Involvement of epigenetic mechanisms in the regulation of telomeres and transposable elements (TEs), genomic regions with the protective and potentially detrimental function, respectively, has been frequently studied. Here, we analyzed telomere lengths in Arabidopsis thaliana plants of Columbia, Landsberg erecta and Wassilevskija ecotypes exposed repeatedly to the hypomethylation drug zebularine during germination. Shorter telomeres were detected in plants growing from seedlings germinated in the presence of zebularine with a progression in telomeric phenotype across generations, relatively high inter-individual variability, and diverse responses among ecotypes. Interestingly, the extent of telomere shortening in zebularine Columbia and Wassilevskija plants corresponded to the transcriptional activation of TEs, suggesting a correlated response of these genomic elements to the zebularine treatment. Changes in lengths of telomeres and levels of TE transcripts in leaves were not always correlated with a hypomethylation of cytosines located in these regions, indicating a cytosine methylation-independent level of their regulation. These observations, including differences among ecotypes together with distinct dynamics of the reversal of the disruption of telomere homeostasis and TEs transcriptional activation, reflect a complex involvement of epigenetic processes in the regulation of crucial genomic regions. Our results further demonstrate the ability of plant cells to cope with these changes without a critical loss of the genome stability.

Institute of Biophysics Academy of Sciences of the Czech Republic Královopolská 135 CZ 61265 Brno Czech Republic

Laboratory of Functional Genomics and Proteomics National Centre for Biomolecular Research Faculty of Science Masaryk University Kotlářská 2 CZ 61137 Brno Czech Republic

Mendel Centre for Plant Genomics and Proteomics Central European Institute for Technology Masaryk University Kamenice 5 CZ 62500 Brno Czech Republic

Zobrazit více v PubMed

Richards E.J., Ausubel F.M. Isolation of a higher eukaryotic telomere from Arabidopsis thaliana. Cell. 1988;53:127–136. doi: 10.1016/0092-8674(88)90494-1. PubMed DOI

Moyzis R.K., Buckingham J.M., Cram L.S., Dani M., Deaven L.L., Jones M.D., Meyne J., Ratliff R.L., Wu J.R. A highly conserved repetitive DNA sequence, (TTAGGG)n, present at the telomeres of human chromosomes. Proc. Natl. Acad. Sci. USA. 1988;85:6622–6626. doi: 10.1073/pnas.85.18.6622. PubMed DOI PMC

Venkatesan S., Khaw A.K., Hande M.P. Telomere biology-insights into an intriguing phenomenon. Cells. 2017;6:15. doi: 10.3390/cells6020015. PubMed DOI PMC

Henderson I.R., Deleris A., Wong W., Zhong X.H., Chin H.G., Horwitz G.A., Kelly K.A., Pradhan S., Jacobsen S.E. The de novo cytosine methyltransferase DRM2 requires intact UBA domains and a catalytically mutated paralog DRM3 during RNA-directed DNA methylation in Arabidopsis thaliana. PLoS Genet. 2010;6:e1001182. doi: 10.1371/journal.pgen.1001182. PubMed DOI PMC

Cokus S.J., Feng S., Zhang X., Chen Z., Merriman B., Haudenschild C.D., Pradhan S., Nelson S.F., Pellegrini M., Jacobsen S.E. Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature. 2008;452:215–219. doi: 10.1038/nature06745. PubMed DOI PMC

Ogrocka A., Polanska P., Majerova E., Janeba Z., Fajkus J., Fojtova M. Compromised telomere maintenance in hypomethylated Arabidopsis thaliana plants. Nucleic Acids Res. 2014;42:2919–2931. doi: 10.1093/nar/gkt1285. PubMed DOI PMC

Vrbsky J., Akimcheva S., Watson J.M., Turner T.L., Daxinger L., Vyskot B., Aufsatz W., Riha K. siRNA-mediated methylation of Arabidopsis telomeres. PLoS Genet. 2010;6:e1000986. doi: 10.1371/journal.pgen.1000986. PubMed DOI PMC

Vaquero-Sedas M.I., Gamez-Arjona F.M., Vega-Palas M.A. Arabidopsis thaliana telomeres exhibit euchromatic features. Nucleic Acids Res. 2011;39:2007–2017. doi: 10.1093/nar/gkq1119. PubMed DOI PMC

Vega-Vaquero A., Bonora G., Morselli M., Vaquero-Sedas M.I., Rubbi L., Pellegrini M., Vega-Palas M.A. Novel features of telomere biology revealed by the absence of telomeric DNA methylation. Genome Res. 2016;26:1047–1056. doi: 10.1101/gr.202465.115. PubMed DOI PMC

Underwood C.J., Henderson I.R., Martienssen R.A. Genetic and epigenetic variation of transposable elements in Arabidopsis. Curr. Opin. Plant. Biol. 2017;36:135–141. doi: 10.1016/j.pbi.2017.03.002. PubMed DOI PMC

Creasey K.M., Zhai J.X., Borges F., Van Ex F., Regulski M., Meyers B.C., Martienssen R.A. miRNAs trigger widespread epigenetically activated siRNAs from transposons in Arabidopsis. Nature. 2014;508:411–415. doi: 10.1038/nature13069. PubMed DOI PMC

Miura A., Yonebayashi S., Watanabe K., Toyama T., Shimada H., Kakutani T. Mobilization of transposons by a mutation abolishing full DNA methylation in Arabidopsis. Nature. 2001;411:212–214. doi: 10.1038/35075612. PubMed DOI

Singer T., Yordan C., Martienssen R.A. Robertson’s Mutator transposons in A. thaliana are regulated by the chromatin-remodeling gene Decrease in DNA Methylation (DDM1) Gene Dev. 2001;15:591–602. doi: 10.1101/gad.193701. PubMed DOI PMC

Stroud H., Hale C.J., Feng S.H., Caro E., Jacob Y., Michaels S.D., Jacobsen S.E. DNA methyltransferases are required to induce heterochromatic re-replication in Arabidopsis. PLoS Genet. 2012;8 doi: 10.1371/journal.pgen.1002808. PubMed DOI PMC

Cheng J.C., Matsen C.B., Gonzales F.A., Ye W., Greer S., Marquez V.E., Jones P.A., Selker E.U. Inhibition of DNA methylation and reactivation of silenced genes by zebularine. J. Natl. Cancer Inst. 2003;95:399–409. doi: 10.1093/jnci/95.5.399. PubMed DOI

Champion C., Guianvarc’h D., Senamaud-Beaufort C., Jurkowska R.Z., Jeltsch A., Ponger L., Arimondo P.B., Guieysse-Peugeot A.L. Mechanistic insights on the inhibition of C5 DNA methyltransferases by zebularine. PLoS ONE. 2010;5:e12388. doi: 10.1371/journal.pone.0012388. PubMed DOI PMC

Ben-Kasus T., Ben-Zvi Z., Marquez V.E., Kelley J.A., Agbaria R. Metabolic activation of zebularine, a novel DNA methylation inhibitor, in human bladder carcinoma cells. Biochem. Pharmacol. 2005;70:121–133. doi: 10.1016/j.bcp.2005.04.010. PubMed DOI

Liu C.H., Finke A., Diaz M., Rozhon W., Poppenberger B., Baubec T., Pecinka A. Repair of DNA damage induced by the cytidine analog zebularine requires ATR and ATM in Arabidopsis. Plant Cell. 2015;27:1788–1800. doi: 10.1105/tpc.114.135467. PubMed DOI PMC

Baubec T., Pecinka A., Rozhon W., Mittelsten Scheid O. Effective, homogeneous and transient interference with cytosine methylation in plant genomic DNA by zebularine. Plant J. 2009;57:542–554. doi: 10.1111/j.1365-313X.2008.03699.x. PubMed DOI PMC

Majerova E., Fojtova M., Mozgova I., Bittova M., Fajkus J. Hypomethylating drugs efficiently decrease cytosine methylation in telomeric DNA and activate telomerase without affecting telomere lengths in tobacco cells. Plant Mol. Biol. 2011;77:371–380. doi: 10.1007/s11103-011-9816-7. PubMed DOI

Griffin P.T., Niederhuth C.E., Schmitz R.J. A comparative analysis of 5-azacytidine- and zebularine-induced DNA demethylation. G3 Genes Genomes Genet. 2016;6:2773–2780. doi: 10.1534/g3.116.030262. PubMed DOI PMC

Shakirov E.V., Shippen D.E. Length regulation and dynamics of individual telomere tracts in wild-type Arabidopsis. Plant Cell. 2004;16:1959–1967. doi: 10.1105/tpc.104.023093. PubMed DOI PMC

Matzke M.A., Mette M.F., Aufsatz W., Jakowitsch J., Matzke A.J.M. Host defenses to parasitic sequences and the evolution of epigenetic control mechanisms. Genetica. 1999;107:271–287. doi: 10.1023/A:1003921710672. PubMed DOI

Yoder J.A., Walsh C.P., Bestor T.H. Cytosine methylation and the ecology of intragenomic parasites. Trends Genet. 1997;13:335–340. doi: 10.1016/S0168-9525(97)01181-5. PubMed DOI

Kato M., Miura A., Bender J., Jacobsen S.E., Kakutani T. Role of CG and non-CG methylation in immobilization of transposons in Arabidopsis. Curr. Biol. 2003;13:421–426. doi: 10.1016/S0960-9822(03)00106-4. PubMed DOI

Baubec T., Finke A., Scheid O.M., Pecinka A. Meristem-specific expression of epigenetic regulators safeguards transposon silencing in Arabidopsis. EMBO Rep. 2014;15:446–452. doi: 10.1002/embr.201337915. PubMed DOI PMC

Hetzl J., Foerster A.M., Raidl G., Scheid O.M. CyMATE: A new tool for methylation analysis of plant genornic DNA after bisulphite sequencing. Plant J. 2007;51:526–536. doi: 10.1111/j.1365-313X.2007.03152.x. PubMed DOI

Sovakova P.P., Magdolenova A., Konecna K., Rajecka V., Fajkus J., Fojtova M. Telomere elongation upon transfer to callus culture reflects the reprogramming of telomere stability control in Arabidopsis. Plant Mol. Biol. 2018;98:81–99. doi: 10.1007/s11103-018-0765-2. PubMed DOI

Xie X.Y., Shippen D.E. DDM1 guards against telomere truncation in Arabidopsis. Plant Cell Rep. 2018;37:501–513. doi: 10.1007/s00299-017-2245-6. PubMed DOI PMC

Anteková K. Analysis of Levels of Transposable Elements Transcripts in Arabidopsis Plants Exposed to the Zebularine during Germination. Masaryk University; Brno, Czech Republic: 2018. Unpublished Results.

Suzuki M.M., Bird A. DNA methylation landscapes: Provocative insights from epigenomics. Nat. Rev. Genet. 2008;9:465–476. doi: 10.1038/nrg2341. PubMed DOI

Polanská P. Diploma Thesis. Masaryk University; Brno, Czech Republic: 2013. Telomeres and Telomerase in Plants with Hypomethylated Genomes.

Vaquero-Sedas M.I., Vega-Palas M.A. Determination of Arabidopsis thaliana telomere length by PCR. Sci. Rep. 2014;4:5540. doi: 10.1038/srep05540. PubMed DOI PMC

Fojtová M., Fajkus P., Polanská P., Fajkus J. Terminal restriction fragments (TRF) method to analyze telomere lengths. Bio Protoc. 2015;5:e1671. doi: 10.21769/BioProtoc.1671. DOI

Dellaporta S.L., Wood J., Hicks J.B. A plant DNA minipreparation: Version II. Plant Mol. Biol. Rep. 1983;1:19–21. doi: 10.1007/BF02712670. DOI

Adamusova K., Khosravi S., Fujimoto S., Houben A., Matsunaga S., Fajkus J., Fojtova M. Two combinatorial patterns of telomere histone marks in plants with canonical and non-canonical telomere repeats. Plant J. 2020;102:678–687. doi: 10.1111/tpj.14653. PubMed DOI

Ijdo J.W., Wells R.A., Baldini A., Reeders S.T. Improved telomere detection using a telomere repeat probe (TTAGGG)n Generated by PCR. Nucleic Acids Res. 1991;19:4780. doi: 10.1093/nar/19.17.4780. PubMed DOI PMC

Pfaffl M.W. Quantification Strategies in Real-Time PCR. In: Bustin S.A., editor. A-Z of Quantitative PCR. International University Line; La Jola, CA, USA: 2004. pp. 87–112.

Clark S.J., Harrison J., Paul C.L., Frommer M. High-sensitivity mapping of methylated cytosines. Nucleic Acids Res. 1994;22:2990–2997. PubMed PMC

Epigenetics for Crop Improvement in Times of Global Change