Epigenetic reprogramming of H3K27me3 and DNA methylation during leaf-to-callus transition in peach

Abstract

Plant tissues are capable of developing unorganized cell masses termed calluses in response to the appropriate combination of auxin and cytokinin. Revealing the potential epigenetic mechanisms involved in callus development can improve our understanding of the regeneration process of plant cells, which will be beneficial for overcoming regeneration recalcitrance in peach. In this study, we report on single-base resolution mapping of DNA methylation and reprogramming of the pattern of trimethylation of histone H3 at lysine 27 (H3K27me3) at the genome-wide level during the leaf-to-callus transition in peach. Overall, mCG and mCHH were predominant at the genome-wide level and mCG was predominant in genic regions. H3K27me3 deposition was mainly detected in the gene body and at the TSS site, and GAGA repetitive sequences were prone to recruit H3K27me3 modification. H3K27me3 methylation was negatively correlated with gene expression. In vitro culture of leaf explants was accompanied by DNA hypomethylation and H3K27me3 demethylation, which could activate auxin- and cytokinin-related regulators to induce callus development. The DNA methylation inhibitor 5-azacytidine could significantly increase callus development, while the H3K27me3 demethylase inhibitor GSK-J4 dramatically reduced callus development. These results demonstrate the roles of DNA methylation and H3K27me3 modification in mediating chromatin status during callus development. Our study provides new insights into the epigenetic mechanisms through which differentiated cells acquire proliferative competence to induce callus development in plants.

References

[1] Ricci A, Sabbadini S, Prieto H et al. Genetic transformation in peach (Prunus persica L.): challenges and ways forward . Plants (Basel). 2020; 9: 971.

[2] Efferth T . Biotechnology applications of plant callus cultures. Engineering. 2019; 5: 50-9.

[3] Feher A. Callus, dedifferentiation, totipotency, somatic embryogenesis: what these terms mean in the era of molecular plant biology? Front Plant Sci. 2019; 10: 536.

[4] Xu S, Lai E, Zhao L et al. Development of a fast and efficient root transgenic system for functional genomics and genetic engineering in peach. Sci Rep. 2020; 10: 2836.

[5] Pérez-Jiménez M, López-Soto MB, Cos-Terrer J . In vitro callus induction from adult tissues of peach (Prunus persica L. Batsch) . In Vitro Cellular & Developmental Biology - Plant. 2013; 49: 79-84.

[6] Ikeuchi M, Ogawa Y, Iwase A et al. Plant regeneration: cellular origins and molecular mechanisms. Development. 2016; 143: 1442-51.

[7] Ikeuchi M, Sugimoto K, Iwase A . Plant callus: mechanisms of induction and repression. Plant Cell. 2013; 25: 3159-73.

[8] Su YH, Liu YB, Zhang XS . Auxin-cytokinin interaction regulates meristem development. Mol Plant. 2011; 4: 616-25.

[9] Ikeuchi M, Favero DS, Sakamoto Y et al. Molecular mechanisms of plant regeneration. Annu Rev Plant Biol. 2019; 70: 377-406.

[10] Atta R, Laurens L, Boucheron-Dubuisson E et al. Pluripotency of Arabidopsis xylem pericycle underlies shoot regeneration from root and hypocotyl explants grown in vitro. Plant J. 2009; 57: 626-44.

[11] Sugimoto K, Jiao Y, Meyerowitz EM . Arabidopsis regeneration from multiple tissues occurs via a root development pathway . Dev Cell. 2010; 18: 463-71.

[12] Fan M, Xu C, Xu K et al. LATERAL ORGAN BOUNDARIES DOMAIN transcription factors direct callus formation in Arabidopsis regeneration. Cell Res. 2012; 22: 1169-80.

[13] Xu L . De novo root regeneration from leaf explants: wounding, auxin, and cell fate transition. Curr Opin Plant Biol. 2018; 41: 39-45.

[14] Ikeuchi M, Rymen B, Sugimoto K . How do plants transduce wound signals to induce tissue repair and organ regeneration? Curr Opin Plant Biol. 2020; 57: 72-7.

[15] Ikeuchi M, Iwase A, Rymen B et al. Wounding triggers callus formation via dynamic hormonal and transcriptional changes. Plant Physiol. 2017; 175: 1158-74.

[16] Argyros RD, Mathews DE, Chiang YH et al. Type B response regulators of Arabidopsis play key roles in cytokinin signaling and plant development. Plant Cell. 2008; 20: 2102-16.

[17] Lee K, Seo PJ . Dynamic epigenetic changes during plant regeneration. Trends Plant Sci. 2018; 23: 235-47.

[18] Saze H, Tsugane K, Kanno T et al. DNA methylation in plants: relationship to small RNAs and histone modifications, and functions in transposon inactivation. Plant Cell Physiol. 2012; 53: 766-84.

[19] Osakabe A, Adachi F, Arimura Y et al. Influence of DNA methylation on positioning and DNA flexibility of nucleosomes with pericentric satellite DNA. Open Biol. 2015; 5: 150128.

[20] Stroud H, Do T, Du J et al. Non-CG methylation patterns shape the epigenetic landscape in Arabidopsis . Nat Struct Mol Biol. 2018; 21: 64-72.

[21] Stroud H, Greenberg MVC, Feng S et al. Comprehensive analysis of silencing mutants reveals complex regulation of the Arabidopsis methylome. Cell. 2013; 152: 352-64.

[22] Zemach A, Kim MY, Hsieh PH et al. The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin. Cell. 2013; 153: 193-205.

[23] Teyssier E, Bernacchia G, Maury S et al. Tissue dependent variations of DNA methylation and endoreduplication levels during tomato fruit development and ripening. Planta. 2008; 228: 391-9.

[24] Stelpflug SC, Eichten SR, Hermanson PJ et al. Consistent and heritable alterations of DNA methylation are induced by tissue culture in maize. Genetics. 2014; 198: 209-18.

[25] Shemer O, Landau U, Candela H et al. Competency for shoot regeneration from Arabidopsis root explants is regulated by DNA methylation. Plant Sci. 2015; 238: 251-61.

[26] Berdasco M, Alcázar R, García-Ortiz MV et al. Promoter DNA hypermethylation and gene repression in undifferentiated Arabidopsis cells. PLoS One. 2008; 3: e3306.

[27] Mozgova I, Munoz-Viana R, Hennig L . PRC2 represses hormone-induced somatic embryogenesis in vegetative tissue of Arabidopsis thaliana . PLoS Genet. 2017; 13: e1006562.

[28] Margueron R, Reinberg D . The Polycomb complex PRC2 and its mark in life. Nature. 2011; 469: 343-9.

[29] Bouyer D, Roudier F, Heese M et al. Polycomb repressive complex 2 controls the embryo-to-seedling phase transition. PLoS Genet. 2011; 7: e1002014.

[30] Chanvivattana Y, Bishopp A, Schubert D et al. Interaction of Polycomb-group proteins controlling flowering in Arabidopsis . Development. 2004; 131: 5263-76.

[31] Krause K, Turck F . Plant epigenetics plant H3K27me3 has finally found its readers. Nat Genet 2018; 50: 1206-8.

[32] He C, Chen XF, Huang H et al. Reprogramming of H3K27me3 is critical for acquisition of pluripotency from cultured Arabidopsis tissues. PLoS Genet. 2012; 8: e1002911.

[33] Nakamura M, Batista RA, Köhler C et al. Polycomb repressive complex 2-mediated histone modification H3K27me3 is associated with embryogenic potential in Norway spruce. J Exp Bot. 2020; 71: 6366-78.

[34] Zhao N, Zhang K, Wang C et al. Systematic analysis of differential H3K27me3 and H3K4me3 deposition in callus and seedling reveals the epigenetic regulatory mechanisms involved in callus formation in rice. Front Genet. 2020; 11: 766.

[35] Jones MA, Covington MF, DiTacchio L et al. Jumonji domain protein JMJD5 functions in both the plant and human circadian systems. Proc Natl Acad Sci USA 2010; 107: 21623-8.

[36] Lu SX, Knowles SM, Webb CJ et al. The Jumonji C domain-containing protein jmj30 regulates period length in the Arabidopsis circadian clock . Plant Physiol. 2011; 155: 906-15.

[37] Gan ES, Xu Y, Wong JY et al. Jumonji demethylases moderate precocious flowering at elevated temperature via regulation of FLC in Arabidopsis . Nat Commun. 2014; 5: 5098.

[38] Okushima Y, Fukaki H, Onoda M et al. ARF7 and ARF19 regulate lateral root formation via direct activation of LBD/ASL genes in Arabidopsis . Plant Cell. 2007; 19: 118-30.

[39] Wang J, Wu B, Lu K et al. The amino acid permease 5 (OsAAP5) regulates tiller number and grain yield in rice. Plant Physiol. 2019; 180: 1031-45.

[40] Xu L, Xu Y, Dong A et al. Novel as1 and as2 defects in leaf adaxial-abaxial polarity reveal the requirement for ASYMMETRIC LEAVES1 and 2 and ERECTA functions in specifying leaf adaxial identity. Development. 2003; 130: 4097-107.

[41] Xu J, Zhou S, Gong X et al. Single-base methylome analysis reveals dynamic epigenomic differences associated with water deficit in apple. Plant Biotechnol J. 2018; 16: 672-87.

[42] Park Y, Wu H . Differential methylation analysis for BS-seq data under general experimental design. Bioinformatics. 2016; 32: 1446-53.

[43] Quadrana L, Almeida J, Asís R et al. Natural occurring epialleles determine vitamin E accumulation in tomato fruits. Nat Commun. 2014; 5: 3027.

[44] Goslin K, Zheng B, Serrano-Mislata A et al. Transcription factor interplay between LEAFY and APETALA1/CAULIFLOWER during floral initiation. Plant Physiol. 2017; 174: 1097-109.

[45] Li H, Durbin R . Fast and accurate long-read alignment with burrows-wheeler transform. Bioinformatics. 2010; 26: 589-95.

[46] Robinson JT, Thorvaldsdóttir H, Winckler W et al. Integrative genomics viewer. Nat Biotechnol. 2011; 29: 24-6.

[47] Kim D, Pertea G, Trapnell C et al. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 2013; 14: R36.

[48] Anders S, Pyl PT, Huber W . HTSeq - a Python framework to work with high-throughput sequencing data. Bioinformatics. 2015; 31: 166-9.

[49] Young MD, Wakefield MJ, Smyth GK et al. Gene ontology analysis for RNA-seq: accounting for selection bias. Genome Biol. 2010; 11: R14.

[50] Mao XZ, Cai T, Olyarchuk JG et al. Automated genome annotation and pathway identification using the KEGG Orthology (KO) as a controlled vocabulary. Bioinformatics. 2005; 21: 3787-93.

[51] Tong Z, Gao Z, Wang F et al. Selection of reliable reference genes for gene expression studies in peach using real-time PCR. BMC Mol Biol. 2009; 10: 71.

[52] Schapira M, Arrowsmith CH . Methyltransferase inhibitors for modulation of the epigenome and beyond. Curr Opin Chem Biol. 2016; 33: 81-7.

[53] Heinemann B, Nielsen JM, Hudlebusch HR et al. Inhibition of demethylases by GSK-J1/J4. Nature. 2014; 514: E1-2.

[54] Hofstetter C, Kampka JM, Huppertz S et al. Inhibition of KDM6 activity during murine ESC differentiation induces DNA damage. J Cell Sci. 2016; 129: 788-803.

[55] Wang GQ, Li H, Meng S et al. Analysis of global methylome and gene expression during carbon reserve mobilization in stems under soil drying. Plant Physiol. 2020; 183: 1809-24.

[56] Fuente L, Conesa A, Lloret A et al. Genome-wide changes in histone H3 lysine 27 trimethylation associated with bud dormancy release in peach. Tree Genet Genomes. 2015; 11: 45.

[57] Xie Q, Frugis G, Colgan D et al. Arabidopsis NAC1 transduces auxin signal downstream of TIR1 to promote lateral root development . Genes Dev. 2000; 14: 3024-36.

[58] Sugimoto K, Gordon SP, Meyerowitz EM . Regeneration in plants and animals: dedifferentiation, transdifferentiation, or just differentiation? Trends Cell Biol. 2011; 21: 212-8.

[59] Shim S, Lee HG, Park OS et al. Dynamic changes in DNA methylation occur in TE regions and affect cell proliferation during leaf-to-callus transition in Arabidopsis . Epigenetics. 2021; 17: 41-58.

[60] Zhong S, Fei Z, Chen YR et al. Single-base resolution methylomes of tomato fruit development reveal epigenome modifications associated with ripening. Nat Biotechnol. 2013; 31: 154-9.

[61] Zhang M, Zhang X, Guo L et al. Single-base resolution methylome of cotton cytoplasmic male sterility system reveals epigenomic changes in response to high-temperature stress during anther development. J Exp Bot. 2020; 71: 951-69.

[62] Niederhuth CE, Bewick AJ, Ji L et al. Widespread natural variation of DNA methylation within angiosperms. Genome Biol. 2016; 17: 194.

[63] Rothkegel K, Espinoza A, Sanhueza D et al. Identification of DNA methylation and transcriptomic profiles associated with fruit mealiness in Prunus persica (L.) Batsch. Front Plant Sci. 2021; 12: 684130.

[64] Seymour DK, Koenig D, Hagmann J et al. Evolution of DNA methylation patterns in the Brassicaceae is driven by differences in genome organization. PLoS Genet. 2014; 10: e1004785.

[65] Zakrzewski F, Schmidt M, Van Lijsebettens M et al. DNA methylation of retrotransposons, DNA transposons and genes in sugar beet (Beta vulgaris L.) . Plant J. 2017; 90: 1156-75.

[66] Li X, Zhu J, Hu F et al. Single-base resolution maps of cultivated and wild rice methylomes and regulatory roles of DNA methylation in plant gene expression. BMC Genomics. 2012; 13: 300.

[67] Belchev I, Tchorbadjieva M, Pantchev I . Effect of 5-azacytidine on callus induction and plant regeneration potential in anther culture of wheat (Triticum aestivum L.) . Bulg J Plant Physiol. 2004; 30: 45-50.

[68] Liu D, Mu Q, Li X et al. The callus formation capacity of strawberry leaf explants is modulated by DNA methylation. Hortic Res. 2022; 9: uhab073.

[69] Jiang D, Berger F . DNA replication-coupled histone modification maintains Polycomb gene silencing in plants. Science. 2017; 357: 1146-9.

[70] Deng W, Buzas DM, Ying H et al. Arabidopsis Polycomb repressive complex 2 binding sites contain putative GAGA factor binding motifs within coding regions of genes . BMC Genomics. 2013; 14: 593.

[71] Zhou S, Liu X, Zhou C et al. Cooperation between the H3K27me3 chromatin mark and non-CG methylation in epigenetic regulation. Plant Physiol. 2016; 172: 1131-41.

[72] Xiang Y, Zhu Z, Han G et al. JMJD3 is a histone H3K27 demethylase. Cell Res. 2007; 17: 850-7.

[73] Kruidenier L, Chung CW, Cheng Z et al. A selective jumonji H3K27 demethylase inhibitor modulates the proinflammatory macrophage response. Nature. 2012; 488: 404-8.

[74] Mandal C, Kim SH, Kang SC et al. GSK-J4-mediated transcriptomic alterations in differentiating embryoid bodies. Mol Cells. 2017; 40: 737-51.

[75] Rath BH, Waung I, Camphausen K et al. Inhibition of the histone H3K27 demethylase UTX enhances tumor cell radiosensitivity. Mol Cancer Ther. 2018; 17: 1070-8.

[76] 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.

[77] Dominguez M, Berger F . Chromatin and the cell cycle meet in Madrid. Development. 2008; 135: 3475-80.

[78] Grafi G, Florentin A, Ransbotyn V et al. The stem cell state in plant development and in response to stress. Front Plant Sci. 2011; 2: 53.

[79] Weinhofer I, Hehenberger E, Roszak P et al. H3K27me3 profiling of the endosperm implies exclusion of polycomb group protein targeting by DNA methylation. PLoS Genet. 2010;6:e1001152.

[80] Lee K, Park OS, Seo PJ . Arabidopsis ATXR2 deposits H3K36me3 at the promoters of LBD genes to facilitate cellular dedifferentiation . Sci Signal. 2017; 10: eaan0316.