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TRENDS in Plant Science
Vol.9 No.2 February 2004
A plant dialect of the histone language
Peter Loidl
Department of Molecular Biology, Innsbruck Medical University, Peter-Mayr-Strasse 4b, A-6020 Innsbruck, Austria
The genome contains all the information needed to
build an organism. However, during differentiation and
development, additional epigenetic information determines the functional state of cells and tissues. This epigenetic information can be introduced by cytosine
methylation and by marking nucleosomal histones. The
code written on histones consists of post-translational
modifications, including acetylation and methylation. In
contrast to the universal nature of the DNA code, the
histone language and its decoding machinery differ
among animals, plants and fungi. Plant cells have
retained totipotency to generate the entire plant and
maintained the ability to dedifferentiate, which suggests that the establishment and maintenance of epigenetic information differs from animals. Here, I aim to
summarize the histone code and plant-specific aspects
of setting and translating the code.
Nuclear DNA is compacted into chromatin, which is a
complex structure built from repeating units, the nucleosomes [1]. These consist of ,145 bp of DNA wrapped
around an octamer of basic proteins, the core histones.
The octamer is formed by two molecules each of histones
H2A, H2B, H3 and H4. At least two different domains can
be distinguished in core histones: a globular domain
involved in histone – histone interactions (containing the
‘histone fold’ motif); and the flexible N-terminal tails of H3
and H4, and N- and C-terminal tails of H2A and H2B. A
series of consecutive nucleosomes produces a ‘beads on a
string’ structure or 10 nm fiber. A further level of compaction is the 30 nm fiber with six nucleosomes per turn in
a solenoid arrangement.
Our traditional picture of eukaryotic chromatin as a
static and largely repressive functional state has, over
recent years, changed to a more complex view of chromatin
as a highly dynamic state that is essential for regulating
cellular functions. The dynamic properties of chromatin
are mediated by multiprotein complexes with different
functions that set marks overlying the stable information
of the DNA. The most prominent factors that influence
chromatin structure and function are enzymes that modify
the histones and chromatin remodeling machines that
utilize ATP. Plant chromatin remodeling complexes have
recently been reviewed in detail [2– 4].
Histones have been conserved during evolution. However, they are dynamically changed by post-translational
modifications. These modifications include acetylation,
methylation, phosphorylation, ubiquitination, glycosylation, ADP ribosylation, carbonylation, sumoylation and
Corresponding author: Peter Loidl ([email protected]).
biotinylation, which can all cause structural and functional rearrangements in chromatin and are therefore
essential elements of the complex ‘epigenetic histone code’
[5,6]. To decipher this code, which is recognized and
interpreted by transcriptional regulators and chromatin
remodeling machines, is one of the central challenges of
chromatin research. In this article, I focus on the methylation and acetylation of core histones (Figure 1) because
little is known about the other types of modification.
DNA methylation and histone modifications
There is ample evidence for an interrelation between DNA
methylation and histone modifications [7]. Cytosine
methylation is important for regulating gene activity
and genome stability in eukaryotes and is correlated with
gene silencing. Silencing governs processes such as X
chromosome inactivation and imprinting in vertebrates,
as well as suppression of transposon movement in higher
plants [8]. DNA methylation also silences protein-coding
genes in plant polyploids [9] and RNA polymerase I genes
[10]. In contrast to the vertebrate genome, in which
methylation is mostly restricted to CG islands, plants and
fungi carry methylation on CG dinucleotides and also on
non-CG cytosines. In Arabidopsis, the cytosine methyltransferase CMT3 is involved in CNG methylation [11].
CMT3 is a member of the plant-specific DNA methyltransferases with a chromodomain [8,12]. A related
enzyme from maize, also carrying a chromodomain, is
involved in the maintenance of CNG methylation [13]. The
link between DNA methylation and histone modifications
was initially supported by two basic observations. Genetic
experiments in Arabidopsis showed that the DDM1 gene,
encoding a protein related to SWI2/SNF2 chromatin
remodeling factors, is implicated in DNA methylation
[14]. A genetic search in Neurospora then revealed the
dim-5 gene, encoding a SET domain protein, to be necessary for DNA methylation [15]. SET domain [Su(var)3-9,
Enhancer-of-zeste, Trithorax] proteins form a protein
family that can influence gene expression through histone
methylation [16]. The Neurospora protein DIM-5 has
histone methyltransferase (HMT) activity and catalyzes
the methylation of lysine-9 in H3; loss of DIM-5 function
blocks DNA methylation and histone H3 methylation [17]. A
related protein has recently been identified in Arabidopsis
that has HMT activity at lysine-9 in H3 and a function for
maintenance of non-CG DNA methylation [18,19].
HMTs set specific marks on nucleosomes
HMTs catalyze the transfer of methyl groups to either
arginine or lysine residues, preferentially within the
N-terminal extensions of histones H3 and H4 (Figure 1). In
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Review
TRENDS in Plant Science
PRSET7
Set8
Ash1
NSD1
PRMT1
PRMT5
Me Ac
Ac
Ac
Ac
Me
Ac*
H4
SGRGKGGKGLGKGGAKRHRKVLRDNIQGIT
3
5
8
16
12
20
20*
+ZmHAT-B
–ZmRpd3
Dot1
Set1
SUV39H1, SUVH4
Ash1
MLL
G9A
Ash1
E(z)
SET9
COMPASS SETDB1
Dim-5
ATX1
KRYPTONITE
Me
DFKTDL
79
G9A
E(z)
H3
Me
Ac
Me Me
P
Ac
Me Ac
Ac
Me Me P
Me
ARTKQTARKSTGGKAPRKQL ATKAARKSAPATGGVK
2 4
9
9
14
1718
CARM1
P
Ac
23
Ac
H2A
-VLLPKKTESHHK
119
Ac
P Ac
12
15
Ub
Ac
PEPAKSAPAPKKGSKKALTKA16
Set2
NSD1
Ub
5
Ac
36
CARM1
CARM1
SGRGKQGCKARAKAKTRS5
26 27
20
H2B
-AVTKYTSSK
120
TRENDS in Plant Science
Figure 1. Core histones are targets for post-translational modifications at distinct
amino acid residues. The modifications depicted are acetylation (Ac, purple),
methylation (Me, green), phosphorylation (P, red) and ubiquitination (Ub, orange).
Methylating enzymes identified to date include PRMT1 [71], CARM1 [72], PRMT5
[73], Set1 [24], Set2 [74], SET7/9 [75], SET8 [76], PR-Set7 [75], SUV39H1 [77],
SUVH4 [25], SETDB1 [78], G9a [79], E(z) [80], KRYPTONITE [18], dim-5 [15], Ash1
[81], MLL [82], Dot1 [20], ATX1 [27] and NSD1 [83]. In plants, ZmHAT-B has been
shown to acetylate specifically lysines (K) 5 and 12 of H4 [84], and the deacetylase
ZmRpd3 can specifically deacetylate this distinct acetylation pattern [67]. The
plant-specific acetylation of lysine 20 of H4 is marked with an asterisk (p); methylation of H3 lysines 14, 18 and 23 has only been detected in plants (http://research.
nhgri.nih.gov/histones/posttrans.shtml) and are not included in the cartoon. A red
frame marks lysine-9 in H3, which can be modified by acetylation as well as methylation in all species investigated so far.
contrast to other modifications, H3 can also be methylated
in the globular domain at lysine-79 [20]. Arginines are
modified up to the mono- or dimethylated state in a
symmetric (both side-chain amino groups are methylated)
or asymmetric (only one side-chain amino group is
dimethylated) manner [21] by protein arginine methyltransferases (PRMTs), which transfer methyl groups from
S-adenosyl methionine to the guanidino nitrogen atoms of
the side chain. PRMTs are grouped into type I enzymes
(asymmetric dimethylation) and type II enzymes (symmetric dimethylation). Lysines can be mono-, di- or
trimethylated by members of the SET-domain-containing
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85
HMT family [22]. Histone methylation currently focuses
considerable research interest because it is associated with
transcriptional regulation and methyl transferases contain well conserved domains among different organisms.
In contrast to other modifications, no histone demethylases have thus far been identified, although theoretical
studies recently predict their existence [23].
Histone methylation is correlated with transcriptional
repression as well as transcriptional activation, even when
it occurs at the same site; H3 lysine-4 methylation in yeast
is important for rDNA silencing [24] but is also involved in
activating gene transcription [25]. This might depend on
the particular gene, the type of the functionally redundant
HMTs involved and the level of methylation (di- or
trimethylated). Only trimethylated lysine-9 in H3 marks
chromatin regions for DNA methylation in Neurospora;
the dimethylated form does not [17]. It is interesting in this
context that trimethylation at lysine-20 of H4 is correlated
with the aging of mammalian cells [26]. An Arabidopsis
homolog of Trithorax, ATX-1, has recently been shown to
function as an activator of homeotic genes in plants; it
specifically methylates H3 lysine-4 and is therefore
involved in chromatin remodeling [27].
In Arabidopsis, euchromatin is characterized by high
levels of dimethylated lysine-4 in H3, whereas high levels
of dimethylated lysine-9 in H3 were observed for heterochromatic chromocenters [28]. It has also been reported for
the Arabidopsis gene DDM1 that DNA methylation
inheritance is dependent on H3 lysine-9 methylation
[29]. However, this might only be true for parts of the
plant genome, because a comparative study over the whole
genome of different plants revealed that, in small genome
plants, high levels of H3 dimethylated lysine-9 were
confined to constitutive heterochromatin, whereas, in
large genome plants, dimethylated lysine-9 was uniformly
distributed. This suggests that large genome plants have
to silence dispersed repetitive sequences also within
euchromatic regions with a high level of methylated H3
lysine-4 [30]. A recent report shows that the methylation
level of H3 lysine-9 is drastically reduced after removal of
CpG methylation in an Arabidopsis mutant lacking the
DNA maintenance methyltransferase MET1 [31]. However, in this particular case, the loss of both CpG
methylation and lysine-9 methylation in H3 at heterochromatic chromocenters had no effect on the structure of
this tightly packed chromatin. An earlier study [32]
showed that chromocenters in a hypomorphic allele of
met1 were reduced in number and size compared with the
wild type. These data emphasize the complex and manifold
mechanisms leading to a particular chromatin structure.
The relationships and hierarchy between DNA methylation, H3 methylation, H4 acetylation and heterochromatin assembly have been investigated in Arabidopsis. As
a result, a tentative model was proposed in which four key
players act in a coordinated manner. Following DNA
replication, maintenance DNA methyltransferase acts on
chromatin with acetylated H4 lysine-16. DNA methylation
precedes and governs H3 lysine-9 methylation. The
chromatin remodeling factor DDM1 could finally trigger
the deacetylation of H4 lysine-16 [32]. However, this model
might not apply to all silenced loci in the Arabidopsis
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genome and other mechanisms can exist for transcriptional regulation in a heterochromatin environment. It
was demonstrated that Arabidopsis mom1 mutants (which
are impaired in the maintenance of gene silencing) exhibit
unaltered nuclear organization, in contrast to ddm1
mutants, which are characterized by a drastic change in
nuclear organization and histone modification pattern
[33]. Analysis of ddm1 mom1 double mutants revealed
that DDM1 and MOM are likely to operate at independent
levels in transcriptional gene silencing. Methylationindependent silencing reinforces the methylation-based
system and thereby prevents rapid epigenetic deregulation in plants with DNA methylation deficiencies [34].
A further level of complexity was introduced by the
finding that RNA interference, chromatin modification
and silencing are interdependent mechanisms [35– 37].
In Arabidopsis, HDA6, a putative Rpd3-type histone
deacetylase (HDAC), enhances DNA methylation induced
by RNA-directed transcriptional silencing [38]. A protein of
the ARGONAUTE family, Arabidopsis AGO4, together
with siRNAs was recently found to direct histone methylation and non-CpG DNA methylation [39]. The few highlighted examples demonstrate that the levels of epigenetic
silencing in plants are multiple and highly complex.
Acetylation signal on histones is reversible
Of the different types of histone modification, acetylation is
the most extensively characterized. e-Amino groups of
lysines in the N-terminal extensions of core histones can be
postsynthetically acetylated by histone acetyltransferases
(HATs) using acetyl-CoA as a cosubstrate; the modification
can be reverted by HDACs, a reaction for which a large
panel of specific inhibitors is available [40]. HATs and
HDACs exist as multiple proteins that belong to distinct
protein families [40,41]; an excellent detailed sequence
and phylogenetic analysis of HATs and HDACs has
recently been published [42].
Although many research reports have been published
on histone acetylation in yeast and vertebrates, little is
still known about the specific functions of histone
acetylation in plants. Studies in animal cells have more
and more revealed that HATs and HDACs not only modify
histones but also many non-histone regulatory proteins
as well as structural proteins: proto-oncogene products
like c-Myc, tumor suppressors like p53 and the retinoblastoma tumor suppressor protein (pRb) and tubulin are
examples of a rapidly growing list of proteins [43– 46].
Therefore, it more and more becomes unclear whether
HATs and HDACs are predominantly histone modifying
enzymes in vivo; they might rather be protein acetyltransferases and deacetylases, and would probably be
better named accordingly.
HATs and HDACs basically fulfill similar functions in
all eukaryotes. The various HATs are well conserved in
their catalytic domains and recruit proteins with homologous functions in different species [42]. By sequence
analysis, four distinct families of HATs can be distinguished: (i) the GNAT-MYST family; (ii) the p300/CBP coactivator family; (iii) the TAFII250-related family; and (iv)
the nuclear receptor coactivator family, which is present in
vertebrates but not in plants or fungi [42].
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Vol.9 No.2 February 2004
There are few reports on plant HATs. In Arabidopsis,
the HAT GCN5 is associated with the transcriptional
adaptor protein ADA2; mutations disrupting ADA2 or
GCN5 had pronounced effects on growth, development and
gene expression patterns [47]. In maize, experiments
using both a transgenic line expressing the GCN5
antisense transcript or a cell line treated with trichostatin
A (a potent HDAC inhibitor) revealed a connection
between the acetylation level of histones and the equilibrium between histone synthesis and degradation [48].
Histone acetylation also has an essential role in cell
differentiation. Increased acetylation of H3 and H4 at
the promoter of a light-regulated plastocyanin gene of
pea was correlated with transcriptional activity in
response to light [49]. The transcriptional enhancer of
the pea plastocyanin gene activates transcription by
associating with the nuclear matrix, thereby triggering
the acetylation of histones on the promoter and altering
chromatin structure [50].
Three families of HDAC have been identified in plants
[42]: (i) members of the RPD3/HDA gene family;
(ii) members of the sirtuin family related to yeast SIR2;
and (iii) members of the HD2 class of enzymes. In contrast
to other eukaryotes, plants contain the HD2-type deacetylases, a plant specific class that is unrelated to the other
HDAC classes [51,52].
In general, HDACs were often correlated with transcriptional repression and gene silencing. HDACs cooperate with HMTs and DNA methyltransferases [53].
Antisense inhibition of an Rpd3-type HDAC led to various
growth and developmental defects [54 – 56]. Overexpression of rice HDAC1 resulted in increased growth rate and
dramatic changes in phenotype [57]. Mutations in the gene
encoding the Rpd3-type HDAC HDA6 of Arabidopsis
revealed it to be associated with transgene silencing
[58]. Similarly, antisense inhibition of an HD2-type HDAC
in Arabidopsis resulted in aborted seed development [59].
Rpd3-, HD2- and HDA1-type deacetylases were able to
repress transcription efficiently in reporter gene assays
[59 –61]. In Brassica, a low temperature responsive transcription factor interacts specifically with an Rpd3-type
HDAC [62]. Together, these data suggest a global role for
HDACs in gene regulation of plants.
Plant-specific peculiarities of histone modifications
The patterns of growth and development differ dramatically between plants and animals. When animals have
developed into adult organisms, growth and morphogenesis cease and cell division mainly replaces dead cells
or specialized cells that undergo continuous turnover. In
plants, morphogenesis and growth continue throughout
the lifetime of the organism. In the absence of migration of
cells, plant morphogenesis is determined by cell division
and expansion. Because cell division occurs preferentially
in meristematic regions, the identity of a cell that leaves
the meristematic region is determined mostly by the
position of the cell relative to the position of its neighbors.
In animals, the identity of cells is mostly determined by
cell lineage. Totipotency of plant cells can refer to single
plant cells that can be isolated and give rise to an entire
Additional lysine residues are acetylated or methylated in
plants
In plants, more lysine residues in the N-terminal histone
regions are subject to modification then in other eukaryotes. Plant H4 can be occasionally acetylated at lysine-20
(Figure 1), eventually leading to penta-acetylated H4 [63].
In animals and fungi, this site is only subject to methylation and it could therefore act as a functional switch in
plant chromatin. A similar situation is present at H3
lysine-9 in all species investigated so far; lysine-9 can be
either acetylated or methylated and it has been shown that
methylation of lysine-9 influences the phosphorylation of
serine 10, which in turn influences the acetylation of
lysine-14 [64]. This interdependence of different modifications might represent the key element of a complex
histone code [65,66]. Plants might have even more
combinatorial possibilities, because another three lysines
of H3 (lysines 14, 18 and 23) can be methylated, apart from
being acetylated (http://research.nhgri.nih.gov/histones/
posttrans.shtml). Taking into account that the nucleosome
consists of two molecules of each of the core histones, the
modification pattern of two H4 molecules, for example, can
be identical or different, giving rise to a great number of
modification states.
Plants are distinguished by a unique HDAC family
Unlike animals and fungi, plants possess the HD2-type
HDAC family [42,51]. This HDAC family has no sequence
relations to other known HDAC classes. HD2-type HDACs
are distantly related to cis–trans isomerases with respect
to DNA sequence but are functionally unrelated [42]. The
enzymatic activity of maize HD2 depends on phosphorylation [51,67]. HD2 might have a function in plant-specific
pathways or have taken over functions corresponding to
those carried out by other HDACs in non-plant organisms.
Possible candidates include members of the SIR2 family,
because this HDAC family is under-represented in
plants compared with animals and fungi. A detailed
phylogenetic analysis indicated that a gene duplication
might have occurred during dicot evolution, suggesting
functional diversification of the HD2 family [42]. It is
interesting in this context that the Arabidopsis genome
is predicted to encode a total of 16 HDAC proteins (http://
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www.chromdb.org/), which is more than the number of
corresponding genes in other eukaryotic organisms outside the plant kingdom. Most of these HDACs have not
been characterized so far and it is not clear whether all of
them display histone specificity in vivo. It might also turn
out that the different subtypes have distinct functions for
particular genes or chromatin areas or only during certain
developmental transitions in individual tissues.
Histone deacetylase ZmHDA1 is post-translationally
regulated by limited proteolysis
It has been recently reported that maize regulates the
activity of an Hda1 homolog by limited proteolysis [60].
ZmHDA1 is synthesized as an enzymatically inactive
protein with an apparent molecular weight of 84 kDa that
is converted to an enzymatically active 48 kDa HDAC by
proteolytic removal of the C-terminal part, presumably by
the aid of a 65 kDa intermediate protein. Interestingly, the
84 kDa precursor HDAC is part of a 300 kDa complex of
unknown function (Figure 2). Only the processed 48 kDa
deacetylase could repress transcription efficiently in a
reporter gene assay. Arabidopsis contains not only an
HDA1-homologous gene (AtHda5; NP_200914) but also a
300 kDa complex
ZmHda1-p84 (no HDAC activity,
function unknown)
p65
P
P
ZmHda1-p84
Enzymatic activation
plant under appropriate culture conditions, or to developmental stem cells in the shoot apical meristem.
With respect to DNA methylation, plants differ from
animals in that DNA methylation patterns can persist
throughout development and can be inherited between
generations, whereas, in vertebrates, DNA methylation is
reprogrammed during early embryogenesis and altered
methylation patterns are not usually transmitted to the
progeny. In addition, plant cells are much more prone to
environmental stress due to their immobility. Altogether,
these basic differences indicate that plants might have
developed mechanisms of gene regulation that are distinct
from those of animals. Indeed, plants differ in the histone
code they use and in the enzymes involved. The differences
discovered so far concern the sites of modification, a whole
plant specific HDAC family as well as distinct ways of
regulating histone modifying enzyme activity.
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(De)phosphorylation
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Limited proteolysis
Review
P
ZmHda1-p48
P
p36
Function unknown
ZmHda1-p48
Full HDAC activity
TRENDS in Plant Science
Figure 2. Maize HDA1 (ZmHda1-p84) is regulated by limited proteolysis and
(de)phosphorylation. The maize histone deacetylase HDA1 is synthesized as an
enzymatically inactive protein that is part of a 300 kDa complex of unknown function; the active enzyme Hda1-p48 arises by proteolytic cleavage involving a putative 65 kDa intermediate protein [60]. Hda1-p48 gains its full enzyme activity and
substrate specificity after dephosphorylation [67]. The cleavage product p36 is present as a distinct protein with unknown function in Arabidopsis.
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Vol.9 No.2 February 2004
distinct gene encoding a small protein of 252 amino acids
(Atg61050; NP_200913); this short protein is highly
homologous to the C-terminal proteolytic cleavage product
of ZmHDA1 and also contains a 17 amino acid stretch
homologous to the N-terminus of ZmHDA1. The 84 kDa
precursor, a 65 kDa intermediate form and the enzymatically active 48 kDa protein exist as phosphorylated forms;
dephosphorylation of p48 stimulates the enzyme activity
and changes the substrate specificity [67]. Mammalian
HDAC1 is also phosphorylated and it has been reported
that phosphorylation alters enzymatic activity and complex formation [68]. It might be that phosphorylation of
ZmHDA1 also determines recruitment of complex components, since the enzymatically active 48 kDa form,
which is presumably dephosphorylated, acts as a protein
monomer. The regulation of maize HDA1 by limited
proteolysis is probably a unique, plant-specific level of
HDAC regulation.
Future prospects and perspectives
Four decades ago, Vincent Allfrey and co-workers [69]
discovered the existence of acetylation and methylation on
histones. With time, it became clear that acetylation does
not function by simple charge neutralization on nucleosomes but rather sets specific regulatory signals in concert
with other modifications [65,70]. We now know that
histone modifications represent additional epigenetic
information on chromatin that alters the functional
TIGQINDRLVKRHRKAGGKGLGKGGKGRGS
Histone H4
?
?
?
?
?
?
Methyl
group
K9
S10
K14
Acetate
group
Phosphate
group
Acetate
group
H
i
s
t
o
n
e
H3
Functional meaning of histone
code element can be influenced by:
• other post-translational modifications
on H3 and H4
• modifications on H2A and H2B
• modifications of core histones of
neighboring nucleosomes
• H1
• non-histone proteins
• regulatory factors
• DNA-methylation
• type of gene
• region of chromatin
• developmental stage
H3
?
?
Methyl
group
K14
S10
Acetate
group
Phosphate
group
?
Histone H4
H
i
s
t
o
n
e
K9
?
acetate
Acetate
group ?
group
?
?
?
TIGQINDRLVKRHRKAGGKGLGKGGKGRGS
TRENDS in Plant Science
Figure 3. Model of interdependence of histone modifications. As outlined earlier [66], different modifications on adjacent sites influence each other. It has been shown that
methylation of H3 lysine-9 (K9) inhibits phosphorylation of serine-10 (S10), and vice versa. The situation is complicated because lysine-9 can alternatively be acetylated.
Similarly, serine-10 phosphorylation and lysine-14 acetylation cross-talk to each other. These modifications occur on one of the two nucleosomal H3 molecules, but the
modification pattern on the second H3 molecule can be different and has a distinct influence on its second counterpart. There might be a direct influence of modifications
of H4 on the modification pattern of H3, and vice versa. Many more factors will change the ‘letters’ of the histone code, leading to a subtle tuning of the functional meaning.
The green arrow at lysine-20 of H4 indicates that this residue can be acetylated or methylated in plants. Question marks indicate the expected yet still unclear interdependent influences of modifications.
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TRENDS in Plant Science
properties of the underlying genetic information; together
with DNA methylation, chromatin remodeling and a range
of non-histone factors, this histone code forms a complex
epigenetic code that formats the genetic text and would
better be named ‘the chromatin code’. At present, we can
translate some words of this chromatin language but it will
probably take decades to be able to translate and read the
entire code.
Figure 3 aims to give an idea of the many open questions
and the different levels of complexity of setting and
translating the chromatin code. At present, we can analyze
the interdependence of modifications exemplified by
methylation of lysine-9, phosphorylation of serine-10 and
acetylation of H3 lysine-14. However, what about the
second H3 molecule in a nucleosome? Does it make a
difference if the modification pattern is ‘asymmetric’
within a nucleosome? What are the influences of modifications in one or both H4 molecules on the modification
pattern of H3? And there are still two molecules each of
H2A and H2B in the nucleosome. What is the effect of
arginine-3 methylation in H4, when the methylation is
introduced to a mono-acetylated rather than a tetraacetylated H4? The number of combinations of different
post-translational marks is enormous and their functional
effects might be widespread. We have little information
about post-translational modifications other than acetylation and methylation, or about the influence of histone H1
and non-histone proteins on the modification patterns of
nucleosomes (Figure 3). Because many non-histone regulatory proteins get modified by HATs and HDACs, the
question arises of whether the histone code is somehow
mirrored on these regulatory proteins for interaction
with histones, chromatin or DNA. It is therefore possible
that the histone code is part of a much more universal
protein code that governs interactions of proteins with
other molecules.
Although many elements of setting and translating the
chromatin code are fairly well conserved throughout
different kingdoms and species, we have to await subtle
or even pronounced differences in the details of this
code. Investigations in plant systems have already
revealed such differences and the special properties of
plant cells and plant genomes, and their unique exposure
and responses to environmental influences suggest a plant
dialect of the chromatin language.
Acknowledgements
I apologize for not citing all relevant literature owing to the enormous
number of papers published on this subject during the past few years, and
the reference limitation. Experimental work in our laboratory was
continuously funded by the Austrian Science Foundation (FWF, P-14528)
and the Austrian National Bank (Jubiläumsfonds P-9000).
References
1 Luger, K. (2003) Structure and dynamic behavior of nucleosomes. Curr.
Opin. Genet. Dev. 13, 127 – 135
2 Lusser, A. (2002) Acetylated, methylated, remodeled: chromatin states
for gene regulation. Curr. Opin. Plant Biol. 5, 437 – 443
3 Reyes, J.C. et al. (2002) Chromatin-remodeling and memory factors.
New regulators of plant development. Plant Physiol. 130, 1090– 1101
4 Wagner, D. (2003) Chromatin regulation of plant development. Curr.
Opin. Plant Biol. 6, 20 – 28
www.sciencedirect.com
Vol.9 No.2 February 2004
89
5 Jenuwein, T. and Allis, C.D. (2001) Translating the histone code.
Science 293, 1074– 1080
6 Turner, B.M. (2002) Cellular memory and the histone code. Cell 111,
285 – 291
7 Dobosy, J.R. and Selker, E.U. (2001) Emerging connections between
DNA methylation and histone acetylation. Cell. Mol. Life Sci. 58,
721 – 727
8 Avramova, Z.V. (2002) Heterochromatin in animals and plants.
Similarities and differences. Plant Physiol. 129, 40 – 49
9 Lee, H-S. and Chen, Z.J. (2001) Protein-coding genes are epigenetically
regulated in Arabidopsis polyploids. Proc. Natl. Acad. Sci. U. S. A. 98,
6753– 6758
10 Chen, Z.J. and Pikaard, C.S. (1997) Epigenetic silencing of RNA
polymerase I transcription: a role for DNA methylation and histone
modification in nucleolar dominance. Genes Dev. 11, 2124 – 2136
11 Bartee, L. et al. (2001) Arabidopsis cmt3 chromomethylase mutations
block non-CG methylation and silencing of an endogenous gene. Genes
Dev. 15, 1753– 1758
12 Henikoff, S. and Comai, L. (1998) A DNA methyltransferase homolog
with a chromodomain exists in multiple forms in Arabidopsis. Genetics
149, 307 – 318
13 Papa, C.M. et al. (2001) Maize chromomethylase Zea methyltransferase2 is required for CpNpG methylation. Plant Cell 13, 1919– 1928
14 Jeddeloh, J.A. et al. (1999) Maintenance of genomic methylation
requires a SWI2/SNF2-like protein. Nat. Genet. 22, 94 – 97
15 Tamaru, H. and Selker, E.U. (2001) A histone H3 methyltransferase
controls DNA methylation in Neurospora crassa. Nature 414, 277 – 283
16 Springer, N.M. et al. (2003) Comparative analysis of SET domain
proteins in maize and Arabidopsis reveals multiple duplications
preceding the divergence of monocots and dicots. Plant Physiol. 132,
907– 925
17 Tamaru, H. et al. (2003) Trimethylated lysine 9 of histone H3 is a mark
for DNA methylation in Neurospora crassa. Nat. Genet. 34, 75 – 79
18 Jackson, J.P. et al. (2002) Control of CpNpG DNA methylation by the
KRYPTONITE histone H3 methyltransferase. Nature 416, 556– 560
19 Malagnac, F. et al. (2002) An Arabidopsis SET domain protein required
for maintenance but not establishment of DNA methylation. EMBO J.
21, 6842 – 6852
20 Feng, Q. et al. (2002) Methylation of H3-lysine 79 is mediated by a new
family of HMTases without a SET domain. Curr. Biol. 12, 1052– 1058
21 Kouzarides, T. (2002) Histone methylation in transcriptional control.
Curr. Opin. Genet. Dev. 12, 198– 209
22 Lachner, M. et al. (2003) An epigenetic road map for histone lysine
methylation. J. Cell Sci. 116, 2117– 2124
23 Chinenov, Y. (2002) A second catalytic domain in the Elp3 histone
acetyltransferases: A candidate for histone demethylase activity?
Trends Biochem. Sci. 27, 115 – 117
24 Briggs, S.D. et al. (2001) Histone H3 lysine 4 methylation is mediated
by Set1 and required for cell growth and rDNA silencing in
Saccharomyces cerevisiae. Genes Dev. 15, 3286– 3295
25 Santos-Rosa, H. et al. (2002) Active genes are tri-methylated at K4 of
histone H3. Nature 419, 407– 411
26 Sarg, B. et al. (2002) Postsynthetic trimethylation of histone H4 at
lysine 20 in mammalian tissues is associated with aging. J. Biol. Chem.
277, 39195 – 39201
27 Alvarez-Venegas, R. et al. (2003) ATX-1, an Arabidopsis homolog of
Trithorax, activates flower homeotic genes. Curr. Biol. 13, 627 – 637
28 Jasencakova, Z. et al. (2003) Histone modifications in Arabidopsis –
high methylation of H3 lysine 9 is dispensable for constitutive
heterochromatin. Plant J. 33, 471 – 480
29 Gendrel, A.V. et al. (2002) Dependence of heterochromatic histone H3
methylation patterns on the Arabidopsis gene DDM1. Science 297,
1871– 1873
30 Houben, A. et al. (2003) Methylation of histone H3 in euchromatin of
plant chromosomes depends on basic nuclear DNA content. Plant J.
33, 967 – 973
31 Tariq, M. et al. (2003) Erasure of CpG methylation in Arabidopsis
alters patterns of histone H3 methylation in heterochromatin. Proc.
Natl. Acad. Sci. U. S. A. 100, 8823 – 8827
32 Soppe, W.J. et al. (2002) DNA methylation controls histone H3 lysine 9
methylation and heterochromatin assembly in Arabidopsis. EMBO J.
21, 6549 – 6559
90
Review
TRENDS in Plant Science
33 Probst, A.V. et al. (2003) Two means of transcriptional reactivation
within heterochromatin. Plant J. 33, 743– 749
34 Scheid, O.M. et al. (2002) Two regulatory levels of transcriptional
gene silencing in Arabidopsis. Proc. Natl. Acad. Sci. U. S. A. 99,
13659 – 13662
35 Grewal, S.I. and Moazed, D. (2003) Heterochromatin and epigenetic
control of gene expression. Science 301, 798 – 802
36 Pickford, A.S. and Cogoni, C. (2003) RNA-mediated gene silencing.
Cell. Mol. Life Sci. 60, 871– 882
37 Stevenson, D.S. and Jarvis, P. (2003) Chromatin silencing: RNA in the
driving seat. Curr. Biol. 13, R13 – R15
38 Aufsatz, W. et al. (2002) HDA6, a putative histone deacetylase needed
to enhance DNA methylation induced by double-stranded RNA.
EMBO J. 21, 6832 – 6841
39 Zilberman, D. et al. (2003) ARGONAUTE4 control of locus-specific
siRNA accumulation and DNA and histone methylation. Science 299,
716 – 719
40 Graessle, S. et al. (2001) Histone acetylation: plants and fungi as model
systems for the investigation of histone deacetylases. Cell. Mol. Life
Sci. 58, 704 – 720
41 Ogryzko, V.V. (2001) Mammalian histone acetyltransferases and their
complexes. Cell. Mol. Life Sci. 58, 683 – 692
42 Pandey, R. et al. (2002) Analysis of histone acetyltransferase and
histone deacetylase families of Arabidopsis thaliana suggests functional diversification of chromatin modification among multicellular
eukaryotes. Nucleic Acids Res. 30, 5036– 5055
43 Gu, W. and Roeder, R.G. (1997) Activation of p53 sequence-specific
DNA binding by acetylation of the p53 C-terminal domain. Cell 90,
595 – 606
44 Chan, H.M. et al. (2001) Acetylation control of the retinoblastoma
tumour-suppressor protein. Nat. Cell Biol. 3, 667– 674
45 Vervoorts, J. et al. (2003) Stimulation of c-Myc transcriptional activity
and acetylation by recruitment of the cofactor CBP. EMBO Rep. 4,
484 – 490
46 Zhang, Y. et al. (2003) HDAC-6 interacts with and deacetylates tubulin
and microtubules in vivo. EMBO J. 22, 1168 – 1179
47 Vlachonasios, K.E. et al. (2003) Disruption mutations of ADA2b and
GCN5 transcriptional adaptor genes dramatically affect Arabidopsis
growth, development, and gene expression. Plant Cell 15, 626– 638
48 Bhat, R.A. et al. (2003) Alteration of GCN5 levels in maize reveals
dynamic responses to manipulating histone acetylation. Plant J. 33,
455 – 469
49 Chua, Y.L. et al. (2001) Targeted histone acetylation and altered
nuclease accessibility over short regions of the pea plastocyanin gene.
Plant Cell 13, 599– 612
50 Chua, Y.L. et al. (2003) The transcriptional enhancer of the pea
plastocyanin gene associates with the nuclear matrix and regulates
gene expression through histone acetylation. Plant Cell 15, 1468– 1479
51 Lusser, A. et al. (1997) Identification of maize histone deacetylase HD2
as an acidic nucleolar phosphoprotein. Science 277, 88 – 91
52 Dangl, M. et al. (2001) Comparative analysis of HD2 type histone
deacetylases in higher plants. Planta 213, 280 – 285
53 Pikaard, C.S. and Lawrence, R.J. (2002) Uniting the paths to gene
silencing. Nat. Genet. 32, 1 – 2
54 Wu, K. et al. (2000) Functional analysis of a RPD3 histone deacetylase
homologue in Arabidopsis thaliana. Plant Mol. Biol. 44, 167– 176
55 Tian, L. and Chen, J.Z. (2001) Blocking histone deacetylation in
Arabidopsis induces pleiotropic effects on plant gene regulation and
development. Proc. Natl. Acad. Sci. U. S. A. 98, 200 – 205
56 Tian, L. et al. (2003) Genetic control of developmental changes induced
by disruption of Arabidopsis histone deacetylase 1 (AtHD1)
expression. Genetics 165, 399 – 409
57 Jang, I-C. et al. (2003) Structure and expression of the rice class-I-type
histone deacetylase genes OsHDAC1-3: OsHDAC1 overexpression in
transgenic plants leads to increased growth rate and altered
architecture. Plant J. 33, 531– 541
58 Murfett, J. et al. (2001) Identification of Arabidopsis histone
deacetylase HDA6 mutants that affect transgene expression. Plant
Cell 13, 1047– 1061
www.sciencedirect.com
Vol.9 No.2 February 2004
59 Wu, K. et al. (2000) Functional analysis of HD2 histone deacetylase
homologues in Arabidopsis thaliana. Plant J. 22, 19 – 27
60 Pipal, A. et al. (2003) Regulation and processing of maize histone
deacetylase HDA1 by limited proteolysis. Plant Cell 15, 1904 – 1917
61 Rossi, V. et al. (2003) A maize histone deacetylase and retinoblastomarelated protein physically interact and cooperate in repressing gene
transcription. Plant Mol. Biol. 51, 401 – 413
62 Gao, M-J. et al. (2003) A novel protein from Brassica napus has a
putative KID domain and responds to low temperature. Plant J. 33,
1073– 1086
63 Waterborg, J.H. (1992) Identification of five sites of acetylation in
alfalfa histone H4. Biochemistry 31, 6211 – 6219
64 Rea, S. et al. (2000) Regulation of chromatin structure by site-specific
histone H3 methyltransferases. Nature 406, 593– 599
65 Loidl, P. (1988) Towards an understanding of the biological function of
histone acetylation. FEBS Lett. 227, 91 – 95
66 Paro, R. (2000) Chromatin regulation: formatting genetic text. Nature
406, 579 – 580
67 Kölle, D. et al. (1999) Different types of maize histone deacetylases are
distinguished by a highly complex substrate and site specificity.
Biochemistry 38, 6769 – 6773
68 Pflum, M.K. et al. (2001) Histone deacetylase 1 phosphorylation
promotes enzymatic activity and complex formation. J. Biol. Chem.
276, 47733 – 47741
69 Allfrey, V.G. et al. (1964) Acetylation and methylation of histones and
their possible role in the regulation of RNA synthesis. Proc. Natl. Acad.
Sci. U. S. A. 51, 786 – 794
70 Strahl, B.D. and Allis, C.D. (2000) The language of covalent histone
modifications. Nature 403, 41 – 45
71 Strahl, B.D. et al. (2001) Methylation of histone H4 at arginine 3 occurs
in vivo and is mediated by the nuclear receptor coactivator PRMT1.
Curr. Biol. 11, 996– 1000
72 Schurter, B.T. et al. (2001) Methylation of histone H3 by coactivatorassociated arginine methyltransferase 1. Biochemistry 40, 5747– 5756
73 Rho, J. et al. (2001) Prmt5, which forms distinct homo-oligomers, is a
member of the protein– arginine methyltransferase family. J. Biol.
Chem. 276, 11393 – 11401
74 Strahl, B.D. et al. (2002) Set2 is a nucleosomal histone H3-selective
methyltransferase that mediates transcriptional repression. Mol. Cell.
Biol. 22, 1298 – 1306
75 Nishioka, K. et al. (2002) Set9, a novel histone H3 methyltransferase
that facilitates transcription by precluding histone tail modifications
required for heterochromatin formation. Genes Dev. 16, 479 – 489
76 Fang, J. et al. (2002) Purification and functional characterization of
SET8, a nucleosomal histone H4-lysine 20-specific methyltransferase.
Curr. Biol. 12, 1086– 1099
77 Lachner, M. et al. (2001) Methylation of histone H3 lysine 9 creates a
binding site for HP1 proteins. Nature 410, 116 – 120
78 Schultz, D.C. et al. (2002) SETDB1: a novel KAP-1-associated
histone H3, lysine 9-specific methyltransferase that contributes to
HP1-mediated silencing of euchromatic genes by KRAB zinc-finger
proteins. Genes Dev. 16, 919 – 932
79 Tachibana, M. et al. (2001) Set domain-containing protein, G9a, is a
novel lysine-preferring mammalian histone methyltransferase with
hyperactivity and specific selectivity to lysines 9 and 27 of histone H3.
J. Biol. Chem. 276, 25309 – 25317
80 Cao, R. et al. (2002) Role of histone H3 lysine 27 methylation in
Polycomb-group silencing. Science 298, 1039 – 1043
81 Beisel, C. et al. (2002) Histone methylation by the Drosophila
epigenetic transcriptional regulator Ash1. Nature 419, 857 – 862
82 Milne, T.A. et al. (2002) MLL targets SET domain methyltransferase
activity to Hox gene promoters. Mol. Cell 10, 1107 – 1117
83 Rayasam, G.V. et al. (2003) NSD1 is essential for early postimplantation development and has a catalytically active SET domain.
EMBO J. 22, 3153 – 3163
84 Kölle, D. et al. (1998) Substrate- and sequential site-specificity of
cytoplasmic histone acetyltransferase of maize and rat liver. FEBS
Lett. 421, 109 – 114