Trans-generation inheritance of methylation patterns in a tobacco transgene following a...

Trans-generation inheritance of methylation patterns ina tobacco transgene following a post-transcriptionalsilencing event

Jana Lunerova-Bedrichova1, Annick Bleys2, Miloslava Fojtova1, Lucie Khaitova1, Anna Depicker2 and Ales Kovarık1,*

1Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., CZ-61265 Brno, Czech Republic, and2Department of Plant Systems Biology, Flanders Institute for Biotechnology, and Department of Molecular Genetics,

Ghent University, B-9052 Ghent, Belgium

Received 19 November 2007; revised 5 February 2008; accepted 26 February 2008; published online 24 April 2008.*For correspondence (fax +420 541211293; e-mail [email protected]).

Summary

We have studied the inheritance of the epigenetic state of tobacco transgenes whose expression was post-

transcriptionally silenced by an invertedly repeated silencer locus. We show that, in hybrids, the coding region

of the target neomycin phosphotransferase (nptII) gene was almost exclusively methylated at CG configu-

rations, and dense non-CG methylation occurred in the 3¢ untranslated region. Homologous sequences in the

silencer locus were heavily methylated at both CG and non-CG motifs. After segregation of the silencer locus,

the CG methylation but not the non-CG methylation of the target genes was transmitted to the progeny. In the

segregants, we observed an overall increase of CG methylation in the target genes, associated with a

re-distribution from the 3¢ end of the coding region towards the middle. This pattern was inherited with some

fluctuation for at least two additional generations in the absence of a detectable T-DNA-derived small RNA

fraction. Thus CG methylation is not cleared during meiosis and may be inherited over generations without

RNA signals being present. These epi-allelic variants re-expressed the reporter gene immediately after

segregation of the trigger, showing that relatively dense CG methylation (approximately 60–80%) imprinted on

most of the coding region (>500 bp) did not reduce expression compared with the parental non-methylated

locus. We propose that the genic CG methylation seen in euchromatic regions of the genome may originate

from ancient post-transcriptional gene silencing events as a result of adventitiously produced methylation-

directing RNA molecules.

Keywords: epi-alleles, plant transgenes, tobacco, epigenetic inheritance, RNA-directed DNA methylation,

post-transcriptional silencing.

Introduction

DNA methylation at cytosine residues is an important tool of

epigenetic memory in most eukaryotic organisms (for

review see Rangwala and Richards, 2004; Vanyushin, 2006).

One of the most prominent features of DNA methylation is

the faithful propagation of its genomic pattern from one

cellular generation to the next. Symmetrical CG methylation

provides a model of how epigenetic information is passed

along to the next generations in both plants and animals.

This so-called maintenance methylase theory is based on

enzyme activity that adds methyl groups to newly replicated

Cs by taking information signals from parental strands. Less

is known about how de novo methylation patterns are

established and how methylation is meiotically transmitted,

i.e. from one generation to the other. Studies involving plant

transgenes revealed that methylation can be induced

in trans by homologous interaction of two or more trans-

gene loci (Matzke et al., 2002). The interaction between the

trigger and target locus may occur through DNA–DNA- or

more frequently RNA–DNA-directed mechanisms. In plants,

in contrast to animals, methylation may occur at various

sequence motifs including CG, CNG and non-symmetrical

sequence contexts, but only the cytosines in CG and CNG

contexts allow transmission of the methylation patterns

based on the parental strand information.

ª 2008 The Authors 1049Journal compilation ª 2008 Blackwell Publishing Ltd

The Plant Journal (2008) 54, 1049–1062 doi: 10.1111/j.1365-313X.2008.03475.x

Methylation usually silences gene expression. For exam-

ple, homologous T-DNA interaction may lead to transcrip-

tional gene silencing (TGS) or post-transcriptional gene

silencing (PTGS). In TGS, the promoter is inactivated

(Matzke et al., 1989; Vaucheret and Fagard, 2001), while in

PTGS the primary transcript is unstable and rapidly

degraded (Vaucheret et al., 2001). In plants, both types of

silencing are associated with de novo methylation of

cognate sequences: TGS is associated with promoter

methylation while PTGS methylation often occurs in coding

sequences. Coding region methylation imposed in trans by

a silencing trigger was observed for the first time during

infection of plants with a viroid (Wassenegger et al., 1994).

In this system, homologous transgene sequences were

silenced and methylated at almost any cytosine residue.

Similarly, upon virus infection, tobacco transgenes carrying

homologous sequences of viral origin were post-transcrip-

tionally silenced and methylated in the coding regions (Ruiz

et al., 1998). PTGS-inducing transgene loci also trigger

methylation of homologous genes in the coding region in

many cases, with one of the first being reported by

Ingelbrecht et al. (1994). However, in contrast to TGS,

PTGS-associated methylation is not always observed

(Wang and Waterhouse, 2000), and the role of coding

region methylation remains enigmatic. There was only

weak upregulation of a post-transcriptionally silenced

transgene upon hypomethylation (Kovarik et al., 2000;

Rodman et al., 2002), and, in one case, PTGS was found

to be dependent on the integrity of DNA methylation loci in

Arabidopsis (Morel et al., 2000). Transcription along

densely methylated genes in inverted repeats or hairpin

constructs was unaffected by heavy methylation of 3¢sequences (Aufsatz et al., 2002; Fojtova et al., 2003; Inge-

lbrecht et al., 1994), suggesting that methylation does not

block elongation, at least if strong promoters are used.

Nevertheless, methylation of the transcribed region may

contribute to reduced expression in those cases where

methylation-sensitive regulatory elements lie in coding

regions (exons or introns) or when elongation rates are

low. In addition, TGS may evolve from PTGS as a result of

spreading of methylation in cis from a coding region into

the promoter (Fojtova et al., 2003). Although both TGS and

PTGS are mechanistically inter-related, many differences

remain. For example, methylation associated with TGS is

often transmitted in a Mendelian manner even in the

absence of a trigger locus (Jones et al., 2001; Park et al.,

1996), and it may be responsible for heritable silencing

phenomena, such as paramutation (Stam and Mittelsten

Scheid, 2005). In contrast, PTGS is meiotically reset in the

absence of the trigger (Jones et al., 2001). The associated

coding region methylation of target genes is also reset,

although methylation patterns of PTGS targets have not

been yet studied in detail using sensitive methods such as

bisulfite sequencing.

In this work, we have addressed the question of epigenetic

inheritance of PTGS-generated epi-alleles. We determined

the methylation status of a silencing and a target locus in F1

hybrids by locus-specific bisulfite genomic sequencing. We

then analyzed the target locus in three succeeding gene-

rations of tobacco plants following segregation of the

silencing trigger. Expression of the reporter neomycin

phosphotransferase (nptII) gene was studied at both protein

and RNA levels to reveal the effect of epi-allelic methylation

in a coding region.

Results

Description of the transgenic loci used

The respective transgenic loci are schematically represented

in Figure 1(a). Transgenic locus 1 in the tobacco line

hemizygous or homozygous for that locus (HeLo1, HoLo1)

contains two copies of the GVCHS287 T-DNA arranged as

an inverted repeat with the nptII genes silenced at the

post-transcriptional level (Van Houdt et al., 1997). The

non-silenced line hemizygous or homozygous for transgenic

locus 2 (HeLo2, HoLo2) contains the GVCHS287 T-DNA

cassette integrated as a single copy. The HeB line carries

transgenic locus B, which consists of three GVCHS287

T-DNA copies, two arranged as direct repeats and the third

located in the same orientation at a distance of approxi-

mately 7 kb (Figure S1; Van Houdt et al., 1997).

Methylation analysis of the silencer locus and

the target in F1 hybrids

In our previous studies, we have characterized several

transgene loci in tobacco (Ingelbrecht et al., 1994; Van Houdt

et al., 1997, 2000a). The invertedly repeated transgenes in

locus 1 (Figure 1a) contain post-transcriptionally silenced

nptII reporter genes that are able to trans-silence any

homologous sequences (Garcia-Perez et al., 2004; Van Houdt

et al., 2000a). Its transcriptionally silenced epi-allele was

unable to transmit the silent state to homologous trans-

genes, suggesting that active transcription of the silencing

locus is needed for trans-PTGS (Fojtova et al., 2006).

Although the methylation status of single-copy genes can

be readily determined by bisulfite genomic sequencing, the

analysis of multi-gene families is more complicated,

because it is often difficult or even impossible to assign

the obtained sequences to a particular locus. Here, we used a

combination of restriction-length polymorphisms and bisul-

fite sequencing to determine the methylation status of two

homologous transgenic loci in the tobacco genome. To

separate the loci in a Lo1/Lo2 hybrid, we digested genomic

DNA using EcoRV restriction endonuclease. In both loci,

EcoRV cuts the 35S promoter immediately 5¢ to the nptII

coding region (Figure 1a). The second EcoRV restriction site

1050 Jana Lunerova-Bedrichova et al.

ª 2008 The AuthorsJournal compilation ª 2008 Blackwell Publishing Ltd, The Plant Journal, (2008), 54, 1049–1062

(a)

(b)

′

′

′

Figure 1. Structure and organization of transgene loci.

(a) Schematic representation of silencing locus 1 and target locus 2. Evidence for the IR character of the T-DNA insertions in locus 1 has been provided elsewhere

(Van Houdt et al., 2000b). Evidence for a single-copy insertion of locus 2 is given by Van Houdt et al. (2000a). The EcoRV enzyme (EV) was used to dissect particular

sub-regions of T-DNA. The diagnostic sites for the methylation analysis of the nptII-transcribed region were SmaI (S) and BamHI (B). P35S, promoter of the

cauliflower mosaic virus; nptII, neomycin phosphotransferase II gene; RB, right T-DNA border; 3¢chs, transcription termination sequence of the chalcone synthase

gene from snapdragon (Antirrhinum majus). Subregions A, B and C analyzed by bisulfite sequencing are shown by dotted lines.

(b) Experimental strategy for isolation of locus-specific bands. Left panel, Southern blot hybridization with the nptII probe of EcoRV-restricted DNA from parental

HoLo1 and HoLo2 lines and a Lo1/Lo2 F1 hybrid. The preparative gel is shown in the middle panel. The right panel shows a control T-DNA-specific PCR on eluted

fractions.

Trans-generation inheritance of DNA methylation 1051


was variable among the loci: in locus 1 (organized as an

inverted repeat), the second site is located in the second

copy of the 35S promoter; in locus 2, the second EcoRV site

is located in the chromosomal DNA downstream from the

right border. As expected, the hybridization signal corre-

sponding to locus 1 was detected in the 3.0 kb region,

whereas the fragment corresponding to locus 2 migrated in

the 1.8 kb region (Figure 1b, left panel). After this diagnostic

hybridization, a preparative agarose gel was established,

using approximately 30 lg of genomic DNA. The gel pieces

comprising the 1.8 � 0.3 and 3.0 � 0.5 kb fragments (Fig-

ure 1b, middle panel) were excised, purified and subjected

to bisulfite treatments. From each fraction, several clones

were sequenced using primers for the B and C regions

(Figure 1a), which comprise more than half of the nptII

coding region and the 3¢ untranslated chs-A region (3¢ UTR),

respectively. The clones derived from the 3.0 kb fragment

corresponding to silencer locus 1 were densely methylated

along the whole sequenced region (Figure 2). In contrast,

the clones derived from the locus 2-specific 1.8 kb fragment

from F1 hybrid genomic DNA showed consistent methyla-

tion in both the CG and non-CG contexts only in the 300 bp

comprising the 3¢ UTR (Figures 3b and 4); the nptII coding

region was methylated exclusively in CG motifs. In a non-

silenced parental plant, locus 2 was found to be nearly

unmethylated (Figure 3a), with only a few methylated cyto-

sines (<0.1% of all Cs) that may be explained by stochastic

background methylation or incomplete bisulfite conversion.

The methylation was further investigated at the popula-

tion level by Southern blot analysis of several individuals

from independent crosses (Figure 5 and Table 1). To analyze

the methylation of both loci in hybrid plants separately, we

carried out double digests of genomic DNAs using methyl-

ation-insensitive and methylation-sensitive enzymes, allow-

ing locus-specific hybridization bands to be revealed

(Figure 1a). The site-specific methylation was studied using

enzymes recognizing the following motifs: SmaI, which cuts

at CCCGGG and is sensitive to methylation of the first and

third Eco47III, which cuts at AGCGCT, and is inhibited by

methylation of the first C; SalI, which cuts at GTCGAC and is

sensitive to methylation of the first C. Non-symmetrical

methylation was analyzed using BamHI (sensitive to methy-

lation of the first C within GGATmCC) digestion. In the

parental HoLo2 line homozygous for the locus 2 target,

these sites were unmethylated, as indicated by complete

digestion of the 1.8 kb EcoRV band (Figure 5 and Figure

S2a). The patterns were consistent in all individuals across

several generations. In silenced Lo1/Lo2 F1 hybrid plants,

SmaI (Figure 5) and SalI (Figure S2a) could not digest the

1.8 kb locus 2-specific EcoRV band, but there was partial

digestion with Eco47III (Figure S2a) and BamHI (Figure 5),

indicating directed trans-methylation of these sites in the

locus 2 target by the locus 1 silencing trigger (Table 1). The

partial digestion of DNAs with BamHI can be explained by

prevalent methylation of the outer C (determined by geno-

mic sequencing), which inhibits the cleavage reaction less

(a)

(b)

Figure 2. Bisulfite genomic sequencing of silen-

cer locus 1 in an F1 hybrid.

(a) Methylation analysis of clones.

(b) Quantitative representation of methylation at

various sequence contexts within the coding

(nptII) and 3¢ end regions. y axis, percentage of

methylated Cs out of the total.



(a)

(b)

(c)

Figure 3. Bisulfite genomic sequencing of target locus 2 before contact with silencer locus 1 (a), in an F1 hybrid (b) and after segregation (c) from the silencer locus.

The profiles of five clones out of ten sequenced are diagrammatically shown. The results for F2 represent an individual plant (randomly selected from seedlings

obtained after selfing of an F1 Lo1/Lo2 hybrid) that no longer contains silencing locus 1, only locus 2. The positions of the restriction sites used for Southern blot

analysis are indicated.



efficiently than methylation of the inner C (http://re-

base.neb.com/rebase/).

Methylation analysis of the target epi-alleles

after segregation of the silencer locus

Self-pollination of a Lo1/Lo2 F1 hybrid resulted in F2 progeny

plants that were screened by Southern blot analysis for

individuals that inherited only the target locus 2. The seg-

regation ratio was close to the expected one, i.e. approxi-

mately 3/16 plants. The methylation status of the target

locus 2 in these F2 segregants (termed lo2-F2) was analyzed

by Southern blotting using methylation-sensitive restriction

enzymes (Figure 5, Figure S2a and Table 1). BamHI com-

pletely digested the 1.8 kb EcoRV band, producing a 1.0 kb

band, indicating the absence of non-symmetrical methyla-

tion. In contrast, the 1.8 kb band was only partially digested

with SmaI, indicating the presence of symmetrical CG

methylation in these cells. Ten randomly selected lo2-F2

segregant plants were selfed and subjected to inbreeding for

another two meiotic cycles yielding independent lines (lo2-

F3 and lo2-F4). Several representatives of the 10 progenies

were analyzed for methylation at restriction sites (Figure 5,

Figure S2a and Table 1). All individuals retained methylation

at the CG sites, as indicated by complete or partial resistance

to digestion with the SmaI, SalI and Eco47III enzymes. In

contrast, none of these F2, F3 and F4 lo2 segregants from a

Lo1/Lo2 hybrid showed resistance to BamHI digestion,

suggesting that non-symmetrical methylation was not

retained. There were no significant differences in methyla-

tion patterns between homozygous (locus 2/locus 2) and

hemizygous (locus 2/)) plants. The second generation of

hybrids that inherited both the silencer locus and the target

locus (Lo1/Lo2 F2, Figure S2b) had methylation patterns

comparable to those of the F1 generation (Lo1/Lo2 F1).

In out-crossed plants that inherited locus 2, CG methyl-

ation was detected at all restriction sites within the 3¢transcribed sequences and the downstream region. To

study the inheritance of the coding region methylation

patterns in detail, we subjected lo2-F2, lo2-F3 and lo2-F4

individuals from two selfed Lo1/Lo2 F1 hybrids to bisulfite

sequencing. The sequencing output in Figure 3(c) shows

non-CG and CG methylation in an F2 individual (line 55). A

total of 51 CG sites were present in region B, of which

approximately 40 were methylated in most clones derived

from the F2 line 55 individual. This value significantly

exceeded that of the F1 hybrid plants, in which only 16–28

Cs were methylated in locus 2 (Figure 3b). For instance,

the CCGG sites at positions +272 and +453 were non-

methylated in F1 clones, while both of these sites were

predominantly methylated at the internal Cs in the segre-

gating F2 progeny. On the other hand, the dense non-CG

methylation seen in the 3¢ UTR of F1 clones was com-

pletely eliminated in F2 clones. The CG methylation was

inherited in the F3 and F4 generations (Figure 4), suggest-

ing that three meiotic cycles were not able to erase the

methylation pattern established in the F1 hybrid. The

methylation patterns in an independent line (line 68) were

similar to those of line 55.

It is known that cell culture may influence global methyl-

ation patterns (Kaeppler et al., 2000; Koukalova et al., 2005)

including transgenes (Fojtova et al., 2003; Meng et al., 2006).

We therefore analyzed the stability of PTGS-generated epi-

alelles of locus 2 in callus cultures derived from a parental F3

plant. Bisulfite sequencing showed that the CG methylation

patterns were remarkably stable over six months of cultiva-

tion (Figure 4).

To study paternal/maternal effects on epi-allelic transmis-

sion, the Lo1/Lo2 F1 hybrid was out-crossed to non-trans-

genic tobacco (Lo1/Lo2 · SR1 $, Lo1/Lo2 · SR1 #), and the

resulting F2 progeny were analyzed for methylation of target

locus 2. Similarly as in the selfing experiment described

above, the hybridization profiles were consistent with

inheritance of CG but not of non-CG methylation. The

bisulfite patterns of all F2 individuals were comparable

(Figure S3), ruling out the hypothesis of differential trans-

Figure 4. Histograms representing the percentage methylation as deter-

mined from bisulfite sequencing of the locus 2 target.

The data were collected from approximately ten clones per experiment and

averaged. The sequenced samples were as follows: target locus 2 in the

parental HeLo2 line (lo2/h2), in F1 Lo1/Lo2 hybrids (lo2-F1) and in three

generations of individuals that did inherit locus 2 but not locus 1 (lo2-F2, lo2-

F3, lo2-F4). Lo2-F3-c is a 6-month-old callus culture. y axis, percentage of

methylated Cs out of the total.



mission of epigenetic information through the male or

female germlines.

Bisulfite sequencing of region A (Figure 1a) revealed that

the P35S promoter was unmethylated in all sequenced lo2-

F2 clones (Figure S4), consistent with the absence of trans-

methylation of promoter sequences in F1 hybrids (Fojtova

et al., 2006). A low level of CG methylation was found in the

5¢ coding sequences (approximately 4% of all CGs).

Figure 5. Population-level analysis of the inheritance of target locus methylation using methylation-sensitive restriction enzymes.

Southern blot hybridization was carried out using the nptII gene probe. Genomic DNAs were pre-digested with methylation-insensitive enzymes ()) to obtain locus-

specific bands (indicated by arrows). The absence of digestion of locus-specific bands with methylation-sensitive enzymes (+) is indicative of transgene methylation.

The diagnostic restriction sites are located at the 3¢ end of the nptII coding region, and the expected lengths of restriction fragments are shown in Figure 1(a). The

upper panels show segregation analysis of Lo1/LoB hybrids and progeny; the analysis of L01/LoB hybrids is shown in the bottom panels. Lo2-F2, Lo2-F3, Lo2-F4 and

LoB-F2 are the progeny of plants that have inherited the epi-allelic variants of locus 2 and locus B, respectively. The lanes marked HoLo2 and HeB contain DNA from

parental non-silenced plants.

Table 1 Breeding strategy and methylation analysis of restriction sites in the target loci in F1 hybrids and progenies

Experiment/crossGeneration/no.individuals Genotype SmaI (+884)d SalI (+870) Eco47III (+1211) BamHI (+877)

Lo1/Lo2 hybrid F1 (18) Lo1)/Lo2) 100a/0b 100/0 0/100 0/100Lo1/Lo2 · Lo1/Lo2 F2 (12) Lo2/); Lo2/Lo2 40/60 80/20 40/60 0/0

F3 (12) Lo2/); Lo2/Lo2 0/100 0/100 40/60 0/0F4 (10) Lo2/); Lo2/Lo2 0/100 ND 40/60 0/0

Lo1/Lo2 · SR1# F2 (6) Lo2/) 80/20 ND ND 0/0Lo1/Lo2 · SR1$ F2 (6) Lo2/) 0/100 ND ND 0/0Lo1/LoB hybrid F1 (10) Lo1)/LoB) 100/0 ND ND 0/100Lo1/LoB · Lo1/LoB F2 (5) LoB/); LoB/LoB 0/100 ND ND 0/0Parental lines

HoLo2 H1–2 (3) Lo2/Lo2 0/0 0/0 0/0 0/0HeLo2 H1–2 (15) Lo2/) 0/0 0/0 0/0 0/0HoLo1 H2 (3) Lo1/Lo1 100/0 100/0 100/0 0/100HeB H2 (6) LoB/) 0/0c ND ND 0/0

aPercentage of individuals with complete methylation of a site.bPercentage of individuals with partial methylation of a site.cWeak resistance to SmaI digestion.dPosition of cutting sites (+1 = transcription start site).ND, not determined.



Repetitiveness does not influence target locus

epi-allelism and its meiotic stability

In plants, the heritable trans-silencing effects are often

associated with the repetitive nature of the acceptor locus

(Stam and Mittelsten Scheid, 2005). Therefore, a locus

bearing three copies of a T-DNA organized as a tandem array

(locus B, Figure S1 ;Van Houdt et al., 1997) was also used as

a target for trans-silencing by locus 1. The methylation was

inspected in F1 (Lo1/LoB hybrid) and segregating loB-F2

progeny by digestion with methylation-insensitive HindIII/

BglII enzymes in combination with methylation-sensitive

SmaI and BamHI enzymes (Figure 5, bottom panels).

Digestion of F1 DNA with BglII and HindIII yielded 6.4 and

2.5 kb bands, corresponding to locus 1 and locus B,

respectively. Neither the 6.4 nor the 2.5 kb bands were di-

gested with SmaI, indicating methylation of these sites at

both loci. In loB-F2 plants, the resistance of the 2.5 kb frag-

ment towards SmaI was maintained, but BamHI digestion

was complete. These results are consistent with the inheri-

tance of methylation at the symmetrical SmaI sites but not

the non-symmetrical BamHI sites after segregation of the

silencing trigger.

Expression analysis in F1 plants and subsequent generations

To study the inheritance of PTGS, we analyzed the RNA in

parental F1 hybrids and the segregating F2 progeny plants

that inherited locus 2 or locus B targets only. The nptII

mRNA levels were analyzed by Northern blot hybridization.

Both Lo1/Lo2 and Lo1/LoB hybrid lines showed negligible

signals compared with the parental non-silenced lines.

In all 50 Lo2 or LoB individuals (from various crosses and

generations, Table 1), the RNA signals were strong and

signal intensities were comparable to those of non-silenced

parental lines (selected blots are shown in Figure 6a). There

were no differences between individuals derived from

different crosses and carrying different target loci. At the

protein level, individuals carrying the methylated epi-alleles

of locus 2 and locus B accumulated high levels of NPTII

protein throughout the three generations analyzed (Fig-

ure 6b). This indicated that PTGS was entirely dependent on

the presence of the silencing trigger locus 1.

No small RNA species are found in segregating progeny

that inherited methylated locus 2 epi-alleles

In many cases, DNA methylation depends on the presence of

RNA signals mediated by small RNA (smRNA) molecules

(Matzke et al., 2007). To understand the observation that the

methylation of the target is maintained after segregation of

the trigger, we analyzed the smRNA fraction in silenced F1

hybrids and segregating progeny that did not inherit the

trigger. Blots containing identical RNA fractions were

hybridized with probes derived from the nptII coding region

(both full length and approximately 400 p of the 5¢ sequence)

and the 3¢ UTR (Figure 7). In silenced Lo1/Lo2 F1 hybrids, all

three probes hybridized to an approximately 21 nt smRNA

fraction. The 3¢ UTR signal was weak compared to those with

the nptII gene probes, despite longer exposure of the

membrane. This can be explained by a relatively high AT

(a)

(b)

Figure 6. Expression analysis of the nptII gene at the RNA and protein levels.

(a) Representative RNA gel-blot hybridizations of the nptII transcripts in

silenced and non-silenced lines. Five micrograms of total RNA were loaded

per lane and hybridized to the nptII DNA probe. HeLo2 and HeB lines were

used as non-silenced controls maintaining the same zygosity level of targets

as in F1 hybrids. The 18S rRNA hybridization bands are shown as loading

controls.

(b) The NPTII protein accumulation level determined by ELISA. The silenced

lines generally had NPTII protein levels close to the detection limit of the

method (5 ng mg)1 protein). The data represent means from two or three

ELISA experiments with two different protein extracts isolated from the same

plant. y-axis, concentration of NPTII per mg of soluble protein in log scale.

SR1, non-transgenic tobacco.



content of the 3¢ UTR and the low stability of hybridizing

RNA–RNA duplexes. In the parental silenced locus 1 line, the

signals were much weaker than in F1 hybrids, suggesting

that the presence of locus 2 caused amplification of smRNA

signals. In segregants that inherited methylated locus 2

epi-alleles, no smRNA signal was visible with any of the

probes used even after longer exposure of the blots. Thus

the presence of smRNAs is correlated with silencing but not

with CG methylation in the body of the gene.

Discussion

Dense CG and non-CG methylation in the silencer locus

The silencer locus 1 showed near complete methylation at

all Cs including CNG in the coding and 3¢ end region. In

plants, CNG methylation catalyzed by CMT3 chromometh-

ylases (Lindroth et al., 2001) is strongly associated with

heterochromatic regions. Similar methylation patterns were

observed in actively transcribed invertedly repeated PAI

genes in Arabidopsis (Mathieu and Bender, 2004), suggest-

ing that these types of heterochromatin are compatible with

transcription. The question arises of how dense non-CG

methylation is maintained and why methylation patterns

established at the trigger and the target do not seem to be

perfect mirror images (see below). One explanation is that

RNA-directed methylation only partially contributes to the

total methylation at the silencing trigger, and its methylation

landscape may respond to additional signals from chroma-

tin established at the inverted repeat. In support, the trans-

criptionally silenced epi-alleles of inverted repeats

maintained dense methylation despite the absence of

detectable transcription (Fojtova et al., 2006; Melquist and

Bender, 2003). Recent observations in Arabidopsis indicate

that non-CG methylation at the inverted repeat depends on

several histone methyltransferase activities (Ebbs and

Bender, 2006).

RNA signals generate region-specific patterning

of methylation at the trans-silenced target

A remarkable aspect of the methylation pattern imposed on

the target during PTGS was a highly localized distribution of

CG and non-CG methylation along the silenced gene: while

approximately 800 bp of the nptII coding region was

methylated exclusively at CG motifs, the downstream

300 bp region (of the 3¢ UTR) was heavily methylated at

nearly all Cs. The dense methylation of the latter is fully

consistent with the classical RNA-directed mechanism of

trans-methylation (Wassenegger, 2000), and there is com-

pelling evidence that the target is trans-silenced and

methylated by an RNA-based mechanism: (i) a transcrip-

tionally silenced epi-allele of the silencing locus (locus 1E)

was not capable of trans-methylation and trans-silencing of

any homologous target for several generations (Fojtova

et al., 2006); (ii) an smRNA fraction composed of degraded

nptII transcripts is readily detected in silenced but not in non-

silenced lines (Figure 7); and (iii) the presence of locus 1 in

the nucleus prevented replication of a tobacco vein mottling

virus carrying homologous nptII sequences (Van Houdt

et al., 2000b).

The question arises as to how the RNA-directed methyl-

ation model can be adopted to explain the strict CG-‘only’

methylation patterns seen in the majority of the coding

Figure 7. Accumulation of T-DNA-specific smRNAs.

smRNA blots were hybridized with RNA probes derived from the full-length nptII coding region (left), approximately 400 bp of the 5¢ coding region (middle) and

approximately 300 bp of the chs-A region (right). The exposure time was 24–48 h. Portions of ethidium bromide-stained gels are shown as loading controls. HeLo2 is

a non-silenced locus 2 line; HeLo1 is a line containing trigger locus 1 in hemizygous condition; Lo1/Lo2 is a trans-silenced hybrid; Lo2-F2 is a segregating progeny

from a Lo1/Lo2 selfed individual. End-labeled oligonucleotides (21 and 25 nt long) were used as size markers.



region. First, structural features of DNA influencing RNA-

directed methylation need to be considered. In our con-

structs, the CG frequency (and GC content) is much higher in

the nptII gene than in the 3¢ region (Figure S5), in which most

of the trans-methylation of non-CG motifs occurred. These

data fit with the hypothesis that the CG-rich areas may be

methylated primarily at CG dinucleotides while the CG-poor

regions may tend to acquire non-CG methylation. In support

of this, 35S promoter mutants lacking CG and CNG sym-

metrical motifs were highly methylated at non-symmetrical

sites compared to the wild-type 35S promoter in tobacco

(Dieguez et al., 1998). Further, the nptII gene is of prokaryotic

origin, while the 3¢ end region in our constructs was derived

from the chalcone synthase A gene (chs-A) of Antirrhinum

majus. The chs-A genes are known to be under epigenetic

control (Koseki et al., 2005). Hypothetically, the chs-A-spe-

cific RNAs could be recognized by endogenous systems of

tobacco and metabolized into methylation-inducing RNA

molecules.

Third, it could be that the primary methylation at all Cs is

seeded at the 3¢ end of the transcribed region by the RNA

silencing trigger and that only CG methylation spreads

upstream into the body of the silenced gene by a process

independent of the silencing trigger. This model is based

on the hypothesis that only a subset of T-DNA-derived

smRNAs is involved in trans-methylation: (i) locus 1 alone

produces only low amounts of smRNAs, despite its heavy

methylation and strong PTGS effect (Figure 7; Van Houdt

et al., 2003); (ii) the levels of 3¢ region-derived smRNAs in

hybrids were at least comparable to those of the coding

region (Figure 7); and (iii) locus 1 alone is not capable of

communicating the silenced message to the homologous

locus in a graft except when combined with locus 2 in a

hybrid (Garcia-Perez et al., 2004). Loci targeted by systemic

silencing do not generally become methylated (Garcia-

Perez et al., 2004; Haque et al., 2007). Perhaps primary

smRNAs emanating from the invertedly repeated locus 1

direct methylation at non-CG motifs, whereas the amplified

smRNAs are involved in spreading of CG methylation into

the body of the gene. In the future, it will be interesting to

analyze loci targeted by transitive silencing using a bisul-

fite method to reveal the methylation patterns generated

by secondary RNAs.

In conclusion, ‘neat’ CG methylation patterns should be

considered a hallmark of trans-PTGS, especially when small

regions are sequenced or assayed by methylation-sensitive

restriction enzymes.

Inheritance of RNA-triggered methylation patterns

The methylation patterns established in a hybrid on a target

were followed over three generations after segregation of

the silencing trigger. The accurately localized non-symmet-

rical CNG methylation was completely lost immediately

after segregation of the trigger even in the densely methy-

lated 3¢ region, and it never reappeared in any subsequent

generation. This is consistent with the requirement for a

constant signal for the maintenance of this type of methyl-

ation (Matzke et al., 2007; Wassenegger, 2000). In contrast,

the CG methylation was maintained in the absence of the

silencing trigger, and became even more pronounced at

many sites compared to the F1 hybrid. The shift towards

more intensive CG methylation in the F2 plant is unexpected,

but is similar to observations in Arabidopsis in which

transcriptionally silenced transgenes were more intensively

methylated in the second generation of hybrids compared to

the first generation (Cao et al., 2003). Our data show that

de novo methylation of CG sites may occur even in the

absence of a silencing trigger. This could potentially be

explained by the transmission of methylation-competent

smRNAs through the germline into the progeny. However,

we think that this is unlikely as we were unable to detect

nptII-specific smRNAs among the F2 plants that inherited

locus 2 but they were readily detected in silenced Lo1/Lo2

and Lo1/LoB hybrids (Figure 7; Fojtova et al., 2006). In the

body of the nptII gene, there were no apparent direct repeats

or unusual DNA structures, features that are suspected to be

involved in methylation inheritance and silencing (Bonnet

et al., 2006; Kinoshita et al., 2006). Together, the data sug-

gest that trans-generation epigenetic inheritance fits a semi-

conservative model of DNA methylation, with de novo

methylation of some CG sites in the first generation. In

support of this, it was found that de novo methylation

activity of a purified animal maintenance methyltransferase

was strongly stimulated by pre-existing methylation (Tol-

lefsbol and Hutchison, 1997). Perhaps NtMET1, a tobacco

analog of the maintenance enzyme (Nakano et al., 2000),

could be involved in de novo methylation of these sites.

Bioinformatic analysis revealed that the genetically most

stable methylation is located in areas that are CG-rich

(Figure S5). This suggests that the CG density and/or

configuration may be critical for the propagation of DNA

methylation patterns after smRNAs have directed their de

novo methylation. Differences in CG dinucleotide content

and distribution could also potentially explain why PTGS-

induced coding region methylation was not transmitted to

the next generation in many studies (Grant-Downton and

Dickinson, 2006). For example, the GFP target was RNA-

trans-methylated during virus-induced silencing in tobac-

co, but lost its methylation immediately after virus

removal (Jones et al., 2001). The GFP gene is relatively

AT-rich, matching the Nicotiana genome average (65%),

and has CG values close to those expected (Figure S5). In

another study, the nos promoter targeted by RNA-directed

methylation transmitted some methylation to the next

generation, while the alpha promoter, which has a CG

content half as high, apparently did not (Kanno et al.,

2005).



Relationship between coding region methylation and

silencing

What function CG methylation might have in the body of a

transgene is a longstanding question. In this study, we show

that CG methylation in the coding region does not correlate

with a suppressive effect on gene expression in >50 plants

screened over four generations. The methylated transgenes

in the segregants displayed the same expression levels as

the non-methylated transgenes in parental plants before

crossing with a plant containing a silencer locus. Thus the

data are consistent with the general absence of meiotic

inheritance of PTGS (Ruiz et al., 1998; Vaucheret et al., 2001).

This also suggests that an RNA-mediated interaction did not

lead to formation of heterochromatin in the target. The

absence of significant CNG methylation in methylated epi-

alleles of locus 2 supports this hypothesis. Similarly, forced

transcription of hairpin templates from strong promoters

was not blocked by methylation of the inverted repeat centre

(Cao et al., 2003). Further, re-expression from silencing tar-

gets despite promoter methylation was observed in mom1

mutants in Arabidopsis (Vaillant et al., 2006). However, there

is some evidence that methylation in the coding region does

influence gene expression. For example, in our previous

study, methylation inhibitors partially released silencing of

the nptII gene within locus 1 (Kovarik et al., 2000), and, in

some cases, maintenance of PTGS appeared to depend on

DNA methylation (Morel et al., 2000). Methylation in the 5¢coding sequence could be more deleterious to transcription

than in downstream sequences (Hohn et al., 1996). Indeed,

the invertedly repeated transgenes within locus 1 contained

dense methylation at both CG and non-CG motifs along the

whole coding region, including the 5¢ untranslated region

(this study and Fojtova et al., 2006). These studies indicated

that the coding region methylation may influence tran-

scription if it occurs in a specific context such as in weak

promoters, around transcription start sites or in downstream

regulatory elements and repeats. Probably none of these

‘auxiliary’ factors were present within the methylated

locus 2 epi-alleles, allowing full recovery of expression

levels upon segregation of the silencing locus.

It is worth noting that the distribution of inherited CG

methylation in the segregated transgene exposed to the

silencer locus in F1 resembles the methylation patterns of

many endogenous genes in Arabidopsis (Zhang et al.,

2006; Zilberman et al., 2007).These whole-genomic studies

revealed methylation in the central genic regions, decreas-

ing towards both 5¢ and 3¢ ends. Perhaps the PTGS-

generated non-silenced epi-alleles of locus 2 adopt the

methylation patterns that are typical for endogenous

genes after trigger locus segregation over time. More

systems need to be analyzed, including tests of epi-allelic

stability under stress conditions. Interestingly, many

actively transcribed housekeeping genes were found

among the methylated fraction of the genome (Zhang

et al., 2006). The current data are consistent with the

hypothesis that these ‘euchromatic’ methylations repre-

sent the remnants of ancient PTGS processes in genome

history.

Experimental procedures

Plant material and genetic crosses

The transgenic system used in this study to analyze homologousinteractions has been described previously (Ingelbrecht et al., 1994;Van Houdt et al., 1997, 2000b). Briefly, all transgenic lines weregenerated by Agrobacterium tumefaciens-mediated transformationof tobacco (Nicotiana tabacum, SR1). The T-DNA-derived planttransformation vector pGVCHS(287) harbors two chimeric genes(Pnos:hpt and P35S:nptII) between the T-DNA borders (Figure 1a).Several rounds of self-fertilization starting from primary transfor-mant GVCHS(287)-1 yielded the stable, homozygous, single-locustransgenic lines HoLo1 (homozygous for PTGS locus 1) and HoLo2(homozygous for the well-expressed locus 2). Plants homozygousfor locus B (HoB; Figure S1) were obtained using the pGVCHS(320)-1 vector carrying essentially the same T-DNA cassette aspGVCHS(287) with minor sequence modifications (Ingelbrechtet al., 1994).

Crosses were performed by emasculating flowers manuallybefore they opened and applying pollen to the stamen. F1 hybridswere obtained by crosses of HoLo1 with HoLo2 or HoB. F1 hybridsLo1/Lo2 and Lo1/LoB were allowed to self-pollinate, yielding F2

progeny. The plants were genotyped by Southern hybridization.Ten randomly selected segregants (termed lo2-F2) from the Lo1/Lo2line were further selfed to obtain lo2-F3 and lo2-F4 generations. Thezygosity of selected individuals was further determined by seedingplants on a kanamycin selection medium: hemizygous and homo-zygous plants were expected to generate 25% and 0% sensitiveprogeny, respectively. Reciprocal backcrosses of the Lo1/Lo2 hybridline to non-transgenic SR1 tobacco plants were carried out to obtainindependent F2 progenies. The genotypes and number of individ-uals analyzed from each cross are given in Table 1. The calluscultures were established using standard procedures.

Southern hybridization

DNA was isolated from fresh fully developed leaves of adult plants(3–4 months old) by a Cetyl trimethylammonium bromide (CTAB)method (Saghai-Maroof et al., 1984). About 20 lg of DNA wasdigested with an excess of restriction enzyme (2 · 20 units), loadedon a 0.9% w/v agarose gel and electrophoresed. The size-separatedfragments were alkali-blotted onto nylon membranes (Hybond XL,GE Healthcare; http://www.gehealthcare.com) and hybridized with32P-labeled DNA probe (DekaLabel kit, MBI, Fermentas; http://www.fermentas.com). The probe was an 830 bp insert of thepGEMnptII plasmid carrying the nptII-coding sequence (Van Houdtet al., 1997). After washing under high stringency, bands werevisualized using a phosphor imager (STORM; GE Healthcare) andthe data were analyzed using ImageQuant software (GE Healthcare).

Bisulfite genomic sequencing

Bisulfite sequencing was performed according to the methoddescribed by Clark et al. (1994) and the protocol described by



Fojtova et al. (2006), with some modifications (protocol 14 at http://www.epigenome-noe.net/researchtools/protocols). Briefly, about30 lg of genomic DNA was digested with an excess of the methyl-ation-insensitive restriction enzyme TruI to delimit sequencedregions. To support complete conversion, the digested DNA wasfirst heat-denatured at 100�C for 5 min, cooled for 5 min, and thendenatured again in 10 M NaOH at room temperature for 30 min.Freshly prepared bisulfite solution (140 ll, prepared as described inprotocol 14) was added directly to the denatured DNA in a 500 llEppendorf tube, and the mixture was incubated in a thermocycler at95�C for 2 min followed by overnight incubation at 55�C. Sub-sequent procedures were performed as described by Fojtova et al.(2006).

The bisulfite-treated DNA was amplified by semi-nested PCR ina 50 ll reaction volume containing 1 · buffer for DyNAzyme(MgCl2-free, Finnzymes; http://www.finnzymes.fi), 0.2 mM dNTPs,0.25 mM forward primer, 0.25 mM reverse primer, 2 units ofDyNAzyme II DNA polymerase (Finnzymes) and 2.5 ll of templatein the first reaction (bisulfite-treated DNA) and 1.5 ll of templatein the second reaction (first PCR product). For amplification ofthe nptII central and 3¢ regions (region B, Figure 1a), the reverseprimer 5¢-YGTTAYAAGAGAGAAATYGYYAATATAG-3¢, a first for-ward primer 5¢-AAATCACCATTCTCTCTCTACAAATC-3¢ and a sec-ond forward primer 5¢-ATCTCCTRTCATCTCACCTTRCTCCT-3¢were designed using mismatches at positions complementaryto potentially methylated cytosines. For amplification of the 3¢nptII and 3¢ end region (region C, Figure 1a), the reverse primer5¢-AYAAYAGYTAYYAGTTTYYTYAAGGGT-3¢, a first forward pri-mer 5¢-ATCTCCTRTCATCTCACCTTRCTCCT-3¢ and a second for-ward primer 5¢-TTCTATCGCCTTCTTAACGAATTCTTCT-3¢ wereused. There was an approximately 40 bp overlap between regionB and C clones. The primers for amplification of the 35Spromoter and 5¢ transcribed region (region A, Figure 1a) aregiven by Fojtova et al. (2006). The PCR program consisted of3 min of initial denaturation at 94�C, followed by 40 cycles of20 sec at 94�C, 45 sec at 55�C and 1 min at 72�C. The programended with an extension step for 10 min at 72�C. The PCRproducts were cloned into a TA vector (pDrive, Qiagen, http://www.qiagen.com/), and 4–8 clones from each sample weresequenced (Biotech GmBH; http://www.vbc-biotech.at).

RNA isolation and Northern blot analysis

Total RNA was isolated from young leaves using the RNeasy PlantMini Kit (Qiagen) according to the manufacturer’s instructions. TheRNA quality was checked by electrophoresis on a 1% w/v agarosegel. For Northern blotting, the RNA was electrophoresed on a 1.2%w/v formaldehyde–agarose gel, which was then washed for 10 minin sterile water to remove the formaldehyde. The RNA was dena-tured in 0.05 M NaOH and blotted onto a Hybond XL membrane(GE Healthcare) in 20· SSC. Radioactively labeled nptII DNA probewas hybridized in ULTRAhyb buffer (Ambion; http://www.ambion.com) for 24 h at 35�C. After washing under low-stringencyconditions, the hybridization bands were visualized using a STORMphosphor imager (GE Healthcare). To evaluate the nptII expressionlevels, the intensities of the nptII hybridization signals were nor-malized to those of the ribosomal RNA bands.

Protein extraction and NPTII ELISA

To extract soluble proteins, lyophilized leaves (20–40 mg of dryweight) were ground in an Eppendorf tube with 200–400 ll ofextraction buffer (0.25 M Tris–HCl, pH 8.0, 1 mM PMSF) and

centrifuged at 20 000 g to remove cell debris. The protein con-centration of the extracts was determined using a protein assay(Bio-Rad, http://www.bio-rad.com/). The NPTII ELISA was per-formed according to the manufacturer’s instructions (Patho-screen-NPTII, Agdia; http://www.agdia.com). The microtiter plateswere read at 405 nm on an ELISA reader (GE Healthcare) using akinetic program (5 min intervals for 2 h).

Isolation and detection of smRNA

The smRNA fraction was isolated according to the protocoldescribed by Hamilton and Baulcombe (1999) with several modifi-cations. The smRNA fraction was enriched by precipitating longnucleic acids in 5% w/v PEG 8000 (Sigma-Aldrich; http://www.sigma.com) and 0.5 M NaCl. After centrifugation (10 000 · g;10 min), the smRNA fraction was precipitated from the supernatantand resuspended in formamide. Up to 50 lg of smRNAs were loa-ded per lane onto a 15% w/v polyacrylamide/50% w/v urea gel. Afterelectrophoresis and gel documentation, RNA was semi-dry-blottedto a Hybond XL membrane at 3 mA cm-2 for 1 h in 0.5· TBE. RNAon the membrane was fixed by cross-linking with carbodiimide(Sigma, http://www.sigmaaldrich.com/; Pall et al., 2007) and bakingat 80�C for 2 h. The single-stranded RNA probes were transcribed inthe sense orientation from linearized pGen-3Zf(+)npt and pGEM-chs-A plasmids with 32P-UTP using an RNAMaxx� high-yieldtranscription kit (Stratagene, http://www.stratagene.com/). The 3¢truncated version of the nptII transcript was obtained by BssHIIdigestion of the pGen-3Zf(+)npt plasmid. The RNA probes werelabeled in an in vitro transcription reaction using plasmids carryingthe nptII and chs-A gene inserts. The hydrolyzed probes werehybridized in ULTRAhyb buffer (Ambion) for 48 h at 30�C, andwashed in 2 · SSC, 0.01% SDS at 30�C, twice 15 min each. Thesignals were visualized using a phosphor imager.

Bioinformatics analysis

The bisulfite sequences were aligned using the PILE-UP programimplemented within the GCG Wisconsin package, and methylationwas analyzed using the Methtools box at http://genome.imb-jena.de/methtools (Grunau et al., 2000). Statistical determinations ofthe methylation density at CG, CHG and CHH motifs wereperformed using the CyMATE tool (Hetzl et al., 2007) at http://www.gmi.oeaw.ac.at/en/cymate-index/cymate-v2/. GC plots wereproduced using the CPGREPORT algorithm (http://www.ebi.ac.uk/cpg).

Distribution of materials

Upon request, all novel materials described in this publication willbe available in a timely manner for non-commercial purposes,subject to requisite permission from any third-party owners of all orparts of the material. Obtaining any permission will be theresponsibility of the person requesting the material.

Acknowledgements

We thank Dr Ortrun Mittelsten-Scheid (Gregor Mendel Institute,Vienna, Austria) for stimulating discussions. The work wassupported by grants from the Grant Agency of the Czech Republic(204/05/H505 and 521/07/0116) and the Academy of Sciences(A600040611 and A50040507). M.F. and A.K. acknowledge theResearch Foundation of Flanders (FWO) for visiting fellowships.



Supplementary Material

The following supplementary material is available for this articleonline:Figure S1. Schematic representation of target locus B.Figure S2. Southern blot methylation analysis of transgene loci inLo1/Lo2 hybrids and segregating progenies.Figure S3. Bisulfite genomic sequencing of the lo2-F2 segregatingprogenies resulting from reciprocal backcrosses of F1 hybrids to anon-transgenic tobacco plant.Figure S4. Bisulfite genomic sequencing of the 5¢ nptII and 35Spromoter of the target locus after trigger segregation (lo2-F2).Figure S5. Bioinformatic analysis of the CG density in the nptII,chs-A and GFP regions.This material is available as part of the online article from http://www.blackwell-synergy.com.Please note: Blackwell publishing are not responsible for thecontent or functionality of any supplementary materials suppliedby the authors. Any queries (other than missing material) should bedirected to the corresponding author for the article.

References

Aufsatz, W., Mette, M.F., van der Winden, J., Matzke, A.J.M. and

Matzke, M. (2002) RNA-directed DNA methylation in Arabidopsis.Proc. Natl Acad. Sci. USA, 99, 16499–16506.

Bonnet, E., Van de Peer, Y. and Rouze, P. (2006) The small RNAworld of plants. New Phytol. 171, 451–468.

Cao, X., Aufsatz, W., Zilberman, D., Mette, M.F., Huang, M.S.,

Matzke, M. and Jacobsen, S.E. (2003) Role of the DRM and CMT3methyltransferases in RNA-directed DNA methylation. Curr. Biol.13, 2212–2217.

Clark, S.J., Harrison, J., Paul, C.L. and Frommer, M. (1994) Highsensitivity mapping of methylated cytosines. Nucleic Acids Res.22, 2990–2997.

Dieguez, M.J., Vaucheret, H., Paszkowski, J. and Mittelsten Scheid,

O. (1998) Cytosine methylation at CG and CNG sites is not aprerequisite for the initiation of transcriptional gene silencing inplants, but it is required for its maintenance. Mol. Gen. Genet.259, 207–215.

Ebbs, M.L. and Bender, J. (2006) Locus-specific control of DNAmethylation by the Arabidopsis SUVH5 histone methyltransfer-ase. Plant Cell, 18, 1166–1176.

Fojtova, M., Van Houdt, H., Depicker, A. and Kovarik, A. (2003)Epigenetic switch from posttranscriptional to transcriptionalsilencing is correlated with promoter hypermethylation. PlantPhysiol. 133, 1240–1250.

Fojtova, M., Bleys, A., Bedrichova, J., Van Houdt, H., Krizova, K.,

Depicker, A. and Kovarik, A. (2006) The trans-silencing capacity ofinvertedly repeated transgenes depends on their epigenetic statein tobacco. Nucleic Acids Res. 34, 2280–2293.

Garcia-Perez, R.D., Van Houdt, H. and Depicker, A. (2004) Spreadingof post-transcriptional gene silencing along the target genepromotes systemic silencing. Plant J. 38, 594–602.

Grant-Downton, R.T. and Dickinson, H.G. (2006) Epigenetics and itsimplications for plant biology 2. The ‘epigenetic epiphany’:epigenetics, evolution and beyond. Ann. Bot. 97, 11–27.

Grunau, C., Schattevoy, R., Mache, N. and Rosenthal, A. (2000)MethTools – a toolbox to visualize and analyze DNA methylationdata. Nucleic Acids Res. 28, 1053–1058.

Hamilton, A.J. and Baulcombe, D.C. (1999) A species of smallantisense RNA in posttranscriptional gene silencing in plants.Science, 286, 950–952.

Haque, A.K.M.N., Yamaoka, N. and Nishiguchi, M. (2007) Cytosinemethylation is associated with RNA silencing in silenced plantsbut not with systemic and transitive RNA silencing throughgrafting. Gene, 396, 321–331.

Hetzl, J., Foerster, A.M., Raidl, G. and Mittelsten Scheid, O. (2007)CyMATE: a new tool for methylation analysis of plant genomicDNA after bisulphite sequencing. Plant J. 51, 526–536.

Hohn, T., Corsten, S., Rieke, S., Muller, M. and Rothnie, H. (1996)Methylation of coding region alone inhibits gene expression inplant protoplasts. Proc. Natl Acad. Sci. USA, 93, 8334–8339.

Ingelbrecht, I., Van Houdt, H., Van Montagu, M. and Depicker, A.

(1994) Posttranscriptional silencing of reporter transgenes intobacco correlates with DNA methylation. Proc. Natl Acad. Sci.USA, 91, 10502–10506.

Jones, L., Ratcliff, F. and Baulcombe, D.F. (2001) RNA-directedtranscriptional gene silencing in plants can be inherited inde-pendently of the RNA trigger and requires Met1 for maintenance.Curr. Biol. 11, 747–757.

Kaeppler, S.M., Kaeppler, H.F. and Rhee, Y. (2000) Epigeneticaspects of somaclonal variation in plants. Plant Mol. Biol. 43, 179–188.

Kanno, T., Aufsatz, W., Jaligot, E., Mette, M.F., Matzke, M. and

Matzke, A.J. (2005) A SNF2-like protein facilitates dynamiccontrol of DNA methylation. EMBO Rep. 6, 649–655.

Kinoshita, Y., Saze, H., Kinoshita, T., Miura, A., Soppe, W.J.,

Koornneef, M. and Kakutani, T. (2006) Control of FWA genesilencing in Arabidopsis thaliana by SINE-related direct repeats.Plant J. 49, 38–45.

Koseki, M., Goto, K., Masuta, C. and Kanazawa, A. (2005) The star-type color pattern in Petunia hybrida ‘Red star’ flowers is inducedby sequence-specific degradation of chalcone synthase RNA.Plant Cell Physiol. 46, 1879–1883.

Koukalova, B., Fojtova, M., Lim, K.Y., Fulnecek, J., Leitch, A.R. and

Kovarik, A. (2005) Dedifferentiation of tobacco cells is associatedwith ribosomal RNA gene hypomethylation, increased tran-scription, and chromatin alterations. Plant Physiol. 139, 275–286.

Kovarik, A., Van Houdt, H., Holy, A. and Depicker, A. (2000) Drug-induced hypomethylation of a posttranscriptionally silencedtransgene locus of tobacco leads to partial release of silencing.FEBS Lett. 467, 47–51.

Lindroth, A.M., Cao, X., Jackson, J.P., Zilberman, D., McCallum,

C.M., Henikoff, S. and Jacobsen, S.E. (2001) Requirement ofCHROMOMETHYLASE3 for maintenance of CpXpG methylation.Science, 292, 2077–2080.

Mathieu, O. and Bender, J. (2004) RNA-directed DNA methylation.J. Cell Sci. 117, 4881–4888.

Matzke, M.A., Primig, G., Trnovsky, J. and Matzke, A.J. (1989)Reversible methylation and inactivation of marker genes insequentially transformed tobacco plants. EMBO J. 8, 643–649.

Matzke, M.A., Aufsatz, W., Kanno, T., Mette, M.F. and Matzke, A.J.

(2002) Homology-dependent gene silencing and host defense inplants. Adv. Genet. 46, 235–275.

Matzke, M., Kanno, T., Huettel, B., Daxinger, L. and Matzke, A.J.

(2007) Targets of RNA-directed DNA methylation. Curr. Opin.Plant Biol. 10, 1–8.

Melquist, S. and Bender, J. (2003) Transcription from an upstreampromoter controls methylation signaling from an inverted repeatof endogenous genes in Arabidopsis. Genes Dev. 17, 2036–2047.

Meng, L., Ziv, M. and Lemaux, P.G. (2006) Nature of stress andtransgene locus influences transgene expression stability inbarley. Plant Mol. Biol. 62, 15–28.

Morel, J.B., Mourrain, P., Beclin, C. and Vaucheret, H. (2000) DNAmethylation and chromatin structure affect transcriptional and



post-transcriptional transgene silencing in Arabidopsis. Curr.Biol. 10, 1591–1594.

Nakano, Y., Steward, N., Sekine, M., Kusano, T. and Sano, H. (2000)A tobacco NtMET1 cDNA encoding a DNA methyltransferase:molecular characterization and abnormal phenotypes of trans-genic tobacco plants. Plant Cell Physiol. 41, 448–457.

Pall, G.S., Codony-Servat, C., Byrne, J., Ritchie, L. and Hamilton, A.

(2007) Carbodiimide-mediated cross-linking of RNA to nylonmembranes improves the detection of siRNA, miRNA and piRNAby Northern blot. Nucleic Acids Res. 35, e60.

Park, Y.D., Papp, I., Moscone, E.A., Iglesias, V.A., Vaucheret, H.,

Matzke, A.J.M. and Matzke, M.A. (1996) Gene silencing mediatedby promoter homology occurs at the level of transcription andresults in meiotically heritable alterations in methylation andgene activity. Plant J. 9, 183–194.

Rangwala, S.H. and Richards, E.J. (2004) The value-added genome:building and maintaining genomic cytosine methylation land-scapes. Curr. Opin. Genet. Dev. 14, 686–691.

Rodman, M., Narendra, S. and Artrus, N. (2002) Progression ofgeminivirus-induced transgene silencing is associated withtransgene methylation. New Phytol. 155, 461–468.

Ruiz, M.T., Voinnet, O. and Baulcombe, D.C. (1998) Initiation andmaintenance of virus-induced gene silencing. Plant Cell, 10, 937–946.

Saghai-Maroof, M.A., Solimam, K.M., Jorgensen, R.A. and Allard,

R.W. (1984) Ribosomal DNA-spacer length polymorphisms inbarley – Mendelian inheritance, chromosomal location and pop-ulation dynamics. Proc. Natl Acad. Sci. USA, 81, 8014–8018.

Stam, M. and Mittelsten Scheid, O. (2005) Paramutation: anencounter leaving a lasting impression. Trends Plant Sci. 10, 283–290.

Tollefsbol, T.O. and Hutchison, C.A., III (1997) Control of methyla-tion spreading in synthetic DNA sequences by the murine DNAmethyltransferase. J. Mol. Biol. 269, 494–504.

Vaillant, I., Schubert, I., Tourmente, S. and Mathieu, O. (2006)MOM1 mediates DNA-methylation-independent silencing ofrepetitive sequences in Arabidopsis. EMBO Rep. 7, 1273–1278.

Van Houdt, H., Ingelbrecht, I., Van Montagu, M. and Depicker, A.

(1997) Post-transcriptional silencing of a neomycin phospho-

transferase II transgene correlates with the accumulation ofunproductive RNAs and with increased cytosine methylation of 3¢flanking regions. Plant J. 12, 379–392.

Van Houdt, H., Kovarik, A., Van Montagu, M. and Depicker, A.

(2000a) Cross-talk between posttranscriptionally silencedneomycin phosphotransferase II transgenes. FEBS Lett. 467, 41–46.

Van Houdt, H., Van Montagu, M. and Depicker, A. (2000b) Bothsense and antisense RNAs are targets for the sense transgene-induced posttranscriptional silencing mechanism. Mol. Gen.Genet. 263, 995–1002.

Van Houdt, H., Bleys, A. and Depicker, A. (2003) RNA targetsequences promote spreading of RNA silencing. Plant Physiol.131, 245–253.

Vanyushin, B.F. (2006) Enzymatic methylation is an epigeneticcontrol of genetic functions of the cell. Biochemistry (Moscow),70, 598–611.

Vaucheret, H. and Fagard, M. (2001) Transcriptional gene silencingin plants: targets, inducers and regulators. Trends Genet. 17, 29–35.

Vaucheret, H., Beclin, C. and Fagard, M. (2001) Post-transcriptionalgene silencing in plants. J. Cell Sci. 114, 3083–3091.

Wang, M.B. and Waterhouse, P.M. (2000) High-efficiency silencingof a beta-glucuronidase gene in rice is correlated with repetitivetransgene structure but is independent of DNA methylation. PlantMol. Biol. 43, 67–82.

Wassenegger, M. (2000) RNA-directed DNA methylation. Plant Mol.Biol. 43, 203–220.

Wassenegger, M., Heimes, S., Riedel, L. and Sanger, H.L. (1994)RNA-directed de novo methylation of genomic sequences inplants. Cell, 76, 567–576.

Zhang, X., Yazaki, J., Sundaresan, A. et al. (2006) Genome-widehigh-resolution mapping and functional analysis of DNA meth-ylation in Arabidopsis. Cell, 126, 1189–1201.

Zilberman, D., Gehring, M., Tran, R.K., Ballinger, T. and Henikoff, S.

(2007) Genome-wide analysis of Arabidopsis thaliana DNAmethylation uncovers an interdependence between methylationand transcription. Nat. Genet. 39, 61–69.



Trans-generation inheritance of methylation patterns in a tobacco transgene following a...

Documents

Transcript of Trans-generation inheritance of methylation patterns in a tobacco transgene following a...