NEWS AND VI EWS

NATURE GENETICS | VOLUME 37 | NUMBER 3 | MARCH 2005 211

Despite our perennial sense of pre-eminence
in the biological world, humans are markedly
similar to rodents. The field of comparative
genomics capitalizes on this fact to identify new
genes and gene regulatory elements. Just how
far can mice take us in understanding humans
and human disease? On page 265 of this issue,
Yu et al.
1
show that progress toward under-
standing an important mechanism thought to
underlie human cancer, aberrant CpG island
methylation, can be advanced substantially by
comparing cancer in mice and humans.
Methylation of cytosines in CpGs is a
normal modification of DNA that helps to
maintain the inactive state of a small subset
of genes and regulates others in response to
stimuli. Regions of the highest CpG content,
called CpG islands, often encompass gene pro-
moters but are usually unmethylated to allow
gene expression in normal cells. In human
cancers, however, a subset of CpG islands
become aberrantly methylated, occasionally
resulting in gene silencing
2,3
. Like genomic
alterations, CpG islands are methylated in a
nonrandom and tumor typespecific fashion
in human tumors, providing formal proof of
differential susceptibility to methylation or
selection of tumor cells that gained a growth
advantage through methylation
4
. But which
among the hundreds of aberrantly methyl-
ated genes contribute to cancer? To address
this question, Yu et al.
1
turned to our distant,
four-legged relatives.
Fehniger and Caligiuri previously created a
line of transgenic mice that undergo an early
expansion in natural killer cells and CD8
+
T
cells
5
. Thirty percent of these preleukemic
mice go on to develop a fatal lymphocytic
leukemia with some pathologic features in
common with human acute lymphoblas-
tic leukemia (ALL). Despite the differences
in the genetic lesions underlying this mouse
model and human leukemias, could the mouse
leukemias help us to understand the epigen-
etic abnormalities of their human counterparts
(Fig. 1)?
Methylation-spotting
To address these questions, Yu et al. used restric-
tion landmark genomic scanning (RLGS),
a reproducible two-dimensional gel-based
method for assessing the methylation status
of thousands of CpG islands at one time
6
. To
identify the CpG islands and their associated
genes, Yu et al.
1
used clones from an arrayed
mouse genomic library that are matched to
specific RLGS fragments.
Their first experiments showed no difference
in CpG island methylation between normal
cells and cells from the preleukemic mice. But
RLGS analysis of 2,447 CpG islands in eight
mouse leukemias showed extensive, nonran-
dom CpG island methylation, as reported for
human tumors including leukemias. Notably,
the overall frequency of methylated CpG
islands in the mouse leukemias (1.88.5%)
also approximated that reported in human
leukemias (08.3%; refs. 7,8). This suggests
that somewhere between early expansion and
leukemia lies the onset, and potentially the
cause, of aberrant CpG island methylation.
Although the overall methylation patterns were
quite similar, the specific methylated genes in
the mouse may be entirely different from those
in human leukemias.
Tumor suppressor ID 4 ALL
Human leukemias are driven in part by chro-
mosomal translocations or hyperploidy, but
additional changes, potentially epigenetic
in nature, are probably also required
9
. From
their extensive RLGS data, Yu et al.
1
focused
a more in-depth analysis on one of the most
commonly methylated genes in the mouse
leukemias, inhibitor of DNA binding 4 (Idb4
Comparative epigenomics of leukemia
Joseph F Costello
Proving that aberrant CpG island methylation has a functional role in human tumorigenesis is a chief goal in
cancer epigenomics. A study now shows that a predictable mouse model of acute lymphocytic leukemia faithfully
recapitulates the pattern, targets and frequency of aberrant methylation observed in its human counterpart and may
soon allow the timing, and perhaps even the cause, of aberrant CpG island methylation to be investigated.
75 million years
Sporadic cancer Induced cancer
RLGS RLGS
Normal Normal Tumor Tumor
Genes inactivated
by methylation
Figure 1 Cross-species approach to understanding cancer epigenomes. Parallel RLGS analyses of
cancers from mice and humans identify new tumor-suppressor genes silenced by methylation (circled
RLGS spots), whose functional importance can then be tested in mice (large arrow).
Joseph F. Costello is in The Brain Tumor
Research Center, Dept. of Neurological Surgery,
Comprehensive Cancer Center, University of
California, San Francisco, California, USA.
e-mail: jcostello@cc.ucsf.edu

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NEWS AND VI EWS
212 VOLUME 37 | NUMBER 3 | MARCH 2005 | NATURE GENETICS
in mouse, ID4 in human). ID genes encode
a subclass of helix-loop-helix proteins that
lack the basic DNA-binding domain and
act as dominant-negative regulators of basic
helix-loop-helix proteins
10,11
. ID4 expression
was downregulated in the mouse and human
leukemias; this downregulation involved vari-
ous levels of aberrant methylation in the ID4
promoter in both organisms. Further data sug-
gested that ID4 downregulation may be a more
general feature in human leukemias, as specific
analysis of human ALL was not reported.
To establish ID4 as a new tumor suppres-
sor, it was necessary to show that ID4 expres-
sion suppresses tumor growth. Clues to how
this might occur came in part from previous
observations that ID4 induces apoptosis in
cultures of astrocytes
12
. Yu and colleagues
then showed that overexpression of ID4 in
an established mouse lymphoid cell line in
low-serum conditions substantially increased
apoptosis, as predicted. These ID4-expressing
cells also had a diminished capacity to grow
as subcutaneous tumors in NOD-SCID mice,
further suggesting that ID4 may act as a tumor
suppressor in xenografts. But it is also possible
that the forced expression of exogenous ID4
might exceed a physiologically relevant level
and have nonspecific effects. Further proof is
needed to confirm that ID4 is a tumor suppres-
sor, potentially using ID4 knock-down in an
appropriate ID4 expressing leukemia cell line
or crossing leukemia-prone mice with viable
ID4-knockout mice
11
.
The role of ID4 in cancer seems to be much
more complicated. In mammary carcinoma
cells, for example, ID4 expression confers
features of transformation
10
, an effect oppo-
site to that expected for a tumor suppressor.
An oncogenic role has also been attributed to
ID4 in human seminomas
10
. More puzzling
is the fact that ID4 is overexpressed in a few
human leukemias; one case involved a specific
translocation of ID4 (ref. 13). In contrast, ID4
is downregulated by methylation in gastric
cancer
14
. Considering also the data from Yu et
al., the effect of ID4 on cell growth and trans-
formation seems to be context-dependent,
stimulating growth in some cell types while
inhibiting growth in others.
The unexpected commonality of the over-
all patterns, frequency and targets of aberrant
methylation identified in this cross-species
approach supports the use of mouse models
to understand the functional role of aberrant
methylation in human cancer. Mouse models of
cancer should also help to determine whether
the specific pattern of aberrant methylation is
influenced by a property of the cell type being
transformed or the particular transforming
gene. Questions aside, 70 million years may
not be so long after all.
1. Yu, L. et al. Nat. Genet. 37, 265274 (2005).
2. Baylin, S. & Bestor, T.H. Cancer Cell 1, 299305
(2002).
3. Jones, P.A. & Baylin, S.B. Nat. Rev. Genet. 3, 415428
(2002).
4. Costello, J.F. et al. Nat. Genet. 24, 132138 (2000).
5. Fehniger, T.A. et al. J. Exp. Med. 193, 219231
(2001).
6. Hatada, I., Hayashizaki, Y., Hirotsune, S., Komatsubara,
H. & Mukai, T. Proc. Natl. Acad. Sci. USA 88, 9523
9527 (1991).
7. Rush, L.J. et al. Cancer Res. 64, 24242433
(2004).
8. Rush, L.J. et al. Blood 97, 32263233 (2001).
9. Pui, C.H., Relling, M.V. & Downing, J.R. N. Engl. J.
Med. 350, 15351548 (2004).
10. Lasorella, A., Uo, T. & Iavarone, A. Oncogene 20,
83268333 (2001).
11. Yun, K., Mantani, A., Garel, S., Rubenstein, J. & Israel,
M.A. Development 131, 54415448 (2004).
12. Andres-Barquin, P.J., Hernandez, M.C. & Israel, M.A.
Exp. Cell. Res. 247, 347355 (1999).
13. Bellido, M. et al. Haematologica 88, 9941001
(2003).
14. Chan, A.S. et al. Oncogene 22, 69466953 (2003).
In eukaryotes, the most abundant covalent
modification of DNA is methylation of cyto-
sine residues at carbon 5 of the pyrimidine
ring. This modification occurs primarily in
the context of a simple sequence (5-CG-3)
and affects both strands of DNA. CpG meth-
ylation serves to increase the coding capacity
of the genomein essence, methylated car-
bon 5 serves as a fifth base in DNA. Regions
of the genome with high levels of methylated
CpG dinucleotides include the inactive X
chromosome in female mammals, imprinted
genes and transposons and their relics
1
, all of
which are associated with stable transcrip-
tional repression. How does the cell read this
information? Additionally, as CpG meth-
ylation is strongly associated with regions of
the genome subject to stable transcriptional
repression, how do cells convert the informa-
tion embedded in cytosine methylation into
a functional state? On page 254 of this issue,
Harikrishnan N and colleagues
2
identify an
association between the methyl CpG binding
protein MeCP2 and human Brahma (Brm),
an ATPase subunit of the human SWI/SNF
complex involved in chromatin remodeling.
These findings establish a link between DNA
methylation and chromatin structure and
provide a new perspective on the mechanism
of methylation-dependent gene regulation.
Silent partner
The information provided by CpG meth-
ylation in eukaryotic cells is interpreted, in
most cases, by a conserved family of proteins
that can interact specifically with methylated
CpG dinucleotides. This methyl CpG bind-
ing domain (MBD) family of proteins is pres-
ent in most eukaryotic organisms (a notable
exception being yeast, which do not methyl-
ate DNA), and its interaction with methylated
DNA has been rigorously characterized
3
.
If the MBD proteins have an important role
in interpreting the methylation mark on DNA,
then how do they translate this into functional
consequences? Several different mechanisms
have been proposed. First, the position of
methylated residues relative to nucleosomes
and their subsequent interaction with MBD
proteins might influence local nucleosome
position. Alternatively, the MBD protein fam-
ily could serve to recruit enzymatic machinery,
which alters the local properties of chromatin,
resulting in stable transcriptional repression.
Harikrishnan N and colleagues
2
focused
on the prototype methyl CpG binding pro-
tein MeCP2. MeCP2 has previously been
SWItching off methylated DNA
Paul A Wade
The mechanism by which cytosine methylation stably represses transcription is of great interest. A new study
provides evidence associating DNA methylation, MeCP2 and the SWI/SNF chromatin-remodeling factor, implicating
local chromatin architecture in DNA methylationdependent transcriptional repression.
Paul A. Wade is in the Laboratory of
Molecular Carcinogenesis, National Institute
of Environmental Health Sciences, Research
Triangle Park, North Carolina, 27709, USA.
e-mail: wadep2@niehs.nih.gov

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