Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Review Article
  • Published:

RNA m6A modification meets plant hormones

Nature Plants volume 11, pages 686–695 (2025)Cite this article

Subjects

Abstract

Plant hormones are essential signalling molecules that control and coordinate diverse physiological processes in plant development and adaptation to ever-fluctuating environments. This hormonal regulation of plant development and environmental responses has recently been shown to extensively involve the most widespread RNA modification, N6-methyladenosine (m6A). Here we discuss the current understanding of the crosstalk between m6A and plant hormones, focusing on their reciprocal regulation, where hormonal signals induce m6A reprogramming and m6A affects hormone biosynthesis and signalling cascades. We also highlight new insights into how m6A contributes to the hormonal control of plant development and stress responses. Furthermore, we discuss future prospects for unveiling the regulatory networks that orchestrate epitranscriptome–hormone interactions and harnessing the related knowledge accrued to enhance crop productivity and resilience in changing environments.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on SpringerLink
  • Instant access to the full article PDF.

USD 39.95

Prices may be subject to local taxes which are calculated during checkout

Fig. 1: Known m6A effector proteins in plants.
Fig. 2: The effects of various phytohormones on m6A modification.
Fig. 3: m6A writers modulate auxin biosynthesis and signalling.
Fig. 4: m6A effectors mediate ABA and SA signalling via various mechanisms.

Similar content being viewed by others

References

  1. Depuydt, S. & Hardtke, C. S. Hormone signalling crosstalk in plant growth regulation. Curr. Biol. 21, R365–R373 (2011).

    CAS  PubMed  Google Scholar 

  2. Waadt, R. et al. Plant hormone regulation of abiotic stress responses. Nat. Rev. Mol. Cell Biol. 23, 680–694 (2022).

    CAS  PubMed  PubMed Central  Google Scholar 

  3. Waadt, R. Phytohormone signaling mechanisms and genetic methods for their modulation and detection. Curr. Opin. Plant Biol. 57, 31–40 (2020).

    CAS  PubMed  Google Scholar 

  4. Santner, A., Calderon-Villalobos, L. I. & Estelle, M. Plant hormones are versatile chemical regulators of plant growth. Nat. Chem. Biol. 5, 301–307 (2009).

    CAS  PubMed  Google Scholar 

  5. Shen, L. S., Liang, Z., Wong, C. E. & Yu, H. Messenger RNA modifications in plants. Trends Plant Sci. 24, 328–341 (2019).

    CAS  PubMed  Google Scholar 

  6. Sharma, B., Prall, W., Bhatia, G. & Gregory, B. D. The diversity and functions of plant RNA modifications: what we know and where we go from here. Ann. Rev. Plant Biol. 74, 53–85 (2023).

    CAS  Google Scholar 

  7. Shao, Y., Wong, C. E., Shen, L. & Yu, H. N6-methyladenosine modification underlies messenger RNA metabolism and plant development. Curr. Opin. Plant Biol. 63, 102047 (2021).

    CAS  PubMed  Google Scholar 

  8. Shi, H., Wei, J. & He, C. Where, when, and how: context-dependent functions of RNA methylation writers, readers, and erasers. Mol. Cell 74, 640–650 (2019).

    CAS  PubMed  PubMed Central  Google Scholar 

  9. Shen, L., Ma, J., Li, P., Wu, Y. & Yu, H. Recent advances in the plant epitranscriptome. Genome Biol. 24, 43 (2023).

    CAS  PubMed  PubMed Central  Google Scholar 

  10. Wong, C. E. et al. Shaping the landscape of N6-methyladenosine RNA methylation in Arabidopsis. Plant Physiol. 191, 2045–2063 (2023).

    CAS  PubMed  PubMed Central  Google Scholar 

  11. Zhang, M. et al. Two zinc finger proteins with functions in m6A writing interact with HAKAI. Nat. Commun. 13, 1127 (2022).

    CAS  PubMed  PubMed Central  Google Scholar 

  12. Růžička, K. et al. Identification of factors required for m6A mRNA methylation in Arabidopsis reveals a role for the conserved E3 ubiquitin ligase HAKAI. New Phytol. 215, 157–172 (2017).

    PubMed  PubMed Central  Google Scholar 

  13. Shen, L. et al. N6-methyladenosine RNA modification regulates shoot stem cell fate in Arabidopsis. Dev. Cell 38, 186–200 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  14. Bodi, Z. et al. Adenosine methylation in Arabidopsis mRNA is associated with the 3′ end and reduced levels cause developmental defects. Front. Plant Sci. 3, 1–10 (2012).

    Google Scholar 

  15. Zhong, S. L. et al. MTA is an Arabidopsis messenger RNA adenosine methylase and interacts with a homolog of a sex-specific splicing factor. Plant Cell 20, 1278–1288 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  16. Shen, L. Functional interdependence of N6-methyladenosine methyltransferase complex subunits in Arabidopsis. Plant Cell 35, 1901–1916 (2023).

    PubMed  PubMed Central  Google Scholar 

  17. Parker, M. T. et al. Nanopore direct RNA sequencing maps the complexity of Arabidopsis mRNA processing and m6A modification. eLife 9, e49658 (2020).

    CAS  PubMed  PubMed Central  Google Scholar 

  18. Warda, A. S. et al. Human METTL16 is a N6-methyladenosine (m6A) methyltransferase that targets pre-mRNAs and various non-coding RNAs. EMBO Rep. 18, 2004–2014 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  19. Pendleton, K. E. et al. The U6 snRNA m6A methyltransferase METTL16 regulates SAM synthetase intron retention. Cell 169, 824–835 e814 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  20. Xu, T. et al. FIONA1-mediated m6A modification regulates the floral transition in Arabidopsis. Adv. Sci. 9, e2103628 (2022).

    Google Scholar 

  21. Wang, C. et al. FIONA1 is an RNA N6-methyladenosine methyltransferase affecting Arabidopsis photomorphogenesis and flowering. Genome Biol. 23, 40 (2022).

    CAS  PubMed  PubMed Central  Google Scholar 

  22. Ma, K. et al. OsEDM2L mediates m6A of EAT1 transcript for proper alternative splicing and polyadenylation regulating rice tapetal degradation. J. Integr. Plant Biol. 63, 1982–1994 (2021).

    CAS  PubMed  Google Scholar 

  23. Cheng, P. et al. RNA N6-methyladenosine modification promotes auxin biosynthesis required for male meiosis in rice. Dev. Cell 57, 246–259 (2022).

    CAS  PubMed  Google Scholar 

  24. Xu, C. et al. R-loop resolution promotes co-transcriptional chromatin silencing. Nat. Commun. 12, 1790 (2021).

    CAS  PubMed  PubMed Central  Google Scholar 

  25. Wang, X. et al. A photoregulatory mechanism of the circadian clock in Arabidopsis. Nat. Plants 7, 1397–1408 (2021).

    CAS  PubMed  Google Scholar 

  26. Jiang, B. et al. Light-induced LLPS of the CRY2/SPA1/FIO1 complex regulating mRNA methylation and chlorophyll homeostasis in Arabidopsis. Nat. Plants 9, 2024–2058 (2023).

    Google Scholar 

  27. Shim, S., Lee, H. G., Lee, H. & Seo, P. J. H3K36me2 is highly correlated with m6A modifications in plants. J. Integr. Plant Biol. 62, 1455–1460 (2020).

    CAS  PubMed  Google Scholar 

  28. Zheng, G. et al. ALKBH5 is a mammalian RNA demethylase that impacts RNA metabolism and mouse fertility. Mol. Cell 49, 18–29 (2013).

    CAS  PubMed  Google Scholar 

  29. Jia, G. F. et al. N6-methyladenosine in nuclear RNA is a major substrate of the obesity-associated FTO. Nat. Chem. Biol. 7, 885–887 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  30. Liang, Z. et al. Epigenetic modifications of mRNA and DNA in plants. Mol. Plant 13, 14–30 (2020).

    CAS  PubMed  Google Scholar 

  31. Mielecki, D. et al. Novel AlkB dioxygenases—alternative models for in silico and in vivo studies. PLoS ONE 7, e30588 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  32. Tang, J. et al. The RNA N6-methyladenosine demethylase ALKBH9B modulates ABA responses in Arabidopsis. J. Integr. Plant Biol. 64, 2361–2373 (2022).

    CAS  PubMed  Google Scholar 

  33. Amara, U., Shoaib, Y. & Kang, H. ALKBH9C, a potential RNA m6A demethylase, regulates the response of Arabidopsis to abiotic stresses and abscisic acid. Plant Cell Environ. 45, 3566–3581 (2022).

    CAS  PubMed  Google Scholar 

  34. Martínez-Pérez, M. et al. Arabidopsis m6A demethylase activity modulates viral infection of a plant virus and the m6A abundance in its genomic RNAs. Proc. Natl Acad. Sci. USA 114, 10755–10760 (2017).

    PubMed  PubMed Central  Google Scholar 

  35. Duan, H. C. et al. ALKBH10B is an RNA N6-methyladenosine demethylase affecting Arabidopsis floral transition. Plant Cell 29, 2995–3011 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  36. Fan, S., Zhang, Y., Zhu, S. & Shen, L. Plant RNA-binding proteins: phase separation dynamics and functional mechanisms underlying plant development and stress responses. Mol. Plant 17, 531–551 (2024).

    CAS  PubMed  Google Scholar 

  37. Wang, X. et al. m6A-dependent regulation of messenger RNA stability. Nature 505, 117–120 (2014).

    PubMed  Google Scholar 

  38. Xu, C. et al. Structural basis for the discriminative recognition of N6-methyladenosine RNA by the human YT521-B homology domain family of proteins. J. Biol. Chem. 290, 24902–24913 (2015).

    CAS  PubMed  Google Scholar 

  39. Li, F., Zhao, D., Wu, J. & Shi, Y. Structure of the YTH domain of human YTHDF2 in complex with an m6A mononucleotide reveals an aromatic cage for m6A recognition. Cell Res. 24, 1490–1492 (2014).

    PubMed  PubMed Central  Google Scholar 

  40. Wu, X. et al. N6-methyladenosine-mediated feedback regulation of abscisic acid perception via phase-separated ECT8 condensates in Arabidopsis. Nat. Plants 10, 469–482 (2024).

    CAS  PubMed  Google Scholar 

  41. Cai, Z. et al. The m6A reader ECT8 is an abiotic stress sensor that accelerates mRNA decay in Arabidopsis. Plant Cell 36, 2908–2926 (2024).

    PubMed  PubMed Central  Google Scholar 

  42. Lee, K. P. et al. The m6A reader ECT1 drives mRNA sequestration to dampen salicylic acid-dependent stress responses in Arabidopsis. Plant Cell 36, 746–763 (2023).

    PubMed Central  Google Scholar 

  43. Song, P. Z. et al. Arabidopsis N6-methyladenosine reader CPSF30-L recognizes FUE signals to control polyadenylation site choice in liquid-like nuclear bodies. Mol. Plant 14, 571–587 (2021).

    CAS  PubMed  Google Scholar 

  44. Hou, Y. F. et al. CPSF30-L-mediated recognition of mRNA m6A modification controls alternative polyadenylation of nitrate signaling-related gene transcripts in Arabidopsis. Mol. Plant 14, 688–699 (2021).

    CAS  PubMed  Google Scholar 

  45. Wei, L. H. et al. The m6A reader ECT2 controls trichome morphology by affecting mRNA stability in Arabidopsis. Plant Cell 30, 968–985 (2018).

    CAS  PubMed  PubMed Central  Google Scholar 

  46. Scutenaire, J. et al. The YTH domain protein ECT2 is an m6A reader required for normal trichome branching in Arabidopsis. Plant Cell 30, 986–1005 (2018).

    CAS  PubMed  PubMed Central  Google Scholar 

  47. Arribas-Hernández, L. et al. An m6A–YTH module controls developmental timing and morphogenesis in Arabidopsis. Plant Cell 30, 952–967 (2018).

    PubMed  PubMed Central  Google Scholar 

  48. Amara, U., Hu, J., Cai, J. & Kang, H. FLK is an mRNA m6A reader that regulates floral transition by modulating the stability and splicing of FLC in Arabidopsis. Mol. Plant 16, 919–929 (2023).

    CAS  PubMed  Google Scholar 

  49. Wang, W. et al. Transcriptome-wide N6-methyladenosine profiling of cotton root provides insights for salt stress tolerance. Environ. Exp. Bot. 194, 104729 (2022).

    CAS  Google Scholar 

  50. Su, T. et al. Transcriptome-wide m6A methylation profile reveals regulatory networks in roots of barley under cadmium stress. J. Hazard. Mater. 423, 127140 (2022).

    CAS  PubMed  Google Scholar 

  51. Hou, N. et al. MdMTA-mediated m6A modification enhances drought tolerance by promoting mRNA stability and translation efficiency of genes involved in lignin deposition and oxidative stress. New Phytol. 234, 1294–1314 (2022).

    CAS  PubMed  Google Scholar 

  52. Govindan, G. et al. mRNA N6-methyladenosine is critical for cold tolerance in Arabidopsis. Plant J. 111, 1052–1068 (2022).

    CAS  PubMed  PubMed Central  Google Scholar 

  53. Gao, Y. et al. Drought induces epitranscriptome and proteome changes in stem-differentiating xylem of Populus trichocarpa. Plant Physiol. 29, 459–479 (2022).

    Google Scholar 

  54. Zheng, H. et al. Analysis of N6-methyladenosine reveals a new important mechanism regulating the salt tolerance of sweet sorghum. Plant Sci. 304, 110801 (2021).

    CAS  PubMed  Google Scholar 

  55. Zhang, G. et al. Unique features of the m6A methylome and its response to drought stress in sea buckthorn (Hippophae rhamnoides Linn.). RNA Biol. 18, 794–803 (2021).

    CAS  PubMed  PubMed Central  Google Scholar 

  56. Yang, D. et al. RNA N6-methyladenosine responds to low-temperature stress in tomato anthers. Front. Plant Sci. 12, 687826 (2021).

    PubMed  PubMed Central  Google Scholar 

  57. Hu, J. et al. N6-methyladenosine mRNA methylation is important for salt stress tolerance in Arabidopsis. Plant J. 106, 1759–1775 (2021).

    CAS  PubMed  Google Scholar 

  58. Cheng, Q. et al. Coordination of m6A mRNA methylation and gene transcriptome in rice response to cadmium stress. Rice 14, 62 (2021).

    CAS  PubMed  PubMed Central  Google Scholar 

  59. Anderson, S. J. et al. N6-methyladenosine inhibits local ribonucleolytic cleavage to stabilize mRNAs in Arabidopsis. Cell Rep. 25, 1146–1157 (2018).

    CAS  PubMed  Google Scholar 

  60. Du, X. M. et al. Global profiling of N6-methyladenosine methylation in maize callus induction. Plant Genome 13, e20018 (2020).

    CAS  PubMed  Google Scholar 

  61. Zhang, B. et al. Defining context-dependent m6A RNA methylomes in Arabidopsis. Dev. Cell 59, 2772–2786 (2024).

    CAS  PubMed  Google Scholar 

  62. Wang, Y. et al. Global N6-methyladenosine profiling revealed the tissue-specific epitranscriptomic regulation of rice responses to salt stress. Int. J. Mol. Sci. 23, 2091 (2022).

    CAS  PubMed  PubMed Central  Google Scholar 

  63. Tang, J., Yang, J., Duan, H. & Jia, G. ALKBH10B, an mRNA m6A demethylase, modulates ABA response during seed germination in Arabidopsis. Front. Plant Sci. 12, 712713 (2021).

    PubMed  PubMed Central  Google Scholar 

  64. Zhang, H. et al. A comprehensive online database for exploring ~20,000 public Arabidopsis RNA-seq libraries. Mol. Plant 13, 1231–1233 (2020).

    CAS  PubMed  Google Scholar 

  65. Fan, W. et al. m6A RNA demethylase AtALKBH9B promotes mobilization of a heat-activated long terminal repeat retrotransposon in Arabidopsis. Sci. Adv. 9, eadf3292 (2023).

    CAS  PubMed  PubMed Central  Google Scholar 

  66. Yu, Z., Zhang, F., Friml, J. & Ding, Z. Auxin signaling: research advances over the past 30 years. J. Integr. Plant Biol. 64, 371–392 (2022).

    CAS  PubMed  Google Scholar 

  67. Du, M., Spalding, E. P. & Gray, W. M. Rapid auxin-mediated cell expansion. Ann. Rev. Plant Biol. 71, 379–402 (2020).

    CAS  Google Scholar 

  68. Zhao, Y. Auxin biosynthesis: a simple two-step pathway converts tryptophan to indole-3-acetic acid in plants. Mol. Plant 5, 334–338 (2012).

    CAS  PubMed  Google Scholar 

  69. Won, C. et al. Conversion of tryptophan to indole-3-acetic acid by TRYPTOPHAN AMINOTRANSFERASES OF ARABIDOPSIS and YUCCAs in Arabidopsis. Proc. Natl Acad. Sci. USA 108, 18518–18523 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  70. Mashiguchi, K. et al. The main auxin biosynthesis pathway in Arabidopsis. Proc. Natl Acad. Sci. USA 108, 18512–18517 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  71. Gate, T., Hill, L., Miller, A. J. & Sanders, D. AtIAR1 is a Zn transporter that regulates auxin metabolism in Arabidopsis thaliana. J. Exp. Bot. 75, 1437–1450 (2024).

    PubMed  Google Scholar 

  72. Korasick, D. A., Enders, T. A. & Strader, L. C. Auxin biosynthesis and storage forms. J. Exp. Bot. 64, 2541–2555 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  73. Ludwig-Muller, J. Auxin conjugates: their role for plant development and in the evolution of land plants. J. Exp. Bot. 62, 1757–1773 (2011).

    PubMed  Google Scholar 

  74. Quint, M., Barkawi, L. S., Fan, K. T., Cohen, J. D. & Gray, W. M. Arabidopsis IAR4 modulates auxin response by regulating auxin homeostasis. Plant Physiol. 150, 748–758 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  75. Rampey, R. A. et al. A family of auxin-conjugate hydrolases that contributes to free indole-3-acetic acid levels during Arabidopsis germination. Plant Physiol. 135, 978–988 (2004).

    CAS  PubMed  PubMed Central  Google Scholar 

  76. LeClere, S., Rampey, R. A. & Bartel, B. IAR4, a gene required for auxin conjugate sensitivity in Arabidopsis, encodes a pyruvate dehydrogenase E1α homolog. Plant Physiol. 135, 989–999 (2004).

    CAS  PubMed  PubMed Central  Google Scholar 

  77. Lasswell, J., Rogg, L. E., Nelson, D. C., Rongey, C. & Bartel, B. Cloning and characterization of IAR1, a gene required for auxin conjugate sensitivity in Arabidopsis. Plant Cell 12, 2395–2408 (2000).

    CAS  PubMed  PubMed Central  Google Scholar 

  78. Davies, R. T., Goetz, D. H., Lasswell, J., Anderson, M. N. & Bartel, B. IAR3 encodes an auxin conjugate hydrolase from Arabidopsis. Plant Cell 11, 365–376 (1999).

    CAS  PubMed  PubMed Central  Google Scholar 

  79. Bartel, B. & Fink, G. R. ILR1, an amidohydrolase that releases active indole-3-acetic acid from conjugates. Science 268, 1745–1748 (1995).

    CAS  PubMed  Google Scholar 

  80. Leyser, O. Auxin signaling. Plant Physiol. 176, 465–479 (2018).

    CAS  PubMed  Google Scholar 

  81. Gray, W. M., Kepinski, S., Rouse, D., Leyser, O. & Estelle, M. Auxin regulates SCF(TIR1)-dependent degradation of AUX/IAA proteins. Nature 414, 271–276 (2001).

    CAS  PubMed  Google Scholar 

  82. Kepinski, S. & Leyser, O. Auxin-induced SCFTIR1–Aux/IAA interaction involves stable modification of the SCFTIR1 complex. Proc. Natl Acad. Sci. USA 101, 12381–12386 (2004).

    CAS  PubMed  PubMed Central  Google Scholar 

  83. Tan, X. et al. Mechanism of auxin perception by the TIR1 ubiquitin ligase. Nature 446, 640–645 (2007).

    CAS  PubMed  Google Scholar 

  84. Arribas-Hernández, L. et al. Recurrent requirement for the m6A–ECT2/ECT3/ECT4 axis in the control of cell proliferation during plant organogenesis. Development 147, dev189134 (2020).

    PubMed  PubMed Central  Google Scholar 

  85. Bhat, S. S. et al. mRNA adenosine methylase (MTA) deposits m6A on pri-miRNAs to modulate miRNA biogenesis in Arabidopsis thaliana. Proc. Natl Acad. Sci. USA 117, 21785–21795 (2020).

    CAS  PubMed  PubMed Central  Google Scholar 

  86. Zemlyanskaya, E. A. et al. N6-adenosine methylation of mRNA integrates multilevel auxin response and ground tissue development in Arabidopsis. Development 150, dev.201775 (2023).

    Google Scholar 

  87. Jiang, J., Zhu, H., Li, N., Batley, J. & Wang, Y. The miR393-target module regulates plant development and responses to biotic and abiotic stresses. Int. J. Mol. Sci. 23, 9477 (2022).

    CAS  PubMed  PubMed Central  Google Scholar 

  88. Windels, D. et al. miR393 is required for production of proper auxin signalling outputs. PLoS ONE 9, e95972 (2014).

    PubMed  PubMed Central  Google Scholar 

  89. Tang, J. et al. OsALKBH9‐mediated m6A demethylation regulates tapetal PCD and pollen exine accumulation in rice. Plant Biotechnol. J. 22, 2410–2423 (2024).

    CAS  PubMed  PubMed Central  Google Scholar 

  90. Huang, X. et al. Cotton (Gossypium hirsutum) VIRMA as an N6-methyladenosine RNA methylation regulator participates in controlling chloroplast-dependent and independent leaf development. Int. J. Mol. Sci. 23, 9887 (2022).

    CAS  PubMed  PubMed Central  Google Scholar 

  91. Hewage, K. A. H. et al. Chemical manipulation of abscisic acid signaling: a new approach to abiotic and biotic stress management in agriculture. Adv. Sci. 7, 2001265 (2020).

    CAS  Google Scholar 

  92. Chen, K. et al. Abscisic acid dynamics, signaling, and functions in plants. J. Integr. Plant Biol. 62, 25–54 (2020).

    CAS  PubMed  Google Scholar 

  93. Thompson, A. J. et al. Abscisic acid biosynthesis in tomato: regulation of zeaxanthin epoxidase and 9-cis-epoxycarotenoid dioxygenase mRNAs by light/dark cycles, water stress and abscisic acid. Plant Mol. Biol. 42, 833–845 (2000).

    CAS  PubMed  Google Scholar 

  94. Raghavendra, A. S., Gonugunta, V. K., Christmann, A. & Grill, E. ABA perception and signalling. Trends Plant Sci. 15, 395–401 (2010).

    CAS  PubMed  Google Scholar 

  95. Park, S. Y. et al. Abscisic acid inhibits type 2C protein phosphatases via the PYR/PYL family of START proteins. Science 324, 1068–1071 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  96. Ma, Y. et al. Regulators of PP2C phosphatase activity function as abscisic acid sensors. Science 324, 1064–1068 (2009).

    CAS  PubMed  Google Scholar 

  97. Fujii, H. et al. In vitro reconstitution of an abscisic acid signalling pathway. Nature 462, 660–664 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  98. Umezawa, T. et al. Type 2C protein phosphatases directly regulate abscisic acid-activated protein kinases in Arabidopsis. Proc. Natl Acad. Sci. USA 106, 17588–17593 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  99. Fujii, H., Verslues, P. E. & Zhu, J. K. Identification of two protein kinases required for abscisic acid regulation of seed germination, root growth, and gene expression in Arabidopsis. Plant Cell 19, 485–494 (2007).

    CAS  PubMed  PubMed Central  Google Scholar 

  100. Fujita, Y. et al. Three SnRK2 protein kinases are the main positive regulators of abscisic acid signaling in response to water stress in Arabidopsis. Plant Cell Physiol. 50, 2123–2132 (2009).

    CAS  PubMed  Google Scholar 

  101. Zhu, J. K. Salt and drought stress signal transduction in plants. Ann. Rev. Plant Biol. 53, 247–273 (2002).

    CAS  Google Scholar 

  102. Luo, W. et al. 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 (2023).

    CAS  PubMed  Google Scholar 

  103. Belda-Palazon, B. et al. FYVE1/FREE1 interacts with the PYL4 ABA receptor and mediates its delivery to the vacuolar degradation pathway. Plant Cell 28, 2291–2311 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  104. Song, P. et al. m6A readers ECT2/ECT3/ECT4 enhance mRNA stability through direct recruitment of the poly(A) binding proteins in Arabidopsis. Genome Biol. 24, 103 (2023).

    CAS  PubMed  PubMed Central  Google Scholar 

  105. Lee, J. H. et al. DWA1 and DWA2, two Arabidopsis DWD protein components of CUL4-based E3 ligases, act together as negative regulators in ABA signal transduction. Plant Cell 22, 1716–1732 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  106. Sheikh, A. H. et al. m6A RNA methylation counteracts dark-induced leaf senescence in Arabidopsis. Plant Physiol. 194, 2663–2678 (2024).

    CAS  PubMed  Google Scholar 

  107. Zhou, L. et al. N6-methyladenosine RNA modification regulates strawberry fruit ripening in an ABA-dependent manner. Genome Biol. 22, 168 (2021).

    CAS  PubMed  PubMed Central  Google Scholar 

  108. Zhou, J. M. & Zhang, Y. Plant immunity: danger perception and signaling. Cell 181, 978–989 (2020).

    CAS  PubMed  Google Scholar 

  109. Kachroo, P., Liu, H. & Kachroo, A. Salicylic acid: transport and long-distance immune signaling. Curr. Opin. Virol. 42, 53–57 (2020).

    CAS  PubMed  Google Scholar 

  110. Prall, W. et al. Pathogen-induced m6A dynamics affect plant immunity. Plant Cell 35, 4155–4172 (2023).

    PubMed  PubMed Central  Google Scholar 

  111. Wang, H. et al. ECT9 condensates with ECT1 and regulates plant immunity. Front. Plant Sci. 14, 1140840 (2023).

    PubMed  PubMed Central  Google Scholar 

  112. Ao, Q., Qiu, T., Liao, F., Hu, Z. & Yang, Y. Knockout of SlYTH2, encoding a YTH domain-containing protein, caused plant dwarfing, delayed fruit internal ripening, and increased seed abortion rate in tomato. Plant Sci. 335, 111807 (2023).

    CAS  PubMed  Google Scholar 

  113. Yin, S. et al. Tomato SlYTH1 encoding a putative RNA m6A reader affects plant growth and fruit shape. Plant Sci. 323, 111417 (2022).

    CAS  PubMed  Google Scholar 

  114. Yin, S., Ao, Q., Tan, C. & Yang, Y. Genome-wide identification and characterization of YTH domain-containing genes, encoding the m6A readers, and their expression in tomato. Plant Cell Rep. 40, 1229–1245 (2021).

    CAS  PubMed  Google Scholar 

  115. Verma, V., Ravindran, P. & Kumar, P. P. Plant hormone-mediated regulation of stress responses. BMC Plant Biol. 16, 86 (2016).

    PubMed  PubMed Central  Google Scholar 

  116. Zhao, X., Dou, L., Gong, Z., Wang, X. & Mao, T. BES1 hinders ABSCISIC ACID INSENSITIVE5 and promotes seed germination in Arabidopsis. New Phytol. 221, 908–918 (2019).

    CAS  PubMed  Google Scholar 

  117. Hu, L. et al. m6A RNA modifications are measured at single-base resolution across the mammalian transcriptome. Nat. Biotechnol. 40, 1210–1219 (2022).

    CAS  PubMed  PubMed Central  Google Scholar 

  118. Anreiter, I., Mir, Q., Simpson, J. T., Janga, S. C. & Soller, M. New twists in detecting mRNA modification dynamics. Trends Biotechnol. 39, 72–89 (2020).

    PubMed  PubMed Central  Google Scholar 

  119. Garalde, D. R. et al. Highly parallel direct RNA sequencing on an array of nanopores. Nat. Methods 15, 201–206 (2018).

    CAS  PubMed  Google Scholar 

  120. Yu, L. et al. CRISPR/dCas13(Rx) derived RNA N6-methyladenosine (m6A) dynamic modification in plant. Adv. Sci. 11, e2401118 (2024).

    Google Scholar 

  121. Shi, C. et al. Programmable RNA N6-methyladenosine editing with CRISPR/dCas13a in plants. Plant Biotechnol. J. 22, 1867–1880 (2024).

    CAS  PubMed  PubMed Central  Google Scholar 

  122. Fang, R., Chen, X., Shen, J. & Wang, B. Targeted mRNA demethylation in Arabidopsis using plant m6A editor. Plant Methods 19, 81 (2023).

    CAS  PubMed  PubMed Central  Google Scholar 

  123. Shen, L. & Yu, H. Epitranscriptome engineering in crop improvement. Mol. Plant 14, 1418–1420 (2021).

    CAS  PubMed  Google Scholar 

  124. Wilson, C., Chen, P. J., Miao, Z. & Liu, D. R. Programmable m6A modification of cellular RNAs with a Cas13-directed methyltransferase. Nat. Biotechnol. 38, 1431–1440 (2020).

    CAS  PubMed  PubMed Central  Google Scholar 

  125. Li, J. et al. Targeted mRNA demethylation using an engineered dCas13b–ALKBH5 fusion protein. Nucleic Acids Res. 48, 5684–5694 (2020).

    CAS  PubMed  PubMed Central  Google Scholar 

  126. Kim, J. S. Precision genome engineering through adenine and cytosine base editing. Nat. Plants 4, 148–151 (2018).

    CAS  PubMed  Google Scholar 

  127. Kang, B. C. et al. Precision genome engineering through adenine base editing in plants. Nat. Plants 4, 427–431 (2018).

    CAS  PubMed  Google Scholar 

  128. Yu, X. et al. Messenger RNA 5′ NAD(+) capping is a dynamic regulatory epitranscriptome mark that is required for proper response to abscisic acid in Arabidopsis. Dev. Cell 56, 125–140 (2021).

    CAS  PubMed  Google Scholar 

  129. Cui, X. et al. 5-Methylcytosine RNA methylation in Arabidopsis thaliana. Mol. Plant 10, 1387–1399 (2017).

    CAS  PubMed  Google Scholar 

  130. Chen, C. et al. TBtools: an integrative toolkit developed for interactive analyses of big biological data. Mol. Plant 13, 1194–1202 (2020).

    CAS  PubMed  Google Scholar 

Download references

Acknowledgements

Figures 1–4 created with BioRender.com. Preparation of this Review was supported by the National Research Foundation Competitive Research Programme (NRF-CRP22-2019-0001) and intramural funding from Temasek Life Sciences Laboratory and the National University of Singapore.

Author information

Authors and Affiliations

  1. Temasek Life Sciences Laboratory, National University of Singapore, Singapore, Singapore

    Lisha Shen & Hao Yu

  2. Department of Biological Sciences, National University of Singapore, Singapore, Singapore

    Hao Yu

Authors
  1. Lisha Shen
    View author publications

    Search author on:PubMed Google Scholar

  2. Hao Yu
    View author publications

    Search author on:PubMed Google Scholar

Corresponding authors

Correspondence to Lisha Shen or Hao Yu.

Ethics declarations

Competing interests

The authors declare no competing interests.

Peer review

Peer review information

Nature Plants thanks Hunseung Kang, Xufeng Wang and Hong-Chao Duan for their contribution to the peer review of this work.

Additional information

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Rights and permissions

Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Shen, L., Yu, H. RNA m6A modification meets plant hormones. Nat. Plants 11, 686–695 (2025). https://doi.org/10.1038/s41477-025-01947-5

Download citation

  • Received:

  • Accepted:

  • Published:

  • Version of record:

  • Issue date:

  • DOI: https://doi.org/10.1038/s41477-025-01947-5

This article is cited by

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing