Mobile transposable elements (TEs) not only participate in genome evolution but also threaten genome integrity. In healthy cells, TEs that encode all of the components that are necessary for their mobility are specifically silenced, yet the precise mechanism remains unknown. Here, we characterize the mechanism used by a conserved class of chromatin remodelers that prevent TE mobility. In the Arabidopsis chromatin remodeler DECREASE IN DNA METHYLATION 1 (DDM1), we identify two conserved binding domains for the histone variant H2A.W, which marks plant heterochromatin. DDM1 is necessary and sufficient for the deposition of H2A.W onto potentially mobile TEs, yet does not act on TE fragments or host protein-coding genes. DDM1-mediated H2A.W deposition changes the properties of chromatin, resulting in the silencing of TEs and, therefore, prevents their mobility. This distinct mechanism provides insights into the interplay between TEs and their host in the contexts of evolution and disease, and potentiates innovative strategies for targeted gene silencing.
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The deep-sequencing (ChIP–seq, RNA-seq and EM-seq) data that support the findings of this study have been deposited to the NCBI Gene Expression Omnibus (GEO) under the accession number GSE150436 and the SRA (BioProject ID: PRJNA689609). All other data supporting the findings of this study are available from the corresponding author on reasonable request. Source data are provided with this paper.
Custom code used to process and analyse the deep-sequencing data, as described in the Methods, is available from the corresponding author on request.
Cosby, R. L., Chang, N. C. & Feschotte, C. Host-transposon interactions: conflict, cooperation, and cooption. Genes Dev. 33, 1098–1116 (2019).
Bourque, G. et al. Ten things you should know about transposable elements. Genome Biol. 19, 199 (2018).
Wicker, T. et al. A unified classification system for eukaryotic transposable elements. Nat. Rev. Genet. 8, 973–982 (2007).
Gagnier, L., Belancio, V. P. & Mager, D. L. Mouse germ line mutations due to retrotransposon insertions. Mob. DNA 10, 15 (2019).
Kidwell, M. G. & Lisch, D. Transposable elements as sources of variation in animals and plants. Proc. Natl Acad. Sci USA 94, 7704–7711 (1997).
Chuong, E. B., Elde, N. C. & Feschotte, C. Regulatory evolution of innate immunity through co-option of endogenous retroviruses. Science 351, 1083–1087 (2016).
Jangam, D., Feschotte, C. & Betran, E. Transposable element domestication as an adaptation to evolutionary conflicts. Trends Genet. 33, 817–831 (2017).
Velanis, C. N. et al. The domesticated transposase ALP2 mediates formation of a novel Polycomb protein complex by direct interaction with MSI1, a core subunit of Polycomb Repressive Complex 2 (PRC2). PLoS Genet. 16, e1008681 (2020).
Rishishwar, L. et al. Evidence for positive selection on recent human transposable element insertions. Gene 675, 69–79 (2018).
Boissinot, S., Davis, J., Entezam, A., Petrov, D. & Furano, A. V. Fitness cost of LINE-1 (L1) activity in humans. Proc. Natl Acad. Sci. USA 103, 9590–9594 (2006).
Payer, L. M. & Burns, K. H. Transposable elements in human genetic disease. Nat. Rev. Genet. 20, 760–772 (2019).
Czech, B. et al. piRNA-guided genome defense: from biogenesis to silencing. Annu. Rev. Genet. 52, 131–157 (2018).
Handler, D. et al. The genetic makeup of the Drosophila piRNA pathway. Mol. Cell 50, 762–777 (2013).
Ozata, D. M., Gainetdinov, I., Zoch, A., O’Carroll, D. & Zamore, P. D. PIWI-interacting RNAs: small RNAs with big functions. Nat. Rev. Genet. 20, 89–108 (2019).
Derkacheva, M. et al. Arabidopsis MSI1 connects LHP1 to PRC2 complexes. EMBO J. 32, 2073–2085 (2013).
Grewal, S. I. & Jia, S. Heterochromatin revisited. Nat. Rev. Genet. 8, 35–46 (2007).
Law, J. A. & Jacobsen, S. E. Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat. Rev. Genet. 11, 204–220 (2010).
Nuthikattu, S. et al. The initiation of epigenetic silencing of active transposable elements is triggered by RDR6 and 21-22 nucleotide small interfering RNAs. Plant Physiol. 162, 116–131 (2013).
Oberlin, S., Sarazin, A., Chevalier, C., Voinnet, O. & Mari-Ordonez, A. A genome-wide transcriptome and translatome analysis of Arabidopsis transposons identifies a unique and conserved genome expression strategy for Ty1/Copia retroelements. Genome Res. 27, 1549–1562 (2017).
Senti, K. A. & Brennecke, J. The piRNA pathway: a fly’s perspective on the guardian of the genome. Trends Genet. 26, 499–509 (2010).
Yu, R., Wang, X. & Moazed, D. Epigenetic inheritance mediated by coupling of RNAi and histone H3K9 methylation. Nature 558, 615–619 (2018).
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. 13, 421–426 (2003).
Mirouze, M. et al. Selective epigenetic control of retrotransposition in Arabidopsis. Nature 461, 427–430 (2009).
Stroud, H. et al. DNA methyltransferases are required to induce heterochromatic re-replication in Arabidopsis. PLoS Genet. 8, e1002808 (2012).
Corem, S. et al. Redistribution of CHH methylation and small interfering RNAs across the genome of tomato ddm1 mutants. Plant Cell 30, 1628–1644 (2018).
Higo, H. et al. DDM1 (decrease in DNA methylation) genes in rice (Oryza sativa). Mol. Genet. Genomics 287, 785–792 (2012).
Hirochika, H., Okamoto, H. & Kakutani, T. Silencing of retrotransposons in Arabidopsis and reactivation by the ddm1 mutation. Plant Cell 12, 357–369 (2000).
Jeddeloh, J. A., Stokes, T. L. & Richards, E. J. Maintenance of genomic methylation requires a SWI2/SNF2-like protein. Nat. Genet. 22, 94–97 (1999).
Mittelsten Scheid, O., Afsar, K. & Paszkowski, J. Release of epigenetic gene silencing by trans-acting mutations in Arabidopsis. Proc. Natl Acad. Sci. USA 95, 632–637 (1998).
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). Genes Dev. 15, 591–602 (2001).
Tan, F. et al. DDM1 represses noncoding RNA expression and RNA-directed DNA methylation in heterochromatin. Plant Physiol. 177, 1187–1197 (2018).
Gendrel, A. V., Lippman, Z., Yordan, C., Colot, V. & Martienssen, R. A. Dependence of heterochromatic histone H3 methylation patterns on the Arabidopsis gene DDM1. Science 297, 1871–1873 (2002).
Soppe, W. J. et al. DNA methylation controls histone H3 lysine 9 methylation and heterochromatin assembly in Arabidopsis. EMBO J. 21, 6549–6559 (2002).
Lippman, Z., May, B., Yordan, C., Singer, T. & Martienssen, R. Distinct mechanisms determine transposon inheritance and methylation via small interfering RNA and histone modification. PLoS Biol. 1, E67 (2003).
Stroud, H. et al. Non-CG methylation patterns shape the epigenetic landscape in Arabidopsis. Nat. Struct. Mol. Biol. 21, 64–72 (2014).
Zemach, A. et al. The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin. Cell 153, 193–205 (2013).
Basenko, E. Y., Kamei, M., Ji, L., Schmitz, R. J. & Lewis, Z. A. The LSH/DDM1 homolog MUS-30 is required for genome stability, but not for DNA methylation in Neurospora crassa. PLoS Genet. 12, e1005790 (2016).
Dunican, D. S. et al. Lsh regulates LTR retrotransposon repression independently of Dnmt3b function. Genome Biol. 14, R146 (2013).
Dennis, K., Fan, T., Geiman, T., Yan, Q. & Muegge, K. Lsh, a member of the SNF2 family, is required for genome-wide methylation. Genes Dev. 15, 2940–2944 (2001).
Zhu, H. et al. Lsh is involved in de novo methylation of DNA. EMBO J. 25, 335–345 (2006).
Ren, J., Finney, R., Ni, K., Cam, M. & Muegge, K. The chromatin remodeling protein Lsh alters nucleosome occupancy at putative enhancers and modulates binding of lineage specific transcription factors. Epigenetics 14, 277–293 (2019).
Lyons, D. B. & Zilberman, D. DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes. eLife 6, e30674 (2017).
Lei, B. et al. A Synthetic approach to reconstruct the evolutionary and functional innovations of the plant histone variant H2A.W. Curr. Biol. 31, 182–191.e5 (2021).
Yelagandula, R. et al. The histone variant H2A.W defines heterochromatin and promotes chromatin condensation in Arabidopsis. Cell 158, 98–109 (2014).
Osakabe, A. et al. Histone H2A variants confer specific properties to nucleosomes and impact on chromatin accessibility. Nucleic Acids Res. 46, 7675–7685 (2018).
Mizuguchi, G. et al. ATP-driven exchange of histone H2AZ variant catalyzed by SWR1 chromatin remodeling complex. Science 303, 343–348 (2004).
Papamichos-Chronakis, M., Watanabe, S., Rando, O. J. & Peterson, C. L. Global regulation of H2A.Z localization by the INO80 chromatin-remodeling enzyme is essential for genome integrity. Cell 144, 200–213 (2011).
Brzeski, J. & Jerzmanowski, A. Deficient in DNA methylation 1 (DDM1) defines a novel family of chromatin-remodeling factors. J. Biol. Chem. 278, 823–828 (2003).
Sengoku, T., Nureki, O., Nakamura, A., Kobayashi, S. & Yokoyama, S. Structural basis for RNA unwinding by the DEAD-box protein Drosophila Vasa. Cell 125, 287–300 (2006).
Talbert, P. B. et al. A unified phylogeny-based nomenclature for histone variants. Epigenetics Chromatin 5, 7 (2012).
Zemach, A. et al. DDM1 binds Arabidopsis methyl-CpG binding domain proteins and affects their subnuclear localization. Plant Cell 17, 1549–1558 (2005).
Workman, J. L. Nucleosome displacement in transcription. Genes Dev. 20, 2009–2017 (2006).
Li, X. et al. Mechanistic insights into plant SUVH family H3K9 methyltransferases and their binding to context-biased non-CG DNA methylation. Proc. Natl Acad. Sci. USA 115, E8793–E8802 (2018).
Deleris, A. et al. Loss of the DNA methyltransferase MET1 Induces H3K9 hypermethylation at PcG target genes and redistribution of H3K27 trimethylation to transposons in Arabidopsis thaliana. PLoS Genet. 8, e1003062 (2012).
Lanciano, S. et al. Sequencing the extrachromosomal circular mobilome reveals retrotransposon activity in plants. PLoS Genet. 13, e1006630 (2017).
Slotkin, R. K. et al. Epigenetic reprogramming and small RNA silencing of transposable elements in pollen. Cell 136, 461–472 (2009).
Rougée, M. et al. Polycomb mutant partially suppresses DNA hypomethylation–associated phenotypes in Arabidopsis. Life Sci. Alliance 4, e202000848 (2020).
Thijssen, P. E. et al. Mutations in CDCA7 and HELLS cause immunodeficiency-centromeric instability-facial anomalies syndrome. Nat. Commun. 6, 7870 (2015).
Ni, K. et al. LSH mediates gene repression through macroH2A deposition. Nat. Commun. 11, 5647 (2020).
Douet, J. et al. MacroH2A histone variants maintain nuclear organization and heterochromatin architecture. J. Cell Sci. 130, 1570–1582 (2017).
Cohen, J. Statistical power analysis. Curr. Dir. Psychol. Sci. 1, 98–101 (1992).
Lister, R. et al. Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133, 523–536 (2008).
Kawakatsu, T. et al. Epigenomic diversity in a global collection of Arabidopsis thaliana accessions. Cell 166, 492–505 (2016).
Lowary, P. T. & Widom, J. New DNA sequence rules for high affinity binding to histone octamer and sequence-directed nucleosome positioning. J. Mol. Biol. 276, 19–42 (1998).
Arimura, Y., Tachiwana, H., Oda, T., Sato, M. & Kurumizaka, H. Structural analysis of the hexasome, lacking one histone H2A/H2B dimer from the conventional nucleosome. Biochemistry 51, 3302–3309 (2012).
Tanaka, Y. et al. Expression and purification of recombinant human histones. Methods 33, 3–11 (2004).
Tachiwana, H. et al. Structural basis of instability of the nucleosome containing a testis-specific histone variant, human H3T. Proc. Natl Acad. Sci. USA 107, 10454–10459 (2010).
Osakabe, A. et al. Vertebrate Spt2 is a novel nucleolar histone chaperone that assists in ribosomal DNA transcription. J. Cell Sci. 126, 1323–1332 (2013).
Lorkovic, Z. J. et al. Compartmentalization of DNA damage response between heterochromatin and euchromatin is mediated by distinct H2A histone variants. Curr. Biol. 27, 1192–1199 (2017).
Ito, T., Takahashi, N., Shimura, Y. & Okada, K. A serine/threonine protein kinase gene isolated by an in vivo binding procedure using the Arabidopsis floral homeotic gene product, AGAMOUS. Plant Cell Physiol. 38, 248–258 (1997).
Wollmann, H. et al. Dynamic deposition of histone variant H3.3 accompanies developmental remodeling of the Arabidopsis transcriptome. PLoS Genet. 8, e1002658 (2012).
Yelagandula, R., Osakabe, A., Axelsson, E., Berger, F. & Kawashima, T. Genome-wide profiling of histone modifications and histone variants in Arabidopsis thaliana and Marchantia polymorpha. Methods Mol. Biol. 1610, 93–106 (2017).
Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).
Ramirez, F. et al. deepTools2: a next generation web server for deep-sequencing data analysis. Nucleic Acids Res. 44, W160–W165 (2016).
Chen, K. et al. DANPOS: dynamic analysis of nucleosome position and occupancy by sequencing. Genome Res. 23, 341–351 (2013).
Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15–21 (2013).
Bray, N. L., Pimentel, H., Melsted, P. & Pachter, L. Near-optimal probabilistic RNA-seq quantification. Nat. Biotechnol. 34, 525–527 (2016).
Soneson, C., Love, M. I. & Robinson, M. D. Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences. F1000Res 4, 1521 (2015).
Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).
Gu, Z., Eils, R. & Schlesner, M. Complex heatmaps reveal patterns and correlations in multidimensional genomic data. Bioinformatics 32, 2847–2849 (2016).
Wickham, H. ggplot2: Elegant Graphics for Data Analysis (Springer, 2016).
Kawashima, T. et al. Dynamic F-actin movement is essential for fertilization in Arabidopsis thaliana. eLife 3, e04501 (2014).
F.B. acknowledges support from the staff at the next-generation sequencing and PlantS facilities at the Vienna BioCenter Core Facilities (VBCF), the BioOptics facility and Molecular Biology Services from the Institute for Molecular Pathology (IMP), and the Molecular Biology Services at the GMI. We thank all members of the Berger laboratory for their technical help and H. Wang for sharing material; E. Sasaki, Z. Harvey, M. Borg, A. Marí-Ordóñez, P. Refsing Andersen and J. M. Watson for discussions and reading of the manuscript. This research was supported by the Japan Society for the Promotion of Science (JSPS) Overseas Research Fellowships (to A.O.), the Austrian Science Fund (FWF): M2539-B21 (to A.O.), P26887, P28320, P32054, P30802 and P33380 (to F.B.), and DK1238 (to B.J. and S.A.M.), the Austrian Academy of Sciences (to F.B., Z.J.L., E.A., S.A., R.P. and R.Y.), MEXT/JSPS 15H05963 and 19H00995 (to T.K.) and JST CREST JPMJCR15O1 (to T.K.).
The authors declare no competing interests.
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Extended Data Fig. 1 Validation of recombinant DDM1 protein and H2A.X or H2A.W pulldown assay with DDM1 fragments. Related to Fig. 1.
a, SDS-PAGE analysis of purified recombinant DDM1 and DDM1 E334N. Proteins were separated by 10% SDS-PAGE and visualized by Coomassie Brilliant Blue staining. Asterisk indicates the degraded products that could not be removed after purification. (Source data shows one of three representative gels obtained). b, Schematic representation of the ATPase assay. Malachite green solution was used to detect free phosphate liberated from ATP by enzyme-catalyzed hydrolysis. c, Graphical representation of the results of ATPase assays with buffer (green), wild type DDM1 (blue), or DDM1 E334N (red), respectively. DNA concentration is expressed as moles of nucleotides. d, The crystal structure of Drosophila RNA helicase protein VASA49 together with the ATP analog (AMPPNP) (PDB ID: 2DB3). The glutamic acid residue at position 400, which coordinates a catalytic water molecule for stabilizing the interaction with ATP, is indicated. e, Sequence alignment between the Glu400 between Drosophila VASA and Arabidopsis DDM1 centered on GLU400, indicated by the blue arrow. Glu400 in VASA corresponds to Glu334 in Arabidopsis. f, h Schematic representation of the DDM1 fragments used in the pulldown assay. g, i SDS-PAGE analysis of the pulldown assay. His6-tagged DDM1 and its truncations (panel g) or GST-tagged DDM1 fragments (panel i) were incubated with histone dimers containing either H2A.X or H2A.W. After pulldown, samples were analyzed by 15% SDS-PAGE and visualized by Coomassie Brilliant Blue. Data in a, g and i represent three independent experiments. Source data are provided in Source Data Extended Data Fig. 1.
Violin plots for the proportion of DNA methylation in CG, CHG, and CHH contexts on protein coding genes (left, n = 27,655), TE fragments not including TEs (middle, n = 25,695), and TEs (right, n = 3,903) in wild type Col-0 (grey) and ddm1 (red).
Extended Data Fig. 3 Genomic distribution of H1, H3K9me2 and H2A.W in ddm1. Related to Figs. 2 and 3.
a, Aggregate profile plots (top) and heatmaps (bottom) of H2A.W, H2A.X, and H1 in Col-0 (grey) and ddm1 (red) over heterochromatic regions, defined by H3K9me2 enrichment. Antibodies against H1 used in this study recognizes both H1.1 and H1.2. b, IGV genome browser snapshot of H1 (black), H2A.W (green), and H3K9me2 (blue) in wild type Col-0 and ddm1. Coloured and grey shading indicate an enriched or depleted signal, respectively. Annotated protein coding genes, TE fragments, and TEs are shown as boxes colored black, pink, or light blue, respectively. c, Aggregate profile plots (top) and heatmaps (bottom) showing distribution of H3K9me2 and H2A.W over TE fragments not including TEs in wild type and ddm1. d, Chromosomal distributions of TEs classified as group 1 (orange; n = 3,257) and group 2 (grey; n = 646) in Fig. 3a for each chromosome. Green boxes represent pericentric heterochromatin. e, f IGV genome browser snapshot of H2A.W (green), H3K9me2 (blue), H3K36me3 (orange), and H3K27me3 (purple) over TEs in wild type Col-0 and ddm1. Coloured and grey shading indicate an enriched or depleted signal, respectively.
Extended Data Fig. 4 RT-qPCR analyses of TEs in complementation lines expressing DDM1 mutant forms. Related to Fig. 4.
a, RT-PCR analyses of transgenic lines. cDNA (+RT) and DNaseI-treated RNA (-RT) were prepared from each plant and used as template for RT-PCR analyses. ACT2 was used as a control for RT-PCR. PCR products were separated by agarose gel and visualized by SYBR Green I staining. b, Bar plots showing the results of RT-qPCR as fold change of enrichment over ACT2 at TEs analyzed in Extended Data Fig. 6c,d from wild type Col-0 (grey), ddm1 (red), ddm1 expressing DDM1-3xFLAG (purple), ddm1 expressing DDM1 ∆N-3xFLAG (green), ddm1 expressing DDM1 ∆C-3xFLAG (orange), or ddm1 expressing DDM1 ∆NC-3xFLAG (brown), respectively. Presented data are means of n = 3 independent biological replicates (each biological replicate has 2 technical repeats); error bars represent SD within biological replicates. Source data are provided in Source Data Extended Data Fig. 4.
a, b, d, e IGV genome browser snapshot of the distribution for H2A.W and H3K9me2 over TEs (panels a and b), protein coding gene (panel d) and TE fragment (panel e) in wild type, ddm1, ddm1 expressing DDM1 FL, DDM1 ∆N, DDM1 ∆C, and DDM1 ∆NC. c, Aggregate profile plots (top) and heatmaps (bottom) showing distribution of H2A.W over TEs in wild type, ddm1, ddm1 expressing DDM1 FL, DDM1 ∆N, DDM1 ∆C, and DDM1 ∆NC.
Extended Data Fig. 6 ChIP-qPCR analyses of H3K9me2 or H2A.W over TEs and Expression of TEs in F1 DDM1/ddm1. Related to Fig. 5.
a, b, Bar plots showing the results of ChIP-qPCR as fold change of H3K9me2 (panel a) or H2A.W (panel b) enrichment over H3 at TEs analyzed in Extended Data Fig. 6c,d from wild type Col-0 (grey), F1 DDM1/ddm1 (blue), or ddm1 (red), respectively. Presented data are means of n = 3 independent biological replicates (each biological replicate has 3 technical repeats); error bars represent SD within biological replicates. The numbers below each TE show the expression level of TEs (log2FoldChange(F1/ddm1)) compared to ddm1 mutant plants. c-e, Bar plots showing relative expression levels of TEs classified as inactivated (blue) or neutral (pink) measured by RT-qPCR from wild type Col-0 (grey), F1 DDM1/ddm1 (blue), or ddm1 (red), respectively. The expression levels of each TE are presented as a fold change over ACT2. Presented data are means of n = 3 independent biological replicates (each biological replicate has 2 technical repeats); error bars represent SD within biological replicates. The dashed lines represent 50% of the ddm1 fold change over ACT2. Source Data are provided in Source Data Extended Data Fig. 6.
Heatmap of the z-transformed expression levels of differentially expressed TEs (n = 1,878) in mutants from wild type Col-0, suvh4;5;6, met1, and ddm1.
Heatmaps showing weighted DNA methylation levels for TEs sorted in categories ‘Inactivated’, ‘neutral’ and ‘other’ in wild type Col-0, ddm1, artificial F1 cross [(Col-0 + ddm1)/2] and F1 cross Col-0 X ddm1 for a CG, b CHG, and c CHH contexts.
Supplementary Figs. 1 and 2
Supplementary Table 1: Sequence list for the DDM1 orthologues across species, which were used for alignment in this study (Fig. 1a and Supplementary Information). Supplementary Table 2: Sequences for primers used in the current study
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Osakabe, A., Jamge, B., Axelsson, E. et al. The chromatin remodeler DDM1 prevents transposon mobility through deposition of histone variant H2A.W. Nat Cell Biol 23, 391–400 (2021). https://doi.org/10.1038/s41556-021-00658-1