Leading Edge

Review

Cancer Epigenetics:
From Mechanism to Therapy
Mark A. Dawson1,2 and Tony Kouzarides1,*
1Gurdon Institute and Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
2Department of Haematology, Cambridge Institute for Medical Research and Addenbrooke’s Hospital, University of Cambridge, Hills Road,
Cambridge CB2 0XY, UK
*Correspondence: [email protected]
http://dx.doi.org/10.1016/j.cell.2012.06.013

The epigenetic regulation of DNA-templated processes has been intensely studied over the last 15
years. DNA methylation, histone modification, nucleosome remodeling, and RNA-mediated target-
ing regulate many biological processes that are fundamental to the genesis of cancer. Here, we
present the basic principles behind these epigenetic pathways and highlight the evidence suggest-
ing that their misregulation can culminate in cancer. This information, along with the promising clin-
ical and preclinical results seen with epigenetic drugs against chromatin regulators, signifies that it
is time to embrace the central role of epigenetics in cancer.

Chromatin is the macromolecular complex of DNA and histone The information conveyed by epigenetic modifications plays
proteins, which provides the scaffold for the packaging of our a critical role in the regulation of all DNA-based processes,
entire genome. It contains the heritable material of eukaryotic such as transcription, DNA repair, and replication. Conse-
cells. The basic functional unit of chromatin is the nucleosome. quently, abnormal expression patterns or genomic alterations
It contains 147 base pairs of DNA, which is wrapped around in chromatin regulators can have profound results and can
a histone octamer, with two each of histones H2A, H2B, H3, lead to the induction and maintenance of various cancers. In
and H4. In general and simple terms, chromatin can be subdi- this Review, we highlight recent advances in our understanding
vided into two major regions: (1) heterochromatin, which is of these epigenetic pathways and discuss their role in oncogen-
highly condensed, late to replicate, and primarily contains inac- esis. We provide a comprehensive list of all the recurrent cancer
tive genes; and (2) euchromatin, which is relatively open and mutations described thus far in epigenetic pathways regulating
contains most of the active genes. Efforts to study the coordi- modifications of DNA (Figure 2), histones (Figures 3, 4, and 5),
nated regulation of the nucleosome have demonstrated that all and chromatin remodeling (Figure 6). Where relevant, we will
of its components are subject to covalent modification, which also emphasize existing and emerging drug therapies aimed at
fundamentally alters the organization and function of these basic targeting epigenetic regulators (Figure 1).
tenants of chromatin (Allis et al., 2007).
The term ‘‘epigenetics’’ was originally coined by Conrad Wad- Characterizing the Epigenome
dington to describe heritable changes in a cellular phenotype Our appreciation of epigenetic complexity and plasticity has
that were independent of alterations in the DNA sequence. dramatically increased over the last few years following the
Despite decades of debate and research, a consensus definition development of several global proteomic and genomic technol-
of epigenetics remains both contentious and ambiguous (Berger ogies. The coupling of next-generation sequencing (NGS) plat-
et al., 2009). Epigenetics is most commonly used to describe forms with established chromatin techniques such as chromatin
chromatin-based events that regulate DNA-templated pro- immunoprecipitation (ChIP-Seq) has presented us with a previ-
cesses, and this will be the definition we use in this review. ously unparalleled view of the epigenome (Park, 2009). These
Modifications to DNA and histones are dynamically laid technologies have provided comprehensive maps of nucleo-
down and removed by chromatin-modifying enzymes in a highly some positioning (Segal and Widom, 2009), chromatin confor-
regulated manner. There are now at least four different DNA mation (de Wit and de Laat, 2012), transcription factor binding
modifications (Baylin and Jones, 2011; Wu and Zhang, 2011) sites (Farnham, 2009), and the localization of histone (Rando
and 16 classes of histone modifications (Kouzarides, 2007; Tan and Chang, 2009) and DNA (Laird, 2010) modifications. In addi-
et al., 2011). These are described in Table 1. These modifications tion, NGS has revealed surprising facts about the mammalian
can alter chromatin structure by altering noncovalent interac- transcriptome. We now have a greater appreciation of the fact
tions within and between nucleosomes. They also serve as that most of our genome is transcribed and that noncoding
docking sites for specialized proteins with unique domains that RNA may play a fundamental role in epigenetic regulation (Ama-
specifically recognize these modifications. These chromatin ral et al., 2008).
readers recruit additional chromatin modifiers and remodeling Most of the complexity surrounding the epigenome comes
enzymes, which serve as the effectors of the modification. from the modification pathways that have been identified.

12 Cell 150, July 6, 2012 ª2012 Elsevier Inc.

Table 1. Chromatin Modifications, Readers, and Their Function
Chromatin Modification Nomenclature Chromatin-Reader Motif Attributed Function
DNA Modifications
5-methylcytosine 5mC MBD domain transcription
5-hydroxymethylcytosine 5hmC unknown transcription
5-formylcytosine 5fC unknown unknown
5-carboxylcytosine 5caC unknown unknown
Histone Modifications
Acetylation K-ac BromodomainTandem, transcription, repair, replication,
PHD fingers and condensation
Methylation (lysine) K-me1, K-me2, K-me3 Chromodomain, Tudor domain, transcription and repair
MBT domain, PWWP domain,
PHD fingers, WD40/b propeller
Methylation (arginine) R-me1, R-me2s, R-me2a Tudor domain transcription
Phosphorylation S-ph, T-ph 14-3-3, BRCT transcription, repair,
(serine and threonine) and condensation
Phosphorylation (tyrosine) Y-ph SH2a transcription and repair
Ubiquitylation K-ub UIM, IUIM transcription and repair
Sumoylation K-su SIMa transcription and repair
ADP ribosylation E-ar Macro domain, PBZ domain transcription and repair
Deimination R/Cit unknown transcription and decondensation
Proline isomerisation P-cis5P-trans unknown transcription
Crotonylation K-cr unknown transcription
Propionylation K-pr unknown unknown
Butyrylation K-bu unknown unknown
Formylation K-fo unknown unknown
Hyroxylation Y-oh unknown unknown
O-GlcNAcylation S-GlcNAc; T-GlcNAc unknown transcription
(serine and threonine)
Modifications: me1, monomethylation; me2, dimethylation; me3, trimethylation; me2s, symmetrical dimethylation; me2a, asymmetrical dimethylation;
and Cit, citrulline. Reader domains: MBD, methyl-CpG-binding domain; PHD, plant homeodomain; MBT, malignant brain tumor domain; PWWP,
proline-tryptophan-tryptophan-proline domain; BRCT, BRCA1 C terminus domain; UIM, ubiquitin interaction motif; IUIM, inverted ubiquitin interaction
motif; SIM, sumo interaction motif; and PBZ, poly ADP-ribose binding zinc finger.
a
These are established binding modules for the posttranslational modification; however, binding to modified histones has not been firmly established.

Recent improvements in the sensitivity and accuracy of mass et al., 2010; Ruthenburg et al., 2011). The latter approach in
spectrometry (MS) instruments have driven many of these particular has uncovered some of the rules governing the recruit-
discoveries (Stunnenberg and Vermeulen, 2011). Moreover, ment of protein complexes to methylated DNA and modified
although MS is inherently not quantitative, recent advances in histones in a nucleosomal context. The next step in our under-
labeling methodologies, such as stable isotope labeling by standing will require a high-resolution in vivo genomic approach
amino acids in cell culture (SILAC), isobaric tags for relative to detail the dynamic events on any given nucleosome during the
and absolute quantification (iTRAQ), and isotope-coded affinity course of gene expression.
tag (ICAT), have allowed a greater ability to provide quantitative
measurements (Stunnenberg and Vermeulen, 2011). Epigenetics and the Cancer Connection
These quantitative methods have generated ‘‘protein recruit- The earliest indications of an epigenetic link to cancer were
ment maps’’ for histone and DNA modifications, which contain derived from gene expression and DNA methylation studies.
proteins that recognize chromatin modifications (Bartke et al., These studies are too numerous to comprehensively detail in
2010; Vermeulen et al., 2010). Many of these chromatin readers this review; however, the reader is referred to an excellent review
have more than one reading motif, so it is important to under- detailing the history of cancer epigenetics (Feinberg and Tycko,
stand how they recognize several modifications either simulta- 2004). Although many of these initial studies were purely correl-
neously or sequentially. The concept of multivalent engagement ative, they did highlight a potential connection between epige-
by chromatin-binding modules has recently been explored netic pathways and cancer. These early observations have
by using either modified histone peptides (Vermeulen et al., been significantly strengthened by recent results from the Inter-
2010) or in-vitro-assembled and -modified nucleosomes (Bartke national Cancer Genome Consortium (ICGC). Whole-genome

Cell 150, July 6, 2012 ª2012 Elsevier Inc. 13

Figure 1. Epigenetic Inhibitors as Cancer Therapies
This schematic depicts the process for epigenetic drug development and the current status of various epigenetic therapies. Candidate small molecules are first
tested in vitro in malignant cell lines for specificity and phenotypic response. These may, in the first instance, assess the inhibition of proliferation, induction of
apoptosis, or cell-cycle arrest. These phenotypic assays are often coupled to genomic and proteomic methods to identify potential molecular mechanisms for the
observed response. Inhibitors that demonstrate potential in vitro are then tested in vivo in animal models of cancer to ascertain whether they may provide
therapeutic benefit in terms of survival. Animal studies also provide valuable information regarding the toxicity and pharmacokinetic properties of the drug. Based
on these preclinical studies, candidate molecules may be taken forward into the clinical setting. When new drugs prove beneficial in well-conducted clinical trials,
they are approved for routine clinical use by regulatory authorities such as the FDA. KAT, histone lysine acetyltransferase; KMT, histone lysine methyltransferase;
RMT, histone arginine methyltransferase; and PARP, poly ADP ribose polymerase.

sequencing in a vast array of cancers has provided a catalog of regulators have raised intriguing correlations between cancer-
recurrent somatic mutations in numerous epigenetic regulators associated DNA hypermethylation and genes marked with
(Forbes et al., 2011; Stratton et al., 2009). A central tenet in ‘‘bivalent’’ histone modifications in multipotent cells (Easwaran
analyzing these cancer genomes is the identification of ‘‘driver’’ et al., 2012; Ohm et al., 2007). These bivalent genes are marked
mutations (causally implicated in the process of oncogenesis). A by active (H3K4me3) and repressive (H3K27me3) histone modi-
key feature of driver mutations is that they are recurrently found fications (Bernstein et al., 2006) and appear to identify transcrip-
in a variety of cancers, and/or they are often present at a high tionally poised genes that are integral to development and
prevalence in a specific tumor type. We will mostly concentrate lineage commitment. Interestingly, many of these genes are
our discussions on suspected or proven driver mutations in targeted for DNA methylation in cancer. Equally intriguing are
epigenetic regulators. recent comparisons between malignant and normal tissues
For instance, malignancies such as follicular lymphoma from the same individuals. These data demonstrate broad
contain recurrent mutations of the histone methyltransferase domains within the malignant cells that contain significant alter-
MLL2 in close to 90% of cases (Morin et al., 2011). Similarly, ations in DNA methylation. These regions appear to correlate
UTX, a histone demethylase, is mutated in up to 12 histologi- with late-replicating regions of the genome associated with the
cally distinct cancers (van Haaften et al., 2009). Compilation of nuclear lamina (Berman et al., 2012). Although there remains little
the epigenetic regulators mutated in cancer highlights histone mechanistic insight into how and why these regions of the
acetylation and methylation as the most widely affected epige- genome are vulnerable to epigenetic alterations in cancer, these
netic pathways (Figures 3 and 4). These and other pathways studies highlight the means by which global sequencing plat-
that are affected to a lesser extent will be described in the forms have started to uncover avenues for further investigation.
following sections. Genetic lesions in chromatin modifiers and global alterations in
Deep sequencing technologies aimed at mapping chromatin the epigenetic landscape not only imply a causative role for
modifications have also begun to shed some light on the origins these proteins in cancer but also provide potential targets for
of epigenetic abnormalities in cancer. Cross-referencing of therapeutic intervention. A number of small-molecule inhibitors
DNA methylation profiles in human cancers with ChIP-Seq have already been developed against chromatin regulators
data for histone modifications and the binding of chromatin (Figure 1). These are at various stages of development, and three

14 Cell 150, July 6, 2012 ª2012 Elsevier Inc.

of these (targeting DNMTs, HDACs, and JAK2) have already
been granted approval by the US Food and Drug Administra-
tion (FDA). This success may suggest that the interest in epige-
netic pathways as targets for drug discovery had been high
over the past decade. However, the reality is that the field of
drug discovery had been somewhat held back due to concerns
over the pleiotropic effects of both the drugs and their targets.
Indeed, some of the approved drugs (against HDACs) have little
enzyme specificity, and their mechanism of action remains
contentious (Minucci and Pelicci, 2006).
The belief and investment in epigenetic cancer therapies may
now gain momentum and reach a new level of support following
the recent preclinical success of inhibitors against BRD4, an
acetyl-lysine chromatin-binding protein (Dawson et al., 2011;
Delmore et al., 2011; Filippakopoulos et al., 2010; Mertz et al.,
2011; Zuber et al., 2011). The molecular mechanisms governing
these impressive preclinical results have also been largely
uncovered and are discussed below. This process is pivotal for
the successful progression of these inhibitors into the clinic.
Figure 2. Cancer Mutations Affecting Epigenetic Regulators of DNA
These results, along with the growing list of genetic lesions in
Methylation
epigenetic regulators, highlight the fact that we have now The 5-carbon of cytosine nucleotides are methylated (5mC) by a family of
entered an era of epigenetic cancer therapies. DNMTs. One of these, DNMT3A, is mutated in AML, myeloproliferative
diseases (MPD), and myelodysplastic syndromes (MDS). In addition to its
catalytic activity, DNMT3A has a chromatin-reader motif, the PWWP domain,
Epigenetic Pathways Connected to Cancer which may aid in localizing this enzyme to chromatin. Somatically acquired
DNA Methylation mutations in cancer may also affect this domain. The TET family of DNA
The methylation of the 5-carbon on cytosine residues (5mC) in hydroxylases metabolizes 5mC into several oxidative intermediates, including
5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carbox-
CpG dinucleotides was the first described covalent modifica-
ylcytosine (5caC). These intermediates are likely involved in the process of
tion of DNA and is perhaps the most extensively characterized active DNA demethylation. Two of the three TET family members are mutated
modification of chromatin. DNA methylation is primarily noted in cancers, including AML, MPD, MDS, and CMML. Mutation types are as
within centromeres, telomeres, inactive X-chromosomes, and follows: M, missense; F, frameshift; N, nonsense; S, splice site mutation; and
T, translocation.
repeat sequences (Baylin and Jones, 2011; Robertson, 2005).
Although global hypomethylation is commonly observed in
malignant cells, the best-studied epigenetic alterations in cancer
are the methylation changes that occur within CpG islands, Three active DNA methyltransferases (DNMTs) have been
which are present in
70% of all mammalian promoters. CpG identified in higher eukaryotes. DNMT1 is a maintenance methyl-
island methylation plays an important role in transcriptional regu- transferase that recognizes hemimethylated DNA generated
lation, and it is commonly altered during malignant transforma- during DNA replication and then methylates newly synthesized
tion (Baylin and Jones, 2011; Robertson, 2005). NGS platforms CpG dinucleotides, whose partners on the parental strand are
have now provided genome-wide maps of CpG methylation. already methylated (Li et al., 1992). Conversely, DNMT3a and
These have confirmed that between 5%–10% of normally unme- DNMT3b, although also capable of methylating hemimethylated
thylated CpG promoter islands become abnormally methylated DNA, function primarily as de novo methyltransferases to estab-
in various cancer genomes. They also demonstrate that CpG lish DNA methylation during embryogenesis (Okano et al., 1999).
hypermethylation of promoters not only affects the expression DNA methylation provides a platform for several methyl-binding
of protein coding genes but also the expression of various proteins. These include MBD1, MBD2, MBD3, and MeCP2.
noncoding RNAs, some of which have a role in malignant trans- These in turn function to recruit histone-modifying enzymes
formation (Baylin and Jones, 2011). Importantly, these genome- to coordinate the chromatin-templated processes (Klose and
wide DNA methylome studies have also uncovered intriguing Bird, 2006).
alterations in DNA methylation within gene bodies and at Although mutations in DNA methyltransferases and MBD
CpG ‘‘shores,’’ which are conserved sequences upstream and proteins have long been known to contribute to developmental
downstream of CpG islands. The functional relevance of these abnormalities (Robertson, 2005), we have only recently become
regional alterations in methylation are yet to be fully deciphered, aware of somatic mutations of these key genes in human malig-
but it is interesting to note that they have challenged the nancies (Figure 2). Recent sequencing of cancer genomes has
general dogma that DNA methylation invariably equates with identified recurrent mutations in DNMT3A in up to 25% of
transcriptional silencing. In fact, these studies have established patients with acute myeloid leukemia (AML) (Ley et al., 2010).
that many actively transcribed genes have high levels of DNA Importantly, these mutations are invariably heterozygous and
methylation within the gene body, suggesting that the context are predicted to disrupt the catalytic activity of the enzyme.
and spatial distribution of DNA methylation is vital in transcrip- Moreover, their presence appears to impact prognosis (Patel
tional regulation (Baylin and Jones, 2011). et al., 2012). However, at present, the mechanisms by which

Cell 150, July 6, 2012 ª2012 Elsevier Inc. 15

these mutations contribute to the development and/or mainte- have a role in both transcriptional activation and silencing,
nance of AML remains elusive. the TET proteins have also been shown to have activating
Understanding the cellular consequences of normal and aber- and repressive functions (Wu and Zhang, 2011). Genome-wide
rant DNA methylation remains a key area of interest, especially mapping of TET1 has demonstrated it to have a strong prefer-
because hypomethylating agents are one of the few epigenetic ence for CpG-rich DNA and, consistent with its catalytic function,
therapies that have gained FDA approval for routine clinical it also been localized to regions enriched for 5mC and 5hmC.
use (Figure 1). Although hypomethylating agents such as azaci- The TET family of proteins derive their name from the
tidine and decitabine have shown mixed results in various solid initial description of a recurrent chromosomal translocation,
malignancies, they have found a therapeutic niche in the myelo- t(10;11)(q22;q23), which juxtaposes the MLL gene with TET1 in
dysplastic syndromes (MDS). Until recently, this group of disor- a subset of patients with AML (Lorsbach et al., 2003). Notably,
ders was largely refractory to therapeutic intervention, and MDS concurrent to the initial description of the catalytic activity for
was primarily managed with supportive care. However, several the TET family of DNA hydroxylases, several reports emerged
large studies have now shown that treatment with azacitidine, describing recurrent mutations in TET2 in numerous hematolog-
even in poor prognosis patients, improves their quality of life ical malignancies (Cimmino et al., 2011; Delhommeau et al.,
and extends survival time. Indeed, azacitidine is the first therapy 2009; Langemeijer et al., 2009) (Figure 2). Interestingly, TET2-
to have demonstrated a survival benefit for patients with MDS deficient mice develop a chronic myelomonocytic leukemia
(Fenaux et al., 2009). The molecular mechanisms governing the (CMML) phenotype, which is in keeping with the high prevalence
impressive responses seen in MDS are largely unknown. of TET2 mutations in patients with this disease (Moran-Crusio
However, recent evidence would suggest that low doses of et al., 2011; Quivoron et al., 2011). The clinical implications of
these agents hold the key to therapeutic benefit (Tsai et al., TET2 mutations have largely been inconclusive; however, in
2012). It is also emerging that the combinatorial use of DNMT some subsets of AML patients, TET2 mutations appear to confer
and HDAC inhibitors may offer superior therapeutic outcomes a poor prognosis (Patel et al., 2012). Early insights into the
(Gore, 2011). process of TET2-mediated oncogenesis have revealed that the
DNA Hydroxy-Methylation and Its Oxidation Derivatives patient-associated mutations are largely loss-of-function muta-
Historically, DNA methylation was generally considered to tions that consequently result in decreased 5hmC levels and
be a relatively stable chromatin modification. However, early a reciprocal increase in 5mC levels within the malignant cells
studies assessing the global distribution of this modification that harbor them. Moreover, mutations in TET2 also appear to
during embryogenesis had clearly identified an active global confer enhanced self-renewal properties to the malignant clones
loss of DNA methylation in the early zygote, especially in the (Cimmino et al., 2011).
male pronucleus. More recently, high-resolution genome-wide Histone Modifications
mapping of this modification in pluripotent and differentiated In 1964, Vincent Allfrey prophetically surmised that histone
cells has also confirmed the dynamic nature of DNA methylation, modifications might have a functional influence on the regulation
evidently signifying the existence of an enzymatic activity within of transcription (Allfrey et al., 1964). Nearly half a century later,
mammalian cells that either erases or alters this chromatin the field is still grappling with the task of unraveling the mecha-
modification (Baylin and Jones, 2011). In 2009, two seminal nisms underlying his enlightened statement. In this time, we
manuscripts describing the presence of 5-hydroxymethylcyto- have learned that these modifications have a major influence,
sine (5hmC) offered the first insights into the metabolism of not just on transcription, but in all DNA-templated processes
5mC (Kriaucionis and Heintz, 2009; Tahiliani et al., 2009). (Kouzarides, 2007). The major cellular processes attributed to
The ten-eleven translocation (TET 1–3) family of proteins have each of these modifications are summarized in Table 1.
now been demonstrated to be the mammalian DNA hydroxy- The great diversity in histone modifications introduces a
lases responsible for catalytically converting 5mC to 5hmC. remarkable complexity that is slowly beginning to be eluci-
Indeed, iterative oxidation of 5hmC by the TET family results in dated. Using transcription as an example, we have learned
further oxidation derivatives, including 5-formylcytosine (5fC) that multiple coexisting histone modifications are associated
and 5-carboxylcytosine (5caC). Although the biological signifi- with activation, and some are associated with repression.
cance of the 5mC oxidation derivatives is yet to be established, However, these modification patterns are not static entities but
several lines of evidence highlight their importance in transcrip- a dynamically changing and complex landscape that evolves in
tional regulation: (1) they are likely to be an essential intermediate a cell context-dependent fashion. Moreover, active and repres-
in the process of both active and passive DNA demethylation, (2) sive modifications are not always mutually exclusive, as evi-
they preclude or enhance the binding of several MBD proteins denced by ‘‘bivalent domains.’’ The combinatorial influence
and, as such, will have local and global effects by altering that one or more histone modifications have on the deposition,
the recruitment of chromatin regulators, and (3) genome-wide interpretation, or erasure of other histone modifications has
mapping of 5hmC has identified a distinctive distribution of this been broadly termed ‘‘histone crosstalk,’’ and recent evidence
modification at both active and repressed genes, including its would suggest that crosstalk is widespread and is of great bio-
presence within gene bodies and at the promoters of bivalently logical significance (Lee et al., 2010).
marked, transcriptionally poised genes (Wu and Zhang, 2011). It should be noted that the cellular enzymes that modify
Notably, 5hmC was also mapped to several intergenic cis-regu- histones may also have nonhistone targets and, as such, it has
latory elements that are either functional enhancers or insulator been difficult to divorce the cellular consequences of individual
elements. Consistent with the notion that 5hmC is likely to histone modifications from the broader targets of many of these

16 Cell 150, July 6, 2012 ª2012 Elsevier Inc.

enzymes. In addition to their catalytic function, many chromatin
modifiers also possess ‘‘reader’’ domains allowing them to bind
to specific regions of the genome and respond to information
conveyed by upstream signaling cascades. This is important,
as it provides two avenues for therapeutically targeting these
epigenetic regulators. The residues that line the binding pocket
of reader domains can dictate a particular preference for
specific modification states, whereas residues outside the
binding pocket contribute to determining the histone sequence
specificity. This combination allows similar reader domains to
dock at different modified residues or at the same amino acid
displaying different modification states. For example, some
methyl-lysine readers engage most efficiently with di/tri-methyl-
ated lysine (Kme2/3), whereas others prefer mono- or unmethy-
lated lysines. Alternatively, when the same lysines are now acet-
ylated, they bind to proteins containing bromodomains (Taverna
et al., 2007). The main modification binding pockets contained
within chromatin-associated proteins is summarized in Table 1.
Many of the proteins that modify or bind these histone modifi-
cations are misregulated in cancer, and in the ensuing sections,
we will discuss the most extensively studied histone modifica-
tions in relation to oncogenesis and novel therapeutics.
Histone Acetylation. The Nε-acetylation of lysine residues is
a major histone modification involved in transcription, chromatin
structure, and DNA repair. Acetylation neutralizes lysine’s posi-
tive charge and may consequently weaken the electrostatic
interaction between histones and negatively charged DNA. For
this reason, histone acetylation is often associated with a more
‘‘open’’ chromatin conformation. Consistent with this, ChIP- Figure 3. Cancer Mutations Affecting Epigenetic Regulators
Seq analyses have confirmed the distribution of histone acetyla- Involved in Histone Acetylation
These tables provide somatic cancer-associated mutations identified in
tion at promoters and enhancers and, in some cases, throughout
histone acetyltransferases and proteins that contain bromodomains (which
the transcribed region of active genes (Heintzman et al., 2007; recognize and bind acetylated histones). Several histone acetyltransferases
Wang et al., 2008). Importantly, lysine acetylation also serves possess chromatin-reader motifs and, thus, mutations in the proteins may
as the nidus for the binding of various proteins with bromodo- alter both their catalytic activities as well as the ability of these proteins to
scaffold multiprotein complexes to chromatin. Interestingly, sequencing of
mains and tandem plant homeodomain (PHD) fingers, which cancer genomes to date has not identified any recurrent somatic mutations in
recognize this modification (Taverna et al., 2007). histone deacetylase enzymes. Abbreviations for the cancers are as follows:
Acetylation is highly dynamic and is regulated by the AML, acute myeloid leukemia; ALL, acute lymphoid leukemia; B-NHL, B-cell
non-Hodgkin’s lymphoma; DLBCL, diffuse large B-cell lymphoma; and TCC,
competing activities of two enzymatic families, the histone transitional cell carcinoma of the urinary bladder. Mutation types are as
lysine acetyltransferases (KATs) and the histone deacetylases follows: M, missense; F, frameshift; N, nonsense; S, splice site mutation; T,
(HDACs). There are two major classes of KATs: (1) type-B, which translocation; and D, deletion.
are predominantly cytoplasmic and modify free histones, and (2)
type-A, which are primarily nuclear and can be broadly classified
into the GNAT, MYST, and CBP/p300 families. some cases, such as the leukemia-associated fusion gene
KATs were the first enzymes shown to modify histones. The MOZ-TIF2, we know a great deal about the cellular conse-
importance of these findings to cancer was immediately quences of this translocation involving a MYST family member.
apparent, as one of these enzymes, CBP, was identified by its MOZ-TIF2 is sufficient to recapitulate an aggressive leukemia
ability to bind the transforming portion of the viral oncoprotein in murine models; it can confer stem cell properties and reacti-
E1A (Bannister and Kouzarides, 1996). It is now clear that vate a self-renewal program when introduced into committed
many, if not most, of the KATs have been implicated in neoplastic hematopoietic progenitors, and much of this oncogenic potential
transformation, and a number of viral oncoproteins are known is dependent on its inherent and recruited KAT activity as well as
to associate with them. There are numerous examples of recur- its ability to bind to nucleosomes (Deguchi et al., 2003; Huntly
rent chromosomal translocations (e.g., MLL-CBP [Wang et al., et al., 2004).
2005] and MOZ-TIF2 [Huntly et al., 2004]) or coding mutations Despite these insights, the great conundrum with regards to
(e.g., p300/CBP [Iyer et al., 2004; Pasqualucci et al., 2011]) unraveling the molecular mechanisms by which histone acetyl-
involving various KATs in a broad range of solid and hematolog- transferases contribute to malignant transformation has been
ical malignancies (Figure 3). Furthermore, altered expression dissecting the contribution of altered patterns in acetylation on
levels of several of the KATs have also been noted in a range histone and nonhistone proteins. Although it is clear that global
of cancers (Avvakumov and Côté, 2007; Iyer et al., 2004). In histone acetylation patterns are perturbed in cancers (Fraga

Cell 150, July 6, 2012 ª2012 Elsevier Inc. 17

et al., 2005; Seligson et al., 2005), it is also well established that Histone Acetylation Readers. The primary readers of Nε-acet-
several nonhistone proteins, including many important onco- ylation of lysine residues are families of proteins that contain an
genes and tumor suppressors such as MYC, p53, and PTEN, evolutionarily conserved binding motif termed a bromodomain.
are also dynamically acetylated (Choudhary et al., 2009). A prag- There are over 40 described human proteins with bromodomains
matic view on this issue is that both histone and nonhistone (Chung and Witherington, 2011). These comprise a diverse
acetylation are likely to be important and, in most part, the group of proteins that function as chromatin remodelers, histone
abundance of substrates has not deterred the enthusiasm for acetyltransferases, histone methyltransferases, and transcrip-
the development of histone acetyltransferase inhibitors (KAT-I). tional coactivators. Many of these proteins also contain several
Although there is only modest structural homology between separate evolutionarily conserved ‘‘chromatin-reading’’ motifs
the different families of KATs, developing specific inhibitors such as PHD fingers, which recognize distinct histone posttrans-
has proven to be fraught with frustration (Cole, 2008). However, lational modifications (Table 1).
recent progress with derivatives of the naturally occurring KAT-I, Until recently, it had not been feasible to therapeutically target
such as curcumin, anacardic acid, and garcinol, as well as the protein-protein interactions with small molecules. However,
synthesis of novel chemical probes, suggest that therapeutically several recent studies have shown that it is possible to develop
targeting the various KATs with some specificity is likely to be highly specific and chemically distinct small molecules against
achieved in the near future (Cole, 2008). the BET family (BRD2, BRD3, BRD4, and BRDt) of bromodo-
Histone Deacetylation. HDACs are enzymes that reverse lysine main proteins (Dawson et al., 2011; Filippakopoulos et al.,
acetylation and restore the positive charge on the side chain. 2010; Nicodeme et al., 2010). The BET family shares a common
There are 18 such enzymes identified, and these are subdivided structural composition featuring tandem amino-terminal bromo-
into four major classes, depending on sequence homology. domains that exhibit high levels of sequence conservation. BET
Class I (HDAC 1-3 and HDAC8) and class II (HDAC 4-7 and proteins play a fundamental role in transcriptional elongation
HDAC 9-10) represent the HDACs most closely related to yeast and cell-cycle progression. Moreover, recurrent translocations
scRpd3 and scHda1, respectively, whereas class IV comprises involving BRD3/4 are associated with the aggressive and invari-
only one enzyme, HDAC11. Class I, II, and IV HDACs share a ably fatal NUT-midline carcinoma (Filippakopoulos et al., 2010)
related catalytic mechanism that requires a zinc metal ion but (Figure 3).
does not involve the use of a cofactor. In contrast, class III Targeting the BET bromodomains is a promising therapeutic
HDACs (sirtuin 1–7) are homologous to yeast scSir2 and employ avenue in cancer. The BET inhibitors have recently been shown
a distinct catalytic mechanism that is NAD+-dependent. Analo- to have excellent efficacy in NUT-midline carcinoma (Filippako-
gous to the KATs, HDACs target both histone and nonhistone poulos et al., 2010) and in a range of hematological malignancies
proteins. Substrate specificity for these enzymes is largely medi- (Dawson et al., 2011; Delmore et al., 2011; Mertz et al., 2011;
ated by components of multisubunit complexes in which HDACs Zuber et al., 2011). A central theme reported in all of the studies
are found, such as Mi2/NuRD, Sin3A, and Co-REST (Bantscheff thus far is the downregulation of MYC transcription following
et al., 2011; Xhemalce et al., 2011). BET inhibition. MYC is a master regulator of cell proliferation
In the context of malignancy, chimeric fusion proteins that are and survival; it is also one of the most common genes dysregu-
seen in leukemia, such as PML-RARa, PLZF-RARa, and AML1- lated in cancer (Meyer and Penn, 2008). Following BET inhibition
ETO, have been shown to recruit HDACs to mediate aberrant with either RNAi or specific BET inhibitors, the expression of
gene silencing, which contributes to leukemogenesis (John- MYC was noted to be substantially decreased in a variety of
stone and Licht, 2003). HDACs can also interact with nonchi- malignant hematopoietic cell lines, including MLL-translocated
meric oncogenes such as BCL6, whose repressive activity is acute myeloid leukemia (Dawson et al., 2011; Zuber et al.,
controlled by dynamic acetylation (Bereshchenko et al., 2002). 2011), multiple myeloma (Delmore et al., 2011), and Burkitt’s
Importantly, inhibitors of histone deactylases (HDAC-I) are able lymphoma (Mertz et al., 2011). Furthermore, murine models of
to reverse some of the aberrant gene repression seen in these diseases confirmed the excellent therapeutic efficacy of
these malignancies and induce growth arrest, differentiation, BET inhibition in vivo.
and apoptosis in the malignant cells (Federico and Bagella, Although MYC has a prominent role in these diseases, it is
2011; Johnstone and Licht, 2003). Based on impressive preclin- unlikely that the profound effects observed by BET inhibition
ical and clinical data, two pan-HDAC inhibitors, Vorinostat and are solely mediated by MYC inhibition. There are many malignant
Romidepsin, have recently been granted FDA approval (Olsen cell lines that overexpress MYC yet fail to respond to BET inhibi-
et al., 2007; Piekarz et al., 2009) for clinical use in patients with tion (Mertz et al., 2011); MYC expression is not always affected
cutaneous T cell lymphoma (Figure 1). Although somatic muta- by BET inhibition (Mertz et al., 2011); MYC is often equally
tions in HDACs do not appear to be prominent in cancer downregulated in responsive and nonresponsive malignant cell
(Figure 3), the expression levels of various HDACs appear to lines (Dawson et al., 2011; Zuber et al., 2011); and, importantly,
be altered in numerous malignancies. Consequently, several MYC overexpression fails to rescue the apoptosis induced by
novel HDAC inhibitors are currently under investigation for clin- BET inhibition (Zuber et al., 2011). The molecular mechanisms
ical use in a broad range of cancers (Federico and Bagella, 2011; governing the efficacy of BET inhibition are slowly being deci-
Johnstone and Licht, 2003). However, the pleiotropic effects of phered. What seems to be clear from the current analyses is
HDACs continue to pose significant challenges in dissecting the that BET inhibitors specifically regulate a small number of genes,
specific effects on histone and nonhistone proteins (Bantscheff and inhibition of transcriptional elongation may be a primary
et al., 2011). mode of action.

18 Cell 150, July 6, 2012 ª2012 Elsevier Inc.

 Histone Methylation. Histones are methylated on the side
chains of arginine, lysine, and histidine residues. Methylation,
unlike acetylation and phosphorylation, does not alter the
overall charge of the molecule. Lysines may be mono-, di-, or
tri-methylated, and arginine residues may be symmetrically
or asymmetrically methylated. The best-characterized sites of
histone methylation are those that occur on lysine residues
and, therefore, these will be the focus of this section. Although
many lysine residues on the various histones are methylated,
the best studied are H3K4, H3K9, H3K27, H3K36, H3K79, and
H4K20. Some of these (H3K4, H3K36, and H3K79) are often
associated with active genes in euchromatin, whereas others
(H3K9, H3K27, and H4K20) are associated with heterochromatic
regions of the genome (Barski et al., 2007). Different methylation
states on the same residue can also localize differently. For
instance, H3K4me2/3 usually spans the transcriptional start
site (TSS) of active genes (Barski et al., 2007), whereas
H3K4me1 is a modification associated with active enhancers
(Heintzman et al., 2009). Similarly, whereas monomethylation
of H3K9 may be seen at active genes, trimethylation of H3K9
is associated with gene repression (Barski et al., 2007).
The enzymatic protagonists for lysine methylation contain a
conserved SET domain, which possesses methyltransferase
activity. The only exception to this is hDOT1L, the enzyme that
methylates H3K79. In contrast to the KATs, the histone lysine
methyltransferases (KMT) tend to be highly specific enzymes
that specifically target certain lysine residues. Cytogenetic
studies, as well as NGS of various cancer genomes, have
demonstrated recurrent translocations and/or coding mutations
in a large number of KMT, including MMSET, EZH2, and MLL
family members (Figure 4).
Whereas the oncogenic effects exerted by the MLL fusions
have been extensively studied and reviewed (Krivtsov and Arm-
strong, 2007), an emerging area of interest is the dichotomous
role of EZH2 in human malignancies. EZH2 is the catalytic
component of the PRC2 complex, which is primarily responsible
for the methylation of H3K27. Early gene-expression studies
implicated the overexpression of EZH2 as a progressive event
that conferred a poor prognosis in prostate and breast cancer
(Margueron and Reinberg, 2011). These initial studies sug-
gested that EZH2 was an oncogene. However, NGS and tar-
geted resequencing of cancer genomes have recently identified
coding mutations within EZH2 in various lymphoid and myeloid Figure 4. Cancer Mutations Affecting Epigenetic Regulators
neoplasms that have somewhat muddied the waters by Involved in Histone Methylation
suggesting both oncogenic and tumor-suppressive roles for Recurrent mutations in histone methyltransferases, demethylases, and
methyllysine binders have been identified in a large number of cancers. These
EZH2. Heterozygous missense mutations resulting in the mutations may significantly alter the catalytic activity of the methyltransferases
substitution of tyrosine 641 (Y641) within the SET domain of or demethylases. In addition, as many of these enzymes also contain chro-
EZH2 were noted in 22% of patients with diffuse large B-cell matin-reader motifs, they may also affect the ability of these proteins to survey
and bind epigenetic modifications. Abbreviations for the cancers are as
lymphoma (Morin et al., 2010). Functional characterization of follows: AML, acute myeloid leukemia; ALL, acute lymphoid leukemia; B-NHL,
this mutation demonstrated that it conferred increased cata- B-cell non-Hodgkin’s lymphoma; DLBCL, diffuse large B-cell lymphoma;
lytic activity and a preference for converting H3K27me1 to HNSCC, head and neck squamous cell carcinoma; FL, follicular lymphoma;
H3K27me2/3, again supporting the contention that EZH2 is an MDS, myelodysplastic syndromes; MPD, myeloproliferative diseases; and
TCC, transitional cell carcinoma of the urinary bladder. Mutation types are as
oncogene (Sneeringer et al., 2010). In contrast, loss-of-function follows: M, missense; F, frameshift; N, nonsense; S, splice site mutation; T,
mutations in EZH2 gene, conferring a poor prognosis, have translocation; D, deletion; and PTD, partial tandem duplication.
been described in the myeloid malignancies (Ernst et al.,
2010; Nikoloski et al., 2010) and T-ALL (Ntziachristos et al., The precise mechanisms by which gain and loss of EZH2
2012; Zhang et al., 2012), suggesting a tumor-suppressive activity culminate in cancers are an area of active investigation.
role for EZH2 in these cell lineages. In light of the varied roles that polycomb proteins play in

Cell 150, July 6, 2012 ª2012 Elsevier Inc. 19

self-renewal and differentiation (Margueron and Reinberg, 2011), is a competitive inhibitor of the a-KG-dependent dioxygenases;
solution of this problem will necessitate vigilance and apprecia- in fact, 2-HG has been shown to adopt a near-identical orienta-
tion of the cellular context within which the mutations arise. The tion within the catalytic core of the JmjC domain (Xu et al., 2011).
increased awareness of the involvement of KMTs in cancer has As 2-HG levels accumulate within the malignant cells, there is
heightened efforts to identify specific inhibitors. These efforts a purported blanket inhibition of the Jumonji class of histone
will only be encouraged by the recent demonstration that demethylases. Accordingly, there is a discernable increase in
small-molecule inhibition of DOT1L shows preclinical promise histone methylation levels (Xu et al., 2011). These remarkable
as a targeted therapy in MLL leukemia (Daigle et al., 2011), findings are yet to be fully investigated, and it will be important
a disease in which aberrant DOT1L activity is ill defined but to determine whether all the Jumonji family members are equally
clearly involved (Krivtsov and Armstrong, 2007). susceptible to 2-HG inhibition. A similar question can be posed
Histone Demethylation. The initial notion that histone lysine for the TET family of enzymes (see above), which also use a-ke-
methylation was a highly stable, nondynamic modification has toglutarate.
now been irrefutably overturned by the identification of two Histone Methylation Readers. The various states of lysine
classes of lysine demethylases (Mosammaparast and Shi, methylation result in considerable physicochemical diversity of
2010). The prima facie example, LSD1 (KDM1A), belongs to lysine; these modification states are read and interpreted by
the first class of demethylases that demethylates lysines via an proteins containing different specialized recognition motifs.
amine oxidation reaction with flavin adenine dinucleotide (FAD) Broadly speaking, the aromatic cages that engage methyllysine
as a cofactor. As this family of enzymes requires a protonated can be divided into two major families, the Royal Family (Tudor
nitrogen to initiate demethylation, they are limited to demethylat- domains, Chromo domains, and malignant brain tumor [MBT]
ing mono- and dimethyllysine. The second and more expansive domains) and PHD fingers. The structural composition of these
class of enzymes is broadly referred to as the Jumonji demethy- domains that allows for this diversity has recently been expertly
lases. They have a conserved JmjC domain, which functions via reviewed (Taverna et al., 2007).
an oxidative mechanism and radical attack (involving Fe(II) and Analogous to the situation with bromodomain proteins,
a-ketoglutarate). The Jumonji family does not require a free several methyllysine readers have also been implicated in cancer
electron pair on the nitrogen atom to initiate catalysis and, (Figure 4). For instance, all three isoforms of the chromodomain
therefore, unlike LSD1, they can demethylate all three methyl protein HP1 have altered expression in numerous cancers (Dia-
lysine states. Unsurprisingly, the multisubunit complexes within lynas et al., 2008). However, thus far, no cancer-specific somatic
which these enzymes reside confer much of their target speci- mutations have been identified in HP1. In contrast, ING family
ficity. As an example, LSD1 can function as a transcriptional members have had coding mutations identified in malignancies
repressor by demethylating H3K4me1/2 as part of the core- such as melanoma and breast cancer, including those that
pressor for RE1-silencing transcription factor (Co-REST) com- specifically target the PHD finger, which recognizes H3K4me3
plex, but its activity is linked to gene activation when it associ- (Coles and Jones, 2009). Despite these findings, neither of the
ates with the androgen receptor to demethylate H3K9me2 aforementioned examples establishes a causal relationship
(Mosammaparast and Shi, 2010). Thus far, recurrent coding between cancer and the abrogation of methyllysine binding at
mutations have been noted in KDM5A (JARID1A), KDM5C chromatin. The best example of this, and indeed a proof of
(JARID1C), and KDM6A (UTX) (Figure 4). Mutations in UTX, in principle for therapeutically targeting methyllysine binders, has
particular, are prevalent in a large number of solid and hemato- recently been shown in a specific form of AML (Wang et al.,
logical cancers. Small-molecule inhibitors of the two families of 2009). Leukemia, induced by the fusion of NUP98 with the
histone demethylases are at various stages of development, PHD finger containing part of JARID1A or PHF23, can be abro-
and this interest will be spurred on by emerging preclinical gated by mutations that negate the ability of the PHD finger to
data showing the therapeutic potential of compounds that inhibit bind H3K4me3. Functional compensation of this effect can be
LSD1/KDM1A in AML (Barretina et al., 2012; Schenk et al., 2012). provided by other PHD fingers that recognize this modification,
Interestingly, recent findings related to recurrent mutations in but not those that do not bind H3K4me3. Moreover, mechanistic
the genes encoding the metabolic enzymes isocitrate dehydro- insights were provided, demonstrating that chromatin binding of
genase-1 (IDH1) and IDH2 have broad implications for the the fusion protein inhibits the deposition of H3K27me3, which
Jumonji class of demethylases, which use a-ketoglutarate leads to the continued expression of critical hematopoietic
(a-KG). IDH1/2 are nicotinamide adenine dinucleotide phos- oncogenes such as HoxA9, Meis1, and Pbx1 (Wang et al.,
phate (NADP)-dependent enzymes that normally catalyze the 2009). In light of these findings, and as result of the structural
oxidative decarboxylation of isocitrate to a-KG, which is associ- diversity present in methyllysine-binding modules, it is likely
ated with the production of NADPH. Mutations in IDH1 and IDH2 that small molecules that disrupt this important protein-protein
are seen in up to 70% of patients with secondary glioblastoma interaction may be effective anticancer agents.
mutiforme and are also noted as recurrent mutations in a range Histone Phosphorylation. The phosphorylation of serine, thre-
of myeloid malignancies, most notably AML (Cimmino et al., onine, and tyrosine residues has been documented on all core
2011). These mutations manifest in a neomorphic enzymatic and most variant histones. Phosphorylation alters the charge
activity that results in the NADPH-dependent reduction of of the protein, affecting its ionic properties and influencing the
a-KG to 2-hydroxyglutarate (2-HG). Consequently, malignant overall structure and function of the local chromatin environ-
cells with IDH1/2 mutations may harbor 2-HG levels that are ment. The phosphorylation of histones is integral to essential
up to 100-fold higher than normal (Cimmino et al., 2011). 2-HG cellular processes such as mitosis, apoptosis, DNA repair,

20 Cell 150, July 6, 2012 ª2012 Elsevier Inc.

 been given a broader application in other malignancies, such
as Hodgkin’s disease and primary mediastinal B-cell lymphoma,
in which this mechanism has been shown to contribute to onco-
genesis (Rui et al., 2010). Given that many small-molecule
inhibitors against kinases are clinically used as anticancer thera-
pies, it is interesting to note that several of these (e.g., JAK2 and
Aurora inhibitors) result in a global reduction in the histone modi-
fications laid down by these enzymes. These agents can there-
fore be considered as potential epigenetic therapies.
Histone phosphorylation is a highly dynamic posttranslational
modification, which is reciprocally controlled by the competing
activities of protein kinases and protein phosphatases. Phos-
phatases, like protein kinases, demonstrate specificity for either
serine/threonine residues or tyrosine residues, or they may have
dual specificity; they are further subdivided based on their
requirement for a metallic ion for their catalytic activity. Although
there is little doubt that histone phosphatases are integral to
chromatin biology, outside of the realm of DNA repair and regu-
lation of mitosis, little is currently known about the function of
these enzymes at chromatin and their potential misadventures
in cancer (Xhemalce et al., 2011).
Figure 5. Cancer Mutations Affecting Epigenetic Regulators The phosphorylation sites on serine, threonine, and tyrosine
Involved in Histone Phosphorylation residues may serve as the binding site for a range of cellular
Recurrent mutations in signaling kinases are one of the most frequent onco-
genic events found in cancer. Some of these kinases signal directly to chro- proteins. Proteins such as MDC1 bind at sites of double-strand
matin. Activating and inactivating mutations of these have been noted in breaks by tethering to gH2AX via its tandem BRCT domain
a range of malignancies. Thus far, BRCA1, which contains a BRCT domain, is (Stucki et al., 2005). Furthermore, the 14-3-3 family of proteins,
the only potential phosphochromatin reader recurrently mutated in cancer. It
should be noted, however, that BRCA1 binding to modified histones via its
of which there are seven mammalian isoforms, contain highly
BRCT domain has not yet been firmly established. As our knowledge about conserved phosphoserine-binding modules which some, such
histone phosphatases and phosphohistone binders increases, we are likely to as 14-3-3z, use to bind H3S10ph and H3S28ph. Many of these
find mutations in many of these proteins that contribute to oncogenesis.
proteins, including 14-3-3z, are abnormally expressed in various
Abbreviations for the cancers are as follows: AML, acute myeloid leukemia;
ALL, acute lymphoid leukemia; CML, chronic myeloid leukemia; NHL, non- human malignancies and, consequently, therapeutically target-
Hodgkin’s lymphoma; MPD, myeloproliferative diseases; and T-PLL, T cell ing them may prove beneficial (Yang et al., 2012).
prolymphocytic leukemia. Mutation types are as follows: M, missense; F, Cancer Mutations in Histone Genes
frameshift; N, nonsense; S, splice site mutation; T, translocation; and D,
deletion. Two recent studies have demonstrated recurrent somatic muta-
tions in genes encoding the replication-independent histone H3
variant H3.3 (H3F3A) and the canonical histone H3.1 (HIST1H3B)
replication, and transcription. Generally speaking, the specific in up to one-third of pediatric glioblastomas (Schwartzentruber
histone phosphorylation sites on core histones can be divided et al., 2012; Wu et al., 2012). These mutations are invariably
into two broad categories: (1) those involved in transcription heterozygous and are clustered such that they primarily result
regulation, and (2) those involved in chromatin condensation. in amino acid substitutions at two critical residues in the tail
Notably, several of these histone modifications, such as of histone H3 (K27M, G34R/G34V). By virtue of the residues
H3S10, are associated with both categories (Baek, 2011). they disrupt, these mutations are likely to have an important
Kinases are the main orchestrators of signal transduction influence on chromatin structure and transcription. The K27M
pathways conveying extracellular cues within the cell. Altered mutation alters the ability of this critical residue to be both meth-
expression, coding mutations, and recurrent translocations ylated and acetylated. These posttranslational modifications of
involving signaling kinases are some of the most frequent onco- H3K27 have different genomic distributions within euchromatin
genic phenomena described in cancer (Hanahan and Weinberg, and heterochromatin; they are recognized by different epige-
2011). Many of these kinases have established roles as signal netic readers and are ultimately associated with different tran-
transducers in the cytoplasm; however, it has recently been scriptional outcomes. Similarly, it is also likely that the G34
recognized that some kinases may also have nuclear functions, mutations, due to their proximity to H3K36, will also influence
which include the phosphorylation of histones (Baek, 2011; Bun- transcription. In support of this contention is the fact that tumors
gard et al., 2010; Dawson et al., 2009) (Figure 5). One such carrying the K27M and G34R/G34V mutations had distinct gene-
enzyme is the nonreceptor tyrosine kinase, JAK2, which is expression profiles, and tumors with the G34V mutation demon-
frequently amplified or mutated in the hematological malignan- strated a global increase in H3K36me3 (Schwartzentruber et al.,
cies. Within the nucleus, JAK2 specifically phosphorylates 2012).
H3Y41, disrupts the binding of the chromatin repressor HP1a, These studies also raise several interesting mechanistic ques-
and activates the expression of hematopoietic oncogenes tions. For instance, given that there are several copies of genes
such as Lmo2 (Dawson et al., 2009). These findings have now encoding for histone H3.1/3.3 within our genome, why do these

Cell 150, July 6, 2012 ª2012 Elsevier Inc. 21

mutated histone proteins get incorporated into nucleosomes?
How do these mutated proteins influence the function of histone
chaperones, nucleosome assembly, stability, and mobility? One
possibility uncovered from these studies suggests that telomere
maintenance and heterochromatin stability may be compro-
mised as a consequence of the H3.3 mutations. Several of
these pediatric glioblastoma multiforme (GBMs) also harbored
mutations in the ATRX/DAXX chromatin-remodeling complex,
which is responsible for the deposition of H3.3. These tumors
with mutations in H3F3A/ATRX/DAXX were associated with
increased alternative lengthening of telomeres and genomic
instability (Schwartzentruber et al., 2012). The ATRX/DAXX
mutations described here are also a seminal feature of pancre-
atic neuroendocrine tumors (Jiao et al., 2011) and highlight
emerging evidence suggesting that mutations in members of
chromatin-remodeling complexes are a common feature in
human malignancy.
Chromatin Remodelers
The myriad of covalent modifications on the nucleosome often
provides the scaffold and context for dynamic ATP-dependent
chromatin remodeling. Based on their biochemical activity and
subunit composition, the mammalian chromatin-remodeling
complexes can be broadly split into four major families: the
switching defective/sucrose nonfermenting (SWI/SNF) family,
Figure 6. Cancer Mutations Affecting Members of the SWI/SNF
the imitation SWI (ISWI) family, the nucleosome remodeling
Chromatin-Remodeling Complex
and deacetylation (NuRD)/Mi-2/chromodomain helicase DNA- SWI/SNF is a multisubunit complex that binds chromatin and disrupts histone-
binding (CHD) family, and the inositol requiring 80 (INO80) family. DNA contacts. The SWI/SNF complex alters nucleosome positioning and
These enzymes are evolutionarily conserved and use ATP as structure by sliding and evicting nucleosomes to make the DNA more
accessible to transcription factors and other chromatin regulators. Recurrent
an energy source to mobilize, evict, and exchange histones. mutations in several members of the SWI/SNF complex have been identified in
Each of these families has distinct domain structures and is a large number of cancers. Abbreviations for the cancers are as follows:
populated by members that contain various chromatin reader B-NHL, B-cell non-Hodgkin’s lymphoma; HNSCC, head and neck squamous
cell carcinoma; OCC, ovarian clear cell carcinoma; and TCC, transitional cell
motifs (SANT domains, bromodomains, and chromodomains)
carcinoma of the urinary bladder. Mutation types are as follows: M, missense;
that confer some regional and context specificity to their chro- F, frameshift; N, nonsense; S, splice site mutation; T, translocation; and D,
matin-remodeling activities (Wang et al., 2007). deletion.
Several members from the various chromatin-remodeling
families, such as SNF5 (Versteege et al., 1998), BRG1 (Wilson
and Roberts, 2011), and MTA1 (Li et al., 2012), were known to motility, and nuclear hormone signaling (Wilson and Roberts,
be mutated in malignancies, raising the possibility that they 2011).
may be bone fide tumor suppressors (Figure 6). Strong evidence Genetic evidence from mouse models has confirmed that
in support of this contention has now emerged from the altered expression of these purported tumor suppressors can
sequencing of cancer genomes. These efforts have highlighted increase the propensity to develop cancer. In the case of
high-frequency mutations in several SWI/SNF complex mem- BRG1, even haploinsufficiency results in increased tumors (Wil-
bers in a range of hematological (Chapman et al., 2011; Morin son and Roberts, 2011). However, despite the wealth of informa-
et al., 2011) and solid malignancies (Gui et al., 2011; Jones tion implicating the SWI/SNF complexes in cancer (Figure 6),
et al., 2010; Tan et al., 2011; Varela et al., 2011; Wang et al., there is no mechanistic evidence to demonstrate that altered
2011). The prevalence of these mutations would suggest that chromatin remodeling due to aberrant chromatin binding or
many of the members of these complexes are involved in the loss of ATPase activity is involved.
development and maintenance of cancer; however, functional Noncoding RNAs
insights into the mechanisms of oncogenesis are only just The high-throughput genomic platforms have established that
beginning to emerge. It is clear that the SWI/SNF complexes virtually the entire genome is transcribed; however, only
2%
have several lineage-specific subunits and interact with tissue- of this is subsequently translated (Amaral et al., 2008). The re-
specific transcription factors to regulate differentiation. They maining ‘‘noncoding’’ RNAs (ncRNAs) can be roughly catego-
also have a reciprocal and antagonistic relationship with the pol- rized into small (under 200 nucleotides) and large ncRNAs. These
ycomb complexes. One possibility, which remains to be formally RNAs are increasingly recognized to be vital for normal develop-
established, is that mutations in SWI/SNF members potentiate ment and may be compromised in diseases such as cancer. The
malignancy by skewing the balance between self-renewal and small ncRNAs include small nucleolar RNAs (snoRNAs), PIWI-
differentiation. Recent data would also suggest a role for the interacting RNAs (piRNAs), small interfering RNAs (siRNAs),
SWI/SNF complexes in regulating cell-cycle progression, cell and microRNAs (miRNAs). Many of these families show a high

22 Cell 150, July 6, 2012 ª2012 Elsevier Inc.

degree of sequence conservation across species and are the clinical arena. The first important issue is that of selectivity.
involved in transcriptional and posttranscriptional gene silencing How can ubiquitously expressed epigenetic regulators serve
through specific base pairing with their targets. In contrast, as selective targets? The answer may lie in the fact that epige-
the long ncRNAs (lncRNAs) demonstrate poor cross-species netic components control a small number of genes instead of
sequence conservation, and their mechanism of action in tran- having global effects on gene expression. For example, the
scriptional regulation is more varied. Notably, these lncRNAs BET protein inhibitors alter only a few hundred genes, and these
appear to have a critical function at chromatin, where they may genes differ depending on cell type (Dawson et al., 2011; Nico-
act as molecular chaperones or scaffolds for various chromatin deme et al., 2010). Thus, these drugs can disrupt a selective
regulators, and their function may be subverted in cancer set of genes. What remains uncertain and imperative to now
(Wang and Chang, 2011). learn is how these epigenetic regulators are targeted to these
One of the best-studied lncRNAs that emerges from the ‘‘essential’’ genes and what makes these genes solely reliant
mammalian HOXC cluster but invariably acts in trans is on certain epigenetic regulators.
HOTAIR. HOTAIR provides a concurrent molecular scaffold for Related to this issue is the observation that epigenetic inhibi-
the targeting and coordinated action of both the PRC2 complex tors lead to dramatic effects in malignant cells, though their
and the LSD1-containing CoREST/REST complex (Wang and normal counterparts remain largely unaltered. This suggests
Chang, 2011). HOTAIR is aberrantly overexpressed in advanced that, during normal homeostasis, epigenetic regulators function
breast and colorectal cancer (Kogo et al., 2011; Wang and in a multitiered and semiredundant manner, but in cancer, they
Chang, 2011), and manipulation of HOTAIR levels within malig- may be required to maintain the expression of a few key target
nant cells can functionally alter the invasive potential of these genes. A slight tip in the balance of this regulation is sufficient
cancers by changing PRC2 occupancy (Wang and Chang, to result in a cell catastrophe. This ‘‘epigenetic vulnerability’’ of
2011). An equally intriguing example that has broad implications certain cancer cells in many ways mirrors the age old axiom of
for both normal development and aberrant targeting of chro- ‘‘oncogene addiction’’ (Weinstein, 2002). Some cancer cells
matin complexes in cancer is the lncRNA HOTTIP. In contrast are reliant on specific epigenetic pathways, whereas normal
to HOTAIR, HOTTIP is expressed from the mammalian HOXA cells have alternative compensating pathways to rely on.
cluster and acts in cis to aid in the transcriptional activation of Finally, it is now also evident from both clinical and preclinical
the 50 HOXA genes (Wang and Chang, 2011). HOTTIP, by means studies that hematopoietic malignancies are clearly more vulner-
of chromatin looping, is brought into close proximity of the able to epigenetic interventions than solid malignancies. Thus,
50 HOXA genes and recruits MLL1 complexes to lay down not all cancers are equally susceptible to epigenetic therapies.
H3K4me3 and potentiate transcription. Given that the 50 HOXA The biology underpinning this observation urgently warrants
cluster plays a seminal role in development and maintenance our attention if epigenetic therapies are to be more widely appli-
of a large number of leukemias, these findings raise the possi- cable. Broadly speaking, even aggressive hematopoietic malig-
bility that abnormal expression and/or function of HOTTIP may nancies, such as AML, appear to harbor as few as ten coding
be a feature of these diseases. mutations; in contrast, the cancer genomes of solid malignan-
Discerning the molecular mechanisms and nuances of RNA- cies appear to be vastly more complex. Furthermore, the in vivo
protein interactions is a pivotal area of chromatin research, as niche occupied by hematopoietic cells offers a very different
the stereochemical nature of these interactions may in the future environment for drug exposure, and hematopoietic cells may
lend itself to specific targeting by innovative small molecules as metabolize these drugs differently than other tissues. Could
cancer therapies. these intrinsic cellular differences account for the varied efficacy
of these agents? Are these therapies being used appropriately in
Perspective and Conclusions the solid malignancies?
Information from global proteomic and genomic techniques has This latter question raises the more fundamental issue of
confirmed many of the hypotheses regarding the molecular rationally designed combination epigenetic therapies. It is likely
causes of cancer, but it has challenged others. The principal that many of these new epigenetic drugs offer synergistic bene-
tenet in oncology—that cancer is a disease initiated and driven fits, and these new therapies may also synergize with conven-
by genetic anomalies—remains uncontested, but it is now clear tional chemotherapies. This strategy of combination therapy
that epigenetic pathways also play a significant role in oncogen- may not only increase therapeutic efficacy but also reduce the
esis. One concern had been that the endpoint of these pathways likelihood of drug resistance.
may not necessarily be epigenetic. However, these concerns are The plethora of genetic lesions in epigenetic regulators offers
ameliorated by the multiplicity of mutations in epigenetic regu- many possible targets for drug discovery and will no doubt
lators, including chromatin-remodeling complexes, and the attract the attention of the pharmaceutical industry. However,
observation that histones themselves are mutated at sites of given the expense of the drug discovery process, what should
key modifications in cancer. In fact, it is now irrefutable that guide the choice of target? The ‘‘drugability’’ of enzymes has
many of the hallmarks of cancer, such as malignant self-renewal, traditionally biased this choice, but the current success of target-
differentiation blockade, evasion of cell death, and tissue inva- ing acetyl-readers may propel other modification readers (e.g.,
siveness are profoundly influenced by changes in the epige- methyl-readers) as the candidates of choice. In addition, one
nome. should not rely solely on the existence of genetic lesions to guide
Despite these assertions, there are still many questions to be the target for drug discovery. There are no genetic lesions re-
answered before we can use our current basic knowledge in ported in histone deacetylases, yet clinically safe and effective

Cell 150, July 6, 2012 ª2012 Elsevier Inc. 23

drugs have been developed against these enzymes. A potential Regions of focal DNA hypermethylation and long-range hypomethylation in
way forward is to use high-throughput genotype/phenotype drug colorectal cancer coincide with nuclear lamina-associated domains. Nat.
Genet. 44, 40–46.
discovery programs in cancer cells, as has been recently re-
ported (Barretina et al., 2012; Garnett et al., 2012). Bernstein, B.E., Mikkelsen, T.S., Xie, X., Kamal, M., Huebert, D.J., Cuff, J., Fry,
B., Meissner, A., Wernig, M., Plath, K., et al. (2006). A bivalent chromatin
Although the biography of cancer will continue to evolve and
structure marks key developmental genes in embryonic stem cells. Cell 125,
surprise us, the prevailing mood within the field of cancer epige- 315–326.
netics is one of optimism. Clearly, the roads leading to effective Bungard, D., Fuerth, B.J., Zeng, P.Y., Faubert, B., Maas, N.L., Viollet, B., Carl-
cancer therapies are long and treacherous, and we do not have ing, D., Thompson, C.B., Jones, R.G., and Berger, S.L. (2010). Signaling kinase
a map to lead us to success. However, what we may now have is AMPK activates stress-promoted transcription via histone H2B phosphoryla-
a promising path to follow. tion. Science 329, 1201–1205.
Chapman, M.A., Lawrence, M.S., Keats, J.J., Cibulskis, K., Sougnez, C.,
ACKNOWLEDGMENTS Schinzel, A.C., Harview, C.L., Brunet, J.P., Ahmann, G.J., Adli, M., et al.
(2011). Initial genome sequencing and analysis of multiple myeloma. Nature
The scope of this review and its space limitations have unfortunately meant 471, 467–472.
that we have not been able to separately cite many of the original publications Choudhary, C., Kumar, C., Gnad, F., Nielsen, M.L., Rehman, M., Walther, T.C.,
that have contributed substantially to the field. We sincerely apologize to the Olsen, J.V., and Mann, M. (2009). Lysine acetylation targets protein complexes
authors of these publications. We would like to thank Drs. Andy Bannister and co-regulates major cellular functions. Science 325, 834–840.
and Brian Huntly for valued input and critical appraisal of the manuscript. Chung, C.W., and Witherington, J. (2011). Progress in the discovery of small-
We would also like to thank Dr. Peter Campbell for sharing data from the Inter- molecule inhibitors of bromodomain—histone interactions. J. Biomol. Screen.
national Cancer Genome Consortium and Prof. Gerald Crabtree for helpful 16, 1170–1185.
discussions. Mark Dawson is supported by a Wellcome-Beit Intermediate
Cimmino, L., Abdel-Wahab, O., Levine, R.L., and Aifantis, I. (2011). TET family
Clinical Fellowship, and the Kouzarides lab is funded by a program grant
proteins and their role in stem cell differentiation and transformation. Cell Stem
from Cancer Research UK (CRUK).
Cell 9, 193–204.
Cole, P.A. (2008). Chemical probes for histone-modifying enzymes. Nat.
REFERENCES
Chem. Biol. 4, 590–597.

Allfrey, V.G., Faulkner, R., and Mirsky, A.E. (1964). Acetylation and methylation Coles, A.H., and Jones, S.N. (2009). The ING gene family in the regulation of
of histones and their possible role in the regulation of RNA synthesis. Proc. cell growth and tumorigenesis. J. Cell. Physiol. 218, 45–57.
Natl. Acad. Sci. USA 51, 786–794. Daigle, S.R., Olhava, E.J., Therkelsen, C.A., Majer, C.R., Sneeringer, C.J.,
Allis, C.D., Jenuwein, T., and Reinberg, D. (2007). Epigenetics (Cold Spring Song, J., Johnston, L.D., Scott, M.P., Smith, J.J., Xiao, Y., et al. (2011). Selec-
Harbor, NY: Cold Spring Harbor Laboratory Press). tive killing of mixed lineage leukemia cells by a potent small-molecule DOT1L
inhibitor. Cancer Cell 20, 53–65.
Amaral, P.P., Dinger, M.E., Mercer, T.R., and Mattick, J.S. (2008). The eukary-
otic genome as an RNA machine. Science 319, 1787–1789. Dawson, M.A., Bannister, A.J., Göttgens, B., Foster, S.D., Bartke, T., Green,
A.R., and Kouzarides, T. (2009). JAK2 phosphorylates histone H3Y41 and
Avvakumov, N., and Côté, J. (2007). The MYST family of histone acetyltrans-
excludes HP1alpha from chromatin. Nature 461, 819–822.
ferases and their intimate links to cancer. Oncogene 26, 5395–5407.
Dawson, M.A., Prinjha, R.K., Dittmann, A., Giotopoulos, G., Bantscheff, M.,
Baek, S.H. (2011). When signaling kinases meet histones and histone modi-
Chan, W.I., Robson, S.C., Chung, C.W., Hopf, C., Savitski, M.M., et al.
fiers in the nucleus. Mol. Cell 42, 274–284.
(2011). Inhibition of BET recruitment to chromatin as an effective treatment
Bannister, A.J., and Kouzarides, T. (1996). The CBP co-activator is a histone for MLL-fusion leukaemia. Nature 478, 529–533.
acetyltransferase. Nature 384, 641–643.
de Wit, E., and de Laat, W. (2012). A decade of 3C technologies: insights into
Bantscheff, M., Hopf, C., Savitski, M.M., Dittmann, A., Grandi, P., Michon, A.- nuclear organization. Genes Dev. 26, 11–24.
M., Schlegl, J., Abraham, Y., Becher, I., Bergamini, G., et al. (2011). Chemo- Deguchi, K., Ayton, P.M., Carapeti, M., Kutok, J.L., Snyder, C.S., Williams, I.R.,
proteomics profiling of HDAC inhibitors reveals selective targeting of HDAC Cross, N.C.P., Glass, C.K., Cleary, M.L., and Gilliland, D.G. (2003). MOZ-TIF2-
complexes. Nat. Biotechnol. 29, 255–265. induced acute myeloid leukemia requires the MOZ nucleosome binding motif
Barretina, J., Caponigro, G., Stransky, N., Venkatesan, K., Margolin, A.A., Kim, and TIF2-mediated recruitment of CBP. Cancer Cell 3, 259–271.
S., Wilson, C.J., Lehár, J., Kryukov, G.V., Sonkin, D., et al. (2012). The Cancer Delhommeau, F., Dupont, S., Della Valle, V., James, C., Trannoy, S., Massé, A.,
Cell Line Encyclopedia enables predictive modelling of anticancer drug sensi- Kosmider, O., Le Couedic, J.P., Robert, F., Alberdi, A., et al. (2009). Mutation in
tivity. Nature 483, 603–607. TET2 in myeloid cancers. N. Engl. J. Med. 360, 2289–2301.
Barski, A., Cuddapah, S., Cui, K., Roh, T.-Y., Schones, D.E., Wang, Z., Wei, G., Delmore, J.E., Issa, G.C., Lemieux, M.E., Rahl, P.B., Shi, J., Jacobs, H.M.,
Chepelev, I., and Zhao, K. (2007). High-resolution profiling of histone methyl- Kastritis, E., Gilpatrick, T., Paranal, R.M., Qi, J., et al. (2011). BET bromodo-
ations in the human genome. Cell 129, 823–837. main inhibition as a therapeutic strategy to target c-Myc. Cell 146, 904–917.
Bartke, T., Vermeulen, M., Xhemalce, B., Robson, S.C., Mann, M., and Kouzar- Dialynas, G.K., Vitalini, M.W., and Wallrath, L.L. (2008). Linking Heterochro-
ides, T. (2010). Nucleosome-interacting proteins regulated by DNA and matin Protein 1 (HP1) to cancer progression. Mutat. Res. 647, 13–20.
histone methylation. Cell 143, 470–484.
Easwaran, H., Johnstone, S.E., Van Neste, L., Ohm, J., Mosbruger, T., Wang,
Baylin, S.B., and Jones, P.A. (2011). A decade of exploring the cancer Q., Aryee, M.J., Joyce, P., Ahuja, N., Weisenberger, D., et al. (2012). A DNA
epigenome - biological and translational implications. Nat. Rev. Cancer 11, hypermethylation module for the stem/progenitor cell signature of cancer.
726–734. Genome Res. 22, 837–849.
Bereshchenko, O.R., Gu, W., and Dalla-Favera, R. (2002). Acetylation inacti- Ernst, T., Chase, A.J., Score, J., Hidalgo-Curtis, C.E., Bryant, C., Jones, A.V.,
vates the transcriptional repressor BCL6. Nat. Genet. 32, 606–613. Waghorn, K., Zoi, K., Ross, F.M., Reiter, A., et al. (2010). Inactivating mutations
Berger, S.L., Kouzarides, T., Shiekhattar, R., and Shilatifard, A. (2009). An of the histone methyltransferase gene EZH2 in myeloid disorders. Nat. Genet.
operational definition of epigenetics. Genes Dev. 23, 781–783. 42, 722–726.
Berman, B.P., Weisenberger, D.J., Aman, J.F., Hinoue, T., Ramjan, Z., Liu, Y., Farnham, P.J. (2009). Insights from genomic profiling of transcription factors.
Noushmehr, H., Lange, C.P., van Dijk, C.M., Tollenaar, R.A., et al. (2012). Nat. Rev. Genet. 10, 605–616.

24 Cell 150, July 6, 2012 ª2012 Elsevier Inc.

Federico, M., and Bagella, L. (2011). Histone deacetylase inhibitors in the associated with poor prognosis in colorectal cancers. Cancer Res. 71,
treatment of hematological malignancies and solid tumors. J. Biomed. 6320–6326.
Biotechnol. 2011, 475641. Kouzarides, T. (2007). Chromatin modifications and their function. Cell 128,
Feinberg, A.P., and Tycko, B. (2004). The history of cancer epigenetics. Nat. 693–705.
Rev. Cancer 4, 143–153.
Kriaucionis, S., and Heintz, N. (2009). The nuclear DNA base 5-hydroxymethyl-
Fenaux, P., Mufti, G.J., Hellstrom-Lindberg, E., Santini, V., Finelli, C., Giagou- cytosine is present in Purkinje neurons and the brain. Science 324, 929–930.
nidis, A., Schoch, R., Gattermann, N., Sanz, G., List, A., et al; International
Krivtsov, A.V., and Armstrong, S.A. (2007). MLL translocations, histone modi-
Vidaza High-Risk MDS Survival Study Group. (2009). Efficacy of azacitidine
fications and leukaemia stem-cell development. Nat. Rev. Cancer 7, 823–833.
compared with that of conventional care regimens in the treatment of
higher-risk myelodysplastic syndromes: a randomised, open-label, phase III Laird, P.W. (2010). Principles and challenges of genomewide DNA methylation
study. Lancet Oncol. 10, 223–232. analysis. Nat. Rev. Genet. 11, 191–203.
Filippakopoulos, P., Qi, J., Picaud, S., Shen, Y., Smith, W.B., Fedorov, O., Langemeijer, S.M., Kuiper, R.P., Berends, M., Knops, R., Aslanyan, M.G.,
Morse, E.M., Keates, T., Hickman, T.T., Felletar, I., et al. (2010). Selective inhi- Massop, M., Stevens-Linders, E., van Hoogen, P., van Kessel, A.G., Ray-
bition of BET bromodomains. Nature 468, 1067–1073. makers, R.A., et al. (2009). Acquired mutations in TET2 are common in myelo-
dysplastic syndromes. Nat. Genet. 41, 838–842.
Forbes, S.A., Bindal, N., Bamford, S., Cole, C., Kok, C.Y., Beare, D., Jia, M.,
Shepherd, R., Leung, K., Menzies, A., et al. (2011). COSMIC: mining complete Lee, J.S., Smith, E., and Shilatifard, A. (2010). The language of histone cross-
cancer genomes in the Catalogue of Somatic Mutations in Cancer. Nucleic talk. Cell 142, 682–685.
Acids Res. 39 (Database issue), D945–D950. Ley, T.J., Ding, L., Walter, M.J., McLellan, M.D., Lamprecht, T., Larson, D.E.,
Fraga, M.F., Ballestar, E., Villar-Garea, A., Boix-Chornet, M., Espada, J., Kandoth, C., Payton, J.E., Baty, J., Welch, J., et al. (2010). DNMT3A mutations
Schotta, G., Bonaldi, T., Haydon, C., Ropero, S., Petrie, K., et al. (2005). in acute myeloid leukemia. N. Engl. J. Med. 363, 2424–2433.
Loss of acetylation at Lys16 and trimethylation at Lys20 of histone H4 is Li, E., Bestor, T.H., and Jaenisch, R. (1992). Targeted mutation of the DNA
a common hallmark of human cancer. Nat. Genet. 37, 391–400. methyltransferase gene results in embryonic lethality. Cell 69, 915–926.
Garnett, M.J., Edelman, E.J., Heidorn, S.J., Greenman, C.D., Dastur, A., Lau,
Li, D.Q., Pakala, S.B., Nair, S.S., Eswaran, J., and Kumar, R. (2012). Metas-
K.W., Greninger, P., Thompson, I.R., Luo, X., Soares, J., et al. (2012). System-
tasis-associated protein 1/nucleosome remodeling and histone deacetylase
atic identification of genomic markers of drug sensitivity in cancer cells. Nature
complex in cancer. Cancer Res. 72, 387–394.
483, 570–575.
Lorsbach, R.B., Moore, J., Mathew, S., Raimondi, S.C., Mukatira, S.T., and
Gore, S.D. (2011). New ways to use DNA methyltransferase inhibitors for the
Downing, J.R. (2003). TET1, a member of a novel protein family, is fused to
treatment of myelodysplastic syndrome. Hematology (Am. Soc. Hematol.
MLL in acute myeloid leukemia containing the t(10;11)(q22;q23). Leukemia
Educ. Program) 2011, 550–555.
17, 637–641.
Gui, Y., Guo, G., Huang, Y., Hu, X., Tang, A., Gao, S., Wu, R., Chen, C., Li, X.,
Margueron, R., and Reinberg, D. (2011). The Polycomb complex PRC2 and its
Zhou, L., et al. (2011). Frequent mutations of chromatin remodeling genes in
mark in life. Nature 469, 343–349.
transitional cell carcinoma of the bladder. Nat. Genet. 43, 875–878.
Mertz, J.A., Conery, A.R., Bryant, B.M., Sandy, P., Balasubramanian, S., Mele,
Hanahan, D., and Weinberg, R.A. (2011). Hallmarks of cancer: the next gener-
D.A., Bergeron, L., and Sims, R.J., III. (2011). Targeting MYC dependence in
ation. Cell 144, 646–674.
cancer by inhibiting BET bromodomains. Proc. Natl. Acad. Sci. USA 108,
Heintzman, N.D., Stuart, R.K., Hon, G., Fu, Y., Ching, C.W., Hawkins, R.D.,
16669–16674.
Barrera, L.O., Van Calcar, S., Qu, C., Ching, K.A., et al. (2007). Distinct and
predictive chromatin signatures of transcriptional promoters and enhancers Meyer, N., and Penn, L.Z. (2008). Reflecting on 25 years with MYC. Nat. Rev.
in the human genome. Nat. Genet. 39, 311–318. Cancer 8, 976–990.

Heintzman, N.D., Hon, G.C., Hawkins, R.D., Kheradpour, P., Stark, A., Harp, Minucci, S., and Pelicci, P.G. (2006). Histone deacetylase inhibitors and the
L.F., Ye, Z., Lee, L.K., Stuart, R.K., Ching, C.W., et al. (2009). Histone modifi- promise of epigenetic (and more) treatments for cancer. Nat. Rev. Cancer 6,
cations at human enhancers reflect global cell-type-specific gene expression. 38–51.
Nature 459, 108–112. Moran-Crusio, K., Reavie, L., Shih, A., Abdel-Wahab, O., Ndiaye-Lobry, D.,
Huntly, B.J., Shigematsu, H., Deguchi, K., Lee, B.H., Mizuno, S., Duclos, N., Lobry, C., Figueroa, M.E., Vasanthakumar, A., Patel, J., Zhao, X., et al.
Rowan, R., Amaral, S., Curley, D., Williams, I.R., et al. (2004). MOZ-TIF2, but (2011). Tet2 loss leads to increased hematopoietic stem cell self-renewal
not BCR-ABL, confers properties of leukemic stem cells to committed murine and myeloid transformation. Cancer Cell 20, 11–24.
hematopoietic progenitors. Cancer Cell 6, 587–596. Morin, R.D., Johnson, N.A., Severson, T.M., Mungall, A.J., An, J., Goya, R.,
Iyer, N.G., Ozdag, H., and Caldas, C. (2004). p300/CBP and cancer. Oncogene Paul, J.E., Boyle, M., Woolcock, B.W., Kuchenbauer, F., et al. (2010). Somatic
23, 4225–4231. mutations altering EZH2 (Tyr641) in follicular and diffuse large B-cell
Jiao, Y., Shi, C., Edil, B.H., de Wilde, R.F., Klimstra, D.S., Maitra, A., Schulick, lymphomas of germinal-center origin. Nat. Genet. 42, 181–185.
R.D., Tang, L.H., Wolfgang, C.L., Choti, M.A., et al. (2011). DAXX/ATRX, MEN1, Morin, R.D., Mendez-Lago, M., Mungall, A.J., Goya, R., Mungall, K.L., Corbett,
and mTOR pathway genes are frequently altered in pancreatic neuroendocrine R.D., Johnson, N.A., Severson, T.M., Chiu, R., Field, M., et al. (2011). Frequent
tumors. Science 331, 1199–1203. mutation of histone-modifying genes in non-Hodgkin lymphoma. Nature 476,
Johnstone, R.W., and Licht, J.D. (2003). Histone deacetylase inhibitors in 298–303.
cancer therapy: is transcription the primary target? Cancer Cell 4, 13–18. Mosammaparast, N., and Shi, Y. (2010). Reversal of histone methylation:
Jones, S., Wang, T.L., Shih, IeM., Mao, T.L., Nakayama, K., Roden, R., Glas, biochemical and molecular mechanisms of histone demethylases. Annu.
R., Slamon, D., Diaz, L.A., Jr., Vogelstein, B., et al. (2010). Frequent mutations Rev. Biochem. 79, 155–179.
of chromatin remodeling gene ARID1A in ovarian clear cell carcinoma. Science Nicodeme, E., Jeffrey, K.L., Schaefer, U., Beinke, S., Dewell, S., Chung, C.W.,
330, 228–231. Chandwani, R., Marazzi, I., Wilson, P., Coste, H., et al. (2010). Suppression of
Klose, R.J., and Bird, A.P. (2006). Genomic DNA methylation: the mark and its inflammation by a synthetic histone mimic. Nature 468, 1119–1123.
mediators. Trends Biochem. Sci. 31, 89–97. Nikoloski, G., Langemeijer, S.M., Kuiper, R.P., Knops, R., Massop, M., Tönnis-
Kogo, R., Shimamura, T., Mimori, K., Kawahara, K., Imoto, S., Sudo, T., Ta- sen, E.R., van der Heijden, A., Scheele, T.N., Vandenberghe, P., de Witte, T.,
naka, F., Shibata, K., Suzuki, A., Komune, S., et al. (2011). Long noncoding et al. (2010). Somatic mutations of the histone methyltransferase gene EZH2
RNA HOTAIR regulates polycomb-dependent chromatin modification and is in myelodysplastic syndromes. Nat. Genet. 42, 665–667.

Cell 150, July 6, 2012 ª2012 Elsevier Inc. 25

Ntziachristos, P., Tsirigos, A., Van Vlierberghe, P., Nedjic, J., Trimarchi, T., on histone H3 (H3K27) in human B-cell lymphomas. Proc. Natl. Acad. Sci.
Flaherty, M.S., Ferres-Marco, D., da Ros, V., Tang, Z., Siegle, J., et al. USA 107, 20980–20985.
(2012). Genetic inactivation of the polycomb repressive complex 2 in T cell Stratton, M.R., Campbell, P.J., and Futreal, P.A. (2009). The cancer genome.
acute lymphoblastic leukemia. Nat. Med. 18, 298–301. Nature 458, 719–724.
Ohm, J.E., McGarvey, K.M., Yu, X., Cheng, L., Schuebel, K.E., Cope, L., Mo- Stucki, M., Clapperton, J.A., Mohammad, D., Yaffe, M.B., Smerdon, S.J., and
hammad, H.P., Chen, W., Daniel, V.C., Yu, W., et al. (2007). A stem cell-like Jackson, S.P. (2005). MDC1 directly binds phosphorylated histone H2AX to
chromatin pattern may predispose tumor suppressor genes to DNA hyperme- regulate cellular responses to DNA double-strand breaks. Cell 123, 1213–
thylation and heritable silencing. Nat. Genet. 39, 237–242. 1226.
Okano, M., Bell, D.W., Haber, D.A., and Li, E. (1999). DNA methyltransferases Stunnenberg, H.G., and Vermeulen, M. (2011). Towards cracking the epige-
Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian netic code using a combination of high-throughput epigenomics and quantita-
development. Cell 99, 247–257. tive mass spectrometry-based proteomics. Bioessays 33, 547–551.
Olsen, E.A., Kim, Y.H., Kuzel, T.M., Pacheco, T.R., Foss, F.M., Parker, S., Tahiliani, M., Koh, K.P., Shen, Y., Pastor, W.A., Bandukwala, H., Brudno, Y.,
Frankel, S.R., Chen, C., Ricker, J.L., Arduino, J.M., and Duvic, M. (2007). Agarwal, S., Iyer, L.M., Liu, D.R., Aravind, L., and Rao, A. (2009). Conversion
Phase IIb multicenter trial of vorinostat in patients with persistent, progressive, of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL
or treatment refractory cutaneous T-cell lymphoma. J. Clin. Oncol. 25, 3109– partner TET1. Science 324, 930–935.
3115.
Tan, M., Luo, H., Lee, S., Jin, F., Yang, J.S., Montellier, E., Buchou, T., Cheng,
Park, P.J. (2009). ChIP-seq: advantages and challenges of a maturing tech- Z., Rousseaux, S., Rajagopal, N., et al. (2011). Identification of 67 histone
nology. Nat. Rev. Genet. 10, 669–680. marks and histone lysine crotonylation as a new type of histone modification.
Pasqualucci, L., Dominguez-Sola, D., Chiarenza, A., Fabbri, G., Grunn, A., Tri- Cell 146, 1016–1028.
fonov, V., Kasper, L.H., Lerach, S., Tang, H., Ma, J., et al. (2011). Inactivating Taverna, S.D., Li, H., Ruthenburg, A.J., Allis, C.D., and Patel, D.J. (2007). How
mutations of acetyltransferase genes in B-cell lymphoma. Nature 471, chromatin-binding modules interpret histone modifications: lessons from
189–195. professional pocket pickers. Nat. Struct. Mol. Biol. 14, 1025–1040.
Patel, J.P., Gönen, M., Figueroa, M.E., Fernandez, H., Sun, Z., Racevskis, J., Tsai, H.C., Li, H., Van Neste, L., Cai, Y., Robert, C., Rassool, F.V., Shin, J.J.,
Van Vlierberghe, P., Dolgalev, I., Thomas, S., Aminova, O., et al. (2012). Prog- Harbom, K.M., Beaty, R., Pappou, E., et al. (2012). Transient low doses of
nostic relevance of integrated genetic profiling in acute myeloid leukemia. N. DNA-demethylating agents exert durable antitumor effects on hematological
Engl. J. Med. 366, 1079–1089. and epithelial tumor cells. Cancer Cell 21, 430–446.
Piekarz, R.L., Frye, R., Turner, M., Wright, J.J., Allen, S.L., Kirschbaum, M.H., van Haaften, G., Dalgliesh, G.L., Davies, H., Chen, L., Bignell, G., Greenman,
Zain, J., Prince, H.M., Leonard, J.P., Geskin, L.J., et al. (2009). Phase II C., Edkins, S., Hardy, C., O’Meara, S., Teague, J., et al. (2009). Somatic muta-
multi-institutional trial of the histone deacetylase inhibitor romidepsin as tions of the histone H3K27 demethylase gene UTX in human cancer. Nat.
monotherapy for patients with cutaneous T-cell lymphoma. J. Clin. Oncol. Genet. 41, 521–523.
27, 5410–5417.
Varela, I., Tarpey, P., Raine, K., Huang, D., Ong, C.K., Stephens, P., Davies, H.,
Quivoron, C., Couronné, L., Della Valle, V., Lopez, C.K., Plo, I., Wagner-Ballon, Jones, D., Lin, M.L., Teague, J., et al. (2011). Exome sequencing identifies
O., Do Cruzeiro, M., Delhommeau, F., Arnulf, B., Stern, M.H., et al. (2011). TET2 frequent mutation of the SWI/SNF complex gene PBRM1 in renal carcinoma.
inactivation results in pleiotropic hematopoietic abnormalities in mouse and is Nature 469, 539–542.
a recurrent event during human lymphomagenesis. Cancer Cell 20, 25–38.
Vermeulen, M., Eberl, H.C., Matarese, F., Marks, H., Denissov, S., Butter, F.,
Rando, O.J., and Chang, H.Y. (2009). Genome-wide views of chromatin struc- Lee, K.K., Olsen, J.V., Hyman, A.A., Stunnenberg, H.G., and Mann, M.
ture. Annu. Rev. Biochem. 78, 245–271. (2010). Quantitative interaction proteomics and genome-wide profiling of
Robertson, K.D. (2005). DNA methylation and human disease. Nat. Rev. epigenetic histone marks and their readers. Cell 142, 967–980.
Genet. 6, 597–610. Versteege, I., Sévenet, N., Lange, J., Rousseau-Merck, M.F., Ambros, P.,
Rui, L., Emre, N.C., Kruhlak, M.J., Chung, H.J., Steidl, C., Slack, G., Wright, Handgretinger, R., Aurias, A., and Delattre, O. (1998). Truncating mutations
G.W., Lenz, G., Ngo, V.N., Shaffer, A.L., et al. (2010). Cooperative epigenetic of hSNF5/INI1 in aggressive paediatric cancer. Nature 394, 203–206.
modulation by cancer amplicon genes. Cancer Cell 18, 590–605. Wang, K.C., and Chang, H.Y. (2011). Molecular mechanisms of long noncod-
Ruthenburg, A.J., Li, H., Milne, T.A., Dewell, S., McGinty, R.K., Yuen, M., ing RNAs. Mol. Cell 43, 904–914.
Ueberheide, B., Dou, Y., Muir, T.W., Patel, D.J., and Allis, C.D. (2011). Recog- Wang, J., Iwasaki, H., Krivtsov, A., Febbo, P.G., Thorner, A.R., Ernst, P., Anas-
nition of a mononucleosomal histone modification pattern by BPTF via multi- tasiadou, E., Kutok, J.L., Kogan, S.C., Zinkel, S.S., et al. (2005). Conditional
valent interactions. Cell 145, 692–706. MLL-CBP targets GMP and models therapy-related myeloproliferative
Schenk, T., Chen, W.C., Göllner, S., Howell, L., Jin, L., Hebestreit, K., Klein, disease. EMBO J. 24, 368–381.
H.U., Popescu, A.C., Burnett, A., Mills, K., et al. (2012). Inhibition of the Wang, G.G., Allis, C.D., and Chi, P. (2007). Chromatin remodeling and cancer,
LSD1 (KDM1A) demethylase reactivates the all-trans-retinoic acid differentia- Part II: ATP-dependent chromatin remodeling. Trends Mol. Med. 13, 373–380.
tion pathway in acute myeloid leukemia. Nat. Med. 18, 605–611. Wang, Z., Zang, C., Rosenfeld, J.A., Schones, D.E., Barski, A., Cuddapah, S.,
Schwartzentruber, J., Korshunov, A., Liu, X.Y., Jones, D.T., Pfaff, E., Jacob, K., Cui, K., Roh, T.Y., Peng, W., Zhang, M.Q., and Zhao, K. (2008). Combinatorial
Sturm, D., Fontebasso, A.M., Quang, D.A., Tönjes, M., et al. (2012). Driver patterns of histone acetylations and methylations in the human genome. Nat.
mutations in histone H3.3 and chromatin remodelling genes in paediatric Genet. 40, 897–903.
glioblastoma. Nature 482, 226–231. Wang, G.G., Song, J., Wang, Z., Dormann, H.L., Casadio, F., Li, H., Luo, J.-L.,
Segal, E., and Widom, J. (2009). From DNA sequence to transcriptional behav- Patel, D.J., and Allis, C.D. (2009). Haematopoietic malignancies caused by
iour: a quantitative approach. Nat. Rev. Genet. 10, 443–456. dysregulation of a chromatin-binding PHD finger. Nature 459, 847–851.
Seligson, D.B., Horvath, S., Shi, T., Yu, H., Tze, S., Grunstein, M., and Kurdis- Wang, K., Kan, J., Yuen, S.T., Shi, S.T., Chu, K.M., Law, S., Chan, T.L., Kan, Z.,
tani, S.K. (2005). Global histone modification patterns predict risk of prostate Chan, A.S., Tsui, W.Y., et al. (2011). Exome sequencing identifies frequent
cancer recurrence. Nature 435, 1262–1266. mutation of ARID1A in molecular subtypes of gastric cancer. Nat. Genet. 43,
Sneeringer, C.J., Scott, M.P., Kuntz, K.W., Knutson, S.K., Pollock, R.M., Ri- 1219–1223.
chon, V.M., and Copeland, R.A. (2010). Coordinated activities of wild-type Weinstein, I.B. (2002). Cancer. Addiction to oncogenes—the Achilles heal of
plus mutant EZH2 drive tumor-associated hypertrimethylation of lysine 27 cancer. Science 297, 63–64.

26 Cell 150, July 6, 2012 ª2012 Elsevier Inc.

Wilson, B.G., and Roberts, C.W. (2011). SWI/SNF nucleosome remodellers Xu, W., Yang, H., Liu, Y., Yang, Y., Wang, P., Kim, S.H., Ito, S., Yang, C., Wang,
and cancer. Nat. Rev. Cancer 11, 481–492. P., Xiao, M.T., et al. (2011). Oncometabolite 2-hydroxyglutarate is a
Wu, H., and Zhang, Y. (2011). Mechanisms and functions of Tet protein-medi- competitive inhibitor of a-ketoglutarate-dependent dioxygenases. Cancer
ated 5-methylcytosine oxidation. Genes Dev. 25, 2436–2452. Cell 19, 17–30.
Wu, G., Broniscer, A., McEachron, T.A., Lu, C., Paugh, B.S., Becksfort, J., Qu, Yang, X., Cao, W., Zhang, L., Zhang, W., Zhang, X., and Lin, H. (2012). Target-
C., Ding, L., Huether, R., Parker, M., et al; St. Jude Children’s Research ing 14-3-3zeta in cancer therapy. Cancer Gene Ther. 19, 153–159.
Hospital–Washington University Pediatric Cancer Genome Project. (2012). Zhang, J., Ding, L., Holmfeldt, L., Wu, G., Heatley, S.L., Payne-Turner, D.,
Somatic histone H3 alterations in pediatric diffuse intrinsic pontine gliomas Easton, J., Chen, X., Wang, J., Rusch, M., et al. (2012). The genetic basis of
and non-brainstem glioblastomas. Nat. Genet. 44, 251–253. early T-cell precursor acute lymphoblastic leukaemia. Nature 481, 157–163.
Xhemalce, B., Dawson, M.A., and Bannister, A.J. (2011). Histone Modifica- Zuber, J., Shi, J., Wang, E., Rappaport, A.R., Herrmann, H., Sison, E.A., Ma-
tions. In Encyclopedia of Molecular Cell Biology and Molecular Medicine goon, D., Qi, J., Blatt, K., Wunderlich, M., et al. (2011). RNAi screen identifies
(Weinheim: Wiley-VCH Verlag). Brd4 as a therapeutic target in acute myeloid leukaemia. Nature 478, 524–528.

Cell 150, July 6, 2012 ª2012 Elsevier Inc. 27