Recent studies have shown that RNA-directed DNA methylation (RdDM) in Arabidopsis thaliana not only requires the production of 24-nucleotide small interfering RNAs (siRNAs) and the de novo DNA methyltransferase DOMAINS REARRANGED METHYLTRANSFERASE 2 (DRM2) but also requires the production of RNA polymerase V (Pol V)-dependent intergenic non-coding (IGN) transcripts. Two crucial RdDM components, ARGONAUTE 4 (AGO4) and SUPPRESSOR OF TY INSERTION 5-LIKE (SPT5L), interact with Pol V-dependent transcripts, which suggests that they serve as a scaffold for the recruitment of the RdDM machinery. This process ultimately leads to DNA methylation and silencing at loci that produce siRNAs and IGN transcripts.
Analyses of transposon expression and DNA methylation patterns in pollen grains and in embryo and endosperm tissues, respectively, suggest that genome-wide decreases in DNA methylation occur during male and female gametogenesis in A. thaliana, which might facilitate enhanced RdDM and transposon silencing in the sperm and egg cells by an unknown mechanism.
Biochemical purification of DNA methyltransferase 3-like (DNMT3L) revealed an interaction between DNMT3L and unmethylated histone 3 lysine 4 (H3K4) tails. As DNMT3L also interacts with the DNMT3A de novo methyltransferase and because H3K4 methylation is anticorrelated with DNA methylation, a model has been proposed in which DNMT3L interaction with unmethylated H3K4 tails targets de novo methylation.
Several recent findings suggest that Piwi-interacting RNAs (piRNAs) target de novo DNA methylation at transposons and other repetitive elements of the genome during male gametogenesis in mammals. piRNA populations isolated early in development were found to be enriched for such sequence elements, and mutations in MILI — a Piwi-clade Ago protein that binds piRNAs — showed DNA methylation defects at the stage of development at which de novo methylation is observed.
Characterization of the Piwi clade of Ago proteins revealed the presence of symmetrical dimethylarginine modifications on several family members from Xenopus laevis, Drosophila melanogaster and mice. Tudor domains are known to interact with this modification, and Tudor domain-containing 1 (TDRD1), a protein with several Tudor domains, interacts with MILI and is required for DNA methylation and transposon silencing.
In mammals, DNA methylation is maintained during DNA replication through the activity of DNMT1, which catalyses the methylation of hemimethylated CG sites in newly synthesized DNA. This activity depends heavily on the presence of ubiquitin-like plant homeodomain and RING finger domain 1 (UHRF1), a protein that specifically recognizes hemimethylated DNA and is proposed to recruit DNMT1 to chromatin.
In A. thaliana, 5-methylcytosine DNA glycosylases and the base excision repair pathway catalyse active DNA demethylation during female gametogenesis and in vegetative plant tissues. Demethylation during gametogenesis is required for imprinting, whereas demethylation in vegetative tissues is proposed to combat robust DNA methylation by the RdDM pathway.
In zebrafish there is evidence for an active DNA demethylation pathway that also involves DNA glycosylase activity and the base excision repair pathway. However, unlike in A. thaliana, in which methylated cytosines are directly recognized and removed, in zebrafish the methylated cytosine is first deaminated by the activation-induced cytosine deaminase (Aid)/apolipoprotein B mRNA-editing enzyme (Apobec) family of proteins, generating a G/T mismatch. This base is then removed by a thymine DNA glycosylase in what seems to be a tightly coupled manner.
In mammals, mechanisms for active DNA demethylation remain unclear. However, an early model proposed a mechanism similar to that recently demonstrated in zebrafish, and a recent study showing that AID is necessary for the reduced levels of DNA methylation normally observed in primordial germ cells also supports this hypothesis. The discovery of the 5-hydroxymethylcytosine modification in certain mammalian cell types led to speculation that this modification could be a substrate for active DNA methylation.
Cytosine DNA methylation is a stable epigenetic mark that is crucial for diverse biological processes, including gene and transposon silencing, imprinting and X chromosome inactivation. Recent findings in plants and animals have greatly increased our understanding of the pathways used to accurately target, maintain and modify patterns of DNA methylation and have revealed unanticipated mechanistic similarities between these organisms. Key roles have emerged for small RNAs, proteins with domains that bind methylated DNA and DNA glycosylases in these processes. Drawing on insights from both plants and animals should deepen our understanding of the regulation and biological significance of DNA methylation.
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Ehrlich, M. et al. Amount and distribution of 5-methylcytosine in human DNA from different types of tissues of cells. Nucleic Acids Res. 10, 2709–2721 (1982).
Bird, A. DNA methylation patterns and epigenetic memory. Genes Dev. 16, 6–21 (2002).
Ramsahoye, B. H. et al. Non-CpG methylation is prevalent in embryonic stem cells and may be mediated by DNA methyltransferase 3a. Proc. Natl Acad. Sci. USA 97, 5237–5242 (2000).
Lister, R. et al. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 462, 315–322 (2009).
Cedar, H. & Bergman, Y. Linking DNA methylation and histone modification: patterns and paradigms. Nature Rev. Genet. 10, 295–304 (2009).
Suzuki, M. M. & Bird, A. DNA methylation landscapes: provocative insights from epigenomics. Nature Rev. Genet. 9, 465–476 (2008).
Henderson, I. R. & Jacobsen, S. E. Epigenetic inheritance in plants. Nature 447, 418–424 (2007).
Cokus, S. J. et al. Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature 452, 215–219 (2008). This study, along with reference 120, provided single-nucleotide resolution, genome-wide mapping of DNA methylation patterns in A. thaliana.
Zhang, X. et al. Genome-wide high-resolution mapping and functional analysis of DNA methylation in Arabidopsis. Cell 126, 1189–1201 (2006).
Kim, J. K., Samaranayake, M. & Pradhan, S. Epigenetic mechanisms in mammals. Cell. Mol. Life Sci. 66, 596–612 (2009).
Goll, M. G. & Bestor, T. H. Eukaryotic cytosine methyltransferases. Annu. Rev. Biochem. 74, 481–514 (2005).
Cheng, X. & Blumenthal, R. M. Mammalian DNA methyltransferases: a structural perspective. Structure 16, 341–350 (2008).
Chan, S. W., Henderson, I. R. & Jacobsen, S. E. Gardening the genome: DNA methylation in Arabidopsis thaliana. Nature Rev. Genet. 6, 351–360 (2005).
Wassenegger, M., Heimes, S., Riedel, L. & Sanger, H. L. RNA-directed de novo methylation of genomic sequences in plants. Cell 76, 567–576 (1994).
Matzke, M., Kanno, T., Daxinger, L., Huettel, B. & Matzke, A. J. RNA-mediated chromatin-based silencing in plants. Curr. Opin. Cell Biol. 21, 367–376 (2009).
Huettel, B. et al. RNA-directed DNA methylation mediated by DRD1 and Pol IVb: a versatile pathway for transcriptional gene silencing in plants. Biochim. Biophys. Acta 1769, 358–374 (2007).
Pikaard, C. S., Haag, J. R., Ream, T. & Wierzbicki, A. T. Roles of RNA polymerase IV in gene silencing. Trends Plant Sci. 13, 390–397 (2008).
Mosher, R. A., Schwach, F., Studholme, D. & Baulcombe, D. C. PolIVb influences RNA-directed DNA methylation independently of its role in siRNA biogenesis. Proc. Natl Acad. Sci. USA 105, 3145–3150 (2008).
Lahmy, S. et al. PolV(PolIVb) function in RNA-directed DNA methylation requires the conserved active site and an additional plant-specific subunit. Proc. Natl Acad. Sci. USA 106, 941–946 (2009).
Ream, T. S. et al. Subunit compositions of the RNA-silencing enzymes Pol IV and Pol V reveal their origins as specialized forms of RNA polymerase II. Mol. Cell 33, 192–203 (2009).
Huang, L. et al. An atypical RNA polymerase involved in RNA silencing shares small subunits with RNA polymerase II. Nature Struct. Mol. Biol. 16, 91–93 (2009).
He, X. J. et al. NRPD4, a protein related to the RPB4 subunit of RNA polymerase II, is a component of RNA polymerases IV and V and is required for RNA-directed DNA methylation. Genes Dev. 23, 318–330 (2009).
Bies-Etheve, N. et al. RNA-directed DNA methylation requires an AGO4-interacting member of the SPT5 elongation factor family. EMBO Rep. 10, 649–654 (2009).
Herr, A. J., Jensen, M. B., Dalmay, T. & Baulcombe, D. C. RNA polymerase IV directs silencing of endogenous DNA. Science 308, 118–120 (2005).
Zhang, X., Henderson, I. R., Lu, C., Green, P. J. & Jacobsen, S. E. Role of RNA polymerase IV in plant small RNA metabolism. Proc. Natl Acad. Sci. USA 104, 4536–4541 (2007).
Haag, J. R., Pontes, O. & Pikaard, C. S. Metal A and metal B sites of nuclear RNA polymerases Pol IV and Pol V are required for siRNA-dependent DNA methylation and gene silencing. PLoS ONE 4, e4110 (2009).
Onodera, Y. et al. Plant nuclear RNA polymerase IV mediates siRNA and DNA methylation-dependent heterochromatin formation. Cell 120, 613–622 (2005).
Pontier, D. et al. Reinforcement of silencing at transposons and highly repeated sequences requires the concerted action of two distinct RNA polymerases IV in Arabidopsis. Genes Dev. 19, 2030–2040 (2005).
Chan, S. W., Zhang, X., Bernatavichute, Y. V. & Jacobsen, S. E. Two-step recruitment of RNA-directed DNA methylation to tandem repeats. PLoS Biol. 4, e363 (2006).
Huettel, B. et al. Endogenous targets of RNA-directed DNA methylation and Pol IV in Arabidopsis. EMBO J. 25, 2828–2836 (2006).
El-Shami, M. et al. Reiterated WG/GW motifs form functionally and evolutionarily conserved ARGONAUTE-binding platforms in RNAi-related components. Genes Dev. 21, 2539–2544 (2007).
Li, C. F. et al. An ARGONAUTE4-containing nuclear processing center colocalized with Cajal bodies in Arabidopsis thaliana. Cell 126, 93–106 (2006).
Li, C. F. et al. Dynamic regulation of ARGONAUTE4 within multiple nuclear bodies in Arabidopsis thaliana. PLoS Genet. 4, e27 (2008).
Wierzbicki, A. T., Haag, J. R. & Pikaard, C. S. Noncoding transcription by RNA polymerase Pol IVb/Pol V mediates transcriptional silencing of overlapping and adjacent genes. Cell 135, 635–648 (2008). This study identifies RNA transcripts that are dependent on Pol V and DRD1 and shows they are required for DNA methylation and silencing but not for siRNA production.
Grewal, S. I. & Elgin, S. C. Transcription and RNA interference in the formation of heterochromatin. Nature 447, 399–406 (2007).
He, X. J. et al. An effector of RNA-directed DNA methylation in Arabidopsis is an ARGONAUTE 4- and RNA-binding protein. Cell 137, 498–508 (2009).
Wierzbicki, A. T., Ream, T. S., Haag, J. R. & Pikaard, C. S. RNA polymerase V transcription guides ARGONAUTE4 to chromatin. Nature Genet. 41, 630–634 (2009).
Ausin, I., Mockler, T. C., Chory, J. & Jacobsen, S. E. IDN1 and IDN2 are required for de novo DNA methylation in Arabidopsis thaliana. Nature Struct. Mol. Biol. 16, 1325–1327 (2009). This study identifies IDN2 as a novel component of the RdDM pathway. The authors show that IDN2 encodes an RNA-binding protein that can interact with dsRNA duplexes containing 5′ overhangs in vitro.
Zheng, B. et al. Intergenic transcription by RNA polymerase II coordinates Pol IV and Pol V in siRNA-directed transcriptional gene silencing in Arabidopsis. Genes Dev. 23, 2850–2860 (2009).
Kanno, T. et al. RNA-directed DNA methylation and plant development require an IWR1-type transcription factor. EMBO Rep. 11, 65–71 (2009).
He, X. J. et al. A conserved transcriptional regulator is required for RNA-directed DNA methylation and plant development. Genes Dev. 23, 2717–2722 (2009).
Kanno, T. et al. Involvement of putative SNF2 chromatin remodeling protein DRD1 in RNA-directed DNA methylation. Curr. Biol. 14, 801–805 (2004).
Kanno, T. et al. A structural-maintenance-of-chromosomes hinge domain-containing protein is required for RNA-directed DNA methylation. Nature Genet. 40, 670–675 (2008).
Smith, L. M. et al. An SNF2 protein associated with nuclear RNA silencing and the spread of a silencing signal between cells in Arabidopsis. Plant Cell 19, 1507–1521 (2007).
Kafri, T. et al. Developmental pattern of gene-specific DNA methylation in the mouse embryo and germ line. Genes Dev. 6, 705–714 (1992).
Monk, M., Boubelik, M. & Lehnert, S. Temporal and regional changes in DNA methylation in the embryonic, extraembryonic and germ cell lineages during mouse embryo development. Development 99, 371–382 (1987).
Reik, W. Stability and flexibility of epigenetic gene regulation in mammalian development. Nature 447, 425–432 (2007).
Sasaki, H. & Matsui, Y. Epigenetic events in mammalian germ-cell development: reprogramming and beyond. Nature Rev. Genet. 9, 129–140 (2008).
Ooi, S. K. et al. DNMT3L connects unmethylated lysine 4 of histone H3 to de novo methylation of DNA. Nature 448, 714–717 (2007). Through the biochemical purification of DNMT3L, this study revealed that this protein copurifies with the de novo DNA methyltransferases as well as with the four core histone proteins. The authors further characterized the interaction between DNMT3L and histones and showed it to be specific for unmethylated H3K9 tails.
Otani, J. et al. Structural basis for recognition of H3K4 methylation status by the DNA methyltransferase 3A ATRX–DNMT3–DNMT3L domain. EMBO Rep. 10, 1235–1241 (2009).
Jia, D., Jurkowska, R. Z., Zhang, X., Jeltsch, A. & Cheng, X. Structure of Dnmt3a bound to Dnmt3L suggests a model for de novo DNA methylation. Nature 449, 248–251 (2007). This paper provides a crystal structure showing that the C-terminal regions of DNMT3A and DNMT3L form a tetrameric complex. Superimposition of a DNA fragment from another crystal structure onto this structure suggests the DNMT3A active sites are positioned approximately ten base pairs apart.
Fournier, C. et al. Allele-specific histone lysine methylation marks regulatory regions at imprinted mouse genes. EMBO J. 21, 6560–6570 (2002).
Delaval, K. et al. Differential histone modifications mark mouse imprinting control regions during spermatogenesis. EMBO J. 26, 720–729 (2007).
Vu, T. H., Li, T. & Hoffman, A. R. Promoter-restricted histone code, not the differentially methylated DNA regions or antisense transcripts, marks the imprinting status of IGF2R in human and mouse. Hum. Mol. Genet. 13, 2233–2245 (2004).
Yamasaki, Y. et al. Neuron-specific relaxation of Igf2r imprinting is associated with neuron-specific histone modifications and lack of its antisense transcript Air. Hum. Mol. Genet. 14, 2511–2520 (2005).
Ciccone, D. N. et al. KDM1B is a histone H3K4 demethylase required to establish maternal genomic imprints. Nature 461, 415–418 (2009).
Okitsu, C. Y. & Hsieh, C. L. DNA methylation dictates histone H3K4 methylation. Mol. Cell. Biol. 27, 2746–2757 (2007).
Weber, M. et al. Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nature Genet. 39, 457–466 (2007).
Meissner, A. et al. Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature 454, 766–770 (2008).
Mohn, F. et al. Lineage-specific polycomb targets and de novo DNA methylation define restriction and potential of neuronal progenitors. Mol. Cell 30, 755–766 (2008).
Guenther, M. G., Levine, S. S., Boyer, L. A., Jaenisch, R. & Young, R. A. A chromatin landmark and transcription initiation at most promoters in human cells. Cell 130, 77–88 (2007).
Zhang, X., Bernatavichute, Y. V., Cokus, S., Pellegrini, M. & Jacobsen, S. E. Genome-wide analysis of mono-, di- and trimethylation of histone H3 lysine 4 in Arabidopsis thaliana. Genome Biol. 10, R62 (2009).
Chotalia, M. et al. Transcription is required for establishment of germline methylation marks at imprinted genes. Genes Dev. 23, 105–117 (2009).
Suetake, I., Shinozaki, F., Miyagawa, J., Takeshima, H. & Tajima, S. DNMT3L stimulates the DNA methylation activity of Dnmt3a and Dnmt3b through a direct interaction. J. Biol. Chem. 279, 27816–27823 (2004).
Chedin, F., Lieber, M. R. & Hsieh, C. L. The DNA methyltransferase-like protein DNMT3L stimulates de novo methylation by Dnmt3a. Proc. Natl Acad. Sci. USA 99, 16916–16921 (2002).
Klimasauskas, S., Kumar, S., Roberts, R. J. & Cheng, X. HhaI methyltransferase flips its target base out of the DNA helix. Cell 76, 357–369 (1994).
Jurkowska, R. Z. et al. Formation of nucleoprotein filaments by mammalian DNA methyltransferase Dnmt3a in complex with regulator Dnmt3L. Nucleic Acids Res. 36, 6656–6663 (2008). This paper provides a biophysical characterization of the tetrameric complex described in reference 51. The characterization shows the formation of nucleoprotein filaments and demonstrates that this complex generates periodic DNA methylation patterns in vitro.
Glass, J. L., Fazzari, M. J., Ferguson-Smith, A. C. & Greally, J. M. CG dinucleotide periodicities recognized by the Dnmt3a–Dnmt3L complex are distinctive at retroelements and imprinted domains. Mamm. Genome 20, 633–643 (2009).
Ferguson-Smith, A. C. & Greally, J. M. Epigenetics: perceptive enzymes. Nature 449, 148–149 (2007).
Gowher, H. & Jeltsch, A. Enzymatic properties of recombinant Dnmt3a DNA methyltransferase from mouse: the enzyme modifies DNA in a non-processive manner and also methylates non-CpG [correction of non-CpA] sites. J. Mol. Biol. 309, 1201–1208 (2001).
Lindroth, A. M. et al. Dual histone H3 methylation marks at lysines 9 and 27 required for interaction with CHROMOMETHYLASE3. EMBO J. 23, 4286–4296 (2004).
Zhao, Q. et al. PRMT5-mediated methylation of histone H4R3 recruits DNMT3A, coupling histone and DNA methylation in gene silencing. Nature Struct. Mol. Biol. 16, 304–311 (2009).
Fabbrizio, E. et al. Negative regulation of transcription by the type II arginine methyltransferase PRMT5. EMBO Rep. 3, 641–645 (2002).
Slotkin, R. K. et al. Epigenetic reprogramming and small RNA silencing of transposable elements in pollen. Cell 136, 461–472 (2009). This study investigates the expression pattern of transposons during plant development and shows they are expressed and active in pollen. However, this reactivation probably only occurs in the vegetative nucleus and not in sperm cells.
Hsieh, T. F. et al. Genome-wide demethylation of Arabidopsis endosperm. Science 324, 1451–1454 (2009). This study, along with reference 76, compares the methylation status of the endosperm and embryo tissues and shows that the endosperm is globally hypomethylated.
Gehring, M., Bubb, K. L. & Henikoff, S. Extensive demethylation of repetitive elements during seed development underlies gene imprinting. Science 324, 1447–1451 (2009). In addition to showing a global decrease in methylation in the endosperm (see reference 75), this study identifies several novel imprinted genes in the A. thaliana genome.
Huh, J. H., Bauer, M. J., Hsieh, T. F. & Fischer, R. L. Cellular programming of plant gene imprinting. Cell 132, 735–744 (2008).
Pina, C., Pinto, F., Feijo, J. A. & Becker, J. D. Gene family analysis of the Arabidopsis pollen transcriptome reveals biological implications for cell growth, division control, and gene expression regulation. Plant Physiol. 138, 744–756 (2005).
Vongs, A., Kakutani, T., Martienssen, R. A. & Richards, E. J. Arabidopsis thaliana DNA methylation mutants. Science 260, 1926–1928 (1993).
Baroux, C., Pecinka, A., Fuchs, J., Schubert, I. & Grossniklaus, U. The triploid endosperm genome of Arabidopsis adopts a peculiar, parental-dosage-dependent chromatin organization. Plant Cell 19, 1782–1794 (2007).
Mosher, R. A. et al. Uniparental expression of PolIV-dependent siRNAs in developing endosperm of Arabidopsis. Nature 460, 283–286 (2009).
Teixeira, F. K. et al. A role for RNAi in the selective correction of DNA methylation defects. Science 323, 1600–1604 (2009).
Aravin, A. A. et al. Double-stranded RNA-mediated silencing of genomic tandem repeats and transposable elements in the D. melanogaster germline. Curr. Biol. 11, 1017–1027 (2001).
Aravin, A. A., Hannon, G. J. & Brennecke, J. The Piwi–piRNA pathway provides an adaptive defense in the transposon arms race. Science 318, 761–764 (2007).
Hutvagner, G. & Simard, M. J. Argonaute proteins: key players in RNA silencing. Nature Rev. Mol. Cell Biol. 9, 22–32 (2008).
Aravin, A. et al. A novel class of small RNAs bind to MILI protein in mouse testes. Nature 442, 203–207 (2006).
Girard, A., Sachidanandam, R., Hannon, G. J. & Carmell, M. A. A germline-specific class of small RNAs binds mammalian Piwi proteins. Nature 442, 199–202 (2006).
Kuramochi-Miyagawa, S. et al. DNA methylation of retrotransposon genes is regulated by Piwi family members MILI and MIWI2 in murine fetal testes. Genes Dev. 22, 908–917 (2008). This study shows that methylation defects in a Piwi clade mutant occur at the time of de novo methylation in male germ cells, which suggests that piRNAs are required for de novo DNA methylation at transposons rather than for the maintenance of pre-existing DNA methylation.
Aravin, A. A., Sachidanandam, R., Girard, A., Fejes-Toth, K. & Hannon, G. J. Developmentally regulated piRNA clusters implicate MILI in transposon control. Science 316, 744–747 (2007).
Aravin, A. A. et al. A piRNA pathway primed by individual transposons is linked to de novo DNA methylation in mice. Mol. Cell 31, 785–799 (2008). This study, along with reference 88, isolated piRNAs from fetal germ cells and showed they are highly enriched for transposon sequences and possess the characteristics of primary and secondary piRNAs.
Brennecke, J. et al. Discrete small RNA-generating loci as master regulators of transposon activity in Drosophila. Cell 128, 1089–1103 (2007).
Gunawardane, L. S. et al. A Slicer-mediated mechanism for repeat-associated siRNA 5′ end formation in Drosophila. Science 315, 1587–1590 (2007).
Carmell, M. A. et al. MIWI2 is essential for spermatogenesis and repression of transposons in the mouse male germline. Dev. Cell 12, 503–514 (2007).
Aravin, A. A. & Bourc'his, D. Small RNA guides for de novo DNA methylation in mammalian germ cells. Genes Dev. 22, 970–975 (2008).
Chen, C. et al. Mouse Piwi interactome identifies binding mechanism of Tdrkh Tudor domain to arginine methylated Miwi. Proc. Natl Acad. Sci. USA 106, 20336–20341 (2009).
Kirino, Y. et al. Arginine methylation of Piwi proteins catalysed by dPRMT5 is required for Ago3 and Aub stability. Nature Cell Biol. 11, 652–658 (2009).
Vagin, V. V. et al. Proteomic analysis of murine Piwi proteins reveals a role for arginine methylation in specifying interaction with Tudor family members. Genes Dev. 23, 1749–1762 (2009).
Reuter, M. et al. Loss of the Mili-interacting Tudor domain-containing protein-1 activates transposons and alters the Mili-associated small RNA profile. Nature Struct. Mol. Biol. 16, 639–646 (2009).
Kojima, K. et al. Associations between PIWI proteins and TDRD1/MTR-1 are critical for integrated subcellular localization in murine male germ cells. Genes Cells 14, 1155–1165 (2009).
Wang, J., Saxe, J. P., Tanaka, T., Chuma, S. & Lin, H. Mili interacts with Tudor domain-containing protein 1 in regulating spermatogenesis. Curr. Biol. 19, 640–644 (2009).
Chuang, L. S. et al. Human DNA-(cytosine-5) methyltransferase–PCNA complex as a target for p21WAF1. Science 277, 1996–2000 (1997).
Schermelleh, L. et al. Dynamics of Dnmt1 interaction with the replication machinery and its role in postreplicative maintenance of DNA methylation. Nucleic Acids Res. 35, 4301–4312 (2007).
Egger, G. et al. Identification of DNMT1 (DNA methyltransferase 1) hypomorphs in somatic knockouts suggests an essential role for DNMT1 in cell survival. Proc. Natl Acad. Sci. USA 103, 14080–14085 (2006).
Spada, F. et al. DNMT1 but not its interaction with the replication machinery is required for maintenance of DNA methylation in human cells. J. Cell Biol. 176, 565–571 (2007).
Bostick, M. et al. UHRF1 plays a role in maintaining DNA methylation in mammalian cells. Science 317, 1760–1764 (2007). This study, along with reference 106, shows that UHRF1 is required for maintaining DNA methylation in mammals. Furthermore, this study demonstrates that the SRA domain of UHRF1 specifically interacts with hemimethylated CG sites and is required for the association of DNMT1 with chromatin.
Sharif, J. et al. The SRA protein Np95 mediates epigenetic inheritance by recruiting Dnmt1 to methylated DNA. Nature 450, 908–912 (2007). See reference 105.
Arita, K., Ariyoshi, M., Tochio, H., Nakamura, Y. & Shirakawa, M. Recognition of hemi-methylated DNA by the SRA protein UHRF1 by a base-flipping mechanism. Nature 455, 818–821 (2008).
Hashimoto, H. et al. The SRA domain of UHRF1 flips 5-methylcytosine out of the DNA helix. Nature 455, 826–829 (2008).
Qian, C. et al. Structure and hemimethylated CpG binding of the SRA domain from human UHRF1. J. Biol. Chem. 283, 34490–34494 (2008).
Avvakumov, G. V. et al. Structural basis for recognition of hemi-methylated DNA by the SRA domain of human UHRF1. Nature 455, 822–825 (2008).
Meilinger, D. et al. Np95 interacts with de novo DNA methyltransferases, Dnmt3a and Dnmt3b, and mediates epigenetic silencing of the viral CMV promoter in embryonic stem cells. EMBO Rep. 10, 1259–1264 (2009).
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).
Huang, J. et al. Lsh, an epigenetic guardian of repetitive elements. Nucleic Acids Res. 32, 5019–5028 (2004).
Woo, H. R., Dittmer, T. A. & Richards, E. J. Three SRA-domain methylcytosine-binding proteins cooperate to maintain global CpG methylation and epigenetic silencing in Arabidopsis. PLoS Genet. 4, e1000156 (2008).
Woo, H. R., Pontes, O., Pikaard, C. S. & Richards, E. J. VIM1, a methylcytosine-binding protein required for centromeric heterochromatinization. Genes Dev. 21, 267–277 (2007).
Hirochika, H., Okamoto, H. & Kakutani, T. Silencing of retrotransposons in Arabidopsis and reactivation by the ddm1 mutation. Plant Cell 12, 357–369 (2000).
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).
Yan, Q., Huang, J., Fan, T., Zhu, H. & Muegge, K. Lsh, a modulator of CpG methylation, is crucial for normal histone methylation. EMBO J. 22, 5154–5162 (2003).
Bernatavichute, Y. V., Zhang, X., Cokus, S., Pellegrini, M. & Jacobsen, S. E. Genome-wide association of histone H3 lysine nine methylation with CHG DNA methylation in Arabidopsis thaliana. PLoS ONE 3, e3156 (2008).
Lister, R. et al. Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133, 523–536 (2008). See reference 8.
Zilberman, D., Gehring, M., Tran, R. K., Ballinger, T. & Henikoff, S. Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. Nature Genet. 39, 61–69 (2007).
Tran, R. K. et al. DNA methylation profiling identifies CG methylation clusters in Arabidopsis genes. Curr. Biol. 15, 154–159 (2005).
Johnson, L. M. et al. The SRA methyl-cytosine-binding domain links DNA and histone methylation. Curr. Biol. 17, 379–384 (2007).
Lindroth, A. M. et al. Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation. Science 292, 2077–2080 (2001).
Bartee, L., Malagnac, F. & Bender, J. Arabidopsis cmt3 chromomethylase mutations block non-CG methylation and silencing of an endogenous gene. Genes Dev. 15, 1753–1758 (2001).
Jackson, J. P., Lindroth, A. M., Cao, X. & Jacobsen, S. E. Control of CpNpG DNA methylation by the KRYPTONITE histone H3 methyltransferase. Nature 416, 556–560 (2002).
Malagnac, F., Bartee, L. & Bender, J. An Arabidopsis SET domain protein required for maintenance but not establishment of DNA methylation. EMBO J. 21, 6842–6852 (2002).
Jackson, J. P. et al. Dimethylation of histone H3 lysine 9 is a critical mark for DNA methylation and gene silencing in Arabidopsis thaliana. Chromosoma 112, 308–315 (2004).
Ebbs, M. L., Bartee, L. & Bender, J. H3 lysine 9 methylation is maintained on a transcribed inverted repeat by combined action of SUVH6 and SUVH4 methyltransferases. Mol. Cell Biol. 25, 10507–10515 (2005).
Ebbs, M. L. & Bender, J. Locus-specific control of DNA methylation by the Arabidopsis SUVH5 histone methyltransferase. Plant Cell 18, 1166–1176 (2006).
Cao, X. et al. Role of the DRM and CMT3 methyltransferases in RNA-directed DNA methylation. Curr. Biol. 13, 2212–2217 (2003).
Johnson, L. M., Law, J. A., Khattar, A., Henderson, I. R. & Jacobsen, S. E. SRA-domain proteins required for DRM2-mediated de novo DNA methylation. PLoS Genet. 4, e1000280 (2008).
Ikeda, Y. & Kinoshita, T. DNA demethylation: a lesson from the garden. Chromosoma 118, 37–41 (2009).
Zhu, J. K. Active DNA demethylation mediated by DNA glycosylases. Annu. Rev. Genet. 43, 143–166 (2009).
Choi, Y. et al. DEMETER, a DNA glycosylase domain protein, is required for endosperm gene imprinting and seed viability in Arabidopsis. Cell 110, 33–42 (2002).
Gong, Z. et al. ROS1, a repressor of transcriptional gene silencing in Arabidopsis, encodes a DNA glycosylase/lyase. Cell 111, 803–814 (2002).
Penterman, J. et al. DNA demethylation in the Arabidopsis genome. Proc. Natl Acad. Sci. USA 104, 6752–6757 (2007).
Ortega-Galisteo, A. P., Morales-Ruiz, T., Ariza, R. R. & Roldan-Arjona, T. Arabidopsis DEMETER-LIKE proteins DML2 and DML3 are required for appropriate distribution of DNA methylation marks. Plant Mol. Biol. 67, 671–681 (2008).
Gehring, M. et al. DEMETER DNA glycosylase establishes MEDEA polycomb gene self-imprinting by allele-specific demethylation. Cell 124, 495–506 (2006).
Morales-Ruiz, T. et al. DEMETER and REPRESSOR OF SILENCING 1 encode 5-methylcytosine DNA glycosylases. Proc. Natl Acad. Sci. USA 103, 6853–6858 (2006).
Agius, F., Kapoor, A. & Zhu, J. K. Role of the Arabidopsis DNA glycosylase/lyase ROS1 in active DNA demethylation. Proc. Natl Acad. Sci. USA 103, 11796–11801 (2006). References 139 and 140 show that DME is an active 5-methylcytosine DNA glycosylase in vitro , and references 140 and 141 show that ROS1 is an active 5-methylcytosine DNA glycosylase in vitro.
Zhu, J., Kapoor, A., Sridhar, V. V., Agius, F. & Zhu, J. K. The DNA glycosylase/lyase ROS1 functions in pruning DNA methylation patterns in Arabidopsis. Curr. Biol. 17, 54–59 (2007).
Penterman, J., Uzawa, R. & Fischer, R. L. Genetic interactions between DNA demethylation and methylation in Arabidopsis. Plant Physiol. 145, 1549–1557 (2007).
Baute, J. & Depicker, A. Base excision repair and its role in maintaining genome stability. Crit. Rev. Biochem. Mol. Biol. 43, 239–276 (2008).
Gehring, M., Reik, W. & Henikoff, S. DNA demethylation by DNA repair. Trends Genet. 25, 82–90 (2009).
Kapoor, A., Agius, F. & Zhu, J. K. Preventing transcriptional gene silencing by active DNA demethylation. FEBS Lett. 579, 5889–5898 (2005).
Malone, C. D. & Hannon, G. J. Small RNAs as guardians of the genome. Cell 136, 656–668 (2009).
Zheng, X. et al. ROS3 is an RNA-binding protein required for DNA demethylation in Arabidopsis. Nature 455, 1259–1262 (2008).
Hajkova, P. et al. Epigenetic reprogramming in mouse primordial germ cells. Mech. Dev. 117, 15–23 (2002).
Hajkova, P. et al. Chromatin dynamics during epigenetic reprogramming in the mouse germ line. Nature 452, 877–881 (2008).
Santos, F., Hendrich, B., Reik, W. & Dean, W. Dynamic reprogramming of DNA methylation in the early mouse embryo. Dev. Biol. 241, 172–182 (2002).
Oswald, J. et al. Active demethylation of the paternal genome in the mouse zygote. Curr. Biol. 10, 475–478 (2000).
Mayer, W., Niveleau, A., Walter, J., Fundele, R. & Haaf, T. Demethylation of the zygotic paternal genome. Nature 403, 501–502 (2000).
Nakamura, T. et al. PGC7/Stella protects against DNA demethylation in early embryogenesis. Nature Cell Biol. 9, 64–71 (2007).
Li, X. et al. A maternal-zygotic effect gene, Zfp57, maintains both maternal and paternal imprints. Dev. Cell 15, 547–557 (2008).
Reese, K. J., Lin, S., Verona, R. I., Schultz, R. M. & Bartolomei, M. S. Maintenance of paternal methylation and repression of the imprinted H19 gene requires MBD3. PLoS Genet. 3, e137 (2007).
Ciccone, D. N. & Chen, T. Histone lysine methylation in genomic imprinting. Epigenetics 4, 216–220 (2009).
Edwards, C. A. & Ferguson-Smith, A. C. Mechanisms regulating imprinted genes in clusters. Curr. Opin. Cell Biol. 19, 281–289 (2007).
Ooi, S. K. & Bestor, T. H. The colorful history of active DNA demethylation. Cell 133, 1145–1148 (2008).
Morgan, H. D., Dean, W., Coker, H. A., Reik, W. & Petersen-Mahrt, S. K. Activation-induced cytidine deaminase deaminates 5-methylcytosine in DNA and is expressed in pluripotent tissues: implications for epigenetic reprogramming. J. Biol. Chem. 279, 52353–52360 (2004).
Rai, K. et al. DNA demethylation in zebrafish involves the coupling of a deaminase, a glycosylase, and Gadd45. Cell 135, 1201–1212 (2008). This study uses zebrafish embryos as a model for studying DNA demethylation and provides evidence that cytosine methylation can be removed through the coordinated activities of 5′ methylcytosine deaminases and thymine mismatch DNA glycosylases.
Hendrich, B., Hardeland, U., Ng, H. H., Jiricny, J. & Bird, A. The thymine glycosylase MBD4 can bind to the product of deamination at methylated CpG sites. Nature 401, 301–304 (1999).
Petronzelli, F. et al. Investigation of the substrate spectrum of the human mismatch-specific DNA N-glycosylase MED1 (MBD4): fundamental role of the catalytic domain. J. Cell Physiol. 185, 473–480 (2000).
Popp, C. et al. Genome-wide erasure of DNA methylation in mouse primordial germ cells is affected by AID deficiency Nature22 Jan 2010 (doi:1038/nature08829). Knocking out AID reduces the genome-wide DNA demethylation observed in PGCs.
Kim, M. S. et al. DNA demethylation in hormone-induced transcriptional derepression. Nature 461, 1007–1012 (2009).
Zhu, B. et al. 5-Methylcytosine DNA glycosylase activity is also present in the human MBD4 (G/T mismatch glycosylase) and in a related avian sequence. Nucleic Acids Res. 28, 4157–4165 (2000).
Tahiliani, M. et al. Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science 324, 930–935 (2009).
Kriaucionis, S. & Heintz, N. The nuclear DNA base 5-hydroxymethylcytosine is present in Purkinje neurons and the brain. Science 324, 929–930 (2009).
Valinluck, V. et al. Oxidative damage to methyl-CpG sequences inhibits the binding of the methyl-CpG binding domain (MBD) of methyl-CpG binding protein 2 (MeCP2). Nucleic Acids Res. 32, 4100–4108 (2004).
Valinluck, V. & Sowers, L. C. Endogenous cytosine damage products alter the site selectivity of human DNA maintenance methyltransferase DNMT1. Cancer Res. 67, 946–950 (2007).
Cannon, S. V., Cummings, A. & Teebor, G. W. 5-Hydroxymethylcytosine DNA glycosylase activity in mammalian tissue. Biochem. Biophys. Res. Commun. 151, 1173–1179 (1988).
Jullien, P. E. et al. Retinoblastoma and its binding partner MSI1 control imprinting in Arabidopsis. PLoS Biol. 6, e194 (2008).
McCabe, M. T., Davis, J. N. & Day, M. L. Regulation of DNA methyltransferase 1 by the pRb/E2F1 pathway. Cancer Res. 65, 3624–3632 (2005).
Kimura, H., Nakamura, T., Ogawa, T., Tanaka, S. & Shiota, K. Transcription of mouse DNA methyltransferase 1 (Dnmt1) is regulated by both E2F-Rb-HDAC-dependent and -independent pathways. Nucleic Acids Res. 31, 3101–3113 (2003).
McCabe, M. T., Low, J. A., Imperiale, M. J. & Day, M. L. Human polyomavirus BKV transcriptionally activates DNA methyltransferase 1 through the pRb/E2F pathway. Oncogene 25, 2727–2735 (2006).
Nicolas, E., Ait-Si-Ali, S. & Trouche, D. The histone deacetylase HDAC3 targets RbAp48 to the retinoblastoma protein. Nucleic Acids Res. 29, 3131–3136 (2001).
Morgan, H. D., Santos, F., Green, K., Dean, W. & Reik, W. Epigenetic reprogramming in mammals. Hum. Mol. Genet. 14, R47–R58 (2005).
Carlson, L. L., Page, A. W. & Bestor, T. H. Properties and localization of DNA methyltransferase in preimplantation mouse embryos: implications for genomic imprinting. Genes Dev. 6, 2536–2541 (1992).
Mertineit, C. et al. Sex-specific exons control DNA methyltransferase in mammalian germ cells. Development 125, 889–897 (1998).
Wilczynska, A., Minshall, N., Armisen, J., Miska, E. A. & Standart, N. Two Piwi proteins, Xiwi and Xili, are expressed in the Xenopus female germline. RNA 15, 337–345 (2009).
Kawaoka, S. et al. The Bombyx ovary-derived cell line endogenously expresses PIWI/PIWI-interacting RNA complexes. RNA 15, 1258–1264 (2009).
Lau, N. C. et al. Abundant primary piRNAs, endo-siRNAs, and microRNAs in a Drosophila ovary cell line. Genome Res. 19, 1776–1785 (2009).
Kawaoka, S. et al. Bombyx small RNAs: genomic defense system against transposons in the silkworm, Bombyx mori. Insect Biochem. Mol. Biol. 38, 1058–1065 (2008).
Lau, N. C., Ohsumi, T., Borowsky, M., Kingston, R. E. & Blower, M. D. Systematic and single cell analysis of Xenopus Piwi-interacting RNAs and Xiwi. EMBO J. 28, 2945–2958 (2009).
We thank members of the Jacobsen laboratory and anonymous reviewers for useful comments and discussion. We apologize to colleagues whose research we did not have space to discuss, especially those studying DNA methylation in other systems, such as maize and Neurospora species. J.A.L. was supported the US National Institutes of Health National Research Service Award 5F32GM820453. This research was supported by US National Institutes of Health grant GM60398. S.E.J. is an investigator at the Howard Hughes Medical Institute.
The authors declare no competing financial interests.
- Epigenetic modifications
Chemical additions to DNA and histones that are associated with changes in gene expression and are heritable but do not alter the primary DNA sequence.
The main protein components of chromatin. The four core histones, H2A, H2B, H3 and H4, form a globular octameric complex called a nucleosome upon which DNA is wrapped. The amino-terminal regions of histone proteins are largely unstructured and are subject to various chemical modifications, including methylation.
- CpG island
A sequence of at least 200 bp with a greater number of CpG sites than expected for its GC content. These regions are often GC rich, typically undermethylated, and are found upstream of many mammalian genes.
- RNA-directed DNA methylation
A plant-specific pathway through which small RNAs (24 nucleotides long) target the de novo methyltransferase DOMAINS REARRANGED METHYLTRANSFERASE 2 (DRM2) to homologous genomic loci to establish DNA methylation, which leads to transcriptional gene silencing.
- RNA interference
A process of post-transcriptional gene silencing in which small RNAs, often generated by the activity of an RNA-dependent RNA polymerase and a Dicer endoribonuclease, are bound by Argonaute proteins and target cleavage of homologous mRNA transcripts.
An RNase III family endonuclease that processes dsRNAs into small interfering RNAs.
Effector proteins of small RNA-directed silencing. Small RNAs guide Argonautes to their RNA targets. Argonaute proteins are characterized by two domains PIWI (a ribonuclease domain) and Piwi Argonaute and Zwille (PAZ; an ssRNA-binding module).
- Chromatin-remodelling factors
Proteins that have the capacity to remodel chromatin, often using the energy of ATP, so that gene transcription can be activated or silenced.
- Small interfering RNAs
2025 nucleotide-long RNAs that are generated from dsRNAs and serve as guides for the cleavage of homologous mRNAs in RNA interference or for the addition of chromatin modifications, including histone and DNA methylation at homologous genomic sequences in transcriptional gene silencing.
- Cajal bodies
Nuclear bodies that are associated with the maturation of ribonucleoprotein complexes.
A densely packaged form of chromatin that is associated with repressive histone modifications, DNA methylation and gene silencing.
- Primordial germ cells
The population of embryonic cells from which germ cells are formed.
- Imprinted genes
Genes in which one allele is expressed in a parent-of-origin-specific manner.
- Bisulphite sequencing
A technique in which the treatment of DNA with bisulphite, which converts cytosines into uracils but does not modify methylated cytosines, is used to determine the DNA methylation pattern.
- Vegetative nucleus
The nucleus of a terminally differentiated vegetative cell. It does not contribute genetic information to subsequent generations.
A multicellular structure that is generated from a haploid spore through mitotic cell divisions and contains the male or female gamete.
The product of fertilization of the central cell of the female gametophyte. It is present in the seeds of most flowering plants and provides nutrition to the developing embryo.
- Primary piRNAs
(Primary Piwi-interacting RNAs.) The products of piRNA precursor transcript processing. These piRNAs have a preference for a 5′ uridine.
- Secondary piRNAs
(Secondary Piwi-interacting RNAs.) The products of a ping-pong amplification cycle. These piRNAs are antisense to primary piRNAs and have a preference for an adenine at position 10.
- Tudor domain
A conserved protein motif that is able to recognize symmetrically dimethylated arginines.
- Base excision repair
A cellular mechanism that repairs damaged DNA and is initiated by the activity of DNA glycosylases.
A genetically distinct population within a widely spread species.
An elongated seed capsule that is formed after fertilization.
Offspring that are produced by crossing two different populations within a single species.
A single diploid cell formed by the union of two haploid germ cells.
An embryonic stage that is characterized by the first definitive lineages.
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Law, J., Jacobsen, S. Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat Rev Genet 11, 204–220 (2010). https://doi.org/10.1038/nrg2719
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