Biochimica et Biophysica Acta 1819 (2012) 222–229

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Biochimica et Biophysica Acta

j o u r n a l h o m e p a g e : w w w. e l s ev i e r. c o m / l o c a t e / b b a g r m

Review

Histone variants and epigenetic inheritance ☆

Gang Yuan a, b, Bing Zhu b,⁎
a
Life Science College, Beijing Normal University, Beijing, 100875, China
b
National Institute of Biological Sciences, Beijing, 102206, China

a r t i c l e i n f o a b s t r a c t

Article history: Nucleosome particles, which are composed of core histones and DNA, are the basic unit of eukaryotic
Received 4 May 2011 chromatin. Histone modifications and histone composition determine the structure and function of the
Received in revised form 8 June 2011 chromatin; this genome packaging, often referred to as “epigenetic information”, provides additional
Accepted 9 June 2011
information beyond the underlying genomic sequence. The epigenetic information must be transmitted from
Available online 17 June 2011
mother cells to daughter cells during mitotic division to maintain the cell lineage identity and proper gene
Keywords:
expression. However, the mechanisms responsible for mitotic epigenetic inheritance remain largely
Histone variant unknown. In this review, we focus on recent studies regarding histone variants and discuss the assembly
Epigenetics pathways that may contribute to epigenetic inheritance. This article is part of a Special Issue entitled: Histone
Chromatin chaperones and Chromatin assembly.
© 2011 Elsevier B.V. All rights reserved.

1. Introduction For mitotic inheritance of histone modification-mediated epigenetic

The eukaryotic genome is compacted into chromatin, which is
composed of basic units termed “nucleosomes” [1]. Each nucleosome
consists of an octameric particle of four core histone proteins (H2A,
H2B, H3 and H4) that bind and wrap 146 base pairs of DNA around the
histone octamer [2]. Histones can be covalently modified by reactions
such as acetylation, methylation, phosphorylation, and ubiquitylation
[3,4]. These chromatin modifications are often recognized by effector
proteins through which they exert their functions [5,6]. In addition to
chromatin post-translational modifications, the importance of histone
variants has been increasingly demonstrated in recent years [7–9].
Epigenetics is usually defined as the study of mitotically and/or
meiotically heritable changes in gene function that cannot be
explained by changes in the DNA sequence [10]. However, the
mechanisms responsible for the inheritance of epigenetic information
during mitotic division remain unknown. The inheritance of DNA CpG
methylation is the most well understood mechanism; several studies
have indicated that there is a semi-conservative segregation of the
symmetric CpG methylation and maintenance of the DNA methylation
by DNMT1 [11–13] with the assistance of PCNA [14] and UHRF1
[15,16]. Because several histone modifications regulate well-estab-
lished epigenetic phenomena, including position effect variegation
[17–19], Polycomb silencing [20–23], and X inactivation [24,25],
researchers are particularly interested in studying the mitotic
inheritance of histone modification-mediated epigenetic information.
☆ This article is part of a Special Issue entitled: Histone chaperones and Chromatin
assembly.
⁎ Corresponding author. Tel.: + 86 10 80728458.
E-mail address: zhubing@nibs.ac.cn (B. Zhu).
information, numerous models have been discussed in review papers
[9,26–34], and several interesting investigations have been recently
published [35–41]. Although increasing knowledge has been obtained
for histone variants, little information is known regarding whether
and/or which histone variants may carry epigenetic information; and
how such epigenetic information passes to the daughter cells during
mitotic division. In this review, we will discuss the deposition of
variant histones and their potential roles in mediating the inheritance
of epigenetic information.
2. H3 variants
The number of H3 histone variants differs among species. All
eukaryotes have a centromere specific H3 (CenH3, or CENP-A in
mammals), which contains an amino acid sequence that differs
significantly from the other H3 histone variants [7]. In addition to
CENP-A, mammals have three ubiquitously expressed H3 variants
(H3.1, H3.2, and H3.3) as well as an H3 isoform that is specifically
expressed in the testis (H3t) [7]. Recently, two primate-specific H3
variants (H3.X and H3.Y) [42] and a hominid-specific variant H3.5
were identified [43]. Other higher eukaryotes have two non-
centromeric H3 variants, H3.3 and H3.1 (identical to mammalian
H3.2). Yeast has only one non-centromeric H3, which is similar to
H3.3 in higher eukaryotes [7].
2.1. CenH3
CENP-A is the first histone variant that was shown to identify
specific chromatin regions, namely the centromeres [27]. CENP-A is
essential for kinetochore formation and chromosome segregation

1874-9399/$ – see front matter © 2011 Elsevier B.V. All rights reserved.
doi:10.1016/j.bbagrm.2011.06.007
 G. Yuan, B. Zhu / Biochimica et Biophysica Acta 1819 (2012) 222–229
[7,44,45]. CENP-A was identified as an H3 variant during co-
purification with other core histones [46], although it shares minimal
sequence similarity with the other H3 histone variants. The other H3
variants, such as H3.1, H3.2 and H3.3, are at the same molecular
weight and differ by only four to five amino acid residues [9]. In
contrast, CENP-A has a variable N-terminus, with no sequence
similarity to the N-terminal region of the other H3 variants [45];
moreover, CENP-A shares only 50% identity in the histone fold domain
with the other H3 histones [47].
2.1.1. CenH3 deposition and genomic distribution
Centromeric DNA is duplicated during the S phase of the cell cycle.
However, unlike canonical histones that are incorporated into
chromatin during the S phase, newly synthesized CENP-A is deposited
during a discrete time period from telophase to the G1 phase in
mammals [48].
In yeast, CenH3 is called “Cse4”, and the specific Cse4 chaperone is
Scm3 [49]. A crystal structure of the Scm3–Cse4–H4 fusion protein
suggests that the complex may form a hexamer (Scm3–Cse4–H4)2
[50]; correspondingly, the formation of a (Scm3–Cse4–H4)2 hexamer
was observed in another study under high salt conditions (2 M NaCl)
[49]. This suggests that Scm3 may bind and deposit (Cse4–H4)2
tetramers. This is in sharp contrast to Asf1, which is a key histone
chaperone for the other H3 histone variants; Asf1 only forms a
complex with the H3-H4 dimers, not with the (H3–H4)2 tetramers
[51–55]. However, a recent report demonstrated a trimeric crystal
structure of a Scm3 fragment associated with a Cse4–H4 dimer, which
argues against the (Scm3–Cse4–H4)2 model [56].
Studies have shown that in mammals, Mis16 and Mis18 function
as upstream factors that bind and recruit CENP-A to the kinetochore; a
double knockdown of the two homologous Mis proteins in HeLa cells
abolished localization of CENP-A to the kinetochore [57]. Although
Mis16 and Mis18 participate in CENP-A deposition, the direct
chaperone that is specific for CENP-A is HJURP [58,59]. The transient
appearance of HJURP precisely coincides with the discrete time period
for CENP-A deposition, and down regulation of HJURP decreases
CENP-A at the centromeres [58,59]. Because HJURP appears at the
centromeres slightly later than Mis18, the Mis18 complex may
function as the licensing factor for CENP-A deposition, while HJURP
likely acts as the direct loading factor for CENP-A [60]. Unlike the Scm3
and Cse4–H4 paradigm in yeast, structural analysis of the human
HJURP–CENP-A–H4 trimeric complex indicates that binding of HJURP
and CENP-A–H4 dimer prevents the formation of a (CENP-A–H4)2
tetramer, which suggests that CENP-A–H4 is deposited as a dimer
rather than a tetramer in mammals [61].
A number of proteins are physically associated with centromeres,
such as the NAC complex (including CENP-B, CENP-C, CENP-H, CENP-
M, CENP-N, CENP-T and CENP-U) [62] and the CENP-H/CENP-I
complex [63]; these protein complexes are important for kinetochore
assembly and may act upstream or downstream of CENP-A incorpo-
ration. Recently, CENP-C and CENP-T have been reported to act
downstream of CENP-A incorporation and ectopic tethering of these
proteins can induce ectopic kinetochore assembly in the absence of
CENP-A incorporation [64].
2.1.2. Defining centromere identity
Once the CenH3 histones are deposited on the centromere, this
centromeric state must be stably maintained. A number of proteins,
including the CENP-A licensing factor HsKNL2 interacting protein
MgcRacGAP (a Rho family activating protein), Ect2 (a Rho family
guanine nucleotide exchange factor), and Cdc42 and Rac (two small
GTPases) are required to stabilize the newly incorporated CENP-A at
the centromeres [65,66]. Because CENP-A occupancy is typically used
to define a centromere, these proteins may help to ensure the
epigenetic inheritance of the centromeric state by stabilizing CENP-A
binding.
223
Because CENP-A is exclusively incorporated at the centromeres,
the protein must be removed after incorrect incorporation at non-
centromere chromatin regions. The Cse4 specific E3 ubiquitin ligase
Psh1 mediates the degradation of non-centromeric Cse4 [67,68].
Although the data clearly indicates that Psh1 plays a role in preventing
Cse4 mislocalization, parallel mechanisms must exist because Psh1
deletion displayed a very mild phenotype unless Cse4 was massively
over expressed [67,68].
The small GTPase and E3 ubiquitin ligase additionally help to
maintain the epigenetic state of centromeres, although CENP-A appears
to be the most important factor. CENP-A's relatively long loop 1 region in
the histone fold domain makes a large area of contact with the
centromeric DNA and contributes to the binding specificity [69–71]. The
structure of the human (CENP-A–H4)2 heterotetramer shows a rotated
CENP-A–CENP-A interface and a strong hydrophobic interaction
between CENP-A and H4, which contributes to the unconventional
shape of the CENP-A-containing nucleosomes [72]. Interestingly, human
neocentromeres can be formed at genomic regions that lack the satellite
DNA sequences that are normally present at the centromeres [73], and
similar events have been observed in fission yeast [74] and plants [75].
Thus, CENP-A binding, rather than the DNA sequence, appears to be a
more important determinant for defining the centromere [76]. Unlike
other histones, CENP-A is not replaced by protamines during mamma-
lian spermatogenesis, which also suggests that CENP-A plays an
important role in defining the centromere [77].
2.1.3. Models for restoring CenH3 nucleosomes or the epigenetic
inheritance of centromeres
Extensive investigations regarding CenH3 have suggested several
models for CenH3-containing nucleosome structures, including: 1) an
octameric nucleosome containing two copies of H2A, H2B, Cen-H3 and
H4, with DNA wrapped in left-handed orientation [62,70,72,78–80]; 2) a
tetrasome containing two copies of CenH3 and H4 but lacking the H2A–
H2B dimers [81]; 3) a hexasome containing two copies of Scm3, CenH3
and H4 [49]; and 4) a hemisome that contains only one copy of H2A, H2B,
CenH3 and H4, with DNA wrapped in a right-handed orientation [82,83].
Despite the uncertainty regarding CenH3 nucleosome composition and
structure, it is generally agreed that CenH3-containing nucleosomes
must be restored to maintain the identity of the centromeres after DNA
duplication. The incorporation of newly synthesized CenH3 begins
during telophase, which occurs much later than centromeric DNA
duplication. Therefore, CenH3 is in shortage for a considerably long
period of time. Several models have been proposed to explain the
chromatin states of the centromeres during this period and define the
mechanisms by which the CenH3-containing nucleosomes are restored.
1) After DNA replication, part of the centromeric region is temporarily
occupied by H3.1 nucleosomes, and CenH3 nucleosomes replace
these transient nucleosomes during the later stages in of the cell
cycle (Fig. 1, left). Based upon this model, the most critical problem is
how to ensure that the CenH3 nucleosomes only replace the H3.1
nucleosomes at the centromeres. Distinct modification patterns on
the interspersed H3.1 nucleosomes at the centromeric regions
[84,85] and the remaining CenH3 nucleosomes at the centromeric
regions may identify these regions for CenH3 replacement. In
mammals, CENP-A and H3.1 nucleosomes are interspaced at the
centromeric regions; however, the CENP-A nucleosomes are
spatially continuous and are often oriented in the same direction,
which aids in kinetochore formation [86]; therefore, epigenetic
information may be provided by the spatially proximal CENP-A
nucleosomes to guide the incorporation of newly synthesized CENP-
A. If this hypothesis is correct, the CenH3 deposition machinery may
be able to recognize this genomic signal. Although we generally
prefer this model, we must point out that it is incompatible with the
data for budding yeast, where each centromere is only composed of
one nucleosome [87].
224 G. Yuan, B. Zhu / Biochimica et Biophysica Acta 1819 (2012) 222–229

Fig. 1. Models for CENP-A inheritance at the centromere. Left: H3.1 nucleosomes are incorporated into the centromeric regions during DNA replication, and the CENP-A nucleosomes
are later incorporated and replace the H3.1 nucleosomes. Middle: DNA replication forms gaps that are devoid of nucleosomes during the S phase, and these gaps are later filled with
newly synthesized CENP-A nucleosomes. Right: DNA replication leads to the formation of hemisomes at the centromeric regions, and newly synthesized CENP-A-H4 dimers pair
with the existing hemisomes to form hybrid nucleosomes. Note: the H2A-H2B dimers were omitted from this illustration for simplicity.

2) During DNA replication, gaps are created at the centromeric regions
that are not filled with canonical nucleosomes and only become
occupied after the incorporation of CenH3 nucleosomes (Fig. 1,
middle). However, long stretches of DNA with reduced nucleosome
protection at the centromeric regions may not be preferable [60]. In
addition, this model is also incompatible with the data for budding
yeast for the same reason mentioned with model 1.
3) During DNA replication, the CenH3 nucleosomes split into two-
halves, where each half occupies one sister chromatid and can
easily incorporate newly synthesized CenH3 molecules. Consistent
with this model, CenH3 nucleosomes were reported to be at the
half height of the canonical nucleosomes [81,82], which suggests a
“hemisome” model for CenH3 nucleosome structure. In this model,
epigenetic information may be maintained at the mono-nucleo-
some level (Fig. 1, right), which agrees well with the data for
budding yeast centromere identity.
2.2. H3.3
acetylated. The histone chaperone Asf1 is also present in both
complexes, which agrees with previous studies that indicated that
Asf1 participates in chromatin assembly [95–98].
Recently, several independent studies have shown that the ATRX-
DAXX complex and DEK are chaperone proteins that play a role in
H3.3 deposition at discrete chromatin regions, including telomeres
and pericentromeric regions [91–94]. These studies are particularly
interesting because they indicate that H3.3, although traditionally
thought to be a marker of euchromatin [8], is also present at hetero-
chromatic regions.
The H3.3 chaperones that have been identified play a role in H3.3
replication-independent deposition. H3.3 can also be deposited in a
replication-dependent manner [99,100], although the chaperone
proteins responsible for replication-dependent H3.3 deposition are
unknown. It is possible that the CAF complex can deposit both H3.1
and H3.3 histones in a replication-dependent manner because the
yeast CAF complex can deposit the only non-centromeric H3, which is
similar to H3.3 [8].

Histone variant H3.3 differs from the canonical H3 by only four

amino acid residues, where three of these residues are clustered in
the α2 helix of the histone fold domain and the other residue is in the
N-terminal tail [9]. Unlike H3.1, which is strictly expressed and
deposited during S phase, H3.3 is expressed and deposited throughout
the cell cycle [88]. The three distinct amino acid residues in the α2
helix are responsible for the replication-independent incorporation of
H3.3 [88], and H3.3 histones are enriched at transcriptionally active
regions [88–90] as well as telomeres and pericentromeric regions
[91–94].
2.2.1. H3.3 deposition and genomic distribution
Biochemical purification of non-chromatic H3 histones in HeLa
cells showed that the canonical H3 histones are deposited by the CAF-
1 complex in a replication-dependent manner, whereas H3.3 histones
are deposited by the HIRA complex in a replication-independent
manner [51]. Both complexes contain HAT1, which corresponds with
previous observations that pre-deposited histones are transiently
2.2.2. H3.3 mediated epigenetic inheritance
The potential of H3.3 to mediate epigenetic inheritance can be
divided into two questions: 1) whether or how H3.3 histone
modifications are maintained in a mitotically heritable manner and
2) whether or how H3.3 histones are incorporated at specific
chromatin regions in a mitotically heritable manner.
Histone variants differ from each other not only in their chromatin
location, but also in their post-translational modifications [101]. For
example, compared with the canonical H3 histone, H3.3 histones are
enriched in post-translational modifications that correlate with gene
expression, such as H3K4 and H3K36 methylation, as well as H3K9,
H3K18, and H3K23 acetylation [54,102–106]. This is consistent with
previous observations that the H3.3 histones are enriched at
transcriptionally active regions of the genome [88–90]. However,
there is little evidence to suggest that the H3.3 histones are more
favorable substrates for the enzymes that mediate these modifica-
tions. The enrichment of these active modifications on H3.3 histone
 G. Yuan, B. Zhu / Biochimica et Biophysica Acta 1819 (2012) 222–229
may simply be because H3.3 deposition and active histone modifica-
tions are both independently correlated with transcriptional activity.
A semi-conservative segregation of the (H3–H4)2 tetramers,
followed by templated modification copying events, was once a
model favored for the mitotic inheritance of histone modification-
mediated epigenetic information. However, most lysine methylations
do not have to be symmetrical within each nucleosome [41], and
canonical (H3–H4)2 tetramers do not split during replication-
dependent chromatin assembly [35]. These recent findings negate
this model as the general mechanism for mitotic inheritance of
histone modification-mediated epigenetic information [33,34,107].
Although a fraction of (H3.3–H4)2 tetramers split in mammalian cells
[35] and similar events occur for the H3.3-like histones in budding
yeast [108], it is unlikely that these events mediate a faithful
duplication of histone modifications within certain subpopulations
of mono-nucleosomes.
On the other hand, the H3.3 histones are clearly enriched at certain
chromatin regions, including actively transcribed genes [88–90] and
heterochromatic regions, such as the telomeres and pericentromeric
regions [91,92,94,109]. However, it remains unclear whether H3.3
histone localization contributes to the transcriptional status of the
underlying DNA. A number of studies suggest that H3.3 plays a role in
maintaining the transcriptional status of the target loci. Nuclear
transfer experiments in Xenopus laevis demonstrated that the
expression of the donor-originated MyoD gene can persist over 24
mitotic divisions and that this epigenetic memory is dependent upon
H3.3 lysine 4 methylation [110,111]. However, the loss of both H3.3
genes in flies leads to a mild transcriptional defect with partial
lethality, and most of the surviving H3.3-null flies develop normally,
except for the male germline [112]. These results suggest that H3.3
histones are not essential for maintaining the epigenetic status of
transcriptionally active genes, which is consistent with the idea that
H3.3 enrichment at euchromatic regions is a consequence, rather than
a determinant, of transcriptional activity. In contrast, H3.3 histones
were reported to be critical for the formation of pericentromeric
heterochromatin [109] and the maintenance of the telomeres [88,93].
Thus, the data indicate that H3.3 histones may play a role in epigenetic
silencing.
3. H2A variants
The H2A and H3 histones are structurally similar [113] and have
several variant forms [7,47]. In addition to the canonical histone H2A,
four H2A variants have been reported in mammals (H2A.Z, H2A.X,
marcoH2A and H2A.Bbd) [47].
3.1. H2A.Z
H2A.Z is highly conserved throughout evolution, it has a single
evolutionary origin and remains distinct from all other H2A variants
[47]. This specialization suggests that H2A.Z has a distinct function
from all other H2A variants. H2A.Z differs from canonical H2A and
other H2A variants mainly in its “docking” domain in the C-terminus
and in the L1 loop where two H2A molecules contact each other
[2,69,114].
3.1.1. H2A.Z deposition and genomic distribution
The SWR1 complex, which is an ATP-dependent chromatin-
remodeling complex, was the first identified H2A.Z chaperone that
mediates H2A.Z deposition [115–117]. Subsequently, the Nap1 and
Chz1 histone chaperones also associate with H2A.Z–H2B dimers, and
these chaperones were proposed to transfer the H2A.Z–H2B dimers to
the SWR1 complex to exchange chromatin H2A-H2B dimers with
H2A.Z–H2B dimers [118]. Recent studies have indicated that Nap1 and
Chz1 are not functionally redundant. Nap1 mediates the nuclear
import of cytosolic H2A.Z–H2B, whereas Chz1 presents the H2A.Z–
225
H2B dimers to the SWR1 complex for final deposition [119]. A recent
study has presented a detailed molecular mechanism of SWR1-
mediated H2A.Z deposition [120]. SWR1 replaces H2A–H2B with
H2A.Z–H2B in a stepwise manner, one copy of the H2A.Z–H2B dimer
at a time, which leads to the formation of intermediate hybrid
nucleosomes that contain both H2A and H2A.Z [120]. Interestingly,
nucleosome-dependent SWR1 ATPase activity is dependent upon the
substrate composition, which indicates that the SWR1 complex can
sense the substrate status and receive a “mission accomplished” signal
to terminate its activity [120].
Genome-wide nucleosome occupancy studies in yeast and flies
have been performed to assess the distribution of H2A.Z nucleosomes.
The H2A.Z nucleosomes are localized to both sides of “nucleosome-
free regions (NFR)” in yeast near the transcription start sites (− 1, + 1
nucleosome) [121,122], while the fly H2A.Z nucleosomes are
predominantly enriched just downstream of the transcription start
sites (+1 nucleosome) [123]. Because the NFRs in yeast are precisely
located between two well-positioned H2A.Z nucleosomes, they may
play a role in the H2A.Z localization pattern. In yeast, the RSC
chromatin-remodeling complex mediates NFR formation at pro-
moters by displacing nucleosomes at the NFR, and the RSC is required
for deposition of the flanking H2A.Z nucleosomes [124]. A previous
study has suggested that in mammals, the “NFRs” at the transcription
start sites were suggested to be consequence of losing the highly labile
nucleosomes consisted of both H2A.Z and H3.3 located at NFRs [125].
The specific localization pattern of H2A.Z nucleosomes near the
transcription start site has been proposed to be an epigenetic marker
for directing or regulating the positioning of downstream nucleo-
somes [126–128]. Therefore, ensuring the correct deposition of H2A.Z
nucleosomes is crucial for the maintenance of epigenetic modifica-
tions at the transcription start site. Recently, the INO80 complex,
which is another ATP-dependent chromatin remodeling complex that
is closely related to the SWR1 complex, was reported to mediate the
replacement of H2A.Z with canonical H2A to ensure proper H2A.Z
distribution at transcription start sites in yeast [129].
3.1.2. H2A.Z mediated epigenetic inheritance
Compared to the (H3–H4)2 tetramers, the H2A–H2B dimers are
much more mobile [130]. Nucleosomes frequently exchange their
H2A–H2B dimers, but rarely exchange their (H3–H4)2 tetramers [35].
Additionally, lysine methylations, which are thought to be the most
stable histone modification [131], predominantly occur on the H3 or
H4 histones [3,4]. Thus, the H2A and H2B histones may not be good
candidates for the propagation of epigenetic information. However, a
number of studies discussed below suggest that H2A.Z may carry
important epigenetic information and maintain the chromatin
transcriptional status.
Transcriptional memory. The yeast genes INO1 and GAL1 localize to
the nuclear periphery upon transcriptional induction. After a short
period of transcriptional repression, the nuclear peripheral INO1 and
GAL1 genes are rapidly reactivated, but not in Htz1 mutant strains
(which cannot encode H2A.Z), which suggests that H2A.Z mediates
epigenetic memory of the previous transcriptional state [132].
Interestingly, transcriptional memory of the yeast GAL genes requires
SWI/SNF activity [133], and SWI/SNF recruitment is dependent upon
H2A.Z [134], which again suggests that H2A.Z mediates epigenetic
transcriptional memory.
Heterochromatin formation and maintenance. Upon differentiation
of cells at the murine inner cell mass (ICM), H2A.Z is first enriched at
pericentromeric heterochromatin and subsequently enriched at other
chromatin regions. Moreover, H2A.Z directly interacts with the
pericentromeric heterochromatin protein INCENP in vivo[135].
H2A.Z depletion caused genome instability and disruption of HP1α
localization at the pericentromeric regions, which suggests that HP1α
function and pericentromeric heterochromatin identity are regulated
by H2A.Z during early embryonic development in mice [136]. In yeast,
226 G. Yuan, B. Zhu / Biochimica et Biophysica Acta 1819 (2012) 222–229
Htz1 acts together with a boundary element to prevent the spread of
heterochromatin. As in htz1Δ cells, Sir2 and Sir3 spread from
telomeric regions to flanking eukaryotic regions and lead to ectopic
heterochromatin formation [137].
3.2. H2A.X
H2A.X is present in nearly all eukaryotes, except nematodes [47].
This histone variant has a histone fold domain that is similar to the
canonical H2A, although it has a unique C-terminal motif termed
SQ(E/D)Ф (where Ф represents a hydrophobic residue) [47,138]. The
H2A.X serine residue at the γ-position of the C terminus can be
phosphorylated (termed γ-H2A.X) after DNA double-strand breaks
(DSB) occur, which has been previously described [139,140].
3.2.1. H2A.X deposition and genomic distribution
Previous studies have shown that H2A.X plays a role in DSB repair;
therefore, H2A.X is viewed as the “histone guardian of the genome”
[141]. Because DSB can potentially occur anywhere in the genome,
H2A.X deposition should be random. Although the FACT protein
complex can mediate the exchange of γ-H2A.X-H2B with unmodified
H2A.X-H2B [142], no specific de novo deposition chaperone for H2A.X
has been identified. Because of the overall sequence similarity between
H2A.X and canonical H2A [47,138], we hypothesize that the same
assembly factor mediates H2A.X and canonical H2A deposition.
3.2.2. The role of H2A.X in meiotic silencing
Aside from the well known function of H2A.X in DSB repair, H2A.X
has also been implicated to play a role in meiosis, growth, tumor
suppression and immune receptor rearrangements [141]. Interest-
ingly, H2A.X knockout mice are sterile [143]. In wild type mice, during
the pachytene stage of spermatogenesis γ-H2A.X is enriched at the
sex chromosomes to initiate meiotic sex chromosome inactivation
(MSCI) and X and Y chromosome condensation, which leads to the
formation of a partially paired sex body. In H2A.X-null mice, this
entire process was impaired [143]. Additionally, previous studies have
indicated that γ-H2A.X also plays a role in meiotic silencing of
unpaired chromosomes in female mice [144].
H3.3-deficient male flies have decreased fertility [112], and it is
interesting to speculate whether these meiotic defects are the results
of impaired meiotic silencing and whether H2A.X and H3.3 play
cooperative roles in these events.
3.3. macroH2A
macroH2A is a vertebrate-specific H2A variant that contains two
distinct domains [145]. Although the N terminal region of macroH2A
is similar to canonical H2A, macroH2A contains a large (200 residue) C
terminal domain termed “the macro domain” that shares no sequence
similarity with any other histone [47]. In mammals, macroH2A is
enriched on the inactive X chromosomes in females [146]. Interest-
ingly, macroH2A is re-localized from centrosomes to inactive X
chromosomes, and this re-localization is dependent on Xist expres-
sion after X inactivation initiation [147,148]; however, X inactivation
initiation is not dependent on macroH2A. Therefore, macroH2A is
thought to be an epigenetic marker of X inactivation and may
contribute to the maintenance of an inactive X chromosome. Several
studies have suggested potential mechanisms where macroH2A
represses gene expression. A previous study has shown that the C-
terminal macro domain of macroH2A interferes with the binding of
transcription factors, and the N-terminal domain impedes chromatin
remodeling via SWI/SNF [149]. In addition, macroH2A can mediate
gene silencing by inhibiting the catalytic activity and substrate
binding capacity of PARP1, which is a nuclear enzyme that is involved
in gene activation [150,151]. Moreover, additional studies have
indicated that macroH2A is involved in autosomal gene silencing.
macroH2A is enriched at developmental genes in human pluripotent
cells in males and regulates the timing of HoxA activation. The
macroH2A distribution pattern at the Hox loci overlaps with PRC2;
therefore, marcoH2A is potentially an epigenetic regulator of key
developmental genes and may cooperate with PRC2 [152].
3.4. H2A.Bbd
H2A.Bbd is the most recently discovered H2A variant; this histone
variant has a truncated C-terminal docking domain [153] and was
named because of its unique genomic distribution, where it is
deficient in inactive X chromosomes (bar body deficient). The
H2A.Bbd nucleosome binds only 116 base pairs of DNA and is less
stable than the canonical nucleosome [154,155]. H2A.Bbd lacks a
small acidic region on the nucleosome surface that is involved in
transcriptional repression and also lacks K119, which is often
ubiquitinated on canonical H2A at transcriptionally inactive regions
[156]. The unique subnuclear localization and key features of H2A.Bbd
suggest that it is involved in gene activation.
4. H4 and H2B histones
Unlike the H3 and H2A histones, which have several variants with
different functions, no ubiquitously expressed H4 and H2B variants
have been reported thus far. Nevertheless, a few tissue-specific H2B
isoforms have been reported, including sperm specific H2B variant
(spH2B), testis specific H2B variants TH2B and H2BFWT [157].
Interestingly, TH2B was proposed to be a platform in specifying
pericentric heterochromatin during late spermiogenesis [158], which
maybe a good target in studying the inheritance of epigenetic states of
pericentric heterochromatin during meiosis. On the other hand,
H2BFWT appears to be enriched at telomere interstitial blocks, and it
has been proposed that H2BFWT may serve as an epigenetic marker
telomeric identity in testis [159].
5. Perspectives
Histone variants are currently the new frontier of chromatin
biology. However, several important questions regarding the mech-
anisms behind epigenetic inheritance and stability remain.
More studies are needed to clarify which histone variants are
involved in epigenetic regulation. Because a key criterion of epigenetics
is that the information is heritable, it is critical to discover which histone
variants play a role in this process and which of their mediated functions
are inherited during mitotic/meiotic division.
The post-translational histone modifications often recruit the
associated effector proteins to exert a function [5,6]. However, few
proteins have been discovered that can bind to and specifically
recognize the variant histones in chromatin context. Several pressing
questions remain, including “How do the histone variants function once
they are deposited?” and “Are the histone variants recognized by
proteins factors like the histone modifications, or do they function solely
by altering the intrinsic properties of the underlying chromatin?”
Acknowledgments
The research of B. Z. is supported by grants from the Chinese Ministry
of Science and Technology (2011CB965300 and 2007AA02Z1A6).
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