Methylation systems have been conserved during the divergence of plants and animals, although they are regulated by different pathways and enzymes. However, studies on the interactions of the epigenomes among evolutionarily distant organisms are lacking. To address this, we studied the epigenetic modification and gene expression of plant chromosome fragments (~30 Mb) in a human-Arabidopsis hybrid cell line. The whole-genome bisulfite sequencing results demonstrated that recombinant Arabidopsis DNA could retain its plant CG methylation levels even without functional plant methyltransferases, indicating that plant DNA methylation states can be maintained even in a different genomic background. The differential methylation analysis showed that the Arabidopsis DNA was undermethylated in the centromeric region and repetitive elements. Several Arabidopsis genes were still expressed, whereas the expression patterns were not related to the gene function. We concluded that the plant DNA did not maintain the original plant epigenomic landscapes and was under the control of the human genome. This study showed how two diverging genomes can coexist and provided insights into epigenetic modifications and their impact on the regulation of gene expressions between plant and animal genomes.

Centre for Research in Biotechnology for Agriculture Universiti Malaya Lembah Pantai Kuala Lumpur 50603 Malaysia

Graduate School of Human Development and Environment Kobe University Kobe Hyogo 657 8501 Japan

Graduate School of Pharmaceutical Sciences Osaka University Suita Osaka 565 0871 Japan

Graduate School of Technology Industrial and Social Sciences Tokushima University Kuramoto Tokushima 770 8503 Japan

Institute of Experimental Botany of the Czech Academy of Sciences Centre of the Region Hana for Biotechnological and Agricultural Research Šlechtitelů 31 779 00 Olomouc Czech Republic

Zobrazit více v PubMed

Blomen V.A., Boonstra J. Stable Transmission of Reversible Modifications: Maintenance of Epigenetic Information through the Cell Cycle. Cell. Mol. Life Sci. 2011;68:27–44. doi: 10.1007/s00018-010-0505-5. PubMed DOI PMC

Feng J.X., Riddle N.C. Epigenetics and Genome Stability. Mamm. Genome. 2020;31:181–195. doi: 10.1007/s00335-020-09836-2. PubMed DOI

Ehrlich M., Gama-Sosa M.A., Huang L.-H., Midgett R.M., Kuo K.C., McCune R.A., Gehrke C. Amount and Distribution of 5-Methylcytosine in Human DNA from Different Types of Tissues or Cells. Nucleic Acids Res. 1982;10:2709–2721. doi: 10.1093/nar/10.8.2709. PubMed DOI PMC

Law J.A., Jacobsen S.E. Establishing, Maintaining and Modifying DNA Methylation Patterns in Plants and Animals. Nat. Rev. Genet. 2010;11:204–220. doi: 10.1038/nrg2719. PubMed DOI PMC

Zhang X., Yazaki J., Sundaresan A., Cokus S., Chan S.W.-L., Chen H., Henderson I.R., Shinn P., Pellegrini M., Jacobsen S.E., et al. Genome-Wide High-Resolution Mapping and Functional Analysis of DNA Methylation in Arabidopsis. Cell. 2006;126:1189–1201. doi: 10.1016/j.cell.2006.08.003. PubMed DOI

Feinberg A.P., Vogelstein B. Hypomethylation Distinguishes Genes of Some Human Cancers from Their Normal Counterparts. Nature. 1983;301:89–92. doi: 10.1038/301089a0. PubMed DOI

Feinberg A.P., Gehrke C.W., Kuo K.C., Ehrlich M. Reduced Genomic 5-Methylcytosine Content in Human Colonic Neoplasia. Cancer Res. 1988;48:1159–1161. PubMed

Jin Z., Liu Y. DNA Methylation in Human Diseases. Genes Dis. 2018;5:1–8. doi: 10.1016/j.gendis.2018.01.002. PubMed DOI PMC

Li E., Zhang Y. DNA Methylation in Mammals. Cold Spring Harb. Perspect. Biol. 2014;6 doi: 10.1101/cshperspect.a019133. PubMed DOI PMC

Chan S.W.-L., Henderson I.R., Jacobsen S.E. Gardening the Genome: DNA Methylation in Arabidopsis Thaliana. Nat. Rev. Genet. 2005;6:351–360. doi: 10.1038/nrg1601. PubMed DOI

Pikaard C.S., Mittelsten Scheid O. Epigenetic Regulation in Plants. Cold Spring Harb. Perspect. Biol. 2014;6 doi: 10.1101/cshperspect.a019315. PubMed DOI PMC

Finnegan E.J., Dennis E.S. Isolation and Identification by Sequence Homology of a Putative Cytosine Methyltransferase from Arabidopsis Thaliana. Nucleic Acids Res. 1993;21:2383–2388. doi: 10.1093/nar/21.10.2383. PubMed DOI PMC

Cao X., Springer N.M., Muszynski M.G., Phillips R.L., Kaeppler S., Jacobsen S.E. Conserved Plant Genes with Similarity to Mammalian de Novo DNA Methyltransferases. Proc. Natl. Acad. Sci. USA. 2000;97:4979–4984. doi: 10.1073/pnas.97.9.4979. PubMed DOI PMC

Goll M.G., Bestor T.H. Eukaryotic Cytosine Methyltransferases. Annu. Rev. Biochem. 2005;74:481–514. doi: 10.1146/annurev.biochem.74.010904.153721. PubMed DOI

Colot V., Rossignol J.-L. Eukaryotic DNA Methylation as an Evolutionary Device. BioEssays. 1999;21:402–411. doi: 10.1002/(SICI)1521-1878(199905)21:5<402::AID-BIES7>3.0.CO;2-B. PubMed DOI

Baulcombe D.C., Dean C. Epigenetic Regulation in Plant Responses to the Environment. Cold Spring Harb. Perspect. Biol. 2014;6:a019471. doi: 10.1101/cshperspect.a019471. PubMed DOI PMC

Greaves I.K., Gonzalez-Bayon R., Wang L., Zhu A., Liu P.-C., Groszmann M., Peacock W.J., Dennis E.S. Epigenetic Changes in Hybrids. Plant Physiol. 2015;168:1197–1205. doi: 10.1104/pp.15.00231. PubMed DOI PMC

Laporte M., Luyer J.L., Rougeux C., Dion-Côté A.-M., Krick M., Bernatchez L. DNA Methylation Reprogramming, TE Derepression, and Postzygotic Isolation of Nascent Animal Species. Sci. Adv. 2019;5:eaaw1644. doi: 10.1126/sciadv.aaw1644. PubMed DOI PMC

Hochstein N., Muiznieks I., Mangel L., Brondke H., Doerfler W. Epigenetic Status of an Adenovirus Type 12 Transgenome upon Long-Term Cultivation in Hamster Cells. J. Virol. 2007;81:5349–5361. doi: 10.1128/JVI.02624-06. PubMed DOI PMC

O’Neill R.J.W., O’Neill M.J., Graves J.A.M. Undermethylation Associated with Retroelement Activation and Chromosome Remodelling in an Interspecific Mammalian Hybrid. Nature. 1998;393:68–72. doi: 10.1038/29985. PubMed DOI

Remus R., Kämmer C., Heller H., Schmitz B., Schell G., Doerfler W. Insertion of Foreign DNA into an Established Mammalian Genome Can Alter the Methylation of Cellular DNA Sequences. J. Virol. 1999;73:1010–1022. doi: 10.1128/JVI.73.2.1010-1022.1999. PubMed DOI PMC

Doerfler W. Epigenetic Consequences of Foreign DNA Insertions: De Novo Methylation and Global Alterations of Methylation Patterns in Recipient Genomes. Rev. Med. Virol. 2011;21:336–346. doi: 10.1002/rmv.698. PubMed DOI

Weber S., Hofmann A., Herms S., Hoffmann P., Doerfler W. Destabilization of the Human Epigenome: Consequences of Foreign DNA Insertions. Epigenomics. 2015;7:745–755. doi: 10.2217/epi.15.40. PubMed DOI

Fitz-James M.H., Tong P., Pidoux A.L., Ozadam H., Yang L., White S.A., Dekker J., Allshire R.C. Large Domains of Heterochromatin Direct the Formation of Short Mitotic Chromosome Loops. eLife. 2020;9:e57212. doi: 10.7554/eLife.57212. PubMed DOI PMC

Wada N., Kazuki Y., Kazuki K., Inoue T., Fukui K., Oshimura M. Maintenance and Function of a Plant Chromosome in Human Cells. ACS Synth. Biol. 2017;6:301–310. doi: 10.1021/acssynbio.6b00180. PubMed DOI

Liu Y., Liaw Y.M., Teo C.H., Cápal P., Wada N., Fukui K., Doležel J., Ohmido N. Molecular Organization of Recombinant Human-Arabidopsis Chromosomes in Hybrid Cell Lines. Sci. Rep. 2021 doi: 10.1038/s41598-021-86130-4. PubMed DOI PMC

Xi Y., Li W. BSMAP: Whole Genome Bisulfite Sequence MAPping Program. BMC Bioinform. 2009;10:232. doi: 10.1186/1471-2105-10-232. PubMed DOI PMC

Krueger F., Andrews S.R. Bismark: A Flexible Aligner and Methylation Caller for Bisulfite-Seq Applications. Bioinformatics. 2011;27:1571–1572. doi: 10.1093/bioinformatics/btr167. 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

Wong N.C., Pope B.J., Candiloro I.L., Korbie D., Trau M., Wong S.Q., Mikeska T., Zhang X., Pitman M., Eggers S., et al. MethPat: A Tool for the Analysis and Visualisation of Complex Methylation Patterns Obtained by Massively Parallel Sequencing. BMC Bioinform. 2016;17:98. doi: 10.1186/s12859-016-0950-8. PubMed DOI PMC

Akalin A., Kormaksson M., Li S., Garrett-Bakelman F.E., Figueroa M.E., Melnick A., Mason C.E. MethylKit: A Comprehensive R Package for the Analysis of Genome-Wide DNA Methylation Profiles. Genome Biol. 2012;13:R87. doi: 10.1186/gb-2012-13-10-r87. PubMed DOI PMC

Chèneby J., Ménétrier Z., Mestdagh M., Rosnet T., Douida A., Rhalloussi W., Bergon A., Lopez F., Ballester B. ReMap 2020: A Database of Regulatory Regions from an Integrative Analysis of Human and Arabidopsis DNA-Binding Sequencing Experiments. Nucleic Acids Res. 2020;48:D180–D188. doi: 10.1093/nar/gkz945. PubMed DOI PMC

Klimopoulos A., Sellis D., Almirantis Y. Widespread Occurrence of Power-Law Distributions in Inter-Repeat Distances Shaped by Genome Dynamics. Gene. 2012;499:88–98. doi: 10.1016/j.gene.2012.02.005. PubMed DOI

Feng S., Cokus S.J., Zhang X., Chen P.-Y., Bostick M., Goll M.G., Hetzel J., Jain J., Strauss S.H., Halpern M.E., et al. Conservation and Divergence of Methylation Patterning in Plants and Animals. Proc. Natl. Acad. Sci. USA. 2010;107:8689–8694. doi: 10.1073/pnas.1002720107. PubMed DOI PMC

Su Z., Han L., Zhao Z. Conservation and Divergence of DNA Methylation in Eukaryotes. Epigenetics. 2011;6:134–140. doi: 10.4161/epi.6.2.13875. PubMed DOI PMC

Long H.K., King H.W., Patient R.K., Odom D.T., Klose R.J. Protection of CpG Islands from DNA Methylation Is DNA-Encoded and Evolutionarily Conserved. Nucleic Acids Res. 2016;44:6693–6706. doi: 10.1093/nar/gkw258. PubMed DOI PMC

Yi S.V. Insights into Epigenome Evolution from Animal and Plant Methylomes. Genome Biol. Evol. 2017;9:3189–3201. doi: 10.1093/gbe/evx203. PubMed DOI PMC

Lienert F., Wirbelauer C., Som I., Dean A., Mohn F., Schübeler D. Identification of genetic elements that autonomously determine DNA methylation states. Nat. Genet. 2011;43:1091–1097. doi: 10.1038/ng.946. PubMed DOI

Krebs A.R., Dessus-Babus S., Burger L., Schübeler D. High-throughput engineering of a mammalian genome reveals building principles of methylation states at CG rich regions. Elife. 2014;3:e04094. doi: 10.7554/eLife.04094. PubMed DOI PMC

Kohli R.M., Zhang Y. TET Enzymes, TDG and the Dynamics of DNA Demethylation. Nature. 2013;502:472–479. doi: 10.1038/nature12750. PubMed DOI PMC

Gallego-Bartolomé J., Gardiner J., Liu W., Papikian A., Ghoshal B., Kuo H.Y., Zhao J.M.-C., Segal D.J., Jacobsen S.E. Targeted DNA Demethylation of the Arabidopsis Genome Using the Human TET1 Catalytic Domain. Proc. Natl. Acad. Sci. USA. 2018;115:E2125–E2134. doi: 10.1073/pnas.1716945115. PubMed DOI PMC

He Y., Ecker J.R. Non-CG Methylation in the Human Genome. Annu. Rev. Genom. Hum. Genet. 2015;16:55–77. doi: 10.1146/annurev-genom-090413-025437. PubMed DOI PMC

Erdmann R.M., Picard C.L. RNA-Directed DNA Methylation. PLoS Genet. 2020;16:e1009034. doi: 10.1371/journal.pgen.1009034. PubMed DOI PMC

Kenchanmane Raju S.K., Ritter E.J., Niederhuth C.E. Establishment, Maintenance, and Biological Roles of Non-CG Methylation in Plants. Essays Biochem. 2019;63:743–755. doi: 10.1042/EBC20190032. PubMed DOI PMC

Matzke M.A., Mosher R.A. RNA-Directed DNA Methylation: An Epigenetic Pathway of Increasing Complexity. Nat. Rev. Genet. 2014;15:394–408. doi: 10.1038/nrg3683. PubMed DOI

Ichikawa K., Tomioka S., Suzuki Y., Nakamura R., Doi K., Yoshimura J., Kumagai M., Inoue Y., Uchida Y., Irie N., et al. Centromere Evolution and CpG Methylation during Vertebrate Speciation. Nat. Commun. 2017;8:1833. doi: 10.1038/s41467-017-01982-7. PubMed DOI PMC

McKinley K.L., Cheeseman I.M. The Molecular Basis for Centromere Identity and Function. Nat. Rev. Mol. Cell Biol. 2016;17:16–29. doi: 10.1038/nrm.2015.5. PubMed DOI PMC

Barra V., Fachinetti D. The Dark Side of Centromeres: Types, Causes and Consequences of Structural Abnormalities Implicating Centromeric DNA. Nat. Commun. 2018;9:4340. doi: 10.1038/s41467-018-06545-y. PubMed DOI PMC

Secco D., Wang C., Shou H., Schultz M.D., Chiarenza S., Nussaume L., Ecker J.R., Whelan J., Lister R. Stress Induced Gene Expression Drives Transient DNA Methylation Changes at Adjacent Repetitive Elements. eLife. 2015;4:e09343. doi: 10.7554/eLife.09343. PubMed DOI PMC

Wan Z.Y., Xia J.H., Lin G., Wang L., Lin V.C.L., Yue G.H. Genome-Wide Methylation Analysis Identified Sexually Dimorphic Methylated Regions in Hybrid Tilapia. Sci. Rep. 2016;6:35903. doi: 10.1038/srep35903. PubMed DOI PMC

Zhao T., Schranz M.E. Network-Based Microsynteny Analysis Identifies Major Differences and Genomic Outliers in Mammalian and Angiosperm Genomes. Proc. Natl. Acad. Sci. USA. 2019;116:2165–2174. doi: 10.1073/pnas.1801757116. PubMed DOI PMC

Li Y., Dai X., Cheng Y., Zhao Y. NPY Genes Play an Essential Role in Root Gravitropic Responses in Arabidopsis. Mol. Plant. 2011;4:171–179. doi: 10.1093/mp/ssq052. PubMed DOI PMC

Tripp B.C., Smith K., Ferry J.G. Carbonic Anhydrase: New Insights for an Ancient Enzyme. J. Biol. Chem. 2001;276:48615–48618. doi: 10.1074/jbc.R100045200. PubMed DOI

Miller S.A., Dykes D.D., Polesky H.F. A Simple Salting out Procedure for Extracting DNA from Human Nucleated Cells. Nucleic Acids Res. 1988;16:1215. doi: 10.1093/nar/16.3.1215. PubMed DOI PMC

Krueger F. Trim Galore. A Wrapper Tool around Cutadapt and FastQC to Consistently Apply Quality and Adapter Trimming to FastQ Files. Babraham Institute; Cambridge, UK: 2015. pp. 516–517.

Tarasov A., Vilella A.J., Cuppen E., Nijman I.J., Prins P. Sambamba: Fast Processing of NGS Alignment Formats. Bioinformatics. 2015;31:2032–2034. doi: 10.1093/bioinformatics/btv098. PubMed DOI PMC

Okonechnikov K., Conesa A., García-Alcalde F. Qualimap 2: Advanced Multi-Sample Quality Control for High-Throughput Sequencing Data. Bioinformatics. 2016;32:292–294. doi: 10.1093/bioinformatics/btv566. PubMed DOI PMC

Ramírez F., Dündar F., Diehl S., Grüning B.A., Manke T. DeepTools: A Flexible Platform for Exploring Deep-Sequencing Data. Nucleic Acids Res. 2014;42:W187–W191. doi: 10.1093/nar/gku365. PubMed DOI PMC

Simon A., Pierre L., Brian H., Phil E. Babraham Bioinformatics-FastQC A Quality Control Tool for High Throughput Sequence Data. [(accessed on 15 January 2021)]; Available online: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/

Quinlan A.R., Hall I.M. BEDTools: A Flexible Suite of Utilities for Comparing Genomic Features. Bioinformatics. 2010;26:841–842. doi: 10.1093/bioinformatics/btq033. PubMed DOI PMC

Han S., Kim D. AtRTPrimer: Database for Arabidopsis Genome-Wide Homogeneous and Specific RT-PCR Primer-Pairs. BMC Bioinform. 2006;7:179. doi: 10.1186/1471-2105-7-179. PubMed DOI PMC