CoChat
Sign Up
Cited by 35Plant Molecular Biology ResearchEpigenetics and DNA MethylationPlant Gene Expression Analysis

Epigenetics and Plant Hormone Dynamics: A Functional and Methodological Perspective

Open access
Rudolf, Jiri, Tomovicova, Lucia, Panzarova, Klara, Fajkus, Jiri, Hejatko, Jan, Skalak, Jan·2024·Journal of Experimental Botany
DOI 10.1093/jxb/erae054PMC PMC11389840
Open this paper in CoChat — free account

Abstract

Plant hormones, pivotal regulators of plant growth, development, and response to environmental cues, have recently emerged as central modulators of epigenetic processes governing gene expression and phenotypic plasticity. This review addresses the complex interplay between plant hormones and epigenetic mechanisms, highlighting the diverse methodologies that have been harnessed to decipher these intricate relationships. We present a comprehensive overview to understand how phytohormones orchestrate epigenetic modifications, shaping plant adaptation and survival strategies. Conversely, we explore how epigenetic regulators ensure hormonal balance and regulate the signalling pathways of key plant hormones. Furthermore, our investigation includes a search for novel genes that are regulated by plant hormones under the control of epigenetic processes. Our review offers a contemporary overview of the epigenetic–plant hormone crosstalk, emphasizing its significance in plant growth, development, and potential agronomical applications.

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1093/jxb/erae054

Cites

1 of 1 references verified0 citation errors · 0 not checkable

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • In bananas, somaclonal variants significantly increased after the eighth subculture while propagation rates declined.

    “In bananas, for instance, somaclonal variants significantly increased after the eighth subculture while propagation rates declined [75], and similar patterns were noted in callus cultures [76,77].”

    From Somaclonal Variation and Clonal Fidelity in Commercial Micropropagation: Challenges and Perspectives (2025) · cites this paper as [75]

    The cited paper’s Cytokinins section discusses epigenetic regulation of plant development, but the passages retrieved do not address banana somaclonal variants or declining propagation rates. Searches for banana, somaclonal variation, the eighth subculture, and propagation rates found no passage supporting the attributed finding. (LLM, conf=0.75)

    Experimental — accuracy not yet measured

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Cites

Flagged first, then by citations

Research works printed but not linked: 305

  1. Aichinger E, Villar CBR, Farrona S, Reyes JC, Hennig L, Köhler C. 2009. CHD3 proteins and polycomb group proteins antagonistically determine cell identity in Arabidopsis. PLoS Genetics 5, e1000605. 19680533 PMC2718830
  2. Allen E, Xie Z, Gustafson AM, Carrington JC. 2005. microRNA-directed phasing during trans-acting siRNA biogenesis in plants. Cell 121, 207– 221. 15851028
  3. Alwutayd KM, Rawat AA, Sheikh AH, et al. 2023. Microbe-induced drought tolerance by ABA-mediated root architecture and epigenetic reprogramming. EMBO Reports 24, e56754. 37278352 PMC10398642
  4. Antoniadi I, Mateo-Bonmatí E, Pernisová M, et al. 2022. IPT9, a cis-zeatin cytokinin biosynthesis gene, promotes root growth. Frontiers in Plant Science 13, 932008. 36311087 PMC9616112
  5. Archacki R, Buszewicz D, Sarnowski TJ, et al. 2013. BRAHMA ATPase of the SWI/SNF chromatin remodeling complex acts as a positive regulator of gibberellin-mediated responses in Arabidopsis. PLoS One 8, e58588. 23536800 PMC3594165
  6. Ariel F, Jegu T, Latrasse D, Romero-Barrios N, Christ A, Benhamed M, Crespi M. 2014. Noncoding transcription by alternative RNA polymerases dynamically regulates an auxin-driven chromatin loop. Molecular Cell 55, 383– 396. 25018019
  7. Ariel F, Lucero L, Christ A, et al. 2020. R-loop mediated trans action of the APOLO long noncoding RNA. Molecular Cell 77, 1055– 1065.e4. 31952990
  8. Aubee JI, Olu M, Thompson KM. 2016. The i6A37 tRNA modification is essential for proper decoding of UUX-leucine codons during rpoS and iraP translation. RNA 22, 729– 742. 26979278 PMC4836647
  9. Autran D, Baroux C, Raissig MT, et al. 2011. Maternal epigenetic pathways control parental contributions to Arabidopsis early embryogenesis. Cell 145, 707– 719. 21620136
  10. Avalbaev AM, Somov KA, Yuldashev RA, Shakirova FM. 2012. Cytokinin oxidase is key enzyme of cytokinin degradation. Biochemistry 77, 1354– 1361. 23244730
  11. Baek D, Shin G, Kim MC, Shen M, Lee SY, Yun D-J. 2020. Histone deacetylase HDA9 with ABI4 contributes to abscisic acid homeostasis in drought stress response. Frontiers in Plant Science 11, 143. 32158458 PMC7052305
  12. Baile F, Gómez-Zambrano A, Calonje M. 2022. Roles of polycomb complexes in regulating gene expression and chromatin structure in plants. Plant Communications 3, 100267. 35059633 PMC8760139
  13. Bajic M, Maher KA, Deal RB. 2018. Identification of open chromatin regions in plant genomes using ATAC-Seq. Methods in Molecular Biology 1675, 183– 201. 29052193 PMC5693289
  14. Barrera-Rojas CH, Rocha GHB, Polverari L, et al. 2020. miR156-targeted SPL10 controls Arabidopsis root meristem activity and root-derived de novo shoot regeneration via cytokinin responses. Journal of Experimental Botany 71, 934– 950. 31642910
  15. Benhamed M, Bertrand C, Servet C, Zhou D-X. 2006. Arabidopsis GCN5, HD1, and TAF1/HAF2 interact to regulate histone acetylation required for light-responsive gene expression. The Plant Cell 18, 2893– 2903. 17085686 PMC1693931
  16. Binder BM. 2020. Ethylene signaling in plants. Journal of Biological Chemistry 295, 7710– 7725. 32332098 PMC7261785
  17. Bisson MMA, Groth G. 2015. Targeting plant ethylene responses by controlling essential protein–protein interactions in the ethylene pathway. Molecular Plant 8, 1165– 1174. 25843012
  18. Bleecker AB, Estelle MA, Somerville C, Kende H. 1988. Insensitivity to ethylene conferred by a dominant mutation in Arabidopsis thaliana. Science 241, 1086– 1089. 17747490
  19. Bourbousse C, Ahmed I, Roudier F, Zabulon G, Blondet E, Balzergue S, Colot V, Bowler C, Barneche F. 2012. Histone H2B monoubiquitination facilitates the rapid modulation of gene expression during Arabidopsis photomorphogenesis. PLoS Genetics 8, e1002825. 22829781 PMC3400566
  20. Boycheva I, Vassileva V, Iantcheva A. 2014. Histone acetyltransferases in plant development and plasticity. Current Genomics 15, 28– 37. 24653661 PMC3958957
  21. Briones-Moreno A, Hernández-García J, Vargas-Chávez C, Blanco-Touriñán N, Phokas A, Úrbez C, Cerdán PD, Coates JC, Alabadí D, Blázquez MA. 2023. DELLA functions evolved by rewiring of associated transcriptional networks. Nature Plants 9, 535– 543. 36914897
  22. Campos-Rivero G, Osorio-Montalvo P, Sánchez-Borges R, Us-Camas R, Duarte-Aké F, De-la-Peña C. 2017. Plant hormone signaling in flowering: an epigenetic point of view. Journal of Plant Physiology 214, 16– 27. 28419906
  23. Carra A, Mica E, Gambino G, Pindo M, Moser C, Pè ME, Schubert A. 2009. Cloning and characterization of small non-coding RNAs from grape. The Plant Journal 59, 750– 763. 19453456
  24. Casanova-Sáez R, Mateo-Bonmatí E, Ljung K. 2021. Auxin metabolism in plants. Cold Spring Harbor Perspectives in Biology 13, a039867. 33431579 PMC7919392
  25. Castro-Camba R, Sánchez C, Vidal N, Vielba JM. 2022. Plant development and crop yield: the role of gibberellins. Plants 11, 2650. 36235516 PMC9571322
  26. Causier B, Ashworth M, Guo W, Davies B. 2012. The TOPLESS interactome: a framework for gene repression in Arabidopsis. Plant Physiology 158, 423– 438. 22065421 PMC3252085
  27. Chamani Mohasses F, Solouki M, Ghareyazie B, Fahmideh L, Mohsenpour M. 2020. Correlation between gene expression levels under drought stress and synonymous codon usage in rice plant by in-silico study. PLoS One 15, e0237334. 32776991 PMC7416939
  28. 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 Phytologist 230, 1967– 1984. 33606283
  29. Chen K, Li G-J, Bressan RA, Song C-P, Zhu J-K, Zhao Y. 2020. Abscisic acid dynamics, signaling, and functions in plants. Journal of Integrative Plant Biology 62, 25– 54. 31850654
  30. Chen L-T, Luo M, Wang Y-Y, Wu K. 2010. Involvement of Arabidopsis histone deacetylase HDA6 in ABA and salt stress response. Journal of Experimental Botany 61, 3345– 3353. 20519338 PMC2905197
  31. Chen L-T, Wu K. 2010. Role of histone deacetylases HDA6 and HDA19 in ABA and abiotic stress response. Plant Signaling & Behavior 5, 1318– 1320. 20930557 PMC3115378
  32. Chen Q, Westfall CS, Hicks LM, Wang S, Jez JM. 2010. Kinetic basis for the conjugation of auxin by a GH3 family indole-acetic acid-amido synthetase. Journal of Biological Chemistry 285, 29780– 29786. 20639576 PMC2943290
  33. Chen W, Tamada Y, Yamane H, Matsushita M, Osako Y, Gao-Takai M, Luo Z, Tao R. 2022. H3K4me3 plays a key role in establishing permissive chromatin states during bud dormancy and bud break in apple. The Plant Journal 111, 1015– 1031. 35699670
  34. Chenarani N, Emamjomeh A, Allahverdi A, Mirmostafa S, Afsharinia MH, Zahiri J. 2021. Bioinformatic tools for DNA methylation and histone modification: a survey. Genomics 113, 1098– 1113. 33677056
  35. Cheng X, Pan M, Zhiguo E, Zhou Y, Niu B, Chen C. 2021. The maternally expressed polycomb group gene OsEMF2a is essential for endosperm cellularization and imprinting in rice. Plant Communications 2, 100092. 33511344 PMC7816080
  36. Cho H, Ryu H, Rho S, et al. 2014. A secreted peptide acts on BIN2-mediated phosphorylation of ARFs to potentiate auxin response during lateral root development. Nature Cell Biology 16, 66– 76. 24362628
  37. Cortijo S, Wardenaar R, Colomé-Tatché M, Johannes F, Colot V. 2014. Genome-wide analysis of DNA methylation in Arabidopsis using MeDIP-chip. Methods in Molecular Biology 1112, 125– 149. 24478012
  38. Covington MF, Harmer SL. 2007. The circadian clock regulates auxin signaling and responses in Arabidopsis. PLoS Biology 5, e222. 17683202 PMC1939880
  39. Cui G, Zhao M, Zhang S, Wang Z, Meng M, Sun F, Zhang C, Xi Y. 2020. MicroRNA and regulation of auxin and cytokinin signalling during post-mowing regeneration of winter wheat (Triticum aestivum L.). Plant Physiology and Biochemistry 155, 769– 779. 32866790
  40. Cui X, Lu F, Qiu Q, et al. 2016. REF6 recognizes a specific DNA sequence to demethylate H3K27me3 and regulate organ boundary formation in Arabidopsis. Nature Genetics 48, 694– 699. 27111035
  41. 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 Physiology 185, 1813– 1828. 33793949 PMC8133595
  42. Cumbie JS, Filichkin SA, Megraw M. 2015. Improved DNase-seq protocol facilitates high resolution mapping of DNase I hypersensitive sites in roots in Arabidopsis thaliana. Plant Methods 11, 42. 26339280 PMC4558764
  43. Delker C, Quint M, Wigge PA. 2022. Recent advances in understanding thermomorphogenesis signaling. Current Opinion in Plant Biology 68, 102231. 35636376
  44. De Lucia F, Crevillen P, Jones AME, Greb T, Dean C. 2008. A PHD-Polycomb Repressive Complex 2 triggers the epigenetic silencing of FLC during vernalization. Proceedings of the National Academy of Sciences, USA 105, 16831– 16836. PMC2579339 18854416
  45. Derkacheva M, Steinbach Y, Wildhaber T, Mozgová I, Mahrez W, Nanni P, Bischof S, Gruissem W, Hennig L. 2013. Arabidopsis MSI1 connects LHP1 to PRC2 complexes. The EMBO Journal 32, 2073– 2085. 23778966 PMC3715863
  46. 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. The Plant Journal 66, 735– 744. 21309869
  47. Du W, Lu Y, Li Q, Luo S, Shen S, Li N, Chen X. 2022. TIR1/AFB proteins: active players in abiotic and biotic stress signaling. Frontiers in Plant Science 13, 1083409. 36523629 PMC9745157
  48. Efroni I, Han S-K, Kim HJ, Wu M-F, Steiner E, Birnbaum KD, Hong JC, Eshed Y, Wagner D. 2013. Regulation of leaf maturation by chromatin-mediated modulation of cytokinin responses. Developmental Cell 24, 438– 445. 23449474 PMC3994294
  49. England JR, Huang J, Jennings MJ, Makde RD, Tan S. 2010. RCC1 uses a conformationally diverse loop region to interact with the nucleosome: a model for the RCC1–nucleosome complex. Journal of Molecular Biology 398, 518– 529. 20347844 PMC2895563
  50. Feng J, Lu J. 2017. LHP1 could act as an activator and a repressor of transcription in plants. Frontiers in Plant Science 8, 2041. 29234344 PMC5712405
  51. Feng J, Shen W-H. 2014. Dynamic regulation and function of histone monoubiquitination in plants. Frontiers in Plant Science 5, 83. 24659991 PMC3952079
  52. Feng S, Cokus SJ, Schubert V, Zhai J, Pellegrini M, Jacobsen SE. 2014. Genome-wide Hi-C analyses in wild type and mutants reveal high-resolution chromatin interactions in Arabidopsis. Molecular Cell 55, 694– 707. 25132175 PMC4347903
  53. Figueiredo DD, Batista RA, Roszak PJ, Köhler C. 2015. Auxin production couples endosperm development to fertilization. Nature Plants 1, 15184. 27251719
  54. Fleming BA, Blango MG, Rousek AA, et al. 2022. A tRNA modifying enzyme as a tunable regulatory nexus for bacterial stress responses and virulence. Nucleic Acids Research 50, 7570– 7590. 35212379 PMC9303304
  55. Foerster AM, Mittelsten Scheid O. 2010. Analysis of DNA methylation in plants by bisulfite sequencing. Methods in Molecular Biology 631, 1– 11. 20204863
  56. Fonouni-Farde C, Christ A, Blein T, et al. 2022. The Arabidopsis APOLO and human UPAT sequence-unrelated long noncoding RNAs can modulate DNA and histone methylation machineries in plants. Genome Biology 23, 181. 36038910 PMC9422110
  57. Forgione I, Muto A, Woloszynska M, Chiappetta AA, Ferrari M, Van Lijsebettens M, Bitonti MB, Bruno L. 2022. Epigenetic mechanisms affect the curled leaf phenotype in the hypomethylated ddc mutant of Arabidopsis thaliana. Plant Science 319, 111254. 35487663
  58. Forgione I, Wołoszyńska M, Pacenza M, Chiappetta A, Greco M, Araniti F, Abenavoli MR, Van Lijsebettens M, Bitonti MB, Bruno L. 2019. Hypomethylated drm1 drm2 cmt3 mutant phenotype of Arabidopsis thaliana is related to auxin pathway impairment. Plant Science 280, 383– 396. 30824017
  59. Furuta K, Kubo M, Sano K, Demura T, Fukuda H, Liu Y-G, Shibata D, Kakimoto T. 2011. The CKH2/PKL chromatin remodeling factor negatively regulates cytokinin responses in Arabidopsis calli. Plant and Cell Physiology 52, 618– 628. 21357580
  60. Gaddam SR, Bhatia C, Gautam H, Pathak PK, Sharma A, Saxena G, Trivedi PK. 2022. Ethylene regulates miRNA-mediated lignin biosynthesis and leaf serration in Arabidopsis thaliana. Biochemical and Biophysical Research Communications 605, 51– 55. 35316763
  61. Galuszka P, Popelková H, Werner T, Frébortová J, Pospíšilová H, Mik V, Köllmer I, Schmülling T, Frébort I. 2007. Biochemical characterization of cytokinin oxidases/dehydrogenases from Arabidopsis thaliana expressed in Nicotiana tabacum L. Journal of Plant Growth Regulation 26, 255– 267.
  62. Ge SX, Jung D, Yao R. 2020. ShinyGO: a graphical gene-set enrichment tool for animals and plants. Bioinformatics 36, 2628– 2629. 31882993 PMC7178415
  63. Geisler MM. 2021. A retro-perspective on auxin transport. Frontiers in Plant Science 12, 756968. 34675956 PMC8524130
  64. Geisler M, Aryal B, di Donato M, Hao P. 2017. A critical view on ABC transporters and their interacting partners in auxin transport. Plant and Cell Physiology 58, 1601– 1614. 29016918
  65. Ghassemian M, Nambara E, Cutler S, Kawaide H, Kamiya Y, McCourt P. 2000. Regulation of abscisic acid signaling by the ethylene response pathway in Arabidopsis. The Plant Cell 12, 1117– 1126. 10899978 PMC149053
  66. Gibb M, Kisiala AB, Morrison EN, Emery RJN. 2020. The origins and roles of methylthiolated cytokinins: evidence from among life Kingdoms. Frontiers in Cell and Developmental Biology 8, 605672. 33240900 PMC7680852
  67. Godwin J, Farrona S. 2022. The importance of networking: plant polycomb repressive complex 2 and its interactors. Epigenomes 6, 8. 35323212 PMC8948837
  68. Gomi K, Sasaki A, Itoh H, Ueguchi-Tanaka M, Ashikari M, Kitano H, Matsuoka M. 2004. GID2, an F-box subunit of the SCF E3 complex, specifically interacts with phosphorylated SLR1 protein and regulates the gibberellin-dependent degradation of SLR1 in rice. The Plant Journal 37, 626– 634. 14756772
  69. Goodman HM, Abelson JN, Landy A, Zadrazil S, Smith JD. 1970. The nucleotide sequences of tyrosine transfer RNAs of Escherichia coli. European Journal of Biochemistry 13, 461– 483. 4315419
  70. Grbić V, Bleecker AB. 1995. Ethylene regulates the timing of leaf senescence in Arabidopsis. The Plant Journal 8, 595– 602.
  71. Gu X, Xu T, He Y. 2014. A histone H3 lysine-27 methyltransferase complex represses lateral root formation in Arabidopsis thaliana. Molecular Plant 7, 977– 988. 24711289
  72. Guo C, Jiang Y, Shi M, Wu X, Wu G. 2021. ABI5 acts downstream of miR159 to delay vegetative phase change in Arabidopsis. New Phytologist 231, 339– 350. 33774835
  73. Gyula P, Baksa I, Tóth T, Mohorianu I, Dalmay T, Szittya G. 2018. Ambient temperature regulates the expression of a small set of sRNAs influencing plant development through NF-YA2 and YUC2. Plant, Cell & Environment 41, 2404– 2417. 29856891
  74. Han H, Adamowski M, Qi L, Alotaibi SS, Friml J. 2021. PIN-mediated polar auxin transport regulations in plant tropic responses. New Phytologist 232, 510– 522. 34254313
  75. Havlová M, Dobrev PI, Motyka V, Štorchová H, Libus J, Dobrá J, Malbeck J, Gaudinová A, Vanková R. 2008. The role of cytokinins in responses to water deficit in tobacco plants over-expressing trans-zeatin O-glucosyltransferase gene under 35S or SAG12 promoters. Plant, Cell & Environment 31, 341– 353. 18088334
  76. He C, Chen X, Huang H, Xu L. 2012. Reprogramming of H3K27me3 is critical for acquisition of pluripotency from cultured arabidopsis tissues. PLoS Genetics 8, e1002911. 22927830 PMC3426549
  77. He Q, Yuan R, Zhang T, et al. 2022. Arabidopsis TIE1 and TIE2 transcriptional repressors dampen cytokinin response during root development. Science Advances 8, eabn5057. 36083905 PMC9462699
  78. Henderson JT, Li H-C, Rider SD, Mordhorst AP, Romero-Severson J, Cheng J-C, Robey J, Sung ZR, de Vries SC, Ogas J. 2004. PICKLE acts throughout the plant to repress expression of embryonic traits and may play a role in gibberellin-dependent responses. Plant Physiology 134, 995– 1005. 14963244 PMC389922
  79. Heyl A, Brault M, Frugier F, Kuderova A, Lindner A-C, Motyka V, Rashotte AM, Schwartzenberg KV, Vankova R, Schaller GE. 2013. Nomenclature for members of the two-component signaling pathway of plants. Plant Physiology 161, 1063– 1065. 23324541 PMC3585578
  80. Hezroni H, Tzchori I, Davidi A, Mattout A, Biran A, Nissim-Rafinia M, Westphal H, Meshorer E. 2011. H3K9 histone acetylation predicts pluripotency and reprogramming capacity of ES cells. Nucleus 2, 300– 309. 21941115 PMC3260568
  81. Himanen K, Woloszynska M, Boccardi TM, De Groeve S, Nelissen H, Bruno L, Vuylsteke M, Van Lijsebettens M. 2012. Histone H2B monoubiquitination is required to reach maximal transcript levels of circadian clock genes in Arabidopsis. The Plant Journal 72, 249– 260. 22762858
  82. Hu T, Manuela D, Hinsch V, Xu M. 2022. PICKLE associates with histone deacetylase 9 to mediate vegetative phase change in Arabidopsis. New Phytologist 235, 1070– 1081. 35460275 PMC9324081
  83. Hu W, Hu S, Li S, Zhou Q, Xie Z, Hao X, Wu S, Tian L, Li D. 2023. AtSAMS regulates floral organ development by DNA methylation and ethylene signaling pathway. Plant Science 334, 111767. 37302530
  84. Huang G, Zhang F, Xie D, Ma Y, Wang P, Cao G, Chen L, Lin S, Zhao Z, Cai Z. 2023. High-throughput profiling of RNA modifications by ultra-performance liquid chromatography coupled to complementary mass spectrometry: methods, quality control, and applications. Talanta 263, 124697. 37262985
  85. Huang X, Tian H, Park J, Oh D-H, Hu J, Zentella R, Qiao H, Dassanayake M, Sun T-P. 2023. The master growth regulator DELLA binding to histone H2A is essential for DELLA-mediated global transcription regulation. Nature Plants 9, 1291– 1305. 37537399 PMC10681320
  86. Jain M, Abu-Shumays R, Olsen HE, Akeson M. 2022. Advances in nanopore direct RNA sequencing. Nature Methods 19, 1160– 1164. 36203024 PMC11388133
  87. Jameson PE. 2023. Zeatin: the 60th anniversary of its identification. Plant Physiology 192, 34– 55. 36789623 PMC10152681
  88. Jameson PE, Song J. 2016. Cytokinin: a key driver of seed yield. Journal of Experimental Botany 67, 593– 606. 26525061
  89. Jégu T, Domenichini S, Blein T, et al. 2015. A SWI/SNF chromatin remodelling protein controls cytokinin production through the regulation of chromatin architecture. PLoS One 10, e0138276. 26457678 PMC4601769
  90. Jia Y, Tian H, Li H, Yu Q, Wang L, Friml J, Ding Z. 2015. The Arabidopsis thaliana elongator complex subunit 2 epigenetically affects root development. Journal of Experimental Botany 66, 4631– 4642. 25998905 PMC4507768
  91. Jiang Y, Wu X, Shi M, Yu J, Guo C. 2022. The miR159–MYB33–ABI5 module regulates seed germination in Arabidopsis. Physiologia Plantarum 174, e13659. 35244224
  92. Jiao Y, Wang Y, Xue D, et al. 2010. Regulation of OsSPL14 by OsmiR156 defines ideal plant architecture in rice. Nature Genetics 42, 541– 544. 20495565
  93. Jin D, Wang Y, Zhao Y, Chen M. 2013. MicroRNAs and their cross-talks in plant development. Journal of Genetics and Genomics 40, 161– 170. 23618399
  94. Jing W, Gong F, Liu G, et al. 2023. Petal size is controlled by the MYB73/TPL/HDA19–miR159–CKX6 module regulating cytokinin catabolism in Rosa hybrida. Nature Communications 14, 7106. PMC10625627 37925502
  95. Jullien PE, Berger F. 2010. Parental genome dosage imbalance deregulates imprinting in Arabidopsis. PLoS Genetics 6, e1000885. 20333248 PMC2841625
  96. Kalve S, De Vos D, Beemster GTS. 2014. Leaf development: a cellular perspective. Frontiers in Plant Science 5, 362. 25132838 PMC4116805
  97. Kamínek M, Pačes V, Corse J, Challice JS. 1979. Effect of stereospecific hydroxylation of N6-(Δ2-isopentenyl)adenosine on cytokinin activity. Planta 145, 239– 243. 24317729
  98. Kang H, Ma J, Wu D, Shen W-H, Zhu Y. 2019. Functional coordination of the chromatin-remodeling factor AtINO80 and the histone chaperones NRP1/2 in inflorescence meristem and root apical meristem. Frontiers in Plant Science 10, 115. 30792730 PMC6374632
  99. Kasahara H, Takei K, Ueda N, Hishiyama S, Yamaya T, Kamiya Y, Yamaguchi S, Sakakibara H. 2004. Distinct isoprenoid origins of cis- and trans-zeatin biosyntheses in Arabidopsis. Journal of Biological Chemistry 279, 14049– 14054. 14726522
  100. Kasschau KD, Xie Z, Allen E, Llave C, Chapman EJ, Krizan KA, Carrington JC. 2003. P1/HC-Pro, a viral suppressor of RNA silencing, interferes with Arabidopsis development and miRNA function. Developmental Cell 4, 205– 217. 12586064
  101. Kaufmann K, Muiño JM, Østerås M, Farinelli L, Krajewski P, Angenent GC. 2010. Chromatin immunoprecipitation (ChIP) of plant transcription factors followed by sequencing (ChIP-SEQ) or hybridization to whole genome arrays (ChIP-CHIP). Nature Protocols 5, 457– 472. 20203663
  102. Kende H, Zeevaart J. 1997. The five ‘classical’ plant hormones. The Plant Cell 9, 1197– 1210. 12237383 PMC156991
  103. Kieber JJ, Rothenberg M, Roman G, Feldmann KA, Ecker JR. 1993. CTR1, a negative regulator of the ethylene response pathway in Arabidopsis, encodes a member of the raf family of protein kinases. Cell 72, 427– 441. 8431946
  104. Kieber JJ, Schaller GE. 2014. Cytokinins. The Arabidopsis Book 12, e0168. 24465173 PMC3894907
  105. Kieber JJ, Schaller GE. 2018. Cytokinin signaling in plant development. Development 145, dev149344. 29487105
  106. Kilian J, Whitehead D, Horak J, Wanke D, Weinl S, Batistic O, D’Angelo C, Bornberg-Bauer E, Kudla J, Harter K. 2007. The AtGenExpress global stress expression data set: protocols, evaluation and model data analysis of UV-B light, drought and cold stress responses. The Plant Journal 50, 347– 363. 17376166
  107. Kim D-H, Sung S. 2017. The binding specificity of the PHD-finger domain of VIN3 moderates vernalization response. Plant Physiology 173, 1258– 1268. 27999085 PMC5291027
  108. Kim J-Y, Yang W, Forner J, Lohmann JU, Noh B, Noh Y-S. 2018. Epigenetic reprogramming by histone acetyltransferase HAG1/AtGCN5 is required for pluripotency acquisition in Arabidopsis. The EMBO Journal 37, e98726. 30061313 PMC6187204
  109. Kim YJ, Wang R, Gao L, et al. 2016. POWERDRESS and HDA9 interact and promote histone H3 deacetylation at specific genomic sites in Arabidopsis. Proceedings of the National Academy of Sciences, USA 113, 14858– 14863. PMC5187680 27930340
  110. Kubo M, Kakimoto T. 2000. The cytokinin-hypersensitive genes of Arabidopsis negatively regulate the cytokinin-signaling pathway for cell division and chloroplast development. The Plant Journal 23, 385– 394. 10929131
  111. Kuchaříková H, Dobrovolná P, Lochmanová G, Zdráhal Z. 2021. Trimethylacetic anhydride-based derivatization facilitates quantification of histone marks at the ms1 level. Molecular & Cellular Proteomics 20, 100114. 34129942 PMC8283018
  112. Kuchaříková H, Plšková Z, Zdráhal Z, Fojtová M, Kerchev P, Lochmanová G. 2022. Quantitative analysis of posttranslational modifications of plant histones. Methods in Molecular Biology 2526, 241– 257. 35657525
  113. Kuhn A, Ramans Harborough S, McLaughlin HM, Natarajan B, Verstraeten I, Friml J, Kepinski S, Østergaard L. 2020. Direct ETTIN–auxin interaction controls chromatin states in gynoecium development. eLife 9, e51787. 32267233 PMC7164952
  114. Kurakawa T, Ueda N, Maekawa M, Kobayashi K, Kojima M, Nagato Y, Sakakibara H, Kyozuka J. 2007. Direct control of shoot meristem activity by a cytokinin-activating enzyme. Nature 445, 652– 655. 17287810
  115. Kuroha T, Tokunaga H, Kojima M, Ueda N, Ishida T, Nagawa S, Fukuda H, Sugimoto K, Sakakibara H. 2009. Functional analyses of LONELY GUY cytokinin-activating enzymes reveal the importance of the direct activation pathway in Arabidopsis. The Plant Cell 21, 3152– 3169. 19837870 PMC2782294
  116. Lafon-Placette C, Le Gac A-L, Chauveau D, et al. 2018. Changes in the epigenome and transcriptome of the poplar shoot apical meristem in response to water availability affect preferentially hormone pathways. Journal of Experimental Botany 69, 537– 551. 29211860
  117. Lafos M, Kroll P, Hohenstatt ML, Thorpe FL, Clarenz O, Schubert D. 2011. Dynamic regulation of H3K27 trimethylation during Arabidopsis differentiation. PLoS Genetics 7, e1002040. 21490956 PMC3072373
  118. Lamichhane TN, Blewett NH, Crawford AK, Cherkasova VA, Iben JR, Begley TJ, Farabaugh PJ, Maraia RJ. 2013. Lack of tRNA modification isopentenyl-A37 alters mRNA decoding and causes metabolic deficiencies in fission yeast. Molecular and Cellular Biology 33, 2918– 2929. 23716598 PMC3719670
  119. Lavy M, Estelle M. 2016. Mechanisms of auxin signaling. Development 143, 3226– 3229. 27624827 PMC5047657
  120. Lee H-J, Jung J-H, Cortés Llorca L, Kim S-G, Lee S, Baldwin IT, Park C-M. 2014. FCA mediates thermal adaptation of stem growth by attenuating auxin action in Arabidopsis. Nature Communications 5, 5473. 25400039
  121. Lee K, Park O-S, Go JY, Yu J, Han JH, Kim J, Bae S, Jung YJ, Seo PJ. 2021. Arabidopsis ATXR2 represses de novo shoot organogenesis in the transition from callus to shoot formation. Cell Reports 37, 109980. 34758306
  122. Lee K, Park O-S, Seo PJ. 2017. Arabidopsis ATXR2 deposits H3K36me3 at the promoters of LBD genes to facilitate cellular dedifferentiation. Science Signaling 10, eaan0316. 29184030
  123. Lee K, Park O-S, Seo PJ. 2018. JMJ30-mediated demethylation of H3K9me3 drives tissue identity changes to promote callus formation in Arabidopsis. The Plant Journal 95, 961– 975. 29923261
  124. Lee K, Seo PJ. 2017. Coordination of matrix attachment and ATP-dependent chromatin remodeling regulate auxin biosynthesis and Arabidopsis hypocotyl elongation. PLoS One 12, e0181804. 28746399 PMC5529009
  125. Li C, Chen C, Gao L, et al. 2015. The Arabidopsis SWI2/SNF2 chromatin remodeler BRAHMA regulates polycomb function during vegetative development and directly activates the flowering repressor gene SVP. PLoS Genetics 11, e1004944. 25615622 PMC4304717
  126. Li C, Gu L, Gao L, et al. 2016. Concerted genomic targeting of H3K27 demethylase REF6 and chromatin-remodeling ATPase BRM in Arabidopsis. Nature Genetics 48, 687– 693. 27111034 PMC5134324
  127. Li C, Liu Y, Shen W-H, Yu Y, Dong A. 2018. Chromatin-remodeling factor OsINO80 is involved in regulation of gibberellin biosynthesis and is crucial for rice plant growth and development. Journal of Integrative Plant Biology 60, 144– 159. 29045007
  128. Li C, Xu J, Li J, Li Q, Yang H. 2014. Involvement of Arabidopsis histone acetyltransferase HAC family genes in the ethylene signaling pathway. Plant and Cell Physiology 55, 426– 435. 24287137
  129. Li H, Torres-Garcia J, Latrasse D, Benhamed M, Schilderink S, Zhou W, Kulikova O, Hirt H, Bisseling T. 2017. Plant-specific histone deacetylases HDT1/2 regulate GIBBERELLIN 2-OXIDASE2 expression to control Arabidopsis root meristem cell number. The Plant Cell 29, 2183– 2196. 28855334 PMC5635991
  130. Li J, Nie X, Tan JLH, Berger F. 2013. Integration of epigenetic and genetic controls of seed size by cytokinin in Arabidopsis. Proceedings of the National Academy of Sciences,USA 110, 15479– 15484. PMC3780859 24003120
  131. Li L, Gallei M, Friml J. 2022. Bending to auxin: fast acid growth for tropisms. Trends in Plant Science 27, 440– 449. 34848141
  132. Li W, Deng M, Wang S, et al. 2023. HISTONE DEACETYLASE 6 interaction with ABSCISIC ACID-INSENSITIVE 5 decreases apple drought tolerance. Plant Physiology 193, kiad468. PMC10663142 37607253
  133. Li W, Wang T, Zhang Y, Li Y. 2016. Overexpression of soybean miR172c confers tolerance to water deficit and salt stress, but increases ABA sensitivity in transgenic Arabidopsis thaliana. Journal of Experimental Botany 67, 175– 194. 26466661
  134. Li Z, Peng J, Wen X, Guo H. 2013. ETHYLENE-INSENSITIVE3 is a senescence-associated gene that accelerates age-dependent leaf senescence by directly repressing miR164 transcription in Arabidopsis. The Plant Cell 25, 3311– 3328. 24064769 PMC3809534
  135. Lin J, Hung F-Y, Ye C, Hong L, Shih Y-H, Wu K, Li QQ. 2020. HDA6-dependent histone deacetylation regulates mRNA polyadenylation in Arabidopsis. Genome Research 30, 1407– 1417. 32759225 PMC7605263
  136. Liu D, Zhao H, Xiao Y, et al. 2022. A cryptic inhibitor of cytokinin phosphorelay controls rice grain size. Molecular Plant 15, 293– 307. 34562665
  137. Liu F, Quesada V, Crevillén P, Bäurle I, Swiezewski S, Dean C. 2007. The Arabidopsis RNA-binding protein FCA requires a lysine-specific demethylase 1 homolog to downregulate FLC. Molecular Cell 28, 398– 407. 17996704
  138. Liu H, Zhang H, Dong YX, Hao YJ, Zhang XS. 2018. DNA METHYLTRANSFERASE1-mediated shoot regeneration is regulated by cytokinin-induced cell cycle in Arabidopsis. New Phytologist 217, 219– 232. 28960381
  139. Liu P-P, Montgomery TA, Fahlgren N, Kasschau KD, Nonogaki H, Carrington JC. 2007. Repression of AUXIN RESPONSE FACTOR10 by microRNA160 is critical for seed germination and post-germination stages. The Plant Journal 52, 133– 146. 17672844
  140. Liu Q, Chen Y-Q. 2009. Insights into the mechanism of plant development: interactions of miRNAs pathway with phytohormone response. Biochemical and Biophysical Research Communications 384, 1– 5. 19366618
  141. Liu Q, Zhang Y-C, Wang C-Y, Luo Y-C, Huang Q-J, Chen S-Y, Zhou H, Qu L-H, Chen Y-Q. 2009. Expression analysis of phytohormone-regulated microRNAs in rice, implying their regulation roles in plant hormone signaling. FEBS Letters 583, 723– 728. 19167382
  142. Liu W, Duttke SH, Hetzel J, et al. 2018. RNA-directed DNA methylation involves co-transcriptional small-RNA-guided slicing of polymerase V transcripts in Arabidopsis. Nature Plants 4, 181– 188. 29379150 PMC5832601
  143. Liu Y, Zhang A, Yin H, Meng Q, Yu X, Huang S, Wang J, Ahmad R, Liu B, Xu Z-Y. 2018. Trithorax-group proteins ARABIDOPSIS TRITHORAX4 (ATX4) and ATX5 function in abscisic acid and dehydration stress responses. New Phytologist 217, 1582– 1597. 29250818
  144. Liu Z, Li J, Wang L, Li Q, Lu Q, Yu Y, Li S, Bai M, Hu Y, Xiang F. 2016. Repression of callus initiation by the miRNA-directed interaction of auxin–cytokinin in Arabidopsis thaliana. The Plant Journal 87, 391– 402. 27189514
  145. Lochmanová G, Ihnatová I, Kuchaříková H, Brabencová S, Zachová D, Fajkus J, Zdráhal Z, Fojtová M. 2019. Different modes of action of genetic and chemical downregulation of histone deacetylases with respect to plant development and histone modifications. International Journal of Molecular Sciences 20, 5093. 31615119 PMC6829310
  146. Long JA, Ohno C, Smith ZR, Meyerowitz EM. 2006. TOPLESS regulates apical embryonic fate in Arabidopsis. Science 312, 1520– 1523. 16763149
  147. Lopes FL, Galvan-Ampudia C, Landrein B. 2021. WUSCHEL in the shoot apical meristem: old player, new tricks. Journal of Experimental Botany 72, 1527– 1535. 33332559
  148. Lucas MC, Novoa EM. 2023. Long-read sequencing in the era of epigenomics and epitranscriptomics. Nature Methods 20, 25– 29. 36635539
  149. Luo M, Wang Y-Y, Liu X, Yang S, Lu Q, Cui Y, Wu K. 2012. HD2C interacts with HDA6 and is involved in ABA and salt stress response in Arabidopsis. Journal of Experimental Botany 63, 3297– 3306. 22368268 PMC3350937
  150. Luo P, Di D, Wu L, Yang J, Lu Y, Shi W. 2022. MicroRNAs are involved in regulating plant development and stress response through fine-tuning of TIR1/AFB-dependent auxin signaling. International Journal of Molecular Sciences 23, 510. 35008937 PMC8745101
  151. Ma S, Tang N, Li X, et al. 2019. Reversible histone H2B monoubiquitination fine-tunes abscisic acid signaling and drought response in rice. Molecular Plant 12, 263– 277. 30578854
  152. Macknight R, Bancroft I, Page T, et al. 1997. FCA, a gene controlling flowering time in Arabidopsis, encodes a protein containing RNA-binding domains. Cell 89, 737– 745. 9182761
  153. Mallory AC, Bartel DP, Bartel B. 2005. MicroRNA-directed regulation of Arabidopsis AUXIN RESPONSE FACTOR17 is essential for proper development and modulates expression of early auxin response genes. The Plant Cell 17, 1360– 1375. 15829600 PMC1091760
  154. Mandal S, Ghorai M, Anand U, et al. 2022. Cytokinins: a genetic target for increasing yield potential in the CRISPR era. Frontiers in Genetics 13, 883930. 35559022 PMC9086551
  155. March E, Farrona S. 2018. Plant deubiquitinases and their role in the control of gene expression through modification of histones. Frontiers in Plant Science 8, 2274. 29387079 PMC5776116
  156. Maric A. 2023. Beyond the genetics of flowering: integration of ethylene signaling and histone methylation controls flowering time. Plant Physiology 192, 2224– 2226. 37067904 PMC10315301
  157. Markulin L, Škiljaica A, Tokić M, Jagić M, Vuk T, Bauer N, Leljak Levanić D. 2021. Taking the wheel—de novo DNA methylation as a driving force of plant embryonic development. Frontiers in Plant Science 12, 764999. 34777448 PMC8585777
  158. Mateo-Bonmatí E, Casanova-Sáez R, Ljung K. 2019. Epigenetic regulation of auxin homeostasis. Biomolecules 9, 623. 31635281 PMC6843323
  159. Mayer KF, Schoof H, Haecker A, Lenhard M, Jürgens G, Laux T. 1998. Role of WUSCHEL in regulating stem cell fate in the Arabidopsis shoot meristem. Cell 95, 805– 815. 9865698
  160. Miao C, Wang Z, Zhang L, Yao J, Hua K, Liu X, Shi H, Zhu J-K. 2019. The grain yield modulator miR156 regulates seed dormancy through the gibberellin pathway in rice. Nature Communications 10, 3822. PMC6707268 31444356
  161. Milutinovic M, Lindsey BE, Wijeratne A, Hernandez JM, Grotewold N, Fernández V, Grotewold E, Brkljacic J. 2019. Arabidopsis EMSY-like (EML) histone readers are necessary for post-fertilization seed development, but prevent fertilization-independent seed formation. Plant Science 285, 99– 109. 31203898
  162. Miyawaki K, Matsumoto-Kitano M, Kakimoto T. 2004. Expression of cytokinin biosynthetic isopentenyltransferase genes in Arabidopsis: tissue specificity and regulation by auxin, cytokinin, and nitrate. The Plant Journal 37, 128– 138. 14675438
  163. Miyawaki K, Tarkowski P, Matsumoto-Kitano M, Kato T, Sato S, Tarkowska D, Tabata S, Sandberg G, Kakimoto T. 2006. Roles of Arabidopsis ATP/ADP isopentenyltransferases and tRNA isopentenyltransferases in cytokinin biosynthesis. Proceedings of the National Academy of Sciences, USA 103, 16598– 16603. PMC1637627 17062755
  164. Mohler K, Ibba M. 2017. Translational fidelity and mistranslation in the cellular response to stress. Nature Microbiology 2, 1– 9. PMC5697424 28836574
  165. Motorin Y, Marchand V. 2021. Analysis of RNA modifications by second- and third-generation deep sequencing: 2020 update. Genes 12, 278. 33669207 PMC7919787
  166. Müller-Xing R, Xing Q. 2022. The plant stem-cell niche and pluripotency: 15 years of an epigenetic perspective. Frontiers in Plant Science 13, 1018559. 36388540 PMC9659954
  167. Nelissen H, De Groeve S, Fleury D, et al. 2010. Plant Elongator regulates auxin-related genes during RNA polymerase II transcription elongation. Proceedings of the National Academy of Sciences, USA 107, 1678– 1683. PMC2824411 20080602
  168. Nelissen H, Fleury D, Bruno L, Robles P, De Veylder L, Traas J, Micol JL, Van Montagu M, Inzé D, Van Lijsebettens M. 2005. The elongata mutants identify a functional Elongator complex in plants with a role in cell proliferation during organ growth. Proceedings of the National Academy of Sciences, USA 102, 7754– 7759. PMC1140448 15894610
  169. Nguyen CT, Tran G-B, Nguyen NH. 2020. Homeostasis of histone acetylation is critical for auxin signaling and root morphogenesis. Plant Molecular Biology 103, 1– 7. 32088831
  170. Nizampatnam NR, Schreier SJ, Damodaran S, Adhikari S, Subramanian S. 2015. microRNA160 dictates stage-specific auxin and cytokinin sensitivities and directs soybean nodule development. The Plant Journal 84, 140– 153. 26287653
  171. Noh Y-S, Amasino RM. 1999. Identification of a promoter region responsible for the senescence-specific expression of SAG12. Plant Molecular Biology 41, 181– 194. 10579486
  172. Ogas J, Kaufmann S, Henderson J, Somerville C. 1999. PICKLE is a CHD3 chromatin-remodeling factor that regulates the transition from embryonic to vegetative development in Arabidopsis. Proceedings of the National Academy of Sciences, USA 96, 13839– 13844. PMC24151 10570159
  173. Orosa-Puente B, Leftley N, von Wangenheim D, et al. 2018. Root branching toward water involves posttranslational modification of transcription factor ARF7. Science 362, 1407– 1410. 30573626
  174. Paces V, Werstiuk E, Hall RH. 1971. Conversion of N6-(Δ2-isopentenyl)adenosine to adenosine by enzyme activity in tobacco tissue. Plant Physiology 48, 775– 778. 16657878 PMC396946
  175. Pajoro A, Muiño JM, Angenent GC, Kaufmann K. 2018. Profiling nucleosome occupancy by MNase-seq: experimental protocol and computational analysis. Methods in Molecular Biology 1675, 167– 181. 29052192
  176. Pajoro A, Severing E, Angenent GC, Immink RGH. 2017. Histone H3 lysine 36 methylation affects temperature-induced alternative splicing and flowering in plants. Genome Biology 18, 102. 28566089 PMC5452352
  177. Park J, Giudicatti AJ, Bader ZE, Han MK, Møller C, Arce AL, Xu Z-Y, Yang SW, Manavella PA, Yun D-J. 2023. The HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENE15–HISTONE DEACETYLASE9 complex associates with HYPONASTIC LEAVES 1 to modulate microRNA expression in response to abscisic acid signaling. The Plant Cell 35, 2910– 2928. 37195876 PMC10396366
  178. Park J, Oh D-H, Dassanayake M, Nguyen KT, Ogas J, Choi G, Sun T. 2017. Gibberellin signaling requires chromatin remodeler PICKLE to promote vegetative growth and phase transitions. Plant Physiology 173, 1463– 1474. 28057895 PMC5291033
  179. Patanun O, Ueda M, Itouga M, et al. 2017. The histone deacetylase inhibitor suberoylanilide hydroxamic acid alleviates salinity stress in Cassava. Frontiers in Plant Science 7, 2039. 28119717 PMC5220070
  180. Pattyn J, Vaughan-Hirsch J, Van de Poel B. 2021. The regulation of ethylene biosynthesis: a complex multilevel control circuitry. New Phytologist 229, 770– 782. 32790878 PMC7820975
  181. Pei H, Ma N, Chen J, Zheng Y, Tian J, Li J, Zhang S, Fei Z, Gao J. 2013a. Integrative analysis of miRNA and mRNA profiles in response to ethylene in rose petals during flower opening. PLoS One 8, e64290. 23696879 PMC3655976
  182. Pei H, Ma N, Tian J, Luo J, Chen J, Li J, Zheng Y, Chen X, Fei Z, Gao J. 2013b. An NAC transcription factor controls ethylene-regulated cell expansion in flower petals. Plant Physiology 163, 775– 791. 23933991 PMC3793057
  183. Peng M, Li Z, Zhou N, Ma M, Jiang Y, Dong A, Shen W-H, Li L. 2018. Linking PHYTOCHROME-INTERACTING FACTOR to histone modification in plant shade avoidance. Plant Physiology 176, 1341– 1351. 29187567 PMC5813548
  184. Pertry I, Václavíková K, Depuydt S, et al. 2009. Identification of Rhodococcus fascians cytokinins and their modus operandi to reshape the plant. Proceedings of the National Academy of Sciences, USA 106, 929– 934. PMC2630087 19129491
  185. Petrén H, Thosteman H, Stift M, Toräng P, Ågren J, Friberg M. 2023. Differences in mating system and predicted parental conflict affect post-pollination reproductive isolation in a flowering plant. Evolution 77, 1019– 1030. 36734045
  186. Plant AR, Larrieu A, Causier B. 2021. Repressor for hire! The vital roles of TOPLESS-mediated transcriptional repression in plants. New Phytologist 231, 963– 973. 33909309
  187. Pontier D, Gan S, Amasino RM, Roby D, Lam E. 1999. Markers for hypersensitive response and senescence show distinct patterns of expression. Plant Molecular Biology 39, 1243– 1255. 10380810
  188. Potter KC, Wang J, Schaller GE, Kieber JJ. 2018. Cytokinin modulates context-dependent chromatin accessibility through the type-B response regulators. Nature Plants 4, 1102– 1111. 30420712
  189. Poulios S, Vlachonasios KE. 2016. Synergistic action of histone acetyltransferase GCN5 and receptor CLAVATA1 negatively affects ethylene responses in Arabidopsis thaliana. Journal of Experimental Botany 67, 905– 918. 26596766
  190. Poulios S, Vlachonasios KE. 2018. Synergistic action of GCN5 and CLAVATA1 in the regulation of gynoecium development in Arabidopsis thaliana. New Phytologist 220, 593– 608. 30027613
  191. Reyes JL, Chua N-H. 2007. ABA induction of miR159 controls transcript levels of two MYB factors during Arabidopsis seed germination. The Plant Journal 49, 592– 606. 17217461
  192. Rizzardi K, Landberg K, Nilsson L, Ljung K, Sundås-Larsson A. 2011. TFL2/LHP1 is involved in auxin biosynthesis through positive regulation of YUCCA genes. The Plant Journal 65, 897– 906. 21251106
  193. Rosa NM, Pfeiffer A, Hill K, et al. 2015. Genome wide binding site analysis reveals transcriptional coactivation of cytokinin-responsive genes by DELLA proteins. PLoS Genetics 11, e1005337. 26134422 PMC4489807
  194. Růžička K, Ljung K, Vanneste S, Podhorská R, Beeckman T, Friml J, Benková E. 2007. Ethylene regulates root growth through effects on auxin biosynthesis and transport-dependent auxin distribution. The Plant Cell 19, 2197– 2212. 17630274 PMC1955700
  195. Rymen B, Kawamura A, Lambolez A, et al. 2019. Histone acetylation orchestrates wound-induced transcriptional activation and cellular reprogramming in Arabidopsis. Communications Biology 2, 404. 31701032 PMC6828771
  196. Saez A, Rodrigues A, Santiago J, Rubio S, Rodriguez PL. 2008. HAB1–SWI3B interaction reveals a link between abscisic acid signaling and putative SWI/SNF chromatin-remodeling complexes in Arabidopsis. The Plant Cell 20, 2972– 2988. 19033529 PMC2613670
  197. Sah SK, Reddy KR, Li J. 2016. Abscisic acid and abiotic stress tolerance in crop plants. Frontiers in Plant Science 7, 571. 27200044 PMC4855980
  198. Sakakibara H. 2006. CYTOKININS: activity, biosynthesis, and translocation. Annual Review of Plant Biology 57, 431– 449. 16669769
  199. Salehin M, Bagchi R, Estelle M. 2015. SCFTIR1/AFB-based auxin perception: mechanism and role in plant growth and development. The Plant Cell 27, 9– 19. 25604443 PMC4330579
  200. Sarnowska EA, Rolicka AT, Bucior E, et al. 2013. DELLA-interacting SWI3C core subunit of switch/sucrose nonfermenting chromatin remodeling complex modulates gibberellin responses and hormonal cross talk in Arabidopsis. Plant Physiology 163, 305– 317. 23893173 PMC3762652

200 of 305 shown

Cited by

Sorted by citations

Authors
Rudolf, J., Tomovicova, L., Panzarova, K., Fajkus, J., Hejatko, J., & Skalak, J.
Affiliations
  • Mendel Centre for Plant Genomics and Proteomics, CEITEC - Central European Institute of Technology, Masaryk University , Kamenice 753/5, CZ-62500 Brno ,
  • Masaryk University (CZ)
  • Photon Systems Instruments , Prumyslova 470, CZ-664 24 Drasov ,
ORCID
Venue
Journal of Experimental Botany
Publisher
Oxford University Press (OUP)
Published
2024-02-19
Volume
75
Issue
17
Pages
5267-5294
ISSN
  • 0022-0957 (ISSN-L)
  • 1460-2431
DOI
10.1093/jxb/erae054
PMC
PMC11389840
OpenAlex
W4391942359
Cited by
35
References
1
Citations by year
2026: 19 · 2025: 13 · 2024: 3
FWCI
1.33
Type
journal article
Language
en
Open access
Licence
Locations
  • Journal of Experimental Botany (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
Funders
European Regional Development Fund-Project, SINGING PLANT
Topics
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Plant Molecular Biology Research
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Plant Gene Expression Analysis
Keywords
plant hormones, epigenetics, epigenetic modifications, phenotypic plasticity, plant growth and development, epigenetic regulators, gene expression regulation, plant adaptation
MeSH terms
Plant Growth Regulators, Plants, Gene Expression Regulation, Plant, Epigenesis, Genetic, Plant Development

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review