A high degree of developmental plasticity enables plants to adapt to continuous, often unfavorable and unpredictable changes in their environment. At the molecular level, adaptive advantages for plants are primarily provided by epigenetic machinery including DNA methylation, histone modifications, and the activity of noncoding RNA molecules. Using a mass spectrometry-based proteomic approach, we examined the levels of acetylated histone peptide forms in Arabidopsis plants with a loss of function of histone deacetylase 6 (HDA6), and in plants germinated in the presence of HDA inhibitors trichostatin A (TSA) and sodium butyrate (NaB). Our analyses revealed particular lysine sites at histone sequences targeted by the HDA6 enzyme, and by TSA- and NaB-sensitive HDAs. Compared with plants exposed to drugs, more dramatic changes in the overall profiles of histone post-translational modifications were identified in hda6 mutants. However, loss of HDA6 was not sufficient by itself to induce hyperacetylation to the maximum degree, implying complementary activities of other HDAs. In contrast to hda6 mutants that did not exhibit any obvious phenotypic defects, the phenotypes of seedlings exposed to HDA inhibitors were markedly affected, showing that the effect of these drugs on early plant development is not limited to the modulation of histone acetylation levels.

Laboratory of Functional Genomics and Proteomics National Centre for Biomolecular Research Faculty of Science Masaryk University 62500 Brno Czech Republic

Mendel Centre for Plant Genomics and Proteomics Central European Institute of Technology Masaryk University 62500 Brno Czech Republic

RECETOX Faculty of Science Masaryk University 62500 Brno Czech Republic

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Brownell J.E., Allis C.D. Special HATs for special occasions: Linking histone acetylation to chromatin assembly and gene activation. Curr. Opin. Genet. Dev. 1996;6:176–184. doi: 10.1016/S0959-437X(96)80048-7. PubMed DOI

Kuo M.H., Allis C.D. Roles of histone acetyltransferases and deacetylases in gene regulation. Bioessays. 1998;20:615–626. doi: 10.1002/(SICI)1521-1878(199808)20:8<615::AID-BIES4>3.0.CO;2-H. PubMed DOI

Chen Z.J., Pikaard C.S. Epigenetic silencing of RNA polymerase I transcription: A role for DNA methylation and histone modification in nucleolar dominance. Genes Dev. 1997;11:2124–2136. doi: 10.1101/gad.11.16.2124. PubMed DOI PMC

Kadosh D., Struhl K. Targeted recruitment of the Sin3-Rpd3 histone deacetylase complex generates a highly localized domain of repressed chromatin in vivo. Mol. Cell Biol. 1998;18:5121–5127. doi: 10.1128/MCB.18.9.5121. PubMed DOI PMC

Ning Y.Q., Chen Q., Lin R.N., Li Y.Q., Li L., Chen S., He X.J. The HDA19 histone deacetylase complex is involved in the regulation of flowering time in a photoperiod-dependent manner. Plant J. 2019;98:448–464. doi: 10.1111/tpj.14229. PubMed DOI

Tanaka M., Kikuchi A., Kamada H. The Arabidopsis histone deacetylases HDA6 and HDA19 contribute to the repression of embryonic properties after germination. Plant Physiol. 2008;146:149–161. doi: 10.1104/pp.107.111674. PubMed DOI PMC

Tian L., Chen Z.J. Blocking histone deacetylation in Arabidopsis induces pleiotropic effects on plant gene regulation and development. Proc. Natl. Acad. Sci. USA. 2001;98:200–205. doi: 10.1073/pnas.98.1.200. PubMed DOI PMC

Zheng M., Liu X.B., Lin J.C., Liu X.Y., Wang Z.Y., Xin M.M., Yao Y.Y., Peng H.R., Zhou D.X., Ni Z.F., et al. Histone acetyltransferase GCN5 contributes to cell wall integrity and salt stress tolerance by altering the expression of cellulose synthesis genes. Plant J. 2019;97:587–602. doi: 10.1111/tpj.14144. PubMed DOI

Pandey R., Muller A., Napoli C.A., Selinger D.A., Pikaard C.S., Richards E.J., Bender J., Mount D.W., Jorgensen R.A. Analysis of histone acetyltransferase and histone deacetylase families of Arabidopsis thaliana suggests functional diversification of chromatin modification among multicellular eukaryotes. Nucleic Acids Res. 2002;30:5036–5055. doi: 10.1093/nar/gkf660. PubMed DOI PMC

Yang X.J., Seto E. Collaborative spirit of histone deacetylases in regulating chromatin structure and gene expression. Curr. Opin. Genet. Dev. 2003;13:143–153. doi: 10.1016/S0959-437X(03)00015-7. PubMed DOI

Murfett J., Wang X.J., Hagen G., Guilfoyle T.J. Identification of arabidopsis histone deacetylase HDA6 mutants that affect transgene expression. Plant Cell. 2001;13:1047–1061. doi: 10.1105/tpc.13.5.1047. PubMed DOI PMC

Aufsatz W., Mette M.F., van der Winden J., Matzke M., Matzke A.J. HDA6, a putative histone deacetylase needed to enhance DNA methylation induced by double-stranded RNA. EMBO J. 2002;21:6832–6841. doi: 10.1093/emboj/cdf663. PubMed DOI PMC

Earley K., Lawrence R.J., Pontes O., Reuther R., Enciso A.J., Silva M., Neves N., Gross M., Viegas W., Pikaard C.S. Erasure of histone acetylation by Arabidopsis HDA6 mediates large-scale gene silencing in nucleolar dominance. Genes Dev. 2006;20:1283–1293. doi: 10.1101/gad.1417706. PubMed DOI PMC

Liu X.C., Yu C.W., Duan J., Luo M., Wang K.C., Tian G., Cui Y.H., Wu K.Q. HDA6 Directly Interacts with DNA Methyltransferase MET1 and Maintains Transposable Element Silencing in Arabidopsis. Plant Physiol. 2012;158:119–129. doi: 10.1104/pp.111.184275. PubMed DOI PMC

Probst A.V., Fagard M., Proux F., Mourrain P., Boutet S., Earley K., Lawrence R.J., Pikaard C.S., Murfett J., Furner I., et al. Arabidopsis histone deacetylase HDA6 is required for maintenance of transcriptional gene silencing and determines nuclear organization of rDNA repeats. Plant Cell. 2004;16:1021–1034. doi: 10.1105/tpc.018754. PubMed DOI PMC

Chen L.T., Luo M., Wang Y.Y., Wu K.Q. Involvement of Arabidopsis histone deacetylase HDA6 in ABA and salt stress response. J. Exp. Bot. 2010;61:3345–3353. doi: 10.1093/jxb/erq154. PubMed DOI PMC

Wang Y.Z., Hu Q., Wu Z.J., Wang H., Han S.M., Jin Y., Zhou J., Zhang Z.F., Jiang J.F., Shen Y., et al. HISTONE DEACETYLASE 6 represses pathogen defence responses in Arabidopsis thaliana. Plant Cell Environ. 2017;40:2972–2986. doi: 10.1111/pce.13047. PubMed DOI

Yu C.W., Liu X.C., Luo M., Chen C.Y., Lin X.D., Tian G., Lu Q., Cui Y.H., Wu K.Q. HISTONE DEACETYLASE6 Interacts with FLOWERING LOCUS D and Regulates Flowering in Arabidopsis. Plant Physiol. 2011;156:173–184. doi: 10.1104/pp.111.174417. PubMed DOI PMC

Finnin M.S., Donigian J.R., Cohen A., Richon V.M., Rifkind R.A., Marks P.A., Breslow R., Pavletich N.P. Structures of a histone deacetylase homologue bound to the TSA and SAHA inhibitors. Nature. 1999;401:188–193. doi: 10.1038/43710. PubMed DOI

Cousens L.S., Gallwitz D., Alberts B.M. Different Accessibilities in Chromatin to Histone Acetylase. J. Biol. Chem. 1979;254:1716–1723. PubMed

Ma X.J., Zhang C., Zhang B., Yang C.P., Li S.J. Identification of genes regulated by histone acetylation during root development in Populus trichocarpa. BMC Genom. 2016;17 doi: 10.1186/s12864-016-2407-x. PubMed DOI PMC

Earley K.W., Shook M.S., Brower-Toland B., Hicks L., Pikaard C.S. In vitro specificities of Arabidopsis co-activator histone acetyltransferases: Implications for histone hyperacetylation in gene activation. Plant J. 2007;52:615–626. doi: 10.1111/j.1365-313X.2007.03264.x. PubMed DOI

Pagano A., Araujo S.D., Macovei A., Dondi D., Lazzaroni S., Balestrazzi A. Metabolic and gene expression hallmarks of seed germination uncovered by sodium butyrate in Medicago truncatula. Plant Cell Environ. 2019;42:259–269. doi: 10.1111/pce.13342. PubMed DOI

Ledvinová D., Mikulášek K., Kuchaříková H., Brabencová S., Fojtová M., Zdráhal Z., Lochmanová G. Filter-Aided Sample Preparation Procedure for Mass Spectrometric Analysis of Plant Histones. Front. Plant Sci. 2018;9:1373. doi: 10.3389/fpls.2018.01373. PubMed DOI PMC

Wu K., Zhang L., Zhou C., Yu C.W., Chaikam V. HDA6 is required for jasmonate response, senescence and flowering in Arabidopsis. J. Exp. Bot. 2008;59:225–234. doi: 10.1093/jxb/erm300. PubMed DOI

Ma X., Lv S., Zhang C., Yang C. Histone deacetylases and their functions in plants. Plant Cell Rep. 2013;32:465–478. doi: 10.1007/s00299-013-1393-6. PubMed DOI

Ueda M., Matsui A., Tanaka M., Nakamura T., Abe T., Sako K., Sasaki T., Kim J.M., Ito A., Nishino N., et al. The Distinct Roles of Class I and II RPD3-Like Histone Deacetylases in Salinity Stress Response. Plant Physiol. 2017;175:1760–1773. doi: 10.1104/pp.17.01332. PubMed DOI PMC

Hartl M., Füßl M., Boersema P.J., Jost J.O., Kramer K., Bakirbas A., Sindlinger J., Plöchinger M., Leister D., Uhrig G., et al. Lysine acetylome profiling uncovers novel histone deacetylase substrate proteins in Arabidopsis. Mol. Syst. Biol. 2017;13:949. doi: 10.15252/msb.20177819. PubMed DOI PMC

Činčárová L., Lochmanová G., Nováková K., Šultesová P., Konečná H., Fajkusová L., Fajkus J., Zdráhal Z. A combined approach for the study of histone deacetylase inhibitors. Mol. Biosyst. 2012;8:2937–2945. doi: 10.1039/c2mb25136a. PubMed DOI

Chang J., Varghese D.S., Gillam M.C., Peyton M., Modi B., Schiltz R.L., Girard L., Martinez E.D. Differential response of cancer cells to HDAC inhibitors trichostatin A and depsipeptide. Br. J. Cancer. 2012;106:116–125. doi: 10.1038/bjc.2011.532. PubMed DOI PMC

Krämer O.H., Zhu P., Ostendorff H.P., Golebiewski M., Tiefenbach J., Peters M.A., Brill B., Groner B., Bach I., Heinzel T., et al. The histone deacetylase inhibitor valproic acid selectively induces proteasomal degradation of HDAC2. EMBO J. 2003;22:3411–3420. doi: 10.1093/emboj/cdg315. PubMed DOI PMC

Marks P.A., Xu W.S. Histone deacetylase inhibitors: Potential in cancer therapy. J. Cell Biochem. 2009;107:600–608. doi: 10.1002/jcb.22185. PubMed DOI PMC

Xu C.R., Liu C., Wang Y.L., Li L.C., Chen W.Q., Xu Z.H., Bai S.N. Histone acetylation affects expression of cellular patterning genes in the Arabidopsis root epidermis. Proc. Natl. Acad. Sci. USA. 2005;102:14469–14474. doi: 10.1073/pnas.0503143102. PubMed DOI PMC

Chen D.H., Huang Y., Jiang C., Si J.P. Chromatin-Based Regulation of Plant Root Development. Front. Plant Sci. 2018;9:1509. doi: 10.3389/fpls.2018.01509. PubMed DOI PMC

Schindelin J., Arganda-Carreras I., Frise E., Kaynig V., Longair M., Pietzsch T., Preibisch S., Rueden C., Saalfeld S., Schmid B., et al. Fiji: An open-source platform for biological-image analysis. Nat. Methods. 2012;9:676–682. doi: 10.1038/nmeth.2019. PubMed DOI PMC

Vizcaíno J.A., Csordas A., Del-Toro N., Dianes J.A., Griss J., Lavidas I., Mayer G., Perez-Riverol Y., Reisinger F., Ternent T., et al. 2016 update of the PRIDE database and its related tools. Nucleic Acids Res. 2016;44:11033. doi: 10.1093/nar/gkw880. PubMed DOI PMC

Aitchison J. The Statistical-Analysis of Compositional Data. J. Roy. Stat. Soc. B Met. 1982;44:139–177. doi: 10.1111/j.2517-6161.1982.tb01195.x. DOI

Hron K., Templ M., Filzmoser P. Imputation of missing values for compositional data using classical and robust methods. Comput. Stat. Data Anal. 2010;54:3095–3107. doi: 10.1016/j.csda.2009.11.023. DOI

R Core Team R: A Language and Environment for Statistical Computing, R Foundation for Statistical Computing: 2018. [(accessed on 15 May 2019)]; Available online: http:// www.R-project.org.

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