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Blood First Edition Paper, prepublished online January 2, 2013; DOI 10.1182/blood-2012-10-451237
The role of chromatin modifiers in normal and malignant hematopoiesis
Jill S. Butler 1,2 and Sharon Y.R. Dent 1-3*
1
Department of Molecular Carcinogenesis at The Virginia Harris Cockrell Cancer
Research Center, The University of Texas MD Anderson Cancer Center Science
Park, Smithville, TX 78957, USA
2
Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer
Center, Houston, TX 77030, USA
3
The Genes & Development Program, Graduate School of Biomedical Sciences,
The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
*To whom correspondence should be addressed
1
Copyright © 2013 American Society of Hematology
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Abstract
Complex developmental processes such as hematopoiesis require a series of
precise and coordinated changes in cellular identity to ensure blood
homeostasis. Epigenetic mechanisms help drive changes in gene expression
that accompany the transition from hematopoietic stem cells to terminally
differentiated blood cells. Genome-wide profiling technologies now provide
valuable glimpses of epigenetic changes that occur during normal
hematopoiesis, and genetic mouse models developed to investigate the in vivo
functions of chromatin modifying enzymes clearly demonstrate significant roles
for these enzymes during embryonic and adult hematopoiesis. Here we will
review the basic science aspects of chromatin modifications and the enzymes
that add, remove, and interpret these epigenetic marks. This overview will
provide a framework for understanding the roles that these molecules during
normal hematopoiesis. Moreover, a number of chromatin modifying enzymes are
involved in hematological malignancies, underscoring the importance of
establishing and maintaining appropriate chromatin modification patterns to
normal hematology.
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Chromatin structure and epigenetic mechanisms
Hematopoiesis is an orderly process that involves the coordination of stem
cell self-renewal, controlled expansion of progenitor cells, and timely
differentiation. Developmental programs, such as hematopoiesis, are
orchestrated by changes in gene expression patterns. These patterns are
directed by transcription factors, and the actions of these factors are strongly
influenced by the chromatin structures of their target genes.
The basic repeat unit of chromatin is the nucleosome, which contains two
copies of each core histone protein, H3, H4, H2A, and H2B and 146 base pairs
of DNA spooled around the histone octamer. Histone H3 and histone H4 form a
heterotetramer at the heart of the nucleosome, and two heterodimers of histones
H2A and H2B associate with the tetramer to complete the octamer. Linker
histones, typified by H1, bind to DNA entering into and exiting from the
nucleosome, thereby providing further structural stability.
Chromatin that is in an open configuration, accessible to transcription
factors and RNA polymerase, is often referred to as euchromatin, reflecting a
less condensed appearance in microscopic images of nuclear sections.
Heterochromatin, in contrast, refers to more densely packed structures that are
generally transcriptionally silent. Regions of the genome that include telomeres
and centromeres are highly heterochromatic. Chromatin organization in other
regions of the genome is more dynamic, reflecting changes in transcriptional
competence and activity. Such plasticity is essential for regulation of various
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cellular processes such as cell division, gene transcription, DNA repair,
replication, and recombination.
The term epigenetics is defined as inherited variation that occurs without
changes in the DNA sequence 1. Epigenetic mechanisms permit a level of
plasticity for the genetic information encoded by the DNA, which allows for the
establishment of cell-specific expression programs. Modifications added to or
removed from the chromatin template that carry epigenetic information include
DNA methylation and histone post-translational modifications. Non-coding RNA
molecules are also emerging as important regulators of gene expression during
hematopoiesis 2,3. However, this review will highlight examples of the essential
roles that chromatin modifying enzymes play during hematopoietic cell
development by regulating the dynamic nature of DNA and specific histone
modifications, namely methylation and acetylation.
DNA modifications
Methylation of a cytosine residue in the context of a CpG dinucleotide
represents a stable regulatory mark in the mammalian genome. Cytosine
methylation (5mC) is generally associated with heterochromatin formation and
transcriptional repression. Conversely, stretches of unmethylated CpG
dinucleotides, termed CpG islands, are often found in the promoters of actively
transcribed genes and support a euchromatic environment. Additional functional
groups were recently discovered to modify the 5-position of cytosine residues,
namely hydroxymethyl (5hmC), formyl (5fC), and carboxyl (5caC), and the
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biological functions of these modifications throughout the genome are now being
discovered 4.
Covalent post-translational modification of histone proteins
Post-translational modifications (PTMs) occurring on histone proteins
regulate chromatin structure in a temporal and spatial manner. Histone
modifications serve both as a signaling mechanism and as binding platforms to
recruit other proteins. Covalent PTMs added to the core histone proteins include
acetylation, methylation, phosphorylation, ubiquitination, sumoylation, ADP
ribosylation, and biotinylation. The ‘writers’ and ‘erasers’ that govern the addition
or removal of these PTMs often demonstrate site specificity, however multiple
enzymes are capable of modifying the same residue within a histone substrate.
Different patterns of histone PTMs have been proposed to act as a ‘code’
in that specific patterns confer specific biological responses 5,6. The ‘histone
code’ hypothesis requires a way for effector molecules to interpret the
information given by histone PTMs to mediate cellular process outside of
chromatin. Protein domains that recognize individual or combinatorial histone
modifications have been termed ‘reading’ or presenting domains 7. As more
histone PTM reading domains are discovered, linking binding patterns to
associated biological responses is becoming more complex. Accumulating
evidence links deregulation of histone PTM interpretation with oncogenic
transformation, highlighting the importance of histone reader proteins 8.
Lysine acetylation and methylation occur on all four of the core histones,
most prevalently on the N-terminal tails. The addition of an acetyl group
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neutralizes the positive charge of the lysine residue, which weakens interactions
between the histones and DNA, facilitating more open and relaxed chromatin
states. Acetylated histones are generally associated with transcriptionally active
genes and euchromatic regions of the genome 9 (Figure 1A). Lysine residues
can accommodate up to three methyl groups (mono-, di-, or tri-), while arginine
residues may be mono- or dimethylated, yielding monomethyl arginine (MMA),
asymmetric dimethyl arginine (ADMA), or symmetric dimethyl arginine (SDMA).
The degree of methylation at a particular lysine or arginine residue is just as
important in influencing biological outcome as the target site (Figure 1).
Chromatin modifications mark genomic regions
Many chromatin modifications are associated with either transcriptional
activation or repression (Table 1), however, there are certainly exceptions to
these assignments. The degree of a modification and where the modifications
are located within genic regions affect the transcriptional outcome. Often,
multiple enzymes modify a particular amino acid residue within a histone protein.
The chromatin modifying enzymes discussed in this review are listed in Table 1
along with their identified substrates, and Figure 1 serves as a general guide for
matching chromatin modifications with transcriptional outcomes. Histone
H3K4me2,3, H3R2me2s, H3K9ac, H3K14ac, K3K27ac and H4K16ac mark
euchromatic regions of the genome, particularly transcriptional enhancer and
promoter regions 10,11,12 (Figure 1A). Histone H3K36me3 is a mark associated
with transcription elongation, and is found in the body and 3’ ends of genes
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(Figure 1A). Methylation of histone H3K79 is largely associated with
transcriptionally active genes, with di- and tri-methylation found near transcription
start sites, and mono-methylation occurring widely across active gene bodies 13.
Histone H3K9me3, H3K27me1,3, and H4K20me3, together with 5mC are
marks of constitutive heterochromatin found in transcriptionally silenced regions
of the genome, such as pericentromeric DNA and the inactive X chromosome
14,15
(Figure 1B). Histone H3K9me2,3, H3K27me3, and H3R2me2a, as well as
5mC mark facultative heterochromatin and are found in transcriptionally
repressed genes that are dynamically regulated 16,17 (Figure 1B). The
aforementioned repressive chromatin marks do not necessarily coexist at the
same promoters. Furthermore, while methylated CpG dinucleotides in gene
promoters and near transcription start sites often confer a repressive
transcriptional state, CpG methylation within gene bodies does not interfere with
transcription 18.
Genomic regions that contain both transcriptional activating and
repressing histone modifications are termed bivalent domains and are prevalent
in undifferentiated ES cells. Bivalent domains consist of small patches of
H3K4me3, near the transcriptional start site within larger regions of H3K27me3 19
(Figure 1C). In addition, 5hmC was recently identified as an additional
epigenetic mark enriched at bivalent domains 20.
In pluripotent ES cells, bivalent domains mark genes that are involved in
cell fate determination and may help to maintain them in a repressed, yet
potentially active, transcriptional state until the onset of differentiation 19.
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Genome-wide mapping of H3K4me3 and H3K27me3 in hematopoietic stem and
progenitor cells revealed the presence of bivalent domains marking genes
involved in lineage specification 21,22. Furthermore, the level of H3K4me3 in the
progenitor cells significantly correlated with the expression of the marked genes
in differentiated cell types 22. These results suggest that the plasticity of the
chromatin landscape is crucial for the transition between multipotent and
differentiated states.
Writers, erasers, and readers of chromatin modifications
Recent literature is replete with examples demonstrating roles for
chromatin modifying enzymes during hematopoiesis. Moreover, genes encoding
these enzymes are frequently disrupted in hematological malignancies (Table 2)
23
. While genome-wide profiling methods provide snapshots of the chromatin
landscape during hematopoiesis, genetic mouse models have afforded insights
into the roles of chromatin modifying enzymes during this process.
DNA methyltransferases (DNMTs) catalyze 5mC
In mammals, the principal enzymes that catalyze cytosine methylation are
members of the DNMT1 and DNMT3 families. DNMT1 primarily serves as a
maintenance enzyme by copying cytosine methylation patterns from a hemimethylated substrate following DNA replication 24. The DNMT3 family includes
two active enzymes, DNMT3a and DNMT3b, each of which is further represented
by several isoforms. DNMT3a and 3b are referred to as de novo
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methyltransferases due to their preference to act on unmethylated DNA
substrates 25.
Conditional deletion of Dnmt1 in hematopoietic stem cells (HSCs) and
progenitor cells revealed that Dnmt1 activity is required for early stages of
hematopoiesis 26,27. Absence of Dnmt1 activity led to decreased self-renewal
capacity 26 and a rapid ablation of the HSC pool 27. Furthermore, mouse HSCs
lacking Dnmt1 were unable to maintain a sufficient population of myeloid cells
due to increased proliferative capacity and decreased differentiation potential of
the myeloid progenitor pool 26.
Deletion of Dnmt3a and 3b, either independently or together, in adult
mouse HSCs indicated that these enzymes are required for self-renewal but not
differentiation or lineage commitment 28. However, a long-term study
investigating the role of Dnmt3a in mouse hematopoiesis demonstrated a
requirement for Dnmt3a activity in maintaining the differentiation potential of
HSCs following serial transplantation into wild-type recipient mice 29.
Furthermore, a complex pattern of genomic cytosine methylation was observed
in Dnmt3a-deficient HSCs, including hypermethylated regions, that might indicate
compensation by other DNMTs 29. Mutations affecting the catalytic activity of
DNMT3A have been identified in nearly one-third of patients with AML or MDS
and are associated with poor clinical outcome, indicating that the function of this
enzyme is crucial to maintain normal hematopoiesis 30-32.
DNMT1, 3a, and 3b physically and functionally interact with one another,
thereby making it more difficult to ascribe the terms “maintenance” or “de novo”
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to any particular enzyme 25. Defining genomic targets of these enzymes will aid
in assigning distinct functions. Taken together, these studies indicate that while
the mechanisms are not yet clearly defined, appropriate expression and activity
of DNA methyltransferases is essential during development and for adult blood
homeostasis.
TET (Ten-eleven translocation) enzymes catalyze 5hmC
The TET family of enzymes, composed of TET1, TET2, and TET3,
catalyze the oxidation of 5mC to 5hmC, which is an intermediate product of DNA
demethylation mechanisms, and is proposed to have functional roles in stem cell
biology 4. The TET enzymes have distinct expression patterns, with TET1
expressed in the fetal liver, TET2 in bone marrow, and both TET2 and TET3 in
peripheral blood 33, suggesting unique functions for these enzymes during
developmental and adult hematopoiesis. Recently, mutations within TET2 were
identified as a prevalent occurrence in myeloid malignancies, prompting intense
investigations to define the molecular function of TET2 during hematopoiesis
34,35
.
Mice lacking Tet2 are viable, but develop hematopoietic malignancies
within 2-6 months 36-39. HSCs obtained from Tet2-deficient mice exhibit
enhanced self-renewal capacity and achieve a greater contribution to peripheral
blood production in transplanted recipients, compared to wild-type HSCs 36-39.
The overall differentiation potential of HSCs was impeded in the absence of Tet2,
with a bias toward expansion of monocyte and macrophage lineages 36-38.
Disease progression resembling human CMML was the most common
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phenotype observed in the Tet2-null mouse models 36,38,39. In addition, myeloid
disorders similar to MPD-like myeloid leukemia, myeloid leukemia with
maturation, and MDS were reported to cause lethality in approximately one-third
of Tet2-null mice 36.
Mutations that disrupt TET2 enzymatic activity and correlate with
decreased global 5hmC levels are observed in patients with myeloid
malignancies 40. TET2 mutations have also been detected in lymphoid
malignancies, suggesting that mutations occur in early hematopoietic progenitors
with myeloid and lymphoid potential 39. Moreover, TET2 mutations identified in
patients are often monoallelic, indicating that haploinsufficiency contributes to
transformation 34,38,39. Heterozygous gain-of-function mutations in the isocitrate
dehydrogenase 1 and 2 (IDH1/2) enzymes, which are prevalent in AML, cause
inhibition of TET2 catalytic activity and result in increased global 5mC levels,
similar to the effect induced by loss of TET2 function 41.
DNA demethylation mechanisms
The passive loss of cytosine methylation following DNA replication is a
widely accepted mechanism for the removal CpG methylation. The direct
removal of a methyl group from DNA is thermodynamically unfavorable 42.
However, recently several pathways have been proposed to mediate indirect, yet
active removal of CpG methylation.
TET enzymes catalyze sequential oxidation reactions that convert 5mC to
5hmC, 5fC, and finally to 5caC, which can be removed by DNA repair
mechanisms 43. An alternative proposed active mechanism is deamination of
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5mC by activation-induced cytidine deaminase (AID), yielding a thymidine base
that is subject to subsequent DNA mismatch repair and base excision repair
mechanisms 42. While these mechanisms do not directly return the methylated
cytosine to an unmodified base, the 5mC functionality is no longer present.
Defining DNA demethylation mechanisms is an active area of investigation that is
likely to yield exciting results in the future.
DNA methylation readers
Methyl binding domains (MBD) recognize and bind to 5mC, and are found
in a conserved family of proteins that includes MBD1, MBD2, MBD3, MBD4, and
MeCP2 44. MBD proteins are generally regarded as mediators of transcriptional
repression by recruiting chromatin modifying enzymes, such as HDACs, to
regions of highly methylated DNA 44. The MBD proteins are not essential for
embryonic development 44, however transgenic mouse model studies have
pointed to a role for Mbd2 in the silencing of embryonic globin gene expression in
adult erythroid cells 45,46.
The SRA domain within UHRF1, a DNMT1 interacting partner, and the
MBD domain of MBD3 were recently reported as readers of 5hmC 47,48. The
UHRF1 SRA domain was previously shown to bind hemimethylated DNA 49. It
will be interesting to learn whether these molecular functions overlap or if they
occur as distinct targeting mechanisms.
The specificity and affinity of MBD domains for 5mC have made them
valuable reagents in defining global cytosine methylation patterns 50. The MBD
domain MBD2 was recently used to affinity-purify methylated DNA fragments
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from mouse HSCs, CMPs, and erythroblasts in order to determine changes in
5mC during myeloid differentiation. Using this method, a high level of 5mC was
detected in mouse HSCs with a dramatic loss of global methylation occurring
during myeloid differentiation 51, similar to results obtained from a DNA
methylation profiling study performed during erythropoiesis using a bisulfitebased method 52. A similar approach employing the MBD domain of MeCP2 was
used to detect DNA methylation changes during later stages of lymphoid
differentiation, however no dramatic change in 5mC patterns were noted 53,
suggesting that global changes in DNA methylation accompany early
differentiation events during hematopoiesis. Notably, the affinity capture
approach can be applied to map the genomic locations of CpG islands using
domains that recognize unmethylated CpG sites 54.
Histone acetyltransferases (HATs) and deacetylases (HDACs)
A number of HAT enzymes have been identified as regulators of
chromatin-templated processes, including gene transcription and DNA repair.
Most HATs function within large multimeric complexes that include targeting
subunits and additional histone modifying activities. In mice, homozygous
deletion of the HAT MOZ leads to reduced numbers of hematopoietic
progenitors, although all lineages are represented, indicating that differentiation
and lineage commitment are not altered 55,56.
Acetylation is a reversible reaction and HDAC enzymes carry out
deacetylation of histones as well as non-histone substrates. The expression of
HDACs 1,2,3 is low in hematopoietic progenitor cells but increases during
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differentiation. However, overexpression of HDAC1 was shown to inhibit myeloid
differentiation 57. HDACs are notoriously linked with hematological malignancies
through their association with leukemogenic fusion proteins, and mediate
aberrant transcriptional repression of genes required for hematopoietic
differentiation 58. Small molecule HDAC inhibitors are used for leukemia therapy
independently, but are more successful when given in combination with other
cytotoxic agents 59. Defining the genomic targets of HDACs will aid in developing
inhibitors that specifically target those enzymes modifying genes involved in
oncogenesis.
Acetylation readers
Many of the enzymes responsible for ‘writing’ and ‘erasing’ histone
modifications contain domains that ‘read’ modifications. Bromodomains are wellcharacterized modules that bind acetylated lysine residues 60. The bromodomain
of the HAT PCAF binds the acetylated N-terminal tail of H3 to promote
transcriptional activation 61 (Figure 2). Moreover, an example of a bromodomain
indirectly promoting chromatin occupancy of a transcriptional regulator was
recently reported. The bromodomain within the bromodomain extra terminal
(BET) family member, BRD3, interacts with acetylated GATA1 to facilitate its
recruitment to genomic targets, including genes involved in erythroid
differentiation 62. Bromodomain-mediated interactions are amenable to small
molecule inhibition strategies 63. Several BET inhibitors show promise as
therapeutic agents for AML through their effective inhibition of leukemia stem and
progenitor cell proliferation and blocking of MLL-mediated transformation 64,65.
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Lysine methyltransferases (KMTs) and demethylases (KDMs)
The majority of mammalian KMTs characterized to date function within
multi-subunit complexes and target the N-terminal tail of histone H3, where they
coordinate with additional histone modifying activities to drive either activation or
repression of transcription. The mixed lineage leukemia (MLL)
methyltransferases carry out methylation of histone H3K4 and are members of
the trithorax group (Trx) family, while enzymes that methylate H3K27 belong to
the polycomb group (PcG) family. The functional antagonism between these
groups of proteins regulates transcription of developmental genes, including the
Hox gene cluster, and establishes patterning during embryonic development in
vertebrates.
MLL1 is required for viability, as MLL1-/- embryos die by E10.5 66. Yolk
sacs derived from MLL1-/- embryos produce fewer and smaller myeloid colonies
than yolk sacs derived from MLL1+/+ embryos, indicating that MLL1 is critical for
primitive hematopoiesis 67. MLL1 is required for HSC and early progenitor selfrenewal during hematopoiesis in the fetal liver 68 as well as in the adult bone
marrow 69. The human MLL1 gene is often disrupted by chromosomal
translocations observed in acute leukemias 70, and defining the molecular
mechanisms underlying transformation remains an active area of investigation 71,
72
. Furthermore, inactivating mutations in other MLL proteins, including MLL2
and MLL3, are observed in various cancers 23.
There are two well-characterized PcG complexes that incorporate multiple
histone modifying activities to mediate transcriptional repression, polycomb
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repressive complex 1 and 2 (PRC1 and PRC2). The enhancer of zeste homolog
2 (EZH2) enzyme functions within the PRC2 complex to catalyze di- and trimethylation of histone H3K27, which is then bound by the PRC1 complex to
maintain transcriptional repression of PcG target genes. EZH2 silences genes
required for cell fate decisions, thus promoting stem cell self-renewal. Fitting with
this role, overexpression of EZH2 enhances the long-term repopulating potential
of hematopoietic stem cells following serial transplantations into mice 73. EZH2 is
required for fetal HSC proliferation and erythropoiesis in the developing embryo,
but loss of EZH2 has only a trivial effect on the function of HSCs in the adult
bone marrow, primarily their ability to contribute to lymphopoiesis 74.
Consistently, EZH2 activity was previously found to be essential during the
early stages of B cell development, but dispensable for the maturation and
activation of pro-B cells 75. Notably, mutations abrogating the catalytic function of
EZH2 were recently identified in acute and chronic myeloid malignancies 76-79,
while gain-of function mutations were identified in B cell lymphomas 80,81,23.
Inhibiting the methyltransferase activity of EZH2 in lymphoma patients carrying
activating mutations might be a promising therapeutic endeavor. Treatment with
an EZH2-specific small molecule inhibitor resulted in decreased lymphoid cell
proliferation in vitro and in mouse xenograft models 82.
A number of point mutations in the polycomb-associated gene addition of
sex combs-like 1 (ASXL1) have been identified in patients with MDS or AML, and
correlate with a poor prognosis 83-86. ASXL1 mutations promote transformation
by decreasing the recruitment of PRC2 to leukemogenic target genes resulting in
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loss of histone H3K27 methylation and transcriptional repression of those genes
87
. Given that gain or loss of function mutations affecting various components of
the PRC2 complex suggests that altering PRC2 activity and/or H3K27
methylation levels in either direction is detrimental to normal hematopoiesis.
The disruptor of telomeric silencing 1-like (DOT1L) enzyme methylates the
globular domain of histone H3 at K79, which correlates with active transcription
88
. Mice deficient for Dot1L exhibit severe anemia and die between E10.5-13.5
89
. Erythroid development was specifically inhibited in Dot1L-null mice, and
altered H3K79 methylation status and expression of the erythroid regulatory
genes, Gata2 and Pu1, was observed 89. Conditional targeting strategies
revealed a role for Dot1L in maintaining adult hematopoiesis as well 90,91.
Notably, aberrant recruitment of DOT1L by several MLL fusion proteins to genes
involved in cellular transformation is a common mechanism underlying MLLmediated leukemogenesis 13,92. Moreover, DOT1L is a promising therapeutic
target in mixed myeloid leukemias in which MLL and/or AF10 oncogenic fusion
proteins are expressed 93,94.
Histone lysine methylation is dynamic and is regulated by lysine (K)
demethylase (KDM) enzymes. Two classes of KDMs acting on histones have
been identified: amine oxidases and jumonji C (JmjC) domain-containing
enzymes. LSD1 was the first histone KDM identified and exhibits dual substrate
specificity for histone H3K4 and K9 95,96. LSD1 interacts with transcriptional
repressors and demethylates histone H3K4me1,2 yielding an unmodified lysine
residue. LSD1 and HDACs1 and 2 interact with the TAL1 transcription factor in
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erythroleukemia cell lines and negatively regulate TAL1 target genes to inhibit
the onset of erythroid differentiation 97. LSD1 also cooperates with the Gfi-1
transcriptional repressors in a lineage-specific manner to regulate
megakaryocytic, granulocytic, and erythroid differentiation 98. Furthermore,
depletion of LSD1 in mice leads to enhanced HSC and progenitor cell
proliferation and deficient erythroid differentiation 99. Regulatory roles for LSD1
in defining hematopoietic lineage commitment highlight the importance of
restricting histone H3K4 methylation patterns to establish and maintain
differentiation programs.
Arginine methyltransferases
Methylation of arginine residues within histone and non-histone proteins is
catalyzed by protein arginine (R) methyltransferases (PRMTs). There are nine
identified enzymes in the mammalian PRMT family (PRMT1-9), which are
generally classified as Type I enzymes (PRMTs 1, 3, 4, 6, 8) that catalyze
asymmetric dimethylation or Type II enzymes (PRMTs 5 and 7) that catalyze
symmetric dimethylation 100. Methylated arginine residues identified in histones
H3 and H4 directly and indirectly regulate transcription.
PRMT1 catalyzes asymmetric dimethylation of histone H4R3
(H4R3me2a), which promotes p300-mediated acetylation of H4K8 and K12,
resulting in transcriptional activation 101. PRMT1 interacts with a leukemogenic
MLL fusion protein (MLL-EEN) to promote transformation of primary
hematopoietic progenitor cells. The oncogenic mechanism is dependent upon
PRMT1-mediated methylation of histone H4R3 and transcriptional activation of
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MLL target genes 102. Furthermore, cross-talk occurring between PRMTs and
KMTs is necessary to establish appropriate histone methylation patterns. For
instance, PRMT6-mediated methylation of histone H3R2me2a indirectly
represses transcription by inhibiting MLL-mediated activity toward histone H3K4
17,103
, and by blocking the association of histone H3K4-methyl binding proteins
104
.
PRMTs influence transcription via methylation of histone and non-histone
substrates, including transcription factors. In human hematopoietic progenitor
cells, PRMT6 physically interacts with RUNX1/AML1 at the promoters of
megakaryocytic genes and maintains a chromatin environment that is repressed,
but primed for transcriptional activation 105. Moreover, PRMT1-mediated
methylation of RUNX1/AML1 itself enhances its ability to activate transcription of
several target genes during hematopoietic differentiation by inhibiting its
association with the SIN3A co-repressor complex 106. PRMT1 also interacts with
an alternatively spliced version of the AML1-ETO leukemogenic fusion protein,
AE9a, and activates transcription of AE9a target genes to enhance
hematopoietic progenitor cell proliferation 107.
Lysine and arginine methylation readers
Methyl lysine binding domains include the plant homeodomain (PHD)
finger, chromo, tudor, malignant brain tumor (MBT), PWWP, and the ankyrin
repeat. Multiple binding domains show affinity for particular lysine or arginine
residues within histone tails, however binding by different effector molecules
depends on whether methylation or acetylation is present (Figure 2). In addition,
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effector binding also depends on the degree of the modification present on a
particular residue, such as me1, me2, me3. These requirements suggest
temporal regulation of binding events to ensure the appropriate interactions occur
between the histone substrate and the binding effector molecule.
Histone modifying enzymes often contain domains that bind modifications.
For instance, the histone demethylase JARID1A contains a C-terminal PHD
finger that binds its substrate, H3K4me2,3 (Figure 2). Translocations occurring
in AML create a JARID1A-NUP98 fusion protein that uses this PHD finger to
aberrantly bind PcG-silenced Hox genes and maintain them in a transcriptionally
active state, resulting in an arrest of hematopoietic differentiation 108.
Furthermore, replacing the JARID1A PHD domain with a PHD domain that reads
unmethylated histone H3K4 fails to induce transformation, supporting the idea
that induced transcriptional activation of temporally regulated genes is crucial to
the leukemogenic mechanism 108. This example demonstrates that aberrant
genomic targeting of a histone modification-reading domain is sufficient to drive
transformation.
The conserved PHD domains within MLL are lost following leukemogenic
translocations 109. It was recently shown that MLL PHD3 binds histone
H3K4me2/3 and is required for localization of wild-type MLL to target gene
promoters to activate transcription 110,111. Introduction of the third PHD finger
(PHD3) into the MLL-ENL fusion protein blocks aberrant HoxC8 gene activation
in an HDAC dependent manner and subsequently inhibits hematopoietic
progenitor transformation 112. Similarly, adding multiple PHD fingers to the MLL-
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AF9 fusion protein inhibits association with the HoxA9 locus and immortalization
of hematopoietic progenitors 109. Taken together, it is evident that loss of the
PHD fingers is a common contributing factor to MLL-mediated leukemogenesis.
Epigenetic mechanisms in normal hematology and in hematological
malignancies
Genomic loci encoding chromatin modifying enzymes are frequently
disrupted in human cancers, and these alterations are especially prevalent in
hematological disorders. It is noteworthy that many modification readers
promote transformation by cooperating with oncogenic enzymes. Loss or gain of
conserved catalytic domains and/or modification reading domains results in
deregulated enzyme activity toward histone and non-histone substrates that
ultimately impacts chromatin structure and function to promote leukemogenesis.
In addition, fusion proteins created by translocations often lead to altered proteinprotein interactions that target histone modifying activities to inappropriate
genomic targets. One significant question that remains is how these enzymes
are targeted to specific genomic loci? DNA methylation and histone modification
patterns are frequently interdependent due to functional interactions between the
enzymes that modify DNA and histones. It is critical to define common DNA
methylation and histone modification patterns, in addition to downstream gene
targets affected by genetic alterations in the writers, erasers, and readers of
chromatin modifications as we look toward the future design of molecular-based
therapies to treat hematological malignancies.
21
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Authorship
Contribution: J.S. Butler and S.Y.R. Dent wrote the manuscript.
Conflict-of-interest disclosure: The authors declare no competing financial
interests.
Correspondence: Sharon Dent, Department of Molecular Carcinogenesis, The
University of Texas MD Anderson Cancer Center Science Park, P.O. Box 389,
Smithville TX 78957; e-mail [email protected]
Acknowledgements
We would like to thank Elizabeth McIvor for helpful comments and discussion on
the manuscript. This work was supported by the Cancer Prevention Research
Institute of Texas (CPRIT) RP100429 to SYR Dent.
REFERENCES
1.
Zhu B, Reinberg D. Epigenetic inheritance: uncontested? Cell research.
2011;21(3):435-441.
2.
Paralkar VR, Weiss MJ. A new 'Linc' between noncoding RNAs and blood
development. Genes Dev. 2011;25(24):2555-2558.
3.
O'Connell RM, Baltimore D. MicroRNAs and hematopoietic cell
development. Current topics in developmental biology. 2012;99:145-174.
4.
Branco MR, Ficz G, Reik W. Uncovering the role of 5hydroxymethylcytosine in the epigenome. Nat Rev Genet. 2011;13(1):7-13.
5.
Jenuwein T, Allis CD. Translating the histone code. Science.
2001;293(5532):1074-1080.
6.
Gardner KE, Allis CD, Strahl BD. Operating on chromatin, a colorful
language where context matters. Journal of molecular biology. 2011;409(1):3646.
7.
Ruthenburg AJ, Allis CD, Wysocka J. Methylation of lysine 4 on histone
H3: intricacy of writing and reading a single epigenetic mark. Mol Cell.
2007;25(1):15-30.
22
From www.bloodjournal.org by guest on June 16, 2017. For personal use only.
8.
Chi P, Allis CD, Wang GG. Covalent histone modifications--miswritten,
misinterpreted and mis-erased in human cancers. Nat Rev Cancer.
2010;10(7):457-469.
9.
Wang Z, Zang C, Rosenfeld JA, et al. Combinatorial patterns of histone
acetylations and methylations in the human genome. Nat Genet. 2008;40(7):897903.
10.
Migliori V, Muller J, Phalke S, et al. Symmetric dimethylation of H3R2 is a
newly identified histone mark that supports euchromatin maintenance. Nature
structural & molecular biology. 2012;19(2):136-144.
11.
Bernstein BE, Kamal M, Lindblad-Toh K, et al. Genomic maps and
comparative analysis of histone modifications in human and mouse. Cell.
2005;120(2):169-181.
12.
Kim TH, Barrera LO, Zheng M, et al. A high-resolution map of active
promoters in the human genome. Nature. 2005;436(7052):876-880.
13.
Steger DJ, Lefterova MI, Ying L, et al. DOT1L/KMT4 recruitment and
H3K79 methylation are ubiquitously coupled with gene transcription in
mammalian cells. Mol Cell Biol. 2008;28(8):2825-2839.
14.
Schotta G, Lachner M, Sarma K, et al. A silencing pathway to induce H3K9 and H4-K20 trimethylation at constitutive heterochromatin. Genes Dev.
2004;18(11):1251-1262.
15.
Plath K, Fang J, Mlynarczyk-Evans SK, et al. Role of histone H3 lysine 27
methylation in X inactivation. Science. 2003;300(5616):131-135.
16.
Barski A, Cuddapah S, Cui K, et al. High-resolution profiling of histone
methylations in the human genome. Cell. 2007;129(4):823-837.
17.
Guccione E, Bassi C, Casadio F, et al. Methylation of histone H3R2 by
PRMT6 and H3K4 by an MLL complex are mutually exclusive. Nature.
2007;449(7164):933-937.
18.
Jones PA. Functions of DNA methylation: islands, start sites, gene bodies
and beyond. Nature reviews Genetics. 2012;13(7):484-492.
19.
Bernstein BE, Mikkelsen TS, Xie X, et al. A bivalent chromatin structure
marks key developmental genes in embryonic stem cells. Cell. 2006;125(2):315326.
20.
Pastor WA, Pape UJ, Huang Y, et al. Genome-wide mapping of 5hydroxymethylcytosine in embryonic stem cells. Nature. 2011;473(7347):394397.
21.
Cui K, Zang C, Roh TY, et al. Chromatin signatures in multipotent human
hematopoietic stem cells indicate the fate of bivalent genes during differentiation.
Cell Stem Cell. 2009;4(1):80-93.
22.
Adli M, Zhu J, Bernstein BE. Genome-wide chromatin maps derived from
limited numbers of hematopoietic progenitors. Nature methods. 2010;7(8):615618.
23.
Butler JS, Koutelou E, Schibler AC, Dent SY. Histone-modifying enzymes:
regulators of developmental decisions and drivers of human disease.
Epigenomics. 2012;4(2):163-177.
23
From www.bloodjournal.org by guest on June 16, 2017. For personal use only.
24.
Song J, Rechkoblit O, Bestor TH, Patel DJ. Structure of DNMT1-DNA
complex reveals a role for autoinhibition in maintenance DNA methylation.
Science. 2011;331(6020):1036-1040.
25.
Ooi SK, O'Donnell AH, Bestor TH. Mammalian cytosine methylation at a
glance. Journal of cell science. 2009;122(Pt 16):2787-2791.
26.
Trowbridge JJ, Snow JW, Kim J, Orkin SH. DNA methyltransferase 1 is
essential for and uniquely regulates hematopoietic stem and progenitor cells. Cell
Stem Cell. 2009;5(4):442-449.
27.
Broske AM, Vockentanz L, Kharazi S, et al. DNA methylation protects
hematopoietic stem cell multipotency from myeloerythroid restriction. Nat Genet.
2009;41(11):1207-1215.
28.
Tadokoro Y, Ema H, Okano M, Li E, Nakauchi H. De novo DNA
methyltransferase is essential for self-renewal, but not for differentiation, in
hematopoietic stem cells. J Exp Med. 2007;204(4):715-722.
29.
Challen GA, Sun D, Jeong M, et al. Dnmt3a is essential for hematopoietic
stem cell differentiation. Nat Genet. 2011;44(1):23-31.
30.
Ley TJ, Ding L, Walter MJ, et al. DNMT3A mutations in acute myeloid
leukemia. The New England journal of medicine. 2010;363(25):2424-2433.
31.
Yan XJ, Xu J, Gu ZH, et al. Exome sequencing identifies somatic
mutations of DNA methyltransferase gene DNMT3A in acute monocytic
leukemia. Nature genetics. 2011;43(4):309-315.
32.
Yamashita Y, Yuan J, Suetake I, et al. Array-based genomic resequencing
of human leukemia. Oncogene. 2010;29(25):3723-3731.
33.
Lorsbach RB, Moore J, Mathew S, Raimondi SC, Mukatira ST, Downing
JR. TET1, a member of a novel protein family, is fused to MLL in acute myeloid
leukemia containing the t(10;11)(q22;q23). Leukemia : official journal of the
Leukemia Society of America, Leukemia Research Fund, UK. 2003;17(3):637641.
34.
Abdel-Wahab O, Mullally A, Hedvat C, et al. Genetic characterization of
TET1, TET2, and TET3 alterations in myeloid malignancies. Blood.
2009;114(1):144-147.
35.
Ko M, Rao A. TET2: epigenetic safeguard for HSC. Blood.
2011;118(17):4501-4503.
36.
Li Z, Cai X, Cai CL, et al. Deletion of Tet2 in mice leads to dysregulated
hematopoietic stem cells and subsequent development of myeloid malignancies.
Blood. 2011;118(17):4509-4518.
37.
Ko M, Bandukwala HS, An J, et al. Ten-Eleven-Translocation 2 (TET2)
negatively regulates homeostasis and differentiation of hematopoietic stem cells
in mice. Proc Natl Acad Sci U S A. 2011;108(35):14566-14571.
38.
Moran-Crusio K, Reavie L, Shih A, et al. Tet2 loss leads to increased
hematopoietic stem cell self-renewal and myeloid transformation. Cancer Cell.
2011;20(1):11-24.
39.
Quivoron C, Couronne L, Della Valle V, et al. TET2 inactivation results in
pleiotropic hematopoietic abnormalities in mouse and is a recurrent event during
human lymphomagenesis. Cancer Cell. 2011;20(1):25-38.
24
From www.bloodjournal.org by guest on June 16, 2017. For personal use only.
40.
Ko M, Huang Y, Jankowska AM, et al. Impaired hydroxylation of 5methylcytosine in myeloid cancers with mutant TET2. Nature.
2010;468(7325):839-843.
41.
Figueroa ME, Abdel-Wahab O, Lu C, et al. Leukemic IDH1 and IDH2
mutations result in a hypermethylation phenotype, disrupt TET2 function, and
impair hematopoietic differentiation. Cancer Cell. 2010;18(6):553-567.
42.
Franchini DM, Schmitz KM, Petersen-Mahrt SK. 5-Methylcytosine DNA
Demethylation: More Than Losing a Methyl Group. Annual review of genetics.
2012.
43.
He YF, Li BZ, Li Z, et al. Tet-mediated formation of 5-carboxylcytosine and
its excision by TDG in mammalian DNA. Science. 2011;333(6047):1303-1307.
44.
Bogdanovic O, Veenstra GJ. DNA methylation and methyl-CpG binding
proteins: developmental requirements and function. Chromosoma.
2009;118(5):549-565.
45.
Rupon JW, Wang SZ, Gaensler K, Lloyd J, Ginder GD. Methyl binding
domain protein 2 mediates gamma-globin gene silencing in adult human
betaYAC transgenic mice. Proceedings of the National Academy of Sciences of
the United States of America. 2006;103(17):6617-6622.
46.
Rupon JW, Wang SZ, Gnanapragasam M, Labropoulos S, Ginder GD.
MBD2 contributes to developmental silencing of the human epsilon-globin gene.
Blood cells, molecules & diseases. 2011;46(3):212-219.
47.
Frauer C, Hoffmann T, Bultmann S, et al. Recognition of 5hydroxymethylcytosine by the Uhrf1 SRA domain. PloS one. 2011;6(6):e21306.
48.
Yildirim O, Li R, Hung JH, et al. Mbd3/NURD complex regulates
expression of 5-hydroxymethylcytosine marked genes in embryonic stem cells.
Cell. 2011;147(7):1498-1510.
49.
Bostick M, Kim JK, Esteve PO, Clark A, Pradhan S, Jacobsen SE. UHRF1
plays a role in maintaining DNA methylation in mammalian cells. Science.
2007;317(5845):1760-1764.
50.
Cross SH, Charlton JA, Nan X, Bird AP. Purification of CpG islands using
a methylated DNA binding column. Nature genetics. 1994;6(3):236-244.
51.
Hogart A, Lichtenberg J, Ajay SS, Anderson S, Margulies EH, Bodine DM.
Genome-wide DNA methylation profiles in hematopoietic stem and progenitor
cells reveal overrepresentation of ETS transcription factor binding sites. Genome
research. 2012;22(8):1407-1418.
52.
Shearstone JR, Pop R, Bock C, Boyle P, Meissner A, Socolovsky M.
Global DNA demethylation during mouse erythropoiesis in vivo. Science.
2011;334(6057):799-802.
53.
Deaton AM, Webb S, Kerr AR, et al. Cell type-specific DNA methylation at
intragenic CpG islands in the immune system. Genome research.
2011;21(7):1074-1086.
54.
Illingworth R, Kerr A, Desousa D, et al. A novel CpG island set identifies
tissue-specific methylation at developmental gene loci. PLoS biology.
2008;6(1):e22.
25
From www.bloodjournal.org by guest on June 16, 2017. For personal use only.
55.
Thomas T, Corcoran LM, Gugasyan R, et al. Monocytic leukemia zinc
finger protein is essential for the development of long-term reconstituting
hematopoietic stem cells. Genes Dev. 2006;20(9):1175-1186.
56.
Katsumoto T, Aikawa Y, Iwama A, et al. MOZ is essential for maintenance
of hematopoietic stem cells. Genes Dev. 2006;20(10):1321-1330.
57.
Wada T, Kikuchi J, Nishimura N, Shimizu R, Kitamura T, Furukawa Y.
Expression levels of histone deacetylases determine the cell fate of
hematopoietic progenitors. The Journal of biological chemistry.
2009;284(44):30673-30683.
58.
Glozak MA, Seto E. Histone deacetylases and cancer. Oncogene.
2007;26(37):5420-5432.
59.
Quintas-Cardama A, Santos FP, Garcia-Manero G. Histone deacetylase
inhibitors for the treatment of myelodysplastic syndrome and acute myeloid
leukemia. Leukemia : official journal of the Leukemia Society of America,
Leukemia Research Fund, UK. 2011;25(2):226-235.
60.
Filippakopoulos P, Knapp S. The bromodomain interaction module. FEBS
letters. 2012;586(17):2692-2704.
61.
Dhalluin C, Carlson JE, Zeng L, He C, Aggarwal AK, Zhou MM. Structure
and ligand of a histone acetyltransferase bromodomain. Nature.
1999;399(6735):491-496.
62.
Lamonica JM, Deng W, Kadauke S, et al. Bromodomain protein Brd3
associates with acetylated GATA1 to promote its chromatin occupancy at
erythroid target genes. Proceedings of the National Academy of Sciences of the
United States of America. 2011;108(22):E159-168.
63.
Vidler LR, Brown N, Knapp S, Hoelder S. Druggability Analysis and
Structural Classification of Bromodomain Acetyl-lysine Binding Sites. Journal of
medicinal chemistry. 2012;55(17):7346-7359.
64.
Dawson MA, Prinjha RK, Dittmann A, et al. Inhibition of BET recruitment to
chromatin as an effective treatment for MLL-fusion leukaemia. Nature.
2011;478(7370):529-533.
65.
Zuber J, Shi J, Wang E, et al. RNAi screen identifies Brd4 as a therapeutic
target in acute myeloid leukaemia. Nature. 2011;478(7370):524-528.
66.
Yu BD, Hess, J. L., Horning, S. E., Brown, G. A., Korsmeyer, S. J. Altered
Hox expression and segmental identity in Mll-mutant mice. Nature.
1995;378(6556):505-508.
67.
Hess JL, Yu BD, Li B, Hanson R, Korsmeyer SJ. Defects in yolk sac
hematopoiesis in Mll-null embryos. Blood. 1997;90(5):1799-1806.
68.
Yagi H, Deguchi K, Aono A, Tani Y, Kishimoto T, Komori T. Growth
disturbance in fetal liver hematopoiesis of Mll-mutant mice. Blood.
1998;92(1):108-117.
69.
Jude CD, Climer L, Xu D, Artinger E, Fisher JK, Ernst P. Unique and
independent roles for MLL in adult hematopoietic stem cells and progenitors. Cell
Stem Cell. 2007;1(3):324-337.
70.
Tkachuk DC, Kohler, S., Cleary, M. L. Involvement of a homolog of
Drosophila Trithorax by 11q23 chromosomal translocations in acute leukemias.
Cell. 1992;71:691-700.
26
From www.bloodjournal.org by guest on June 16, 2017. For personal use only.
71.
Bernt KM, Armstrong SA. Targeting epigenetic programs in MLLrearranged leukemias. Hematology / the Education Program of the American
Society of Hematology American Society of Hematology Education Program.
2011;2011:354-360.
72.
Smith E, Lin C, Shilatifard A. The super elongation complex (SEC) and
MLL in development and disease. Genes & development. 2011;25(7):661-672.
73.
Kamminga LM, Bystrykh LV, de Boer A, et al. The Polycomb group gene
Ezh2 prevents hematopoietic stem cell exhaustion. Blood. 2006;107(5):21702179.
74.
Mochizuki-Kashio M, Mishima Y, Miyagi S, et al. Dependency on the
polycomb gene Ezh2 distinguishes fetal from adult hematopoietic stem cells.
Blood. 2011;118(25):6553-6561.
75.
Su IH, Basavaraj A, Krutchinsky AN, et al. Ezh2 controls B cell
development through histone H3 methylation and Igh rearrangement. Nat
Immunol. 2003;4(2):124-131.
76.
Nikoloski G, Langemeijer SM, Kuiper RP, et al. Somatic mutations of the
histone methyltransferase gene EZH2 in myelodysplastic syndromes. Nat Genet.
2010;42(8):665-667.
77.
Makishima H, Jankowska AM, Tiu RV, et al. Novel homo- and hemizygous
mutations in EZH2 in myeloid malignancies. Leukemia. 2010;24(10):1799-1804.
78.
Ernst T, Chase AJ, Score J, et al. Inactivating mutations of the histone
methyltransferase gene EZH2 in myeloid disorders. Nat Genet. 2010;42(8):722726.
79.
Jankowska AM, Makishima H, Tiu RV, et al. Mutational spectrum analysis
of chronic myelomonocytic leukemia includes genes associated with epigenetic
regulation: UTX, EZH2 and DNMT3A. Blood. 2011.
80.
Morin RD, Johnson NA, Severson TM, et al. Somatic mutations altering
EZH2 (Tyr641) in follicular and diffuse large B-cell lymphomas of germinal-center
origin. Nat Genet. 2010;42(2):181-185.
81.
Chase A, Cross NC. Aberrations of EZH2 in cancer. Clinical cancer
research : an official journal of the American Association for Cancer Research.
2011;17(9):2613-2618.
82.
McCabe MT, Ott HM, Ganji G, et al. EZH2 inhibition as a therapeutic
strategy for lymphoma with EZH2-activating mutations. Nature. 2012.
83.
Gelsi-Boyer V, Trouplin V, Adelaide J, et al. Mutations of polycombassociated gene ASXL1 in myelodysplastic syndromes and chronic
myelomonocytic leukaemia. British journal of haematology. 2009;145(6):788-800.
84.
Bejar R, Stevenson K, Abdel-Wahab O, et al. Clinical effect of point
mutations in myelodysplastic syndromes. The New England journal of medicine.
2011;364(26):2496-2506.
85.
Metzeler KH, Becker H, Maharry K, et al. ASXL1 mutations identify a highrisk subgroup of older patients with primary cytogenetically normal AML within
the ELN Favorable genetic category. Blood. 2011;118(26):6920-6929.
86.
Gelsi-Boyer V, Brecqueville M, Devillier R, Murati A, Mozziconacci MJ,
Birnbaum D. Mutations in ASXL1 are associated with poor prognosis across the
27
From www.bloodjournal.org by guest on June 16, 2017. For personal use only.
spectrum of malignant myeloid diseases. Journal of hematology & oncology.
2012;5:12.
87.
Abdel-Wahab O, Adli M, LaFave LM, et al. ASXL1 mutations promote
myeloid transformation through loss of PRC2-mediated gene repression. Cancer
Cell. 2012;22(2):180-193.
88.
Feng Q, Wang H, Ng HH, et al. Methylation of H3-lysine 79 is mediated by
a new family of HMTases without a SET domain. Curr Biol. 2002;12(12):10521058.
89.
Feng Y, Yang Y, Ortega MM, et al. Early mammalian erythropoiesis
requires the Dot1L methyltransferase. Blood. 2010;116(22):4483-4491.
90.
Jo SY, Granowicz EM, Maillard I, Thomas D, Hess JL. Requirement for
Dot1l in murine postnatal hematopoiesis and leukemogenesis by MLL
translocation. Blood. 2011;117(18):4759-4768.
91.
Nguyen AT, He J, Taranova O, Zhang Y. Essential role of DOT1L in
maintaining normal adult hematopoiesis. Cell Res. 2011;21(9):1370-1373.
92.
Okada Y, Feng Q, Lin Y, et al. hDOT1L links histone methylation to
leukemogenesis. Cell. 2005;121(2):167-178.
93.
Daigle SR, Olhava EJ, Therkelsen CA, et al. Selective killing of mixed
lineage leukemia cells by a potent small-molecule DOT1L inhibitor. Cancer Cell.
2011;20(1):53-65.
94.
Chen L, Deshpande A, Banka D, et al. Abrogation of MLL-AF10 and
CALM-AF10 mediated transformation through genetic inactivation or
pharmacological inhibition of the H3K79 methyltransferase Dot1l. Leukemia :
official journal of the Leukemia Society of America, Leukemia Research Fund,
UK. 2012.
95.
Shi Y, Lan F, Matson C, et al. Histone demethylation mediated by the
nuclear amine oxidase homolog LSD1. Cell. 2004;119(7):941-953.
96.
Metzger E, Wissmann M, Yin N, et al. LSD1 demethylates repressive
histone marks to promote androgen-receptor-dependent transcription. Nature.
2005;437(7057):436-439.
97.
Hu X, Li X, Valverde K, et al. LSD1-mediated epigenetic modification is
required for TAL1 function and hematopoiesis. Proc Natl Acad Sci U S A.
2009;106(25):10141-10146.
98.
Saleque S, Kim J, Rooke HM, Orkin SH. Epigenetic regulation of
hematopoietic differentiation by Gfi-1 and Gfi-1b is mediated by the cofactors
CoREST and LSD1. Mol Cell. 2007;27(4):562-572.
99.
Sprussel A, Schulte JH, Weber S, et al. Lysine-specific demethylase 1
restricts hematopoietic progenitor proliferation and is essential for terminal
differentiation. Leukemia. 2012.
100. Bedford MT, Clarke SG. Protein arginine methylation in mammals: who,
what, and why. Mol Cell. 2009;33(1):1-13.
101. Wang H, Huang ZQ, Xia L, et al. Methylation of histone H4 at arginine 3
facilitating transcriptional activation by nuclear hormone receptor. Science.
2001;293(5531):853-857.
102. Cheung N, Chan LC, Thompson A, Cleary ML, So CW. Protein argininemethyltransferase-dependent oncogenesis. Nat Cell Biol. 2007;9(10):1208-1215.
28
From www.bloodjournal.org by guest on June 16, 2017. For personal use only.
103. Hyllus D, Stein C, Schnabel K, et al. PRMT6-mediated methylation of R2
in histone H3 antagonizes H3 K4 trimethylation. Genes Dev. 2007;21(24):33693380.
104. Iberg AN, Espejo A, Cheng D, et al. Arginine methylation of the histone H3
tail impedes effector binding. J Biol Chem. 2008;283(6):3006-3010.
105. Herglotz J, Kuvardina ON, Kolodziej S, et al. Histone arginine methylation
keeps RUNX1 target genes in an intermediate state. Oncogene. 2012.
106. Zhao X, Jankovic V, Gural A, et al. Methylation of RUNX1 by PRMT1
abrogates SIN3A binding and potentiates its transcriptional activity. Genes &
development. 2008;22(5):640-653.
107. Shia WJ, Okumura AJ, Yan M, et al. PRMT1 interacts with AML1-ETO to
promote its transcriptional activation and progenitor cell proliferative potential.
Blood. 2012;119(21):4953-4962.
108. Wang GG, Song J, Wang Z, et al. Haematopoietic malignancies caused
by dysregulation of a chromatin-binding PHD finger. Nature.
2009;459(7248):847-851.
109. Muntean AG, Giannola D, Udager AM, Hess JL. The PHD fingers of MLL
block MLL fusion protein-mediated transformation. Blood. 2008.
110. Milne TA, Kim J, Wang GG, et al. Multiple interactions recruit MLL1 and
MLL1 fusion proteins to the HOXA9 locus in leukemogenesis. Mol Cell.
2010;38(6):853-863.
111. Chang PY, Hom RA, Musselman CA, et al. Binding of the MLL PHD3
finger to histone H3K4me3 is required for MLL-dependent gene transcription. J
Mol Biol. 2010;400(2):137-144.
112. Chen J, Santillan DA, Koonce M, et al. Loss of MLL PHD finger 3 is
necessary for MLL-ENL-induced hematopoietic stem cell immortalization. Cancer
Res. 2008;68(15):6199-6207.
29
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Table 1. Chromatin modifying enzymes
Enzyme
Writer/Eraser
Transcriptional
outcome
Activation
Activation
Activation
Activation
Eraser
Chromatin
modification
H3K4me
H3K79me
H4R3me2a
H3ac
H4ac
H3ac
H3ac
H3K27me
H3ac
H4ac
H3K4me
H3K9me
H3K4me
MLL1, 2, 3, 4, 5
DOT1L
PRMT1
p300
Writer
Writer
Writer
Writer
MOZ
PCAF
EZH2
HDAC1, 2, 3
Writer
Writer
Writer
Eraser
KDM1A (LSD1)
Eraser
KDM5A
(JARID1A)
PRMT6
DNMT1, 3a, 3b
Tet1, 2, 3
AID
Writer
Writer
Writer/Eraser
Eraser
H3R2me2a
5mC
5hmC/5mC
5mC
Repression
Repression
TBD
TBD
30
Activation
Activation
Repression
Repression
Repression
Repression
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Table 2. Chromatin modifying enzymes are essential for hematopoiesis
Enzyme
Moz
Mll1
Ezh2
Dot1L
Lsd1
Epigenetic
activity
Histone
acetylation
Histone
methylation
Histone
methylation
Histone
methylation
Dnmt1
Histone
demethylation
DNA 5mC
Dnmt3a
Tet2
DNA 5mC
DNA 5hmC
Targeting
strategy
KO
Role in HSC
self-renewal
Yes
Lineagespecific role
No
55
KO
KO
Yes
Yes
Myeloid
Myeloid
56
67
KO
Yes
No
68
CKO; Mx1-Cre,
lysozyme M-Cre,
CD19-Cre, lck-Cre
CKO; Mx1-Cre
Yes
No
69
--
Lymphoid
75
CKO; Tie2-Cre,
Rosa26-Cre
Inducible KO;
Rosa26-Cre-ER
No
Erythroid &
Lymphoid
MPPs &
Myeloid
74
Inducible KO;
Rosa26-Cre-ER
KO
CKD; global
Yes
90
-Yes
MPPs &
Myeloid
Erythroid
Myeloid
CKO; Mx1-Cre
CKO; Mx1-Cre
hypomorph
CKO; Mx1-Cre
KO
KO
CKO; Vav-Cre,
Ella-Cre, Mx1-Cre
KO
CKO; Mx1-Cre
Yes
Yes
Myeloid
Lymphoid
26
27
Yes
Yes
Yes
Yes
LT-HSCs
Myeloid
Myeloid
Myeloid
29
37
36
38
Yes
Lymphoid &
Myeloid
39
Yes
Refs
91
89
99
Abbreviations are as follows: Conditional knock-out (CKO); conditional knock-down (CKD);
5-methyl cytosine (5mC); 5-hydroxy-methyl cytosine (5HmC); multipotent progenitor (MPP);
long term hematopoietic stem cell (LT-HSC)
31
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FIGURE LEGENDS
Figure 1. Histone modifications mark dynamically regulated genes.
In all panels, shades of green indicate active marks while shades of pink
represent repressive marks. Orange and yellow mark regions of 5mC and
5hmC, respectively. (A) The distribution of histone methylation and acetylation
marks, along with the degree of methylation, is illustrated across the promoter
region, TSS (transcriptional start site) and gene body of a transcriptionally active
gene. (B) Histone H3 methylation and DNA methylation are found in the
promoter region and surrounding the TSS in transcriptionally repressed genes.
(C) Bivalent chromatin domains consist of discrete pockets of histone H3K4me3
within large regions of histone H3K27me3. DNA 5hmC is also found in bivalent
domains.
Figure 2. Modification binding domains interpret histone PTMs.
Domains from various histone interacting proteins are depicted along with the
PTMs that they bind on histone H3. Multiple reading domains can interact with a
single modified site, as illustrated for histone H3K4, K9, K27, K36. Interactions
may also change depending on the modification present at the site, as shown for
acetylation or methylation of histone H3K9 and K36. The colors represent
different PTMs and associated binding domains, which are depicted as follows:
pink – methylation; green – acetylation
1
From www.bloodjournal.org by guest on June 16, 2017. For personal use only.
Prepublished online January 2, 2013;
doi:10.1182/blood-2012-10-451237
The role of chromatin modifiers in normal and malignant hematopoiesis
Jill S. Butler and Sharon Y.R. Dent
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