Nucleic Acids Research, 2003, Vol. 31, No. 5 1387-1391
© 2003 Oxford University Press
De novo cytosine methylation in the differentiating macronucleus of the stichotrichous ciliate Stylonychia lemnae
Stefan Juranek,
Hans-Joachim Wieden1 and
Hans J. Lipps*
Institute of Cell Biology and
1 Institute of Physical Biochemistry, University Witten/Herdecke, Stockumer Strasse 10, D-58448 Witten, Germany
*To whom correspondence should be addressed. Tel: +49 2302 669144; Fax: +49 2302 669220; Email: lipps{at}uni-wh.de
Received December 23, 2002; Accepted January 9, 2003
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ABSTRACT
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Dramatic DNA reorganization and elimination processes occur
during macronuclear differentiation in ciliates. In this study
we analyzed whether cytosine methylation of specific sequences
plays a functional role during DNA rearrangement. Three classes
of sequences, macronuclear-destined sequences (MDSs, pCE7),
members from a large family of transposon-like elements and
micronuclear-specific sequences (pLJ01), differing in their
structure and future destiny during nuclear differentiation,
were studied in the micronucleus, the developing macronucleus
and, when present, in the mature macronucleus. While the MDSs
become processed to a 1.1 and 1.3 kb gene-sized macronuclear
DNA molecule, the family of transposon-like elements represented
by MaA81 becomes removed late in the course of polytene chromosome
formation. The micronuclear-specific sequence pLJ01 is eliminated
together with bulk micronuclear DNA during degradation of polytene
chromosomes. No methylated cytosine could be detected in the
vegetative macronucleus and no difference in methylation pattern
was observed either between micronucleus and developing macronucleus
in MDSs or in a micronuclear-specific sequence. However, a significant
percentage of the cytosines contained in the transposon-like
element becomes methylated
de novo in the course of macronuclear
differentiation. This is the first demonstration that cytosine
methylation in specific sequences occurs during macronuclear
differentiation and may provide a first step towards understanding
epigenetic factors involved in DNA processing.
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INTRODUCTION
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In eukaryotic cells methylation of cytosine residues very frequently
correlates with the silencing of genes (
1) and formation of
heterochromatin (
2) and it seems to be essential for genomic
imprinting and development in mammalian organisms (reviewed
in
3,
4). Once a specific methylation pattern is established
it can be stably propagated by the action of maintenance methyltransferases
(reviewed in
5). The methylation pattern is established by
de novo methyltransferases while demethylation is achieved either
by suppression of maintenance DNA methyltransferase followed
by the passive loss of methyl groups during replications or
by the action of specific demethylases (
6). In vertebrate nuclei
cytosine methylation occurs predominantly at the sequence CpG,
although other sequence motifs in which cytosine methylation
occurs are described (
7). In addition to cytosine methylation
the methylation of adenosine has been described in a variety
of organisms including ciliates (
8). Only recently cytosine
methylation has been described to occur early during
Drosophila embryogenesis using very sensitive detection techniques (
7,
9).
Eukaryotic organisms in which cytosine methylation has not yet
been found are yeast,
Caenorhabditis (
7) and the nuclei of stichotrichous
ciliates.
Vegetative cells of ciliated protozoa contain two types of nuclei: macronuclei and micronuclei. While the DNA-rich macronucleus is transcriptionally very active expressing all the RNAs required for vegetative growth, the diploid micronucleus seems to be transcriptionally inert and its main function only becomes obvious during sexual reproduction. In the course of this process of conjugation, haploid micronuclei are exchanged between sexual partners where they fuse with a remaining haploid micronucleus to form a diploid zygote nucleus. This nucleus divides mitotically and one of the daughter nuclei differentiates into a new micronucleus, whereas the other forms a new macronucleus while the old macronucleus degenerates. In spirotrichous ciliates, such as Euplotes, Oxytricha or Stylonychia, macronuclear differentiation is accompanied by massive DNA rearrangement and DNA elimination events (Fig. 1). In a first DNA synthesis phase, which eventually leads to the formation of polytene chromosomes, short non-coding DNA sequences (internal eliminated sequences, IESs) interrupting macronuclear- destined sequences (MDSs) and part of transposon-like sequences (10) are spliced off the DNA. As the polytene chromosomes become degraded, a large percentage of DNA is eliminated and in the course of this process the remaining DNA becomes fragmented into short DNA molecules (gene-sized pieces, gsp) ranging in size between
0.4 and 40 kb, to which telomeric sequences are added de novo. These short gene-sized DNA molecules carry the genes that will be transcribed in the vegetative macronucleus (11). So far, modification of nucleotides was only analyzed in the macronuclei and micronuclei of several ciliates using HPLC and methylation-dependent cleavage assays. Methylated cytosines have been detected in macronuclear DNA of Blepharisma (12) and Colpoda (13), whereas only methylated adenine was found in macronuclear DNA of most other ciliates (8,1417).

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Figure 1. Schematic diagram of macronuclear development indicating major events during this process [modified after Prescott (11) and Kraut et al. (30)].
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During macronuclear differentiation MDSs have to be discriminated
from sequences to be eliminated. This elimination process can
be regarded as the most extreme form of irreversible silencing.
We therefore analyzed the DNA not only from vegetative nuclei
but also from the developing macronucleus (macronuclear anlagen)
with respect to methylation of cytosines using RP-HPLC. Moreover,
specific sequences, such as macronuclear precursor sequences,
micronuclear-specific sequences and a family of transposon-like
elements, were analyzed in detail for cytosine methylation in
the various nuclei using a bisulphate-based PCR strategy (
18).
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MATERIALS AND METHODS
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Growth of Stylonychia lemnae cells, isolation of nuclei and DNA
Vegetative
Stylonychia cells were cultivated as described earlier
(
19). Conjugations were set up under conditions described previously
(
19). Isolation of macronuclei, micronuclei and anlagen of different
stages of development and preparation of DNA followed the protocols
described previously (
19,
20).
RP-HPLC
For RP-HPLC, DNA (100 µg) was needle sheared and completely digested to nucleosides using Benzonase (Novagen, 300 U, 24 h), nuclease P1 (Roche, 10 U, 24 h) and alkaline phosphatase (Roche, 10 U, 3 h). The nucleosides were analyzed on a LIChrosorb RP-18 (7 µm) column (Merck) according to Gowher et al. (21). DNA was analyzed in the presence and absence of 5 µg methylcytidine (Sigma).
Bisulphite reaction and strand specific PCR
Bisulphite treatment was done according to the method described by Clark et al. (18) with some minor modifications. For each reaction 25 µg DNA isolated from the different nuclei was used in a volume of 100 µl. The genomic DNA was needle sheared, denatured in 0.3 M NaOH (45°C for 30 min). Sulphonation was done in 5 mM 0.1 M hydroquinone, 3.6 M sodium bisulphite, pH 5.0 (55°C for 6 h). Free bisulphite was removed using the Promega DNA clean-up-system. Alkali desulphonation was performed in 0.3 M NaOH (45°C for 30 min). The DNA was then ethanol precipitated and resuspended in 250 µl ddH2O. Aliquots of 510 µl were used in each PCR. PCR conditions were 15 min 94°C initial denaturation, 35 cycles of 45 s 94°C, 45 s 53°C, 45 s 72°C followed by a final extension of 15 min at 72°C to enable TA cloning using the pGEM-T easy system by Promega. A hotstart Taq polymerase (Genecraft) was used. In the first PCR, primer combination (a) was used and in the following, nested reaction primer combination (b) (see Table 1), with the exception of P13/P14 where the nested PCR was not necessary. Due to the structural instability of the bisulphite treated template (18) only short regions of the sequences of interest could be amplified in one reaction.
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RESULTS
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DNA was isolated from macronuclei, micronuclei and macronuclear
anlagen of the stichotrichous ciliate
Stylonychia (
19,
20), digested
with nucleases and phosphatases and subjected to RP-HPLC analysis.
A typical elution profile showing the positions of cytosine
and methylated cytosine is shown in Figure
2. Methylated cytosine
could not be detected in any case. Since this technique would
not allow the detection of very low amounts (<0.1 µg
methylcytosine/100 µg total DNA) of this nucleoside we
decided to use the bisulphite-based PCR strategy to analyze
exemplary sequences for the presence of methylated cytosines.

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Figure 2. RP-HPLC analysis of anlagen DNA in an early stage of polytenization. DNA (100 µg) was analyzed in the presence (broken line) and absence (continuous line) of 5 µg methylcytidine. Similar profiles were observed for micronuclear, macronuclear and anlagen DNA of different stages of development.
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The following sequences with different destinies during macronuclear
differentiation were further analyzed using PCR. The observed
cytosine methylation pattern was compared in the micronucleus,
the macronuclear anlagen and, if processed, also in the mature
macronucleus (Fig.
3). (i) A cluster of MDSs (pCE7) that become
processed in the mature macronucleus to a 1.1 and 1.3 kb gsp
(
22). In micronuclear DNA these two MDSs are separated by a
10 bp spacer region and interrupted by five IESs (Fig.
3A).
(ii) Members (for which clone MaA81 is one example) of a family
of transposon-like elements showing very high sequence identity
(>90%) present in about 50007000 copies per haploid
genome whose removal starts late during polytene chromosome
formation but before fragmentation of DNA occurs. However, the
exact mechanisms by which these elements are removed has not
yet been determined and it is not clear whether all members
of this family become excised during polytene chromosome formation
or become eliminated during chromosome breakdown. This element
consists of two long direct repeats flanking the truncated version
of a macronuclear-specific sequence and a 16mer telomeric repeat
(
23,
24) (Fig.
3B). (iii) A 800 bp micronuclear-specific DNA
sequence (pLJ01) isolated from a micronuclear gene library (Fig.
3C). This sequence hybridizes to micronuclear DNA and to DNA
isolated from late polytene chromosome stage but not to macronuclear
DNA. Thus pLJ01 becomes eliminated together with bulk micronuclear
DNA as part of the DNA elimination process. Its copy number
was estimated to be below 20 copies per haploid genome (data
not shown). pLJ01 shows no structural homology to transposon-like
elements and most likely represents an intergenic DNA-spacer
separating MDS clusters in the micronuclear genome. Six bisulphite
conversions were performed with DNA isolated from the different
nuclei. Sequence data were obtained from six to ten cloned PCR
fragments from each set of sequences. Results from these analyses
are summarized in Table
2. An alignment of the sequences of
several cloned PCR products are provided as Supplementary Material.

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Figure 3. Sequences chosen for further analysis by PCR of bisulphite treated DNA (for explanation see text). Bars indicate the regions investigated. The position of the primer pairs for nested PCR are indicated by P1 to P12 (A)/(B) respectively (see Table 1). (A) pCE7, (B) MaA81, (C) pLJ01.
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Although cytosine methylation was not detected in the analyzed
sequences from macronuclear DNA, methylated cytosines were found
in pCE7 in both the micronuclei and the macronuclear anlagen.
In these sequences cytosine methylation was exclusively observed
in the symmetric sequence motif CCWGG at the internal cytosine.
This sequence motif is found seven times in pCE7 of which one
motif is in the micronuclear-specific sequence upstream of the
1.1 kb MDS, four are found in its 5'-subtelomeric region, one
in its 3'-subtelomeric region and one in the 5'-subtelomeric
region of the 1.3 kb MDS. However, cytosines in this motif are
not necessarily methylated. The modified nucleotides are only
found in the micronuclear-specific sequence flanking the 1.1
kb gsp homologous sequence and in its 5'-subtelomeric region.
No other cytosine methylation could be detected in pCE7. This
methylation pattern was identical in different bisulphite conversions
and PCRs (for sequence data see Supplementary Material). Also
no cytosine methylation could be found in the micronuclear-specific
sequence pLJ01. Most interestingly no cytosine methylation can
be detected in the transposon-like element in the micronucleus
but a significant percentage of cytosines becomes methylated
(

25%) in the analyzed region of this element (PCR product obtained
with primers P5/P6) in the course of macronuclear differentiation.
In all analyses the methylation pattern observed was identical
and the nucleotide differences between different clones were
<2% (for sequence data see Supplementary Material) demonstrating
that probably all members of this family are modified early
during macronuclear development. Interestingly methylation in
these elements appeared clustered within 500 bp of these elements.
In contrast to the methylation sites found in conjunction with
the MDSs in the micronucleus and macronuclear anlagen, no specific
sequence motif could be identified that is linked to cytosine
methylation in the transposon-like element during macronuclear
differentiation.
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DISCUSSION
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The methylation of cytosines has been attributed to be relevant
in the silencing of genes, imprinting and the formation of heterochromatin.
Ciliated protozoa, especially spirotrichous ciliates such as
Euplotes,
Oxytricha and
Stylonychia, represent attractive models
for studying programmed DNA rearrangement and elimination processes.
Various reports approached the question whether cytosine methylation
occurs in these cells. Methylated cytosines were shown to be
present in macronuclear DNA of
Blepharisma (
12) and
Colpoda (
13). Only methylated adenine could be found in the macronucleus
of most other species using standard chromatographic techniques
(
8,
14
17). In these studies only DNA from the two nuclei
occurring in the vegetative cell, macronucleus and micronucleus,
were analyzed. Since a dramatic nuclear remodeling and differentiation
process occurs only after sexual reproduction, we investigated
the problem of cytosine methylation again and included DNA from
various stages of the developing macronucleus. Since methylated
cytosines could not be detected by RP-HPLC, the level of modified
cytosines has to be <0.1 µg per 100 µg genomic
DNA. We therefore used PCR as a more sensitive technique on
a set of DNA sequences known to have different destinies during
the process of DNA remodeling in
S.lemnae: MDSs that become
processed to a functional macronuclear DNA molecule, a family
of transposon-like elements whose removal starts late during
polytene chromosome formation and a micronuclear-specific sequence
being eliminated with bulk micronuclear DNA after the breakdown
of polytene chromosomes. In contrast to
Colpoda (
13) and
Blepharisma (
12) no modification of cytosine could be found in the mature
macronucleus of
Stylonychia whereas a low level of cytosine
methylation occurring in the sequence motif CCWGG was found
in the micronuclear-specific sequences upstream of one MDS and
in its subtelomeric region. This methylation was identical in
the micronucleus and the macronuclear anlagen suggesting that
it is not involved in nuclear differentiation but may be relevant
in the silencing of these sequences in the micronucleus and
the developing macronucleus. CCWGG was already described as
a prokaryotic methylation motif (
25) and was recently found
in mammalian cells possibly being involved in B cell lymphoma
gene silencing (
26). No cytosine methylation was found in the
micronuclear-specific sequence pLJ01 eliminated with bulk micronuclear
DNA in the micronucleus or the macronuclear anlagen. However,
a dramatic difference in cytosine methylation extent is observed
in the transposon-like element between micronuclei and developing
macronuclei. While no cytosine is methylated in micronuclear
DNA, cytosines are methylated
de novo in this element during
macronuclear differentiation. Excision of transposon-like elements
has been extensively studied in
Euplotes. Part of them are excised
before breakdown of polytene chromosomes (
10,
27) in the form
of heterochromatic chromatin rings (
28) and evidence has been
provided that chromatin configuration plays an important role
in this excision process (
29). Our data suggest that
de novo methylation of cytosines is involved in the formation of heterochromatic
regions, which could be a necessary prerequisite for correct
removal of transposon-like elements during macronuclear differentiation.
In summary, we show for the first time a low level of cytosine methylation in micronuclear DNA of S.lemnae of the sequence motif CCWGG and demonstrate that the cytosines in a class of sequences, whose removal starts before elimination of bulk DNA, become de novo methylated during macronuclear differentiation. This implies two different DNA methylation systems in the cell. Maintenance methyltransferases are involved in the preservation of the methylation status in micronuclei. In this case methylation is observed exclusively in one sequence motif. A de novo methyltransferase will methylate cytosines in a very specific class of DNA sequences in the course of macronuclear differentiation. This may be a first step towards understanding epigenetic factors involved in programmed DNA reorganization.
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SUPPLEMENTARY MATERIAL
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Supplementary Material is available at NAR Online.
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ACKNOWLEDGEMENTS
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This work was supported by grants from the Deutsche Forschungsgemeinschaft,
the National Science Foundation (grant number 128-6114-1) and
the Alfried von Bohlen and Halbach Foundation.
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