Content uploaded by Carmen Cantemir
Author content
All content in this area was uploaded by Carmen Cantemir on Nov 20, 2014
Content may be subject to copyright.
MOLECULAR AND CELLULAR BIOLOGY, Apr. 2003, p. 2709–2719 Vol. 23, No. 8
0270-7306/03/$08.00⫹0 DOI: 10.1128/MCB.23.8.2709–2719.2003
Copyright © 2003, American Society for Microbiology. All Rights Reserved.
Endogenous Assays of DNA Methyltransferases: Evidence for
Differential Activities of DNMT1, DNMT2, and DNMT3 in
Mammalian Cells In Vivo
Kui Liu, Yun Fei Wang, Carmen Cantemir, and Mark T. Muller*
Department of Molecular Genetics, Ohio State University, Columbus, Ohio 43210
Received 17 December 2002/Accepted 14 January 2003
While CpG methylation can be readily analyzed at the DNA sequence level in wild-type and mutant cells, the
actual DNA (cytosine-5) methyltransferases (DNMTs) responsible for in vivo methylation on genomic DNA are
less tractable. We used an antibody-based method to identify specific endogenous DNMTs (DNMT1, DNMT1b,
DNMT2, DNMT3a, and DNMT3b) that stably and selectively bind to genomic DNA containing 5-aza-2ⴕ-
deoxycytidine (aza-dC) in vivo. Selective binding to aza-dC-containing DNA suggests that the engaged DNMT
is catalytically active in the cell. DNMT1b is a splice variant of the predominant maintenance activity DNMT1,
while DNMT2 is a well-conserved protein with homologs in plants, yeast, Drosophila, humans, and mice.
Despite the presence of motifs essential for transmethylation activity, catalytic activity of DNMT2 has never
been reported. The data here suggest that DNMT2 is active in vivo when the endogenous genome is the target,
both in human and mouse cell lines. We quantified relative global genomic activity of DNMT1, -2, -3a, and -3b
in a mouse teratocarcinoma cell line. DNMT1 and -3b displayed the greatest in vivo binding avidity for
aza-dC-containing genomic DNA in these cells. This study demonstrates that individual DNMTs can be
tracked and that their binding to genomic DNA can be quantified in mammalian cells in vivo. The different
DNMTs display a wide spectrum of genomic DNA-directed activity. The use of an antibody-based tracking
method will allow specific DNMTs and their DNA targets to be recovered and analyzed in a physiological
setting in chromatin.
In eukaryotes, DNA methylation is an epigenetic encryption
system that is essential for proper gene regulation (for reviews
see references 2, 4, 7, 23, 29, and 30). Defects in methylation
lead to diverse disorders from mental retardation to immune
deficiencies, and there is particularly strong evidence that
methylation defects create a favorable environment for malig-
nant transformation (2, 3). Pharmacologic alterations in meth-
ylation of specific genes have also been correlated with tumor
response to chemotherapy and patient survival; thus, methyl-
ation regulation and the enzymes that catalyze the process
represent important areas for treating cancer (2, 30).
The enzymatic machinery that mediates methylation in-
volves a number of DNA (cytosine-5) methyltransferase
(DNMT) isoforms, including DNMT1, DNMT1b, DNMT2,
DNMT3a, and DNMT3b (and a host of DNMT3 splice vari-
ants) (4, 29, 30). Dnmt1,Dnmt3a, and Dnmt3b are independent
genes and essential; embryos lacking both copies of Dnmt1 or
Dnmt3b die before birth, whereas Dnmt3a-nulls survive about
4 weeks (18, 21). Heterozygous mutants appear normal and are
fertile (18, 21). The murine DNMT3a and -3b enzymes appear
to possess de novo methylation activity (based upon plasmid
methylation), and there is evidence that they act on different
DNA targets in vivo (12). No transmethylase activity has been
found with DNMT2, and biallelic deletions appear to possess
normal methylation patterns (8, 22). How different DNMTs
are directed to specific sites in vivo is not well understood,
although DNA sequence, chromatin structure, or ancillary in-
teracting factors (or a combination of these) are obvious can-
didates. In order to sort out which specific DNMTs are respon-
sible for methylation of selected DNA targets, one needs to
examine individual methylases in vivo under physiological con-
ditions. Achieving this objective is complicated when one con-
siders that the most prevalent methylase is DNMT1, with
DNMT3a and -3b being barely detectable (31), while there
exist additional minor forms, including DNMT2 and DNMTb
(5, 8, 13, 22). Recently, a cell line knockout of Dnmt1 was
characterized (28) that displayed nearly normal global genomic
methylation. Other methylases must be active in this case. For
example, DNMT3b is thought to be the additional activity that
cooperates with DNMT1 to maintain cellular DNA methyl-
ation patterns (28). Additional minor but active DNMTs that
are physiologically relevant exist (8, 13, 22). Minor methylating
activities may be less robust overall (relative to DNMT1) but
have important consequences if key regulatory genes are their
targets.
We have developed a method to facilitate elucidation of the
methylation machinery that acts in a chromosomal setting. The
approach is based on studies showing that DNA methyltrans-
ferases have a fleeting covalent association with the DNA
substrate; however, when 5-aza-2⬘-deoxycytidine (aza-dC) is
present, the covalent DNA-protein intermediate is arrested,
leading to adducts that have consequences in global methyl-
ation (9, 15, 33, 34). Consequently, active methylases become
stoichiometrically removed from the active nuclear pool, lead-
ing to hypomethylation of the genome. We have used an an-
tibody-based method to detect and quantify the physical inter-
* Corresponding author. Mailing address: Department of Molecular
Genetics, Ohio State University, 484 West 12th Ave., Columbus, OH
43210. Phone: (614) 292-1914. Fax: (614) 292-4702. E-mail: muller.2
@osu.edu.
2709
action of several different DNMTs on the genome of the cell in
vivo.
MATERIALS AND METHODS
Reagents. The topoisomerase I (topo I) antibody was isolated from serum of
scleroderma patients and was donated by TopoGEN, Inc. (www.topogen.com)
(Columbus, Ohio). Anti-DNMT1 rabbit antibody was prepared by using a com-
mercial antibody production service (Research Genetics) and was raised against
a synthetic peptide derived from the N-terminal region. Anti-DNMT1b rabbit
antibody was prepared against a peptide unique to the additional exon not
present in DNMT1 (5, 13). All peptide antibodies were immunoaffinity purified
and tested by enzyme-linked immunosorbent assay and Western blotting for
appropriate reactivity. Anti-DNMT2 antibody prepared against DNMT2 was
provided by X. Cheng and Anti-DNMT3a and -3b antibodies (specific for mouse
DNMT3) were provided by K. Robertson. All DNMT antisera were verified for
specificity by Western blotting by using crude extracts. Camptothecin (CPT) and
etoposide (VP16) were provided by TopoGEN, (in 100% dimethyl sulfoxide),
and aza-dC was from Sigma Chemical Co. (St. Louis, Mo.). aza-dC was prepared
fresh just prior to use.
Cell culture. HeLa, WI-38, HCT-116 (wild type), and HCT-116 Dnmt1
⫺/⫺
(27) cell lines in this study were cultured in Dulbecco’s modified Eagle medium
supplemented with 10% fetal bovine serum (CellGro, Inc., Herndon, Va.). Jur-
kat cells were grown in RPMI medium supplemented with 10% fetal bovine
serum. HCT-116 cells were kindly supplied by B. Vogelstein and S. Baylin.
Mouse teratocarcinoma cell line P19 was provided by K. Robertson. Cells were
grown in a humidified atmosphere of 5% CO
2
–95% air at 37°C.
Nuclear protein preparation, band depletions, and Western blotting analysis.
To prepare samples for Western blotting, cells were washed twice with cold
phosphate-buffered saline and resuspended in 1 ml of buffer A (100 mM NaCl,
50 mM KCl, 20 mM Tris-HCl, pH 7.5, 0.1 mM EDTA, 0.1 mM phenylmethyl-
sulfonyl fluoride, 10% glycerol, 0.2% NP-40, and 0.1% Triton X-100). Following
incubation on ice (10 min), nuclei were centrifuged (2,000 ⫻g, 10 min) and lysed
in 100 lof1⫻electrophoresis sample buffer and boiled for 2 to 3 min. The
samples were separated by gradient sodium dodecyl sulfate (SDS)-polyacryl-
amide gel electrophoresis, followed by electroblot transfer to nitrocellulose.
Immune complexes were illuminated by using the BM Chemiluminescence West-
ern blotting kit (mouse/rabbit) (Boehringer Mannheim GmbH, Mannheim, Ger-
many) as described previously (20).
ICM analysis. The method for detecting DNMT-genomic DNA adducts is
based upon technology developed to measure topoisomerase-DNA adducts (36)
(Fig. 1C). Cells were treated with aza-dC as specified by each experiment. It is
essential that negative controls (no drug treatment) be included in each analysis.
Typically 1 ⫻10
7
to 5 ⫻10
7
cells were used for each ICM analysis (a single
100-mm dish, although the method works equally well with adherent and non-
adherent cells). Following drug treatment, the medium was removed by suction
and the cells were lysed by immediate addition at 37°C of 1% Sarkosyl in
Tris-EDTA (TE) (10 mM Tris-HCl, pH 7.5, 1 mM EDTA). For a 100-mm petri
dish, 2 ml of Sarkosyl lysis solution was used; the plates were swirled several
times to promote complete dispersion and lysis of the monolayer. For Jurkat
(suspension) cells, the cells were deposited by centrifugation, the supernatant
were decanted and cells were lysed with 3 ml of 1% Sarkosyl–TE as described
above. The lysate was then gently sheared (18-gauge needle) and layered onto a
step CsCl gradient made in a Beckman SW41 polyallomer centrifuge tube (14 by
89 mm). The gradients are composed of four layers (2 ml each) of different
densities of CsCl made in TE as follows: a stock solution of CsCl was made fresh
by dissolving 120 g of CsCl in 70 ml of sterile TE (final density of 1.86 g/ml;
refractive index of 1.414). From this stock, four solutions (A to D) were prepared
as follows: solution A, 0.075 volumes of TE plus 0.925 volumes of CsCl stock;
solution B, 0.2 volumes of TE plus 0.8 volumes of CsCl stock, solution C, 0.45
volumes of TE plus 0.55 volumes of CsCl stock, and solution D, 0.55 volumes of
TE plus 0.45 volumes of CsCl stock. By using a 5-ml pipette, 2 ml each of
solutions A, B, C, and D from bottom to top of tube was layered. The lysates
were overlaid onto step gradients that were topped and balanced with mineral oil
followed by centrifugation (30,000 rpm for 20 h at 20°C with a Beckman SW41
rotor). The gradient was fractionated into 0.4-ml aliquots by piercing the bottom
of the tube. The DNA peak, which comes out near the bottom of the tube, is
easily identified by notable increases in viscosity. To accurately locate DNA-
containing fractions, 30 l of each fraction is diluted into 270 l of water and
absorbance is measured at 260 nm. Peak fractions were pooled, and the DNA
concentration was accurately measured by either fluorometry or UV spectros-
copy. The DNA pools can be stored indefinitely at ⫺20°C. DNA concentrations
were all adjusted to equivalence and were verified by loading a fixed amount
FIG. 1. DNMT reaction mechanism and the ICM assay. (A) Meth-
ylation on non-aza-dC-containing DNA proceeds via a nucleophilic
attack by cysteine thiolate of DNMT at the C-6 on cytosine followed by
a second nucleophilic attack at C-5 by the methyl group of S-adeno-
sylmethionine (methyl donor). This results in the transfer of the methyl
group to C-5 and an intermediate that is resolved by elimination of
DNMT at C-6 and abstraction of a proton from C-5. (B) Mechanism
of action on aza-dC-substituted DNA involves a methyl transfer at the
N-5 of aza-dC and formation of a stable or covalent complex between
enzyme and DNA that is resistant to ionic detergents, high ionic
strength, and temperature (viz., conditions that dissociate proteins that
are noncovalently bound to DNA) (9, 10, 15, 34). (C) Overview of the
ICM assay. The endogenous DNMT reaction in vivo shows the enzyme
in either a one-dimensional search mode (scanning for suitable CpG
targets in chromatin) in a weak binding mode (enzyme paused over a
chromatin-accessible CpG site in vivo) or in the covalent DNMT-DNA
complex mode with aza-dC-substituted DNA. Direct addition of Sar-
kosyl lyses the cells and disrupts weak (noncovalent) protein-DNA
complexes in chromatin; however, aza-dC-induced DNMT-DNA com-
plexes are not dissociable under these conditions. The viscous lysate is
sheared and overlaid onto a step CsCl gradient (Materials and Meth-
ods) that resolves DNA from the bulk, excess free protein and debris
in a single step (35, 38, 39). Proteins stably bound to the DNA are
dragged down to the 1.7-g/ml fraction of the gradient. The DNA
fraction contains DNMTs only when the cells have been prelabeled
with aza-dC. Specific DNMTs are quantified in the DNA peak by
Western slot blotting. Note that the material at the top of the gradient
gives a nonspecific Western blot signal due to the excess of membra-
nous debris and cannot be relied on to measure free DNMT. To
demonstrate that the DNA peak-associated DNMT signal is real (and
not carryover from the top of the gradient), the DNA peak can be
collected and rebanded in CsCl to give quantitative recovery of the
DNMT signal in a second gradient (data not shown). The ICM data
were not affected by digestion of lysates with RNase A prior to cen-
trifugation; therefore, RNase digestion was deemed unnecessary.
2710 LIU ET AL. MOL.CELL.BIOL.
(from 50 to 200 ng of each DNA sample) onto a 1% agarose gel, followed by
electrophoresis (150 V for 10 min) and staining with 0.5 g of ethidium bro-
mide/ml (30 min) and destaining with water for 15 min. Gels were photographed
and band intensities were compared between samples to verify that DNA con-
centrations were identical.
Immunodetection of proteins in the DNA peak. Immunoblotting with a stan-
dard slot blot manifold (Schleicher & Schuell, Keene, N.H.) was carried out on
the DNA pool from each gradient as follows: Hybond enhanced chemilumines-
cence nitrocellulose membranes (cut to fit a slot blot manifold) were soaked for
15 min in 25 mM sodium phosphate buffer, pH 6.5, at room temperature. The
slot blot manifold was assembled by placing two pieces of Whatman no. 1 filter
paper under the nitrocellulose membrane. The viscosity of the DNA was reduced
by shearing with a 21- or 25-gauge needle and a 1-ml syringe. The DNA samples
(typically from 20 to 100 l) were diluted with an equal volume of 25 mM sodium
phosphate buffer (pH 6.5) and were applied to the slot blot device under vacuum
until all traces of liquid were drawn down. The membrane was removed from the
manifold and was immediately immersed in 25 mM phosphate buffer, pH 6.5, for
5 min at room temperature. Membranes were then equilibrated in Tris-buffered
saline–Tween (TBST) (20 mM Tris-HCl, pH 7.5, 137 mM NaCl, 0.1% Tween 20)
for 15 min with gentle agitation, followed by blocking with TBST containing 5%
nonfat dried milk for 2 to3hatroom temperature. The blots were then washed
three times with TBST for 10 min each at room temperature. The primary
antibody was diluted as appropriate (1:1,000 to 1:10,000) in 10 to 50 ml of TBST.
Blots were incubated with primary antibody for6hatroom temperature, fol-
lowed by washing three or four times with TBST (10 min per wash, with gentle
agitation). The blots were processed to illuminate the immune complexes in
either of two ways. In the first method, the nitrocellulose membranes were
incubated with in 30 ml of TBST containing 0.4 Ci of
125
I-protein A/ml for 2 h
at room temperature. Following several washes with TBST (10 min each, with
agitation at room temperature), the membranes were air dried, wrapped in Saran
Wrap, and visualized by autoradiography. The second method involved visual-
ization of complexes by chemiluminescence with Amersham’s enhanced chemi-
luminescence kit. The primary antibody incubation step was for1hatroom
temperature, followed by three TBST washes as described above. The blots were
incubated with horseradish peroxidase-conjugated secondary antibody for 30 min
at room temperature and washed four times in TBST, followed by detection as
per the kit protocol. Blot signals were quantified by either densitometry of
autoradiograms or on a phosphorimager, and results were expressed as arbitrary
signals per microgram of DNA. All ICM data were verified by three independent
experiments.
RESULTS
The ICM technique. We have developed an in vivo assay that
measures the physical interaction between DNMT and the
genome (ICM assay for in vivo complex of methylase). The
ICM assay is based upon known details about the reaction
mechanism of this class of enzymes (15, 34), and it was previ-
ously demonstrated that DNMT1-DNA adducts survive harsh
conditions of high salt and detergent (9). The enzyme engages
DNA in an intermediate complex where the DNA (at a target
cytosine) is covalently linked to the methyltransferase. This
covalent intermediate is transient and is released in the last
step of the reaction sequence. The interaction of DNMT with
the 5-aza-substituted cytosine in DNA (in the presence of
S-adenosylmethionine) results in formation of an irreversible
protein-genomic DNA adduct. Essentially, the catalytic center
of DNMT becomes covalently bound to the 6 position of cy-
tosine (Fig. 1A and B). An overview of the ICM assay is shown
in Fig. 1C. To validate the specificity and resolving power of
the ICM technique, we focused initially on the predominant
DNA methylation activity, DNMT1, by using a peptide anti-
body prepared against the amino terminus of DNMT1 that
does not share homology with other DNMTs (for other than
DNMT1b, see below and Materials and Methods). The results
(Fig. 2A) clearly show that, in the presence of aza-dC, a strong
DNMT1 signal was detected in the DNA peak (row 1). The
DNMT1 signal in the DNA fraction required aza-dC (compare
rows 1 and 2 [Fig. 2A]). The ability of the anti-DNMT1 anti-
body to detect a specific polypeptide on Western blots is shown
in Fig. 2B (lane 2).
In order to determine whether the entire DNMT1 signal in
the DNA peak off CsCl was physically bound to DNA and to
ensure that essentially all DNMT in the DNA peak is attached
to DNA, the following experiments were carried out: DNA was
recovered from aza-dC-treated cells and digested exhaustively
with DNase I. DNMT1 was then evaluated for electrophoretic
mobility shifting on Western blots before and after digestion
(Fig. 2C). Prior to digestion (Fig. 2C, lane 2), little if any
distinct DNMT1 signal was visible; however, after DNase I, a
strong band appeared (Fig. 2C, lane 3), which was shifted to a
higher molecular weight (relative to free DNMT1 in a nuclear
extract [Fig. 2C, lane 1]). The molecular mass increase (esti-
mated to be 8 to 10 kDa) corresponds to roughly 20 to 30
nucleotides of DNA stably bound to DNMT1. These results
show that any DNMT1 signal in the DNA peak is bound to
genomic DNA. An independent verification of this idea comes
from the following experiment: the DNA peak from aza-dC-
treated cells was pooled, dialyzed, and rerun on a second CsCl
gradient. The DNMT1 signal in the DNA fraction was quan-
titatively recovered (data not shown). From these experiments
we conclude that DNMT1 is present in the DNA fraction due
to its association with genomic DNA and not to adventitious
trapping or cross contamination with the free DNMT1 present
at the top of the gradient. Since the complexes survive through
two rounds of centrifugation (48 h), we conclude that they are
not reversing at least over this time period.
To examine specificity and efficiency of the ICM assay for
detecting a specific DNMT isoform, additional experiments
were required. First, we analyzed mutant and wild-type HCT-
116 cells for “band depletion”of DNMT1 on Western blots.
WI-38 (control cells) and wild-type HCT-116 cells show the
presence of DNMT1 at its expected molecular weight (Fig.
2D); however, the polypeptide signal is reduced substantially
after exposure to aza-dC due to the binding of DNMT1 to the
genomic DNA (it is band depleted in this case; compare lanes
3 and 4 and lanes 5 and 6 in Fig. 2D). The degree to which the
band is depleted in this analysis reflects the efficiency of trap-
ping of DNMT1 on the genome of the cell. These data show
that 75 to 80% of the DNMT1 in the cell is lost after aza-dC
treatment in this experiment. The fact that a normal cell line
(WI-38 diploid fibroblasts) and a tumor cell line (HCT-116)
both displayed this high degree of efficiency demonstrates that
the ICM efficiency is consistent in cells with diverse growth
phenotypes. An additional control using a mutant HCT-116
cell line lacking both copies of DNMT1 (27) confirms that the
signal detected (filled arrow [Fig. 2D]) is indeed the DNMT1
polypeptide (it is missing in the mutant). Moreover, aza-dC
treatment of the mutant cell line had no effect on the polypep-
tide profile (Fig. 2D, lanes 1 and 2). Second, ICM results on
the HCT-116 wild type and Dnmt1
⫺/⫺
mutants (Fig. 2E) are
mutually consistent with the band depletion data. These data
reveal that in Dnmt1
⫺/⫺
mutant cells the antibody did not
detect any DNMT1 in the DNA peak (even after aza-dC treat-
ment). DNMT1 protein was detected only in the wild-type
HCT-116 cells prelabeled with aza-dC.
Since slot blotting is not based upon molecular weight (relies
VOL. 23, 2003 IN VIVO ACTION OF DNMT 2711
FIG. 2. ICM and band depletion analysis of Dnmt1
⫺/⫺
and Dnmt1
⫹/⫹
HCT-116 colon cancer cells with and without aza-dC. (A) ICM assay
results with HeLa cells. Approximately 3 ⫻10
7
HeLa cells in exponential growth were untreated or treated with 5 M aza-dC for 24 h; following
Sarkosyl lysis, the DNA was banded in CsCl, the gradient was fractionated, and the DNA peak was located by UV absorbance. Individual fractions
were slot blotted onto membranes and probed with anti-DNMT1 antibody as described in Materials and Methods. Each slot corresponds to the
gradient fraction shown in the graph (top fractions of gradient not shown). (B) Western blotting of DNMT1 in HeLa cell extracts. Nuclear extracts
(100 g) were subjected to SDS-polyacrylamide gel electrophoresis, and the Western blots were probed with anti-DNMT1 antibody as described
in Materials and Methods. Lane 1, stained gel (molecular weight markers indicated); and lane 2, autoradiogram. (C) Electrophoretic mobility
shifts. HeLa cells were treated with aza-dC exactly as described for panel A and were subjected to ICM. The DNA was recovered and dialyzed
2712 LIU ET AL. MOL.CELL.BIOL.
on antibody specificity), it is important to show that covalent
binding of a heterologous protein to genomic DNA does not
generate a signal in the DNA peak when probed with anti-
DNMT1 antibody. We utilized topoisomerase poisons to ex-
amine this possibility. Exponentially growing HeLa Cells were
first incubated with aza-dC, and the cells were then pulsed with
a topo II drug (VP16) or a topo I drug (CPT) for 30 min prior
to harvest. These conditions promote covalent trapping of topo
II or topo I on genomic DNA (37). Western probing of the
ICM Western blot with anti-DNMT1 probe from cells treated
with VP16 or CPT but not exposed to aza-dC (Fig. 3A) gave no
detectable signal. This control demonstrates specificity of the
ICM, since these conditions clearly promote topo-DNA com-
plexes (compare Fig. 3C; data for topo II antibody probe not
shown). As expected, combining VP16/aza-dC or CPT/aza-dC
also yielded a positive DNMT1 signal in the DNA peak (Fig.
3B). Short exposure to CPT elevated DNMT1-DNA com-
plexes by about 25 to 30% (compare aza-dC and CPT and
aza-dC alone [Fig. 3B]). The effect was not large but was
reproducible (four experiments) and was not seen in aza-dC/
VP16 (topo II)-treated cells.
Kinetics of complex formation with different DNMT iso-
forms. The time course of DNMT1 complex formation was
analyzed by the ICM in exponentially growing HeLa cells (Fig.
4A). At the shortest time tested (2.5 h), the highest level of
complex formation was detected (two- to threefold greater
than later time points); however, complexes stabilized at a
fixed but lower level over a period of 73 h. In a variety of
human and mouse cell lines tested, DNMT1 complexes formed
rapidly (within 10 min, earliest time tested, not shown) and
were subsequently (usually within 6 h) reduced to basal, stable
levels as depicted in Fig. 4B with Jurkat cells.
Endogenous covalent DNA binding of different DNMTs can
be analyzed by using the ICM technique with the appropriate
antibodies. The splice variant DNMT1b has been identified as
a minor methylase activity in vitro (5, 13). We used the ICM to
examine whether this enzyme is an endogenous, functional
methylase that targets the genome. DNMT1b differs from
DNMT1 by the addition of 16 amino acid residues (between
exons 4 and 5). We raised a peptide antibody to this 16-amino-
acid region and used it to probe Western blots from an ICM
analysis (Fig. 5). Since the 16 amino acids are unique to
DNMT1b, this antibody detects only the splice variant, even in
the presence of excess DNMT1. The rate of complex accumu-
lation was essentially identical for both DNMT1 isoforms;
however, DNMT1b represents about 10% (⫾3% in repeat
experiments) of DNMT1 complex yield. Complex formation
was maximal for both isoforms at drug concentrations in the 1
to 10 M range (data not shown). As expected, we did not
detect DNMT1b by using the ICM on Dnmt1
⫺/⫺
biallelic
knockout deletions (data not shown).
DNMT2 is a well-conserved enzyme of both eukaryotes and
prokaryotes; however, despite the presence of a number of
sequence motifs common to active DNMTs, this isoform has
not been shown to possess in vitro activity (8), nor is it essential
for de novo or maintenance methylation events in embryonic
stem cells (22). We examined DNMT2 activity in HeLa cells by
using the ICM assay. When the ICM blots were probed with
anti-DNMT2 antibody (8), we found an aza-dC-dependent
signal associated with genomic DNA (Fig. 5). The signal was
much weaker than that of DNMT1 (ca. 5%). The time course
of DNMT2-DNA adduct formation was very different from
that of DNMT1 and -1b isoforms, suggesting that the former
activity is regulated independent from the known maintenance
activities. The data show that DNMT1, -1b, and -2 are differ-
entially trapped on aza-dC-labeled genomic DNA.
The availability of well-characterized antibodies to mouse
DNMTs allowed us to compare DNMT isoforms in a single cell
line (mouse teratocarcinoma cell line P19). We compared
DNMT1, DNMT2, DNMT3a, and DNMT3b in P19 cells
treated with different concentrations of aza-dC (Fig. 6A). ICM
analyses were carried out on all four different DNMTs by using
the appropriate antibody probes. We selected a time after
aza-dC addition when the complex formation had stabilized (8
h [Fig. 5]). Western blot experiments evaluated each DNMT
isoform to demonstrate antibody specificity (except for
DNMT1, which is shown in Fig. 2B). Westerns blots were also
compared from aza-dC-treated and untreated cells for
DNMT2, -3a, and -3b (Fig. 6A) to evaluate the efficiency of
adduct formation with these different isoforms. (As noted
above, substantial band depletion was seen with DNMT1 fol-
lowing aza-dC [Fig. 2D] treatment, suggesting that the effi-
ciency of adduct formation was greater than 75%.) In parallel,
complex formation was measured by the ICM assay (at fixed
genomic DNA concentrations indicated in Fig. 6 and with
increasing amounts of aza-dC). Quantitation of DNMT-DNA
complexes based on band depletion was difficult, although we
note that, for the three DNMTs tested, it appears that signals
were slightly reduced by aza-dC; thus, complex formation was
much less efficient (estimated to be 10%) for these DNMTs
than for DNMT1 (Fig. 2D). We note however that all isoforms
were still detected by the ICM assay. ICM data revealed that
DNMT2 and DNMT3a complex formation was roughly three-
to fivefold lower than that of DNMT3b (at 8 h after drug
addition). DNMT1 complexes were the most abundant of all,
as noted with HeLa cells (note that 10-fold less DNA was
against TNM (10 mM Tris-HCl, pH 8.0, 1 mM EDTA, and 10 mM MgCl
2
), and aliquots were removed for digestion with 50 g of DNase I/ml
(60 min at 37°C). DNA was immunoprecipitated with anti-DNMT1 antibody and was analyzed by SDS-polyacrylamide gel electrophoresis followed
by Western blotting (probed with anti-DNMT1 antibody). Lane 1, HeLa nuclear extract control showing the position of DNMT1 polypeptide from
non-drug-treated cells. Lane 2, anti-DNMT1 immunoprecipitated DNA (from CsCl gradient) before DNase I digestion. Lane 3, same as lane 2,
after DNase I digestion. (D) Band depletion analysis of DNMT1 in Dnmt1
⫹/⫹
and Dnmt1
⫺/⫺
HCT-116 and WI-38 cell lines. Cells (10
7
/dish) were
exponentially growing when treated (or not as indicated on the top of the blot) with 5 M aza-dC for 12 h at 37°C in tissue culture medium plus
10% bovine calf serum. Nuclear proteins were extracted for SDS-polyacrylamide gel electrophoresis and Western blotting as described in Materials
and Methods by using anti-DNMT1 antibody probe. The large filled arrow marks the position of the DNMT1 polypeptide band. (E) ICM analysis
of DNMT1 in HCT-116 Dnmt1
⫹/⫹
and Dnmt1
⫺/⫺
cells. Cells were treated with aza-dC or untreated as described for panel D above and were
subjected to the ICM analysis. The DNA peak was pooled, and its concentration was measured. Either 0.4, 0.8, or 1.6 g of DNA was slot blotted
onto a membrane, which was probed with DNMT1 antibody.
VOL. 23, 2003 IN VIVO ACTION OF DNMT 2713
loaded for DNMT1 than for the others in the ICM data shown
in Fig. 6). DNMT3a complexes were clearly less common than
those of DNMT3b. The differences between DNMT2, -3a, and
-3b complexes (by ICM) are not reflected at the polypeptide
level. In Fig. 6B, extracts were probed with a mixture of anti-
sera to get an idea of the relative amount of each isoform in the
same extract. DNMT2 and -3a were similar, while less
DNMT3b was detected. These data suggest that P19 cells pos-
sess catalytically active DNMT1, -2, -3a, and -3b, with DNMT1
and -3b having the greatest amount of methylation activity
directed at the endogenous genome.
DISCUSSION
The ICM assay is based on known details about the reaction
mechanism of this class of enzymes where a putative covalent
complex forms between the target cytosine and DNA methyl-
transferase (9, 15, 33, 34). Under normal circumstances, the
FIG. 3. Combined effects of topo I and II trapping on DNMT1 adduct formation. HeLa cells (exponentially growing; 4 ⫻10
7
cells/ICM) were
cultured for 24 h without or with aza-dC (5 M), followed by 30 min of exposure to VP16 (10 M) or CPT (50 M) as indicated and subjected
to the ICM assay. Increasing amounts of DNA (from 1 to 10 g) were spotted on the membrane. (A) Two cultures were treated with either VP16
or CPT and probed with anti-DNMT1 antibody. (B) Three plates were treated with aza-dC alone or with aza-dC/VP16 and aza-dC/CPT as
indicated. Increasing amounts of DNA were spotted and probed with anti-DNMT1 antibody. Panel C shows several controls where the blot was
probed with anti-topo I antibody.
2714 LIU ET AL. MOL.CELL.BIOL.
covalent intermediate is transient and quickly resolves as the
enzyme turns over; however, when aza-dC has been inserted
into the DNA, this interaction results in the formation of an
irreversible protein-genomic DNA complex. The catalytic cen-
ter of DNMT becomes covalently bound to the 6 position of
the cytosine ring (9, 15, 33, 34). Thus, in order to trap DNMT
on the genome in vivo, aza-dC must be present. DNMT is
presumably a typical DNA binding protein and will be in either
a linear search mode over DNA or weakly bound in a complex
with DNA and other ligands in chromatin. Upon making con-
tact and gaining access to the aza-dC target site, DNMT-DNA
complexes form that resist dissociation with protein denatur-
ants, and these adducts do not readily reverse. With regard to
the ICM technique described here, ionic detergents arrest the
enzyme activity and at the same time disrupt the bulk of elec-
trostatic protein-DNA complexes in the cell. DNA is then
purified (without proteases) by CsCl gradient centrifugation,
which completely dissociates noncovalent protein-DNA inter-
actions and gives complete resolution of DNA from free pro-
tein with a recovery of 95 to 100%. This DNA is highly purified
and free of bulk chromosomal proteins (such as histones) and
has not been treated with proteases or phenol. An antibody
probe is then used to quantify DNMT levels in the DNA
fraction from the gradient. Several points should be stressed
about the use and application of this technology. The method
gives a snapshot of DNMT activity on the genome of any given
cell or tissue that represents the physical interactions between
DNMT and genomic DNA at the time of cell lysis. By analogy
to well-characterized prokaryotic methyltransferases, aza-dC is
a necessary in order to drive adduct formation (6). The fact
that methylation can be also detected at aza-dC sites (6, 10) is
mutually consistent with the notion that ICM detection of
aza-dC DNA-DNMT adducts represents bona fide methyl-
ation sites. The method is quantitative and can be used with
virtually any cell or tissue as long as the genome can be pre-
labeled with aza-dC. Since the ICM relies on monospecific
antibody probes, it is highly specific for a given DNMT isoform
and provides insight on the behavior of a given DNMT in vivo.
For example, DNMT1 is strongly S phase dependent, based on
the ICM (M. T. Muller and Y. F. Wang, unpublished data);
FIG. 4. ICM time course and aza-dC dose response in different cell lines. (A and B) Time course of DNMT1 adduct formation. HeLa cells
(A) or Jurkat cells (B) in exponential growth were treated with 5 M aza-dC or untreated. Panel A shows the ICM slot blot for a single DNA
concentration of 3 g. Panel B shows the digitized data where the ICM signal was arbitrarily assigned unit values based upon phosphorimaging
of a single DNA concentration on the ICM slot blot.
VOL. 23, 2003 IN VIVO ACTION OF DNMT 2715
therefore, the assay is most likely detecting events at DNA
replication forks or very soon after nascent DNA synthesis.
The following pieces of evidence attest to the validity of the
ICM method for quantifying DNMT-DNA interactions in vivo.
(i) We note that there is a total dependence on preincorpo-
ration of aza-dC. That dependence, based upon collective data
from a number of different labs (6, 9, 10, 15, 33, 34), suggests
that catalytically active methylases are being detected.
(ii) Western blotting experiments demonstrate that DNMT
polypeptide bands are depleted by aza-dC treatment. The loss
of the signal is due to adduct formation on genomic DNA,
which renders the trapped DNMT nonextractable. When
tested, band depletion is always attended by an increase in
DNMT in the DNA peak fraction of a CsCl gradient. Neither
band depletion nor adducts were seen in HCT-116 Dnmt1
⫺/⫺
deletion mutants (27) (with a DNMT1 antibody probe). The
band depletion data also reveal the overall efficiency of com-
plex formation. Any reduction in the amount of total polypep-
tide should be directly proportional to the number of enzyme
molecules stably bound to the genome. The efficiency is quite
high (⬎75%) for the maintenance enzyme DNMT1, which is
the predominant activity in cells. In contrast, murine DNMT2,
-3a, and -3b band depletions were much less obvious and prob-
ably no more than 10%. While all of these were detected by
ICM assay, the low efficiency may reflect the low relative ac-
tivity (or high DNA sequence selectivity in chromatin) of these
isoforms relative to maintenance methylation; however, addi-
tional data will be required to confirm this. It is safe to say that
our present data show that all of these isoforms stably and
selectively bind aza-dC- substituted DNA in vivo. These data
suggest that, in mouse P19 cells, DNMT2, -3a, and -3b are
active and that DNMT3b displays higher ICM activity than
does DNMT2 or -3a. In human and mouse cells tested,
DNMT2 binding to genomic DNA was clearly detectable but
was also consistently lower than for other isoforms.
(iii) The ICM method does not detect other covalently
bound proteins that associate with genomic DNA. Genomic
DNA from cells treated with topoisomerase poisons (that are
known to induce topoisomerase adducts) does not contain
detectable DNMT. It is very unlikely that our DNMT antibod-
ies are detecting nonmethylase proteins that may be stably
bound to the genome. In contrast, treating with topoisomerase
poisons plus aza-dC gives strong signals for both classes of
covalent DNA binding proteins. The finding that topo I com-
plexes are enhanced by aza-dC supports the notion that DNA-
DNMT1 complexes are sites of DNA damage and that topo I
is being recruited to these regions to assist in repair or recom-
bination to remove the lesions (20, 32, 37).
(iv) The ICM complexes recovered from CsCl gradients
were found to contain a DNMT1 polypeptide with a small
DNA fragment following extensive digestion with DNase I.
Essentially all of the DNMT1 was electrophoretically shifted
due to the single-stranded nucleic acid tail that was covalently
bound. This result shows that all of the DNMT1 found in the
DNA peak is stably (covalently) bound to nucleic acid. We
FIG. 5. Comparative analysis of DNMT1, DNMT1b, and DNMT2 in HeLa cells. HeLa cells in exponential growth (4 ⫻10
7
/ICM assay) were
treated with 5 M aza-dC for the times indicated (“0”corresponds to a negative control) and were subjected to the ICM analysis by using two
different probes: anti-DNMT1 (top row) and anti-DNMT1b (middle row) and anti-DNMT2 antibody (bottom). The amount (in micrograms) of
DNA loaded per slot is indicated on the right side of the blot.
2716 LIU ET AL. MOL.CELL.BIOL.
estimate that 20 to 30 nucleotides remained; however, accurate
estimates in this size range (⬎200 kDa) are crude at best.
The ICM method is antibody based and can be used to
biochemically track different DNMT isoforms that engage an
aza-dC-labeled genome. We show that in fact the DNMT1b
variant is quite an active DNA methylase in vivo and mirrors
the action of the more abundant DNMT1 activity (DNMT1b
complexes being roughly 10% of DNMT1). This ratio is close
to that predicted by mRNA expression analysis (13) but is
higher than expected based upon Western blotting data (5).
While total DNMT1b may be low, it can bind efficiently to
aza-dC-substituted genomic DNA, suggesting robust methyl-
ation activity in vivo. Our collective data show that the DNA-
hypomethylating drug aza-dC has multiple targets in vivo. In
double knockouts of Dnmt1 and Dnmt3b (28), the DNMT1b
splice variant would also be absent; however, based upon the
ICM, this variant may contribute to the global methylation
patterns in vivo in wild type cells. Understanding isoform-
specific methylation in vivo is further complicated by studies
showing the existence of multiple isoforms of DNMT3b, some
of which are inactive in vitro (1). In our present study, we could
not examine different DNMT3b isoforms due to the lack of
specific antisera; however, the ICM has the potential to resolve
these issues in a biologically relevant context.
The availability of monospecific mouse antibodies allowed
us to compare several DNMT isoforms in the murine system.
Our data show that DNMT1, -3a, -3b, and -2 stably and spe-
cifically bind aza-dC-substituted genomes, suggesting that
these are all active transmethylases in mouse P19 embryonic
carcinoma cells (Fig. 6). Based upon the ICM assay, it appears
that, after 8 h of aza-dC treatment, DNMT3b displayed con-
siderably higher (four- to fivefold) global activity than did
DNMT2 and -3a; however, DNMT3b expression was about
half the levels of DNMT3a and DNMT2. A possible explana-
tion is that the endogenous catalytic activity of each DNMT is
regulated by other proteins or by accessibility of a DNA target
in chromatin (recently reviewed in reference 29). For example,
DNMT3b colocalizes to pericentromeric heterochromatin,
which, as a repetitive element, may represent a localized sink
for DNMT3b activity. Alternatively, this may simply be a
unique feature of embryonic carcinoma cells; however, recent
results showing that DNMT3b works coordinately with
DNMT1 in maintaining genomic methylation states (28) sup-
port the notion that DNMT3b and -1 are operating at higher
levels in vivo.
In the two species tested (human and mouse), our data
suggest that DNMT2 is a catalytically active transmethylase in
a chromosomal setting. DNMT2 is extremely well conserved,
and a homolog exists in Drosophila melanogaster. Moreover, it
has recently been reported that the fly genome contains
5-methyl cytosine (11, 19); thus, it is logical to presume that a
functional methylase exists, although none has been reported.
Additional support for this idea comes from reports that
aza-dC is cytotoxic in D. melanogaster (17). As noted, DNMT2
is thus far the most highly conserved of all DNMTs containing
key motifs found in other active methyltransferases (conserved
proline-cysteine dipeptide active sites, for example). DNMT2
homologs have been found in plants, yeast, flies, mice, and
humans (29); thus, given its evolutionary conservation, detect-
ing catalytic activity in humans and mice might predict its
FIG. 6. Comparing endogenous DNMTs in mouse cells. (A) P19
cell cultures in exponential growth (4 ⫻10
7
/dish) were treated with 0,
0.5, 5, or 20 M aza-dC for 8 h. Half of the cultures were subjected to
the ICM analysis (slot blots labeled ICM on top) by using anti-DNMT
probes indicated on the left. Nuclear extracts were prepared (from
duplicate cultures) and were analyzed by SDS-polyacrylamide gel elec-
trophoresis and Western blotting by using the probes shown on the
left. For the Western blots (150 g of protein per lane) only the 0 and
0.5 M aza-dC samples are shown. For the ICM analysis, all concen-
trations of aza-dC titration are shown, with use of a fixed amount of
DNA in each slot (3 or 0.3 g as indicated). (B) An admixture of
antibodies was used for two P19 nuclear extracts (150 g/lane) pre-
pared from cells treated with 0 or 0.5 M aza-dC (8 h).
VOL. 23, 2003 IN VIVO ACTION OF DNMT 2717
activity in the fruit fly. Clearly additional studies will be nec-
essary to resolve these issues.
The time course of DNMT1-DNA complex formation fol-
lowing addition of aza-dC showed that DNMT1 adducts were
consistently higher after short exposure to aza-dC and that,
with time, the adduct formation decreased to a lower (but
stable) level. A logical interpretation is that short drug expo-
sures may saturate the genome with all active DNMT1; thus,
adduct accumulation is maximum early. The subsequent reduc-
tion in total DNMT1-DNA adducts suggests two possibilities:
first, we cannot rule out that aza-dC- treated cells are simply
dying off due to cytotoxic consequences of the drug; however,
we note that, under our experimental conditions (5 M aza-
dC), we did not detect an increase in dead cells (compared to
negative controls) by flow cytometry in the first 24 h following
drug addition (data not shown). After 24 h, we start to see a
time-dependent increase in cell death and apoptosis. Second,
the reduction in adducts might also suggest that they are
healed or repaired. If this is the case, we conclude that these
adducts are perceived and that sites of DNA damage (9, 15, 16)
and cellular mechanisms exist to deal with DNMT1-DNA ad-
duct formation. A precedent for cellular mechanisms that re-
verse covalent protein-DNA adducts has been reported in eu-
karyotes (14, 26, 40); therefore, it seems likely that enzymatic
(or other) means exist to reverse (or repair) the DNMT1-DNA
adducts. The finding that aza-dC stimulates recombination in
the fruit fly (24, 25) further suggests that recombination repair
may be the adduct reversal that we report here. These reversal
pathways are of obvious importance to the application of hy-
pomethylating drugs in the treatment of cancer. Further eval-
uation of the biological consequences of DNMT1 adducts in
repair- proficient and -deficient cell lines is ongoing to examine
this specific point (Wang and Muller, unpublished).
ACKNOWLEDGMENTS
We thank B. Vogelstein and S. Baylin (Johns Hopkins University)
for generously providing the HCT-116 cell lines used in this study. We
also thank Christoph Plass (Ohio State University) and Keith Robert-
son (National Cancer Institute) for helpful discussions, reagents, and
input on this work and X. Cheng (Emory University) for providing an
anti-DNMT2 antibody probe.
REFERENCES
1. Aoki, A., I. Suetake, J. Miyagawa, T. Fujio, T. Chijiwa, H. Sasaki, and S.
Tajima. 2001. Enzymatic properties of de novo type mouse DNA (cyto-
sine-5) methyltransferases. Nucleic Acids Res. 29:3506–3512.
2. Baylin, S. B., M. Esteller, M. R. Rountree, K. E. Bachman, K. Schuebel and
J. G. Herman. 2001. Aberrant patterns of DNA methylation, chromatin
formation and gene expression in cancer. Hum. Mol. Genet. 10:687–692.
3. Belinsky, S. A., K. J. Nikula, W. A. Palmisano, R. Michels, G. Saccomanno,
E. Gabrielson, S. B. Baylin, and J. G. Herman. 1998. Aberrant methylation
of p16INK4a is an early event in lung cancer and a potential biomarker for
early diagnosis. Proc. Natl. Acad. Sci. USA 95:11891–11896.
4. Bestor, T. 2000. The DNA methyltransferases of mammals. Hum. Mol.
Genet. 9:2395–2402.
5. Bonfils, C., N. Beaulieu, E. Chan, J. Cotton-Montpetit, and A. R. MacLeod.
2000. Characterization of the human DNA methyltransferase splice variant
Dnmt1b. J. Biol. Chem. 275:10754–10760.
6. Brank, A. S., R. Eritja, R. G. Barcia, V. E. Marquez, and J. K. Christman.
2002. Inhibition of HhaI DNA (Cytosine-C5) methyltransferase by oligode-
oxyribonucleotides containing 5-aza-2⬘-deoxycytidine: examination of the in-
tertwined roles of co-factor, target, transition state structure and enzyme
conformation. J. Mol. Biol. 323:53–67.
7. Costello, J. F., and C. Plass. 2001. Methylation matters. J. Med. Genet.
38:285–303.
8. Dong, A. Y., J. A. Yoder, A. Zhang, L. Zhou, T. H. Bestor, and X. Cheng.
2001. Structure of human DNMT2, an enigmatic DNA methyltransferase
homolog that displays denaturant-resistant binding to DNA. Nucleic Acids
Res. 29:439–448.
9. Ferguson, A., P. Vertino, J. Spitzner, S. Baylin, M. Muller, and N. Davidson.
1997. Role of estrogen receptor gene demethylation and DNA methyltrans-
ferase-DNA adduct formation in 5⬘-aza-2⬘deoxycytidine-induced cytoxicity
in human breast cancer cells. J. Biol. Chem. 272:32260–32266.
10. Gabbara, S., and A. S. Bhagwat. 1995. The mechanism of inhibition of DNA
(cytosine-5-)-methyltransferase by 5-azacytosine is likely to involve methyl
transfer to the inhibitor. Biochem. J. 307:87–92.
11. Gowher, H., O. Leismann, and A. Jeltsch. 2000. DNA of Drosophila mela-
nogaster contains 5-methylcytosine. EMBO J. 19:6918–6923.
12. Hsieh, C.-L. 1999. In vivo activity of murine de novo methyltransferases,
Dnmt3a and Dnmt3b. Mol. Cell. Biol. 19:8211–8218.
13. Hsu, D.-W., M.-J. Lin, T.-L. Lee, S.-C. Wen, X. Chen, and C.-K. J. Shen.
1999. Two major forms of DNA (cytosine-5) methyltransferase in human
somatic tissues. Proc. Natl. Acad. Sci. USA 96:9751–9756.
14. Interthal, H., J. J. Pouliot, and J. J. Champoux. 2001. The tyrosyl-DNA
phosphodiesterase Tdp 1 is a member of the phospholipase D superfamily.
Proc. Natl. Acad. Sci. USA 98:12009–12014.
15. Juttermann, R., E. Li, and R. Jaenisch. 1994. Toxicity of 5-aza-2⬘-deoxycy-
tidine to mammalian cells is mediated primarily by covalent trapping of
DNA methyltransferase rather than DNA demethylation. Proc. Natl. Acad.
Sci. USA 91:11797–11801.
16. Karpf, A. R., B. C. Moore, T. O. Ririe, and D. A. Jones. 2001. Activation of
the p53 DNA damage response pathway after inhibition of DNA methyl-
transferase by 5-aza-2⬘-deoxycytidine. Mol. Pharmacol. 59:751–757.
17. Katz, A. J. 1985. Genotoxicity of 5-azacytidine in somatic cells of Drosophila.
Mutat. Res. 143:195–199.
18. Li, E., T. Bestor, and R. Jaenisch. 1992. Targeted mutation of the DNA
methyltransferase gene results in embryonic lethality. Cell 69:915–926.
19. Lyko, F., B. H. Ramsahoye, and R. Jaenisch. 2000. DNA methylation in
Drosophila melanogaster. Nature 408:538–540.
20. Mao, Y., S. Okada, L. Chang, and M. T. Muller. 2000. p53 dependence of
topoisomerase I recruitment in vivo. Cancer Res. 60:4538–4543.
21. Okano, M., D. Bell, D. Haber, and E. Li. 1999. DNA methyltransferases
Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian
development. Cell 99:247–257.
22. Okano, M., S. Xie, and E. Li. 1998. Dnmt2 is not required for de novo and
maintenance methylation of viral DNA in ES cells. Nucleic Acids Res.
26:2536–2540.
23. Ordway, J. M., and T. Curran. 2002. Methylation matters: modeling a man-
ageable genome. Cell Growth Differ. 13:149–162.
24. Osgood, C. J., and S. M. Seward. 1989. 5-Azacytidine induces sex chromo-
some loss and interchange in immature germ cells of Drosophila mei-9
males. Environ. Mol. Mutag. 14:135–145.
25. Pontecorvo, G., A. Avitabile, G. Esposito, G. Migliaccio, and M. Carfagna.
1992. Induced crossing-over in Drosophila melanogaster germ cells of DNA
repair-proficient and repair-deficient (mei-9L1) males following larval feed-
ing with 5-azacytidine and mitomycin C. Mutat. Res. 266:93–98.
26. Pouliot, J. J., K. C. Yao, C. A. Robertson, and H. A. Nash. 1999. Yeast gene
for a tyr-DNA phosphodiesterase that repairs topoisomerase I complexes.
Science 286:552–555.
27. Rhee, I., K. Jair, R. Yen, C. Lengauer, J. Herman, K. Kinzler, B. Vogelstein,
S. Baylin, and K. E. Schuebel. 2001. CpG methylation is maintained in
human cancer cells lacking DNMT1. Nature 404:1003–1007.
28. Rhee, I., K. E. Bachman, B. H. Park, K. W. Jair, R. W. Yen, K. E. Schuebel,
H. Cui, A. P. Feinberg, C. Langeur, K. W. Kinzler, S. B. Baylin, and B.
Vogelstein. 2002. DNMT1 and DNMT3b cooperate to silence genes in hu-
man cancer cells. Nature 416:552–556.
29. Robertson, K. D. 2002. DNA methylation and chromatin—unraveling the
tangled web. Oncogene 21:5361–5379.
30. Robertson, K. D. 2001. DNA methylation, methyltransferases, and cancer.
Oncogene 20:3139–3155.
31. Robertson, K., et al. 1999. The human DNA methyltransferases (DNMTs) 1,
3a and 3b: coordinate mRNA expression in normal tissues and overexpres-
sion in tumors. Nucleic Acids Res. 27:2291–2298.
32. Rosenstein, B. S., D. Subramanian, and M. T. Muller. 1997. The involve-
ment of topoisomerase I in the induction of DNA-protein crosslinks and
DNA single-strand breaks in cells of ultraviolet-irradiated human and frog
cell lines. Radiat. Res. 148:575–579.
33. Santi, D., C. E. Garrett, and P. J. Barr. 1983. On the mechanism of inhibition
of DNA-cytosine methyltransferases by cytosine analogs. Cell 33:9–15.
34. Santi, D. V., A. Normant, and C. E. Garrett. 1984. Covalent bond formation
between a DNA-cytosine methyltransferase and DNA containing 5-azacy-
tosine. Proc. Natl. Acad. Sci. USA 81:6993–6997.
35. Subramanian, D., E. Kraut, A. Staubus, D. Young, and M. T. Muller. 1995.
Analysis of topoisomerase I complexes in patients being treated with topo-
tecan. Cancer Res. 55:2097–2103.
36. Subramanian, D., C. Sommer Furbee, and M. T. Muller. 2000. ICE bioassay.
Isolating in vivo complexes of enzyme to DNA. Methods Mol. Biol. 95:137–
147.
37. Subramanian, D., B. Rosenstein, and M. T. Muller. 1998. Ultraviolet-in-
2718 LIU ET AL. MOL.CELL.BIOL.
duced DNA damage stimulates topoisomerase I-DNA complex formation in
vivo: possible relationship with DNA repair. Cancer Res. 58:976–984.
38. Trask, D. K., J. A. DiDonato, and M. T. Muller. 1984. Rapid detection and
isolation of covalent DNA/protein complexes: application to topoisomerase
I and II. EMBO J. 3:671–676.
39. Trask, D. K., and M. T. Muller. 1988. Stabilization of type I topoisomerase-
DNA covalent complexes by actinomycin D. Proc. Natl. Acad. Sci. USA
85:1417–1421.
40. Yang, S., A. B. Burgin, B. N. Huizenga, C. A. Robertson, K. C. Yao, and H. A.
Nash. 1996. A eukaryotic enzyme that can disjoin dead-end covalent com-
plexes between DNA and type I topoisomerases. Proc. Natl. Acad. Sci. USA
93:11534–11539.
VOL. 23, 2003 IN VIVO ACTION OF DNMT 2719
