Plant J. 2008 Dec; 56(5): 814–823.
Published online 2008 Aug 26. doi:  10.1111/j.1365-313X.2008.03640.x
PMCID: PMC2667643

Cooperative activity of DNA methyltransferases for maintenance of symmetrical and non-symmetrical cytosine methylation in Arabidopsis thaliana


Maintenance of cytosine methylation in plants is controlled by three DNA methyltransferases. MET1 maintains CG methylation, and DRM1/2 and CMT3 act redundantly to enforce non-CG methylation. RPS, a repetitive hypermethylated DNA fragment from Petunia hybrida, attracts DNA methylation when transferred into Petunia or other species. In Arabidopsis thaliana, which does not contain any RPS homologues, RPS transgenes are efficiently methylated in all sequence contexts. To test which DNA methylation pathways regulate RPS methylation, we examined maintenance of RPS methylation in various mutant backgrounds. Surprisingly, CG methylation was lost in a drm1/2/cmt3 mutant, and non-CG methylation was almost completely eliminated in a met1 mutant. An unusual cooperative activity of all three DNA methyltransferases is therefore required for maintenance of both CG and non-CG methylation in RPS. Other unusual features of RPS methylation are the independence of its non-CG methylation from the RNA-directed DNA methylation (RdDM) pathway and the exceptional maintenance of methylation at a CCmTGG site in some epigenetic mutants. This is indicative of activity of a methylation system in plants that may have evolved from the DCM methylation system that controls CCmWGG methylation in bacteria. Our data suggest that strict separation of CG and non-CG methylation pathways does not apply to all target regions, and that caution is required in generalizing methylation data obtained for individual genomic regions.

Keywords: DNA methylation, MET1, DRM2, CMT3, DCM-like methylation


DNA methylation has evolved from an immune function in bacteria to a regulator of gene expression and genome structure in higher eukaryotes. In bacteria, methylation targets are determined on the basis of their DNA sequence, as type II DNA methyltransferases methylate short recognition sequences, providing protection against methylation-sensitive endonucleases that target the same sequence (Wilson, 1988). In higher eukaryotes, DNA methylation systems have to fulfil new functions that are not compatible with the universal distribution of DNA methylation marks across the genome. For example, inactivation of parasitic sequences or compartmentalization of heterochromatic regions require selective establishment and clonal inheritance of DNA methylation patterns based on de novo and maintenance methylation systems. The evolution and adaptation of prokaryotic DNA methylation systems was probably a requirement for higher eukaryotes to manage their large genomes (Bestor, 1990), and a comparison of the features of DNA methylation systems present in higher eukaryotes may help us to understand this evolutionary process.

Plants show three cytosine methylation types, CG, CNG and CNN methylation, which are regulated by three DNA methylation functions. DNMT1-like METHYLTRANSFERASE 1 (MET1) controls CG methylation (Finnegan and Dennis, 1993; Saze et al., 2003). CHROMOMETHYLASE 3 (CMT3) is the main enzyme controlling methylation at CNG sites (Lindroth et al., 2001) but also affects CNN methylation (Bartee et al., 2001). Two members of the DOMAINS REARRANGED METHYLTRANSFERASE family, DRM1 and DRM2, are also responsible for CNN methylation (Cao and Jacobsen, 2002a), thus CNG and CNN methylation are therefore controlled redundantly by CMT3, DRM1 and DRM2 (Chan et al., 2005). While the symmetry of CG methylation targets provides a means for maintenance after replication, non-symmetrical methylation (NSM) patterns can only be maintained via continuous de novo methylation, which requires defined helper functions. NSM patterns are maintained by three partially overlapping pathways that can be distinguished by their effects on individual target regions.

NSM of endogenous repeats at the flowering time locus FWA and at the repeat element MEA-ISR requires a 24 nt siRNA whose production is controlled by the two largest subunits of RNA-DEPENDENT POLYMERASE IV (NRPD1a and NRPD1b), RNA-DEPENDENT RNA POLYMERASE 2 (RDR2), DICER-LIKE 3 (DCL3) and ARGONAUTE4 (AGO4). It has been proposed that, within a nucleolar processing centre, NRPD1a-generated RNA is copied by RDR2 into dsRNA, which DCL3 cleaves into 24 nt siRNAs that assemble with an AGO4/NRPD1b-containing silencing complex (Li et al., 2006; Pontes et al., 2006). This complex guides DRM2 (the more highly expressed member of the DRM family; Cao and Jacobsen, 2002a) to its target regions, where it induces NSM (Chan et al., 2004).

NSM at the SINE element AtSN1 uses a combination of the RNAi pathway and a second pathway in which CMT3 is guided to the target region by histone H3 lysine 9 dimethylation (H3K9me2), which is established by the suppressor of variegation-enhancer of zeste-trithorax (SET) domain protein SUVH4/KRYPTONITE (KYP) (Jackson et al., 2002). An essential regulator both for the RNAi pathway and the KYP-dependent pathway is the putative SNF2 chromatin remodelling protein DRD1 (Kanno et al., 2004). DRD1 works together with the 24 nt siRNA pathway in the establishment of DNA methylation, with DRM2 and CMT3 maintaining DNA methylation (Chan et al., 2006).

NSM at the pericentromeric retrotransposon Ta3 does not require the siRNA pathway and is also independent of DRD1. Instead, Ta3 methylation is regulated by CMT3- and KYP-based histone H3K9me2 methylation in an alternative DRD1-independent pathway (Chan et al., 2006).

We have previously described the RPS sequence element from Petunia hybrida, which acts as a hot spot for de novo DNA methylation when transferred into the Arabidopsis genome (Muller et al., 2002). There is no indication that the RPS element is transcribed, and it has been suggested that RPS attracts DNA methylation via its palindromic structures (Muller et al., 2002). To test the influence of epigenetic regulators on RPS-specific methylation patterns, we crossed a methylated RPS transgene into various Arabidopsis mutant backgrounds. Surprisingly, we found that the three methyltransferases MET1, CMT3 and DRM1/2 are all required cooperatively for RPS methylation both at CG and non-CG sites.


The transgenic Arabidopsis line RA5 contains a single copy of the RPS transgene, which is heavily methylated (Muller et al., 2002). We used this line for crosses with epigenetic pathway mutants to test their effects on maintenance of RPS methylation. RPS methylation was first examined in the putative chromatin remodelling mutants drd1 and ddm1 (Figure 1). DDM1 had no influence on the methylation of cytosines in any context but methylation levels were significantly affected in drd1, especially at non-CG targets, as CNG and CNN methylation levels dropped to below 10% of the wild-type levels for these targets. CG-specific methylation was also reduced in drd1, especially at two CG sites in the 5′ region. In contrast to the significant hypomethylation of CNG sites, methylation at the second C residue within a CCTGG sequence was only moderately reduced in the drd1 mutant.

Figure 1
RPS methylation in putative chromatin remodelling mutants

As a next step, we compared RPS methylation patterns in lines carrying mutations of four genes required for NSM mediated by the RNAi pathway or the KYP-dependent pathway (Figure 2). In all four lines, both CNG and CNN methylation levels were reduced, with kyp2 and dcl3 having the strongest impact. The only exception was again methylation at the CCmTGG site, which was not significantly altered in any of the four mutants. Surprisingly, CG methylation was also reduced in kyp2, dcl3 and ago4. In rdr2, most CG targets remained hypermethylated, except for the two cytosines in the 5′ region that were also affected in drd1.

Figure 2
RPS methylation in mutants of the RNA-directed DNA methylation pathway

RPS methylation was then tested in the three DNA methyltransferase mutants (Figure 3). Surprisingly, DNA methylation was significantly reduced in all lines irrespective of the sequence context. In met1, hypomethylation affected CG sites, and non-CG methylation was also almost eliminated. The mildest effects were detectable in cmt3, in which C residues in all sequence contexts were hypomethylated, but this effect was less pronounced at the CCmTGG site, at some central CNN sites and at CG sites in the 3′ region. The most significant hypomethylation effect was observed in the drm1/2mutant double mutant and a drm1/2/cmt3 triple mutant, in which methylation was almost completely eliminated, with only some traces of CNN methylation. Maintenance of RPS-specific CG methylation can therefore not be guaranteed by MET1 alone but requires both DRM1/2 and CMT3. Equally, DRM1/2 and CMT3 are necessary but not sufficient for maintenance of CNG and CNN methylation, which also requires MET1. Maintenance of methylation at the CCmTGG site also required DRM1/2, MET1, and, to a lesser extent, CMT3.

Figure 3
RPS methylation in DNA methyltransferase mutants

Although some hypomethylation was detectable in rdr2, kyp2, dcl3 and ago4, neither CNG nor CNN methylation were eliminated. This result was in accordance with the assumption that, while the RNAi pathway may augment RPS methylation, it is not essential for its maintenance. The analysis of RPS-specific small RNAs (Figure 4) also supports this model. Petunia, which contains a large pool of methylated RPS copies and RPS homologues, shows a strong signal for RPS-specific small RNAs. A very faint signal of similar size was also detectable in the RA5 line, which has a single methylated RPS copy, but the small RNA is no longer detectable in the rdr2 line, which still shows a significant level of RPS methylation (Figure 2). The small RNA in RA5 may therefore reflect an enhancement of RPS methylation via the RNAi pathway, but basic levels of RPS methylation can be maintained without the RNAi pathway. To test whether this independence also applies to initiation of RPS-specific methylation, we transformed an rdr2 mutant with an RPS construct and analysed methylation patterns in three independent transformants (Figure 5). All three lines showed a low but significant methylation level for the RPS transgene, which suggests that RPS methylation is not only maintained but can also be initiated in the absence of the RNAi pathway.

Figure 5
De novo methylation of RPS does not depend on RDR2
Figure 4
Analysis of RPS-specific small RNAs

Apart from the joint requirement for various methyltransferases and the independence of non-CG methylation from the small RNA pathway, another unusual feature of RPS was that its methylation was dependent on MET1 but not influenced by DDM1, as these two functions jointly regulate CG methylation for a number of endogenes and transgenic loci. To test whether the plant genome contains other regions with methylation patterns that are independent of DDM1, we cloned genomic DNA of a ddm1 mutant after digestion with GlaI, which requires methylated cytosines for restriction. GlaI cleaves fully methylated CGCG sites, ACGC and GCGC sites which contain at least three methylated C residues, and GCGT sites with at least two methylated residues (Tarasova et al., 2008). When digested with GlaI, ddm1 genomic DNA no longer contains the characteristic bands that are indicative of methylated repetitive regions in the wild-type (Figure 6a). A faint background level suggested that a small fraction of the ddm1 DNA was digested by GlaI. After cloning this fraction, we sequenced nine regions and used the highly integrated single-base resolution maps at (Lister et al., 2008) to examine their methylation profiles in wild-type and DNA methyltransferase mutants. Eight of the nine cloned regions represented genes with CG methylation regions located in the central and/or 3′ coding region. One clone comprised a methylated repeat region next to the 3′ UTR of At4g14365, which contained CG and non-CG methylation targets. In all cloned regions, CG methylation is abolished in met1 and retained in the drm1/2/cmt3 triple mutant. The non-CG methylation pattern in the region near the At4g14365 gene is lost in the drm1/2/cmt3 triple mutant and retained in met1 (Table 1). We selected regions from three clones with CG methylation (Figure 6b) and from the only clone with CG and non-CG methylation (Figure 6c) for bisulfate analysis of ddm1 DNA, which confirmed that all clones maintained their methylation pattern in ddm1. Like RPS methylation, methylation in some euchromatic regions is therefore independent of DDM1. In contrast to RPS, however, CG and non-CG patterns in these regions are separately controlled by MET1 and DRM1/2/CMT3 activity.

Table 1
Clones isolated after GlaI digestion of ddm1 genomic DNA
Figure 6
Methylation patterns of cloned genomic regions in ddm1


The RPS element was selected in a screen for Petunia DNA elements that destabilize the expression of an adjacent marker gene (tenLohuis et al., 1995). RPS belongs to a group of middle repetitive, dispersed and hypermethylated homologues. Repetitiveness, however, is not a prerequisite for hypermethylation, as RPS transgenes are efficient methylation targets in Arabidopsis, which lacks any significant RPS homology. As attempts to identify RPS transcripts had been unsuccessful, it had been proposed that RPS hypermethylation was independent of the RdDM pathway (Muller et al., 2002). Our analysis of RPS methylation patterns in plants bearing mutations in chromatin-remodelling enzymes, RdDM pathway functions and DNA methyltransferases supports this model, and identifies some unusual requirements for maintenance of RPS methylation.

RPS methylation is independent of DDM1

One surprising observation was that RPS-specific DNA methylation was unaltered in the ddm1 mutant. DDM1 has similarities to members of the SWI/SNF family of adenosine triphosphate-dependent chromatin-remodelling proteins, suggesting an indirect role in DNA methylation, control of methylation and transcriptional inactivation of transposons (Miura et al., 2001), heterochromatic repeats (Steimer et al., 2000) and transgenes (Mittelsten Scheid et al., 1998). In ddm1 mutants, repetitive sequences are quickly demethylated, while hypomethylation of many low-copy regions occurs progressively (Jeddeloh et al., 1998). In contrast, RPS-specific methylation is fully maintained in ddm1.

Hypermethylation of RPS in a ddm1 background is surprising in view of the very strong hypomethylation of RPS in the met1 mutant, as DDM1 and MET1 usually show close cooperativity. Efficient maintenance of RNA-directed DNA methylation requires the activity of DDM1 and MET1 (Aufsatz et al., 2002), which are also essential for silencing of elements that are potentially independent of the RDM pathway and for which no small RNAs have been found (Rangwala and Richards, 2007). As far as we are aware, the only example of a locus that is differently affected by DDM1 and MET1 is Sadhu6-1, a non-autonomous retroposon that is reactivated in met1 but not in ddm1; CG methylation levels for Sadhu6-1 are reduced from 95% to 62% in met1 but only to 83% in ddm1 (Rangwala and Richards, 2007). For RPS, we see a similar but even more drastic discrepancy, with CG methylation levels decreasing from 89% to 11% in met1 but only to 82% in ddm1.

Our search for other genomic regions with CG methylation patterns that remained unaltered in a ddm1 mutant background identified several genes that all contained methylated CG blocks in the centre or 3′ half of their coding regions. As for RPS, CG methylation of all these genes was eliminated in met1 (Lister et al., 2008) but maintained in ddm1. DDM1 is therefore essential for DNA methylation of certain but not all genomic regions. It is tempting to speculate that repetitive or heterochromatic regions are prime targets for DDM1, while unique or euchromatic regions are methylated independently of DDM1. Repetitiveness may, however, not be sufficient for a region to come under DDM1 control, as we found a block of methylated CG and non-CG targets in a repetitive region near the 3′ UTR of At4g14365 that are also independent of DDM1.

RdDM pathway functions enhance RPS methylation but are not essential for maintenance or initiation of RPS methylation

The general reduction of DNA methylation levels in drd1, kyp2, dcl3, ago4 and rdr2 suggests that RdDM pathways contribute to the maintenance of RPS methylation. However, this effect is not specific for non-CG methylation targets, and this is most obvious in kyp2 and dcl3 backgrounds for which CG methylation levels fall from 89% to 12% and 21%, respectively. This contrasts with reports regarding the conservation of CG methylation in dcl3 at MEA-ISR, AtSN1 and IR-71 (Henderson et al., 2006). For kyp, a moderate reduction of CG methylation from 16% to 6% has been reported for Superman (SUP), but CG methylation at FWA, TSI, TA3 and at a 180-bp centromeric repeat remains unchanged (Jackson et al., 2002).

Although drd1, kyp2, dcl3, ago4 and rdr2 all show a hypomethylation effect, none of the mutants inhibits RPS methylation completely, and a similar basic level of methylation is also observed in RPS transgenes after transfer into rdr2. The basic methylation level in all five mutants, the lack of an RPS-specific siRNA in the rdr2 background and the failure to detect RPS-specific transcripts suggest that the initial RPS methylation level is established independently of RdRM pathways. The enhanced methylation levels and the presence of an RPS-specific siRNA in RA5 suggest that basal methylation levels are amplified via the RdRM pathway. It has been suggested that siRNA production requires NRPD1a to transcribe either a methylated target region (Herr et al., 2005) or locus-specific nascent transcripts (Pontes et al., 2006) or dsRNA (Vaucheret, 2005). Our data support a signal function for methylated RPS DNA in the initiation of siRNA production.

The separation between CG and non-CG methylation pathways is lost in RPS

Another surprising feature of RPS methylation is the influence of the various DNA methyltransferases on methylation of cytosines outside their usual target sequence context. These characteristics are not shared by the cloned DDM1-independent methylation targets, for which we see a clear separation between MET1-controlled CG methylation and DRM1/2/CMT3-controlled non-CG methylation. MET1 was therefore expected to regulate RPS-specific CG methylation only, which did actually drop from 89 to 11% in met1. However, CNG methylation was also reduced from 76% to 3.8% and CNN methylation decreased from 33% to 0.6%. There are a few reports indicating that MET1 is important for the maintenance of CNG methylation at other loci (Rangwala and Richards, 2007), but these effects are relatively modest compared to the very drastic reduction of RPS-specific non-CG methylation in met1. Equally surprising, RPS-specific hypomethylation in the drm1 drm2 background was not limited to non-CG targets but also included CG methylation, which decreased from 89 to 2% in drm1/2 and was completely eliminated in the drm1/2/cmt3 triple mutant. The presence of MET1 is therefore not sufficient to maintain CG methylation of RPS. This contrasts with reports on FWA, MEA-IR and SUP, for which CG methylation remains unaltered in the drm1/2/cmt3 triple mutant, reflecting the primary importance of MET1 for CG methylation (Cao and Jacobsen, 2002b). In line with our observations for RPS, the drm2 single mutation has been shown to cause a moderate reduction in both CG and CNG methylation at 5S rDNA (Mathieu et al., 2007).

The unusual influence of DRM1/2, CMT3, DCL3 and KYP on the maintenance of CG methylation, and the participation of MET1 in maintaining CNG and CNN methylation, make RPS a very unusual methylation target. Our results suggest that maintenance of RPS methylation requires mutual enforcement of symmetrical and non-symmetrical DNA methylation systems, and that all methylation patterns are significantly reduced or lost if either of the two systems is compromised. This may reflect a cooperative effect whereby MET1, DRM1/2 and CMT3 only gain access to RPS jointly, or it may be the result of methylation-sensitive auxiliary factors that guide methyltransferases to RPS. The latter model implies that, for example, CG methylation is required for binding of DRM1/2 and CMT3 guiding factors, and non-CG methylation enables binding of the MET1 guiding factors. Loss of CG methylation would then compromise maintenance of non-CG methylation and vice versa.

A DCM-like methylation site is independent of RDM functions

Although RPS is so far the only target requiring the cooperative activity of MET1, CMT3 and DRM1/2, its special regulation indicates that sequence- or locus-specific factors should be taken into account to understand the composition of DNA methylation patterns. This conclusion is also supported by the observation that CG methylation patterns at certain loci are controlled by DDM1, while CG targets at other loci are independent of DDM1. In addition, some of our results highlight how careful we need to be in interpreting methylation data for individual sites as indicators for a locus. Among the seven CG sites in the analysed RPS region, for example, we detected at two sites a 90% reduction of DNA methylation in rdr2, but methylation at the other five sites does not change at all. The most significant exception, however, is the conservation of CNG methylation at a CCmTGG site in RDM mutant backgrounds. This implies that CCmTGG methylation at this site is independent of a small RNA pathway. DRD1 may have a moderate influence on maintenance of CCmTGG methylation, probably by facilitating access to the region for regulatory proteins or methyltransferases.

The presence of a CCWGG methylation system in mammals illustrates the transmission of DCM-like methylation systems into eukaryotes. Initially, CCmWGG methylation was interpreted as maintenance of CNG methylation when it was detected in CCmWGG-methylated plasmid DNA that had been transferred into the genome of mouse cell lines (Clark et al., 1995). The discovery of CCmWGG methylation in retroviral DNA (Lorincz et al., 2000) and in endogenous promoter regions (Malone et al., 2001), however, argues in favour of a de novo CCmWGG methylation activity in mammals. This is also the most likely explanation for our results. Due to the absence of CCmWGG methylation in Agrobacterium tumefaciens (Gomez-Eichelmann et al., 1991), the transferred T-DNA is unmethylated when transferred into the plant genome, and CCmTGG methylation is established de novo in the transformed plant. CCmTGG methylation is significantly reduced or lost in all DNA methyltransferase mutants, which implies that MET1, DRM1/2 and CMT3 either help to recruit an unknown CCTGG methyltransferase to the RPS region, or that the CCTGG site is efficiently labelled as a target for methylation, mediated by joint activity of the three methyltransferases.

Our date demonstrate that, at least for certain loci, DNA methylation patterns cannot exclusively be interpreted as the result of a specific DNA methylation function or pathway. To fully understand the dynamics of DNA maintenance, it will be important to consider target-specific characteristics that influence the accessibility and cooperativity of methyltransferases or their auxiliary factors. This may also contribute to a better understanding of the high levels of methylation polymorphism (Vaughn et al., 2007) and locus-specific methylation variation (Fischer et al., 2008).

Experimental procedures

Plant material

All plants were grown under 8 h short-day conditions at 22°C. Arabidopsis thaliana mutants used in this study and their ecotypes are described in Appendix S1. The Arabidopsis line RA5 containing a single copy of a p35S GUS/RPS transgene (Muller et al., 2002) was used for crosses with the various mutants. Progeny plants were selfed, and homozygous mutant genotypes were selected by allele-specific PCR on F2 populations. The presence of the transgene was selected by histochemical assay for the expression of GUS activity (Jefferson et al., 1987).

Plasmid design and transformation

For analysis of de novo RPS methylation in rdr2, pGreen 0049 (Hellens et al., 2000) harbouring a 35S–Luc reporter gene and a kanamycin resistance marker was used as a vector, digested with HindIII and ligated with a 1.6-kb RPS HindIII fragment isolated from p35S GUS/RPS (Muller et al., 2002). Transgenic lines were isolated after transforming rdr2 with the resulting construct pGreen49+RPS (Clough and Bent, 1998).

Bisulfite sequencing

The sequence of the RPS region analysed by bisulfite sequencing is shown in Figure S2. Genomic DNA was isolated using a GenElute plant genomic DNA miniprep kit (Sigma-Aldrich, and subjected to bisulfite treatment using an Epitect bisulfite kit (Qiagen, according to the manufacturer’s instructions, except that the procedure was repeated twice to disrupt secondary structures and ensure complete conversion. A 1-μg aliquot of input DNA was used for the conversion reaction. In order to test whether this treatment leads to complete C→T conversion, 20 pg of an RPS-containing plasmid was mixed with 1 μg of wild-type DNA for a reconstitution control experiment, and complete conversion was confirmed.

To analyse the RPS top strand, primers RPS-top-F and RPS-top-R were used (Appendix S1). PCR was carried out using Go Taq polymerase (Promega, under the following conditions: 94°C for 4 min, 51°C for 2 min and 72°C for 1 min (two cycles), then 94°C for 1 min, 51°C for 2 min and 72°C for 1 min (38 cycles), generating a 421-bp product. PCR products were separated on a 1% agarose gel and the DNA was excised and cleaned up using a QIAquick gel extraction kit (Qiagen). The purified fragment was then cloned using a TOPO-TA cloning kit (Invitrogen, according to the manufacturer’s recommendations, and recombinant plasmids were transferred into one shot MACH-Ti competent cells (Invitrogen). Transformants were selected on LB culture plates with 50 μg ml−1 kanamycin and 40 mg ml−1 X-gal, and colonies were selected for plasmid isolation using a QIAprep spin miniprep kit (Qiagen).

Analysis of bisulfite-treated genomic sequencing lines

For each line, 9–20 clones were sequenced and sequences were exported into the BioEdit program (Hall, 1999). Aligned sequences were saved in FASTA format and were analysed by the MethTools2 program ( The tab files returned by MethTools were pasted into an Excel spreadsheet to calculate and illustrate DNA methylation frequencies at individual cytosine residues. Bisulfite sequencing data were also analysed by the CyMATE programme (Hetzl et al., 2007) and are presented in Figure S3.

Analysis of methylation patterns in regions cloned after Gla I digestion of ddm1 DNA

The following regions were selected for bisulfite sequencing: At1g02010 – chromosome 1, positions 350 334–350 576; At3g53580 – chromosome 3, positions 19 877 246–19 877 428; At4g10140 – chromosome 4, positions 6 324 044–6 324 271; At4g14365, chromosome 4, positions 8 271 333–8 271 568. Sequence data are provided in Figure S2.

Detection of small RNAs

About 50 μg of small low-molecular-weight RNA was isolated from rosette leaves (Hamilton and Baulcombe, 1999), separated on a 15% denaturing polyacrylamide gel, and transferred onto a Hybond Nx membrane (Amersham, by carbodiimide-mediated cross-linking (Pall et al., 2007). A RNA single-strand probe was generated by T7 RNA polymerase transcription of a plasmid template in the presence of α32P-labelled UTP. Primers BsF (5′-CCCAACACCTTGGAATGATTGC-3′) and BsR (5′-AGGAGGTATCTGTCTTCTTTTTTAC-3′) were used for amplification of an RPS fragment, which was cloned into pGEM-T Easy vector (Promega). As a positive control, an oligonucleotide with sequence complementary to miR159 was labelled with T4 polynucleotide kinase and γ32P-ATP.


A.S. was funded by the European Commission Framework 6 Marie Curie Early Stage Training Scheme AGAPE (contract number MEST-CT-2004-504318). We would like to thank Dr Marjori Matzke and Dr Ortrun Mittelsten Scheid (Gregor Mendel Institute of Molecular Plant Biology, Vienna) for mutant lines.

Supporting information

Additional Supporting Information may be found in the online version of this article:

Figure S1. Identification of mutant lines and list of oligonucleotides.

Figure S2. Sequence of regions analysed by genomic sequencing.

Figure S3. RPS bisulfite data in CyMATE format.

Please note: Wiley-Blackwell are not responsible for the content or functionality of any supporting materials supplied by the authors. Any queries (other than missing material) should be directed to the corresponding author for the article.


  • Aufsatz W, Mette MF, van der Winden J, Matzke AJM, Matzke M. RNA-directed DNA methylation in Arabidopsis. Proc. Natl Acad. Sci. USA. 2002;99:16499–16506. [PMC free article] [PubMed]
  • Bartee L, Malagnac F, Bender J. Arabidopsis cmt3 chromomethylase mutations block non-CG methylation and silencing of an endogenous gene. Genes Dev. 2001;15:1753–1758. [PMC free article] [PubMed]
  • Bestor TH. DNA methylation – evolution of a bacterial immune function into a regulator of gene-expression and genome structure in higher eukaryotes. Philos. Trans. R. Soc. Lond. B Biol. Sci. 1990;326:179–187. [PubMed]
  • Cao X, Jacobsen SE. Role of the Arabidopsis DRM methyltransferases in de novo DNA methylation and gene silencing. Curr. Biol. 2002a;12:1138. [PubMed]
  • Cao XF, Jacobsen SE. Locus-specific control of asymmetric and CpNpG methylation by the DRM and CMT3 methyltransferase genes. Proc. Natl Acad. Sci. USA. 2002b;99:16491–16498. [PMC free article] [PubMed]
  • Chan SWL, Zilberman D, Xie Z, Johansen LK, Carrington JC, Jacobsen SE. RNA silencing genes control de novo DNA methylation. Science. 2004;303:1336. [PubMed]
  • Chan SWL, Henderson IR, Jacobsen SE. Gardening the genome: DNA methylation in Arabidopsis thaliana. Nat. Rev. Genet. 2005;6:351–360. [PubMed]
  • Chan SWL, Henderson IR, Zhang XY, Shah G, Chien JSC, Jacobsen SE. RNAi, DRD1, and histone methylation actively target developmentally important non-CG DNA methylation in Arabidopsis. PLoS Genet. 2006;2:791–797. [PMC free article] [PubMed]
  • Clark SJ, Harrison J, Frommer M. CpNpG methylation in mammalian cells. Nat. Genet. 1995;10:20–27. [PubMed]
  • Clough SJ, Bent AF. Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana. Plant J. 1998;16:735–743. [PubMed]
  • Finnegan E, Dennis E. Isolation and identification by sequence homology of a putative cytosine methyltransferase from Arabidopsis thaliana. Nucleic Acids Res. 1993;21:2383–2388. [PMC free article] [PubMed]
  • Fischer U, Kuhlmann M, Pecinka A, Schmidt R, Mette MF. Local DNA features affect RNA-directed transcriptional gene silencing and DNA methylation. Plant J. 2008;53:1–10. [PubMed]
  • Gomez-Eichelmann MC, Levy-Mustri A, Ramirez-Santos J. Presence of 5-methylcytosine in CC(A/T)GG sequences (Dcm methylation) in DNAs from different bacteria. J. Bacteriol. 1991;173:7692–7694. [PMC free article] [PubMed]
  • Hall TA. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp. Ser. 1999;41:95–98.
  • Hamilton AJ, Baulcombe DC. A species of small antisense RNA in posttranscriptional gene silencing in plants. Science. 1999;286:950–952. [PubMed]
  • Hellens R, Mullineaux P, Klee H. Technical focus: a guide to Agrobacterium binary Ti vectors. Trends Plant Sci. 2000;5:446–451. [PubMed]
  • Henderson IR, Zhang X, Lu C, Johnson L, Meyers BC, Green PJ, Jacobsen SE. Dissecting Arabidopsis thaliana DICER function in small RNA processing, gene silencing and DNA methylation patterning. Nat. Genet. 2006;38:721–725. [PubMed]
  • Herr AJ, Jensen MB, Dalmay T, Baulcombe DC. RNA polymerase IV directs silencing of endogenous DNA. Science. 2005;308:118–120. [PubMed]
  • Hetzl J, Foerster AM, Raidl G, Mittelsten Scheid O. CyMATE: a new tool for methylation analysis of plant genomic DNA after bisulfite sequencing. Plant J. 2007;51:526–536. [PubMed]
  • Jackson JP, Lindroth AM, Cao XF, Jacobsen SE. Control of CpNpG DNA methylation by the KRYPTONITE histone H3 methyltransferase. Nature. 2002;416:556–560. [PubMed]
  • Jeddeloh JA, Bender J, Richards EJ. The DNA methylation locus DDM1 is required for maintenance of gene silencing in Arabidopsis. Genes Dev. 1998;12:1714–1725. [PMC free article] [PubMed]
  • Jefferson RA, Kavanagh TA, Bevan MW. GUS fusions: beta-glucuronidase as a sensitive and versatile gene fusion marker in higher plants. EMBO J. 1987;6:3901–3907. [PMC free article] [PubMed]
  • Kanno T, Mette MF, Kreil DP, Aufsatz W, Matzke M, Matzke AJM. Involvement of putative SNF2 chromatin remodeling protein DRD1 in RNA-directed DNA methylation. Curr. Biol. 2004;14:801–805. [PubMed]
  • Li CF, Pontes O, El-Shami M, Henderson IR, Bernatavichute YV, Chan SWL, Lagrange T, Pikaard CS, Jacobsen SE. An ARGONAUTE4-containing nuclear processing center colocalized with Cajal bodies in Arabidopsis thaliana. Cell. 2006;126:93–106. [PubMed]
  • Lindroth AM, Cao X, Jackson JP, Zilberman D, McCallum CM, Henikoff S, Jacobsen SE. Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation. Science. 2001;292:2077–2080. [PubMed]
  • Lister R, O’Malley RC, Tonti-Filippini J, Gregory BD, Berry CC, Millar AH, Ecker JR. Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell. 2008;133:523–536. [PMC free article] [PubMed]
  • tenLohuis M, Muller A, Heidmann I, Niedenhof I, Meyer P. A repetitive DNA fragment carrying a hot spot for de novo DNA methylation enhances expression variegation in tobacco and petunia. Plant J. 1995;8:919–932. [PubMed]
  • Lorincz MC, Schubeler D, Goeke SC, Walters M, Groudine M, Martin DIK. Dynamic analysis of proviral induction and de novo methylation: implications for a histone deacetylase-independent, methylation density-dependent mechanism of transcriptional repression. Mol. Cell. Biol. 2000;20:842–850. [PMC free article] [PubMed]
  • Malone CS, Miner MD, Doerr JR, Jackson JP, Jacobsen SE, Wall R, Teitell M. CmC(A/T)GG DNA methylation in mature B cell lymphoma gene silencing. Proc. Natl Acad. Sci. USA. 2001;98:10404–10409. [PMC free article] [PubMed]
  • Mathieu O, Reinders J, Čaikovski M, Smathajitt C, Paszkowski J. Transgenerational stability of the Arabidopsis epigenome is coordinated by CG methylation. Cell. 2007;130:851–862. [PubMed]
  • Mittelsten Scheid O, Afsar K, Paszkowski J. Release of epigenetic gene silencing by trans-acting mutations in Arabidopsis. Proc. Natl Acad. Sci. USA. 1998;95:632–637. [PMC free article] [PubMed]
  • 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. [PubMed]
  • Muller A, Marins M, Kamisugi Y, Meyer P. Analysis of hypermethylation in the RPS element suggests a signal function for short inverted repeats in de novo methylation. Plant Mol. Biol. 2002;48:383–399. [PubMed]
  • Pall GS, Codony-Servat C, Byrne J, Ritchie L, Hamilton A. Carbodiimide-mediated cross-linking of RNA to nylon membranes improves the detection of siRNA, miRNA and piRNA by Northern blot. Nucleic Acids Res. 2007;35:e60. [PMC free article] [PubMed]
  • Pontes O, Li CF, Nunes PC, Haag J, Ream T, Vitins A, Jacobsen SE, Pikaard CS. The Arabidopsis chromatin-modifying nuclear siRNA pathway involves a nucleolar RNA processing center. Cell. 2006;126:79–92. [PubMed]
  • Rangwala SH, Richards EJ. Differential epigenetic regulation within an Arabidopsis retroposon family. Genetics. 2007;176:151–160. [PMC free article] [PubMed]
  • Saze H, Scheid OM, Paszkowski J. Maintenance of CpG methylation is essential for epigenetic inheritance during plant gametogenesis. Nat. Genet. 2003;34:65–69. [PubMed]
  • Steimer A, Amedeo P, Afsar K, Fransz P, Scheid OM, Paszkowski J. Endogenous targets of transcriptional gene silencing in Arabidopsis. Plant Cell. 2000;12:1165–1178. [PMC free article] [PubMed]
  • Tarasova GV, Nayakshina TN, Degtyarev SKH. Substrate specificity of new methyl-directed DNA endonuclease GlaI. BMC Mol. Biol. 2008;9:7. [PMC free article] [PubMed]
  • Vaucheret H. RNA polymerase IV and transcriptional silencing. Nat. Genet. 2005;37:659–660. [PubMed]
  • Vaughn MW, Tanurdzi M, Lippman Z, et al. Epigenetic natural variation in Arabidopsis thaliana. PLoS Biol. 2007;5:e174. [PMC free article] [PubMed]
  • Wilson GG. Type II restriction-modification systems. Trends Genet. 1988;4:314–318. [PubMed]

Articles from The Plant Journal are provided here courtesy of Wiley-Blackwell, John Wiley & Sons
PubReader format: click here to try


Save items

Related citations in PubMed

See reviews...See all...

Cited by other articles in PMC

See all...


  • Compound
    PubChem chemical compound records that cite the current articles. These references are taken from those provided on submitted PubChem chemical substance records. Multiple substance records may contribute to the PubChem compound record.
  • Gene
    Gene records that cite the current articles. Citations in Gene are added manually by NCBI or imported from outside public resources.
  • GEO Profiles
    GEO Profiles
    Gene Expression Omnibus (GEO) Profiles of molecular abundance data. The current articles are references on the Gene record associated with the GEO profile.
  • HomoloGene
    HomoloGene clusters of homologous genes and sequences that cite the current articles. These are references on the Gene and sequence records in the HomoloGene entry.
  • MedGen
    Related information in MedGen
  • Protein
    Protein translation features of primary database (GenBank) nucleotide records reported in the current articles as well as Reference Sequences (RefSeqs) that include the articles as references.
  • PubMed
    PubMed citations for these articles
  • Substance
    PubChem chemical substance records that cite the current articles. These references are taken from those provided on submitted PubChem chemical substance records.

Recent Activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...