Carcinogenesis vol.23 no.7 pp.1103–1109, 2002
The impact of chromatin in human cancer: linking DNA
methylation to gene silencing
Esteban Ballestar and Manel Esteller1
Cancer Epigenetics Laboratory, Molecular Pathology Program, Centro
Nacional de Investigaciones Oncologicas, 28029 Madrid, Spain
1To whom correspondence should be addressed
For decades, chromatin was considered to be an inert
structure whose only role was the compacting and confining
progress in this field over the last 10 years has dramatically
elevated chromatin to a key position in the control of gene
activity. Its role in mediating the transformation of a
On one side of this story there is the discovery that aberrant
methylation patterns in an increasing number of tumour
suppressor and DNA repair genes determine carcinogenetic
transformation; while on the other side, there is the exist-
ence of a series of methyl-DNA binding activities that
recruit co-repressor complexes and modify the structure
of the chromatin to produce a transcriptionally silenced
state. Although this field has seen rapid progress in recent
years, detailed mechanisms by which this machinery modi-
fies chromatin structure to its appropriate state and the
specific targeting of repressor complexes have yet to be
resolved. In this review we present the models of how
repressor complexes may modify chromatin structure and
mediate silencing of tumour suppressor and DNA repair
DNA methylation involvement in cancer has become one of
the hottest topics in cancer research. A major breakthrough in
the field within the last 5 years has been the recognition of
the key role of chromatin as a mediator between DNA
methylation and transcriptional silencing of genes relevant to
cancer. The spectacular progress over the past decade in
research in the areas of chromatin and DNA methylation has
prepared the ground for the meeting of two traditionally
Progress in the field of chromatin research: from an inert
structure to an active entity
For decades, chromatin roles were limited to DNA compaction
and subsequent gene repression. In the 1970s, a combination
of physical and molecular biology techniques revealed that
chromatin consists of a repetitive nucleoprotein complex, the
nucleosome (1). This particle comprises a histone octamer,
with two copies of each of the histones H2A, H2B, H3 and
H4, wrapped by 147 bp of DNA. In the octamer, histones H3
and H4 are assembled in a tetramer, which is flanked by two
Abbreviations: DMT, DNA methyltransferases; HATS, histone acetyltrans-
ferases; HDACs, histone deacetylases; MBD, methyl-CpG binding domain.
© Oxford University Press
H2A–H2B dimers. A variable length of DNA completes the
second turn around the histone octamer and interacts with a
fifth histone, named H1. After the discovery of the nucleosome,
subsequent structural studies refined our knowledge of its
structure. The chromatin, a monotonous array of nucleosomes,
according to early models, seemed to be a static structure in
which little room was left for regulatory functions of gene
activity. Once the repetitive nature of the chromatin had
been defined and its structural details delineated, interest in
chromatin decreased. Much of the effort on transcriptional
regulation during the 1980s focused on the further definition
of cis-acting elements and trans-acting factors involved in the
transcription process (see ref. 2 for review). A remarkable
exception to the little progress made in chromatin research
during those years was the recognition of the existence of
strict nucleosome positioning around eukaryotic genes, which
suggested that histones might have specific effects on the
transcription process. The early 1990s witnessed the high-
resolution description of the histone octamer, the protein
component of the nucleosome (3). The new data showed the
existence of an architectural motif, the histone fold, which is
shared by all core histones, and is responsible for their
dimerization within the octamer. Furthermore, the histone fold
was also found in several regulatory proteins. Their assembly
into nucleosomal structures may confer specialized functions
on individual chromosomal domains (4). In addition, the
existence of histone variants, encoded by multiple genes,
contributes to a unique nucleosomal architecture, and this
heterogeneity can be exploited to regulate a wide range of
nuclear functions (4). Another important source of heterogen-
eity in chromatin is provided by the occurrence of histone
modifications at their protruding N-termini. Although histone
acetylation has been known since the mid 1960s (5) and its
relationship with transcriptional activation was long suspected,
its exact consequences have remained unclear for years.
This has partly been because attempts to isolate histone
acetyltransferases (HATs) and histone deacetylases (HDACs)
failed for almost three decades. Acetylation, the major post-
translational modification of histones, occurs at the lysine
residues of their highly conserved N-terminal tails. This
modification reduces the positive net charge of the histones
and was originally thought to weaken histone–DNA contacts
facilitating accessibility to transcriptional factors (6). Although
it is not clear that acetylation affects intranucleosomal contacts,
the discovery that histone acetylation does alleviate the repress-
ive effects of chromatin enhanced the interest in the role of
nucleosomes in gene control. During the mid 1990s HATs and
HDACs started to be isolated and cloned (7). HATs and
HDACs were shown to be components of large co-activator
and co-repressor complexes. The isolation of HAT and HDAC
complexes shed light on the mechanisms by which chromatin
is modified in order to yield a transcriptionally active or
inactive structure. In parallel, other histone post-translational
modifications, such as phosphorylation and methylation have
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Received December 21, 2001; revised and accepted February 12, 2002