNA demethylation. New Phytol. 2022; 233: 1202-19

[145]

Du J, Johnson LM, Groth M. et al. Mechanism of DNA methylation directed histone methylation by KRYPTONITE. Mol Cell . 2014; 55: 495-504

PDF (2411KB)

170

Accesses

0

Citation

Detail

Sections
Recommended

/