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NATURE GENETICS|VOLUME 37 |NUMBER 3 |MARCH 2005 21 1

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 265of this issue,

Yu et al.1show that progress toward under-

standing an important mechanism thought to

underlie human cancer, aberrant CpG islandmethylation, 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 genomicalterations, 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 methylation4. But which

among the hundreds of aberrantly methyl-

ated genes contribute to cancer? To address

this question, Yu et al.1turned 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

cells5. Thirty percent of these preleukemicmice 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-spottingTo 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 time6. Toidentify the CpG islands and their associated

genes, Yu et al.1used 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 thosein human leukemias.

Tumor suppressor ID 4 ALLHuman leukemias are driven in part by chro-

mosomal translocations or hyperploidy, but

additional changes, potentially epigenetic

in nature, are probably also required9. From

their extensive RLGS data, Yu et al.1focused

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 faithfullyrecapitulates 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 NormalTumor 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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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 proteins10,11. ID4expression

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 ID4downregulation 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 astrocytes12. 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-expressingcells 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 mice11.

The role of ID4 in cancer seems to be much

more complicated. In mammary carcinoma

cells, for example, ID4 expression confers

features of transformation10, an effect oppo-

site to that expected for a tumor suppressor.

An oncogenic role has also been attributed to

ID4 in human seminomas10. 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

cancer14. Considering also the data from Yuet

al., the effect of ID4 on cell growth and trans-

formation seems to be context-dependent,

stimulating growth in some cell types whileinhibiting 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. USA88, 9523

9527 (1991).

7. Rush, L.J. et al. Cancer Res. 64, 24242433

(2004).

8. Rush, L.J. et al. Blood97, 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. Development131, 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. Oncogene22, 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. Regionsof the genome with high levels of methylated

CpG dinucleotides include the inactive X

chromosome in female mammals, imprinted

genes and transposons and their relics1, 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 colleagues2identify 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 partnerThe 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 characterized3.

If the MBD proteins have an important role

in interpreting the methylation mark on DNA,

then how do they translate this into functionalconsequences? 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 colleagues2 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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