![](x2_files/shim.gif) Originally published in Science Express on
11 December 2003 Science,
Vol 303, Issue 5658, 644-649, 30 January 2004
[DOI: 10.1126/science.1092727]
Epigenetic Dynamics of Imprinted X Inactivation During Early
Mouse Development Ikuhiro
Okamoto,1 Arie P. Otte,2
C. David Allis,3 Danny
Reinberg,4 Edith Heard1*
The initiation of X-chromosome inactivation is thought to be
tightly correlated with early differentiation events
during mouse development. Here, we show that although
initially active, the paternal X chromosome undergoes
imprinted inactivation from the cleavage stages, well
before cellular differentiation. A reversal of the
inactive state, with a loss of epigenetic marks such as
histone modifications and polycomb proteins, subsequently
occurs in cells of the inner cell mass (ICM), which give
rise to the embryo-proper in which random X inactivation
is known to occur. This reveals the remarkable plasticity
of the X-inactivation process during preimplantation
development and underlines the importance of the ICM in
global reprogramming of epigenetic marks in the early
embryo.
1 CNRS UMR218, Curie Institute, 26 rue d'Ulm, Paris
75005, France. 2 Swammerdam Institute for Life
Sciences, BioCentrum Amsterdam, University of Amsterdam, 1018 TV
Amsterdam, Netherlands. 3 Rockefeller University, Box
78, 1230 York Avenue, New York, NY 10021, USA. 4
Department of Biochemistry, Division of Nucleic Acids Enzymology,
Howard Hughes Medical Institute, University of Medicine and
Dentistry of New Jersey, Robert Wood Johnson Medical School,
Piscataway, NJ 08854, USA.
* To whom correspondence
should be addressed. E-mail: edith.heard@curie.fr
In mammals, dosage compensation between XX females and XY males
is achieved by inactivating one of the two X chromosomes
during early female embryogenesis (1).
Classical biochemical and cytological analyses have
suggested that in XX mouse embryos, there are three waves
of X inactivation during development, correlating with
the three earliest differentiation steps (2).
In the first two lineages to differentiate, the
trophectoderm and primitive endoderm of the blastocyst,
which contribute to the extraembryonic tissues, X
inactivation is subject to imprinting, with exclusive
inactivation of the paternal X chromosome (Xp) (3,
4).
This seems to be due to an imprint on the maternal X
chromosome (Xm) to remain active, as well as a paternal
imprint to inactivate (5).
By the third wave of differentiation, in epiblast cells
derived from the ICM, X inactivation is random, affecting
either the Xp or the Xm (6,
7).
Initiation of both imprinted and random X inactivation
are dependent on a unique, untranslated RNA (Xist) that
coats the X chromosome in cis and triggers its silencing
(8,
9).
In embryonic stem (ES) cells, which can recapitulate the
random form of X inactivation upon in vitro differentiation,
Xist RNA coating of the X chromosome is rapidly followed
(within one to two cell cycles) by gene silencing (10).
During early development, Xist is expressed from
the two- to four-cell stage onward (11–13).
Early Xist expression is exclusively of paternal
origin (11);
the maternal Xist allele is repressed until the
morula stage (12).
Despite the early Xist RNA coating of the Xp at the
four-cell stage (12),
the first cytologically detectable signs of X
inactivation (a heteropycnotic, asynchronously
replicating Xp) occur several cell divisions later, at
about the 50-cell stage in the trophectoderm (14,
15).
The reasons for this apparent delay, which contrasts with
the rapidity of X inactivation that occurs after Xist RNA
coating in differentiating ES cells, remain unclear.
Furthermore, even though both the Xm and Xp are clearly
active immediately after fertilization based on allozyme
analysis (16–18),
reverse transcription polymerase chain reaction (RT-PCR)
studies have suggested that paternal alleles of some
X-linked genes show lower transcriptional activity than
their maternal counterparts during early embryogenesis
(19,
20).
Indeed, it has been suggested that a predisposition of
the XP to inactivate may be carried over from its passage
through the male germ line, where the Xp and the Y
chromosome together form the highly condensed,
heterochromatic sex vesicle, and this could underly
imprinted X inactivation (21).
Xist RNA and early chromatin changes on Xp. A number of
unresolved questions thus surround the initiation and
kinetics of imprinted X inactivation. We set out to
address these questions with techniques that enable us to
examine the status of the Xist RNA–coated Xp in
individual cells during early preimplantation embryogenesis.
Embryos from the two-cell to the blastocyst stage were
isolated by flushing from the oviduct or uterus and
analyzed directly, without in vitro culture, which can
potentially lead to perturbations in epigenetic
regulation. Using RNA fluorescence in situ hybridization
(FISH), a domain of Xist RNA accumulation could be
detected in all interphase blastomeres from the four-cell
stage onward (Figs. 1
and 2
and fig. S1). These findings are consistent with previous
studies (12,
13,
22,
23).
We could detect a small punctate signal but no Xist RNA
accumulation in a proportion of two-cell embryos (in the
G2 phase based on developmental timing). At
the four-cell stage, when paternal Xist RNA is just
starting to accumulate, the Xist RNA domain was often
small (Fig.
2 and fig. S3). We examined the early chromatin
status of the Xp chromosome by means of Xist RNA FISH
combined with immunofluorescence. In particular, we
looked for Xp enrichment in H3 histones methylated at
lysines 9 (K9) and 27 (K27) and for its association with
the Eed and Enx1 polycomb group proteins (see table S1 for
antibodies), because all of these marks have been shown
to be characteristics of the X chromosome undergoing
inactivation, and therefore represent candidates for the
predisposition of the Xp to inactivate (24–27).
Methylation of H3K9, in particular, has been reported to
be associated with the Xp in the sex vesicle during
spermatogenesis (28).
When we examined four- and eight-cell stage embryos, no
sign of either H3K9 and H3K27 methylation enrichment or of
Eed and Enx1 accumulation could be detected on the Xist
RNA–coated Xp (Fig.
1). At the 16-cell stage, however, these marks could
be detected on the Xp in some blastomeres (Fig.
1 and fig. S2). Their similar time of onset on the Xp
is consistent with Enx1 being the histone
methyltransferase responsible for H3K27 methylation
(26,
27).
This is also the time window previously described for
accumulation of the histone H2A variant, macroH2A, on the
X chromosome (29),
suggesting that major chromatin changes on the Xp begin
at this stage. The proportion of blastomeres in which the
Xp carried the Eed, Enx1, and H3K27 methylation marks
varied considerably between embryos at the 16- to 32-cell
stages (Fig.
1, i and r). By the blastocyst stage, however, the Xp
carried these marks in the majority (>90%) of
blastomeres. Methylation of H3K9 on the Xp showed
different kinetics, with a later onset, which were first
detected in embryos with >32 cells (Fig.
1 and fig. S2). By the midblastocyst stage, almost
all trophectoderm cells had an Xp enriched in H3K9
methylation (Fig.
1, p and q). The later appearance of H3K9 methylation
on the Xp suggests that this mark may be independently
deposited, perhaps as a consequence of H3K27
methylation.
Fig. 1. Eed, Enx1, and histone
H3 methylation enrichment on the Xp in preimplantation
embryos. Immunolabeling (red) with antibodies against Eed
(a to d), Enx1 (e to h), H3
di/trimethyl K27 (j to m), and H3 dimethyl K9
(n to q) was combined with Xist RNA FISH
(green). 4',6'-diamidino-2-phenylindole (DAPI) staining is
shown in blue. For each stage, an intact embryo and enlarged
representative nucleus or nuclei are shown. The arrowheads
indicate which cells are shown enlarged above each embryo. The
number of embryos with blastomeres showing Xp enrichment of
Eed and Enx1 (i) or H3K27 and H3K9 methylation
(r) are shown. [View
Larger Version of this Image (56K GIF file)]
|
Fig. 2. Loss of histone H3K4
methylation, H3K9 acetylation, and RNA PolII from the Xp in
early preimplantation embryos. Immunolabeling (red) with
antibodies was combined with Xist RNA FISH (green).
4',6'-diamidino-2-phenylindole (DAPI) staining is shown in
blue. Hypoacetylation of H3K9 (a to d) and
hypomethylation of H3K4 (e to h) are seen in
some blastomeres from the eight-cell stage. Two focal planes
of the same four-cell embryo are shown illustrating the
initiation of RNA PolII exclusion (detected with antibody H5)
in some blastomeres (j and k) but not in others
(l and m). Eight-cell and sixteen-cell embryos
show complete RNA PolII exclusion from the Xp in most
blastomeres (n to q). Arrowheads indicate which
cells of the intact embryo are shown as an enlarged version.
Kinetics of these changes on the Xp are shown in (i)
and (r). [View
Larger Version of this Image (50K GIF file)]
|
We also examined the timing of X-chromosome–wide
hypoacetylation of H3K9 and hypomethylation of H3K4.
These are early events during random X inactivation in
differentiating ES cells; they occur within the same time
window as H3K9 and K27 methylation (24,
26,
30).
At the four-cell stage, no or very little depletion for
these histone modifications could be detected at the site
of Xist RNA accumulation (Fig.
2, a to d, and fig. S3A). However, at the 8-cell
stage, both hypoacetylation of H3K9 and hypomethylation
of H3K4 could be detected at the Xp in some blastomeres (Fig.
2, c to f), and by the 32-cell stage, the proportion
of blastomeres with an Xp carrying these marks had risen
to over 90% (Fig.
2i). Thus, hypoacetylation of H3K9 and
hypomethylation of H3K4 occur after Xist RNA coating of
the Xp chromosome, but precede Eed/Enx1 accumulation and
H3K27 and K9 methylation.
Transcriptional activity of the Xp. The surprisingly early
appearance of these chromatin changes on the Xp suggested
that the initiation of Xp inactivation could be more
precocious than previously thought. Studies on the
developmental timing of Xp inactivation have, in the
past, involved analysis at the posttranscriptional level
(RT-PCR) (19,
20)
or posttranslational level [allozyme analyses, LacZ, and
green fluorescent proteins (GFPs)] (4,
31,
32)
and were hampered by the use of pools of embryos or cells,
as well as the unknown half-lives of the X-linked
transcripts and proteins assayed. We therefore decided to
assess Xp silencing more directly, at the level of
transcription and in single cells. Using an antibody (H5)
that recognizes the elongating form of RNA polymerase II
(RNA PolII), which is normally present only in
transcriptionally engaged chromatin (33),
we assessed the presence or absence of RNA PolII from the
Xist RNA domain as a marker of transcriptional activity
or silencing of the Xp. In differentiating female ES
cells, we found that RNA PolII exclusion from the X
chromosome is one of the earliest events in the
X-inactivation process, after Xist RNA coating (34).
Using this approach in preimplantation embryos, we could
see no exclusion of RNA PolII at or around the location
of the Xist pinpoint signal detected in two-cell,
G2 stage embryos (fig. S3). The first signs of
exclusion of RNA PolII from the site of Xist RNA
accumulation on the Xp could be detected at the four-cell
stage (Fig.
2, j to m). The number of blastomeres showing this
pattern increased from one or two at the 4-cell stage to
almost 100% by the 32-cell stage (Fig.
2r and fig. S3, i to l). The early initiation of
transcriptional silencing of the Xp was confirmed with
RNA FISH to detect nascent transcripts of the X-linked
Chic1/Brx gene. At the two-cell stage, two Chic1/Brx
signals, one of which was adjacent to the Xist
pinpoint, could be seen in some embryos (fig. S3). At the
8-cell stage a Chic1/Brx RNA signal could
be detected on the Xp within the Xist RNA domain in some
blastomeres, but by the 16-cell stage, this pattern was
never seen in more than one blastomere (35).
Taken together, our data point to the initiation of
transcriptional inactivation of the Xp from the four- to
eight-cell stage, which is much earlier than previously
thought. Before this, at the two-cell stage, the Xp seems
to be active. Inactivation appears to be triggered by
Xist RNA coating of the Xp and affects most if not all
blastomeres by the 32-cell stage. Imprinted X inactivation
thus initiates before any overt signs of cellular
differentiation.
Inactivation status of the Xp in the ICM. By the late
morula/early blastocyst stage (the first sign of the
blastocoel cavity), our findings suggest that essentially
all blastomeres contain an inactive Xp, as assessed by
RNA PolII exclusion, histone modifications, and Eed/Enx1
association. An important implication of this is that the
Xp must be inactive even in the ICM, which gives rise to
the epiblast. However, it is well known that random and
not imprinted paternal inactivation occurs in this lineage.
To resolve this paradox, we investigated the activity
status of the Xp specifically in the ICM, using
immunosurgery to isolate ICMs and eliminate all
trophectoderm cells. When this procedure was performed on
early blastocysts, the isolated ICM cells were found to
contain a Xist RNA domain from which RNA PolII staining
was excluded (fig. S4, e and f) and which was associated
with H3K9 hypoacetylation, H3K4 hypomethylation, H3K9 and
K27 methylation, and Eed and Enx1 accumulation (Fig.
3, k to n) (35).
Thus, exactly as predicted by our kinetic analysis, the
Xist RNA–coated Xp appears to be inactive in all cells,
including those of the ICM, up to the early blastocyst
stage. However, when ICM immunosurgery was performed on
later (expanded or hatching) blastocysts, we found that,
in contrast to trophectoderm cells, in the majority of
ICM cells, Xist RNA appeared to be dispersed or absent and
no Eed- or Enx-enriched domain could be found. Thus,
during ICM growth, Xist RNA coating of the Xp is lost,
and this is tightly coupled to loss of Eed and Enx1
accumulation on the Xp (Fig.
3h). However, the majority of these cells still contained
what appeared to be an X-chromosome domain enriched in
H3K27 methylation, even in the absence of Xist RNA
coating. In ICMs from the latest blastocysts recovered,
some cells had also lost the H3K9 and K27 methylation
domain, even though these modifications could clearly be
detected elsewhere in the nucleus (Fig.
3, q and r). Histone H3K9 and K27 methylation are
therefore also lost on the Xp over time in the ICM, but
after the dissociation of Xist RNA, Eed, and Enx1 (Fig.
4a).
Fig. 3. Blastocysts and ICM
cells isolated at different stages with immunosurgery (42)
are shown. Eed, Enx1, or H3 di/tri-meK27 was detected by
immunolabeling (red) combined with Xist RNA FISH.
4',6'-diamidino-2-phenylindole (DAPI) staining is shown in
blue. Representative trophectoderm cells (arrowheads) with Eed
(a and b) and Enx1 (i and j)
accumulation on the Xist RNA–coated chromosome are shown. Eed
staining and Xist RNA FISH in ICM cells derived from early,
late, and cultured blastocysts is shown (c to
g). Xist RNA FISH and Enxl staining (k to
n) or H3 di/trimethyl K27 staining (o to
r) in ICM cells derived from early and late blastocysts
are shown. The decreasing proportions of cells showing Eed,
Enx1, or H3 di/tri-meK27 enrichment in the ICM are summarized
(h). [View
Larger Version of this Image (75K GIF file)]
|
Fig. 4. The kinetics of
transcriptional inactivation, histone modifications, and
polycomb group protein association on the Xist RNA–coated Xp
in preimplantation embryos are summarized (A), and a
schematic representation of the order events is shown
(B). Findings not shown here but reported by others (13,
14,
28)
are shown in italics. [View
Larger Version of this Image (36K GIF file)]
|
We also isolated the ICM from early blastocysts by
immunosurgery and cultured them for 24 hours. In this
procedure, the outgrowing cells are believed to be of the
primitive endoderm type (15,
36).
All outgrowing cells were found to have a Xist RNA domain
that showed the chromatin characteristics observed in
morulas and in the trophectoderm (Fig.
3g) (35),
suggesting that the inactive state of the Xp is probably
maintained upon differentiation of the primitive endoderm
lineage. On the other hand, in cells at the center of the
ICM, reversal of the inactive state (loss of Xist RNA
coating, as well as loss of Eed and Enx association)
could be detected, as in ICMs isolated directly from late
blastocysts.
Conclusions. We have made a number of findings concerning
the process of X inactivation during early mouse
development. We show that the imprint on the Xp is
unlikely to be due to its global chromatin status but
rather to the early activity of the paternal Xist
gene. We also show that, although the Xp is initially
active in early cleavage female embryos, it becomes
rapidly inactivated after accumulation of Xist RNA at the
four-cell stage, as assessed by the exclusion of RNA
PolII, the absence of nascent X-linked transcripts, and
the appearance of H3K4 hypomethylation and H3K9
hypoacetylation. Polycomb group proteins, which are
believed to be involved in the early maintenance of the
repressed state in several systems (37)
and X inactivation in particular (26,
27),
subsequently accumulate on the Xp and H3K27 methylation
occurs. The variable time of onset we observed for these
early maintenance marks over the 16- to 32-cell stage may
explain the potential reversibility of Xp imprinted
inactivation in some embryos, under abnormal
circumstances such as in XpO (with no Xm and a single Xp)
mice (38)
or in androgenotes (XpXp) (22).
From the 32-cell stage onward, however, we show that the
Xp carries these epigenetic marks in virtually all cells
of female embryos and maintains them in the trophectoderm
and primitive endoderm. In these lineages, they are
presumably further "locked in" by the shift in
replication timing of the Xp (14).
However, during ICM growth, we found that X inactivation
is reversed. A rapid loss of Xist RNA coating of the Xp
was observed, accompanied by the loss of Eed and Enx1
association, and this was followed by a more gradual loss
of the H3 methylation marks, presumably by dilution of
old nucleosomes through cell division. By the time
implantation occurs, the Xp is no longer inactive and random
inactivation of either the Xp or the Xm can occur in cells
of the epiblast. The kinetics of these events are shown
in Fig.
4a, together with the order of events during
development (Fig.
4b).
Our study reveals that the inactive state of the Xp and
associated epigenetic marks are highly labile during
preimplantation development. Their reversal in the ICM
may be a reflection of more global reprogramming events
occurring at this stage of development (39).
The reasons for such a dynamic cycle of Xp inactivation,
followed by reactivation, followed by random X
inactivation in the mouse are unclear but could be due to
a combination of evolutionary pressure to silence the Xp
early in development, as predicted by the parental genome
conflict theory (40),
together with the efficient reprogramming activity of the
ICM.
Finally, in a study investigating X inactivation in cloned
mouse embryos (41),
a GFP transgene carried by a somatic cell–derived
inactive X chromosome, was shown to be reactivated after
transfer into an enucleated oocyte, but then became
preferentially inactivated in extraembryonic tissues. In
light of the results we present here, these findings are
consistent with the idea that the presence of a
transcribing Xist gene, whether paternally inherited or
of somatic cell origin, is likely to be the only "imprint"
required to trigger the chromatin modifications and
epigenetic marks that lead to preferential X inactivation
in the cleavage stage embryo.
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We thank N. Takagi, V. Colot, and J.
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Sibarita for help with 3D microscopy; and S. Yoshida for her
encouragement. I.O. was supported by the Japanese Society for
the Promotion of Science. This work was funded by the CNRS,
the Association pour la Recherche sur le Cancer, and the
Fondation pour la Recherche Medicale. |
Supporting Online Material
www.sciencemag.org/cgi/content/full/1092727/DC1
Materials and Methods
Figs. S1 to S4
Table S1
References and Notes
20 October 2003; accepted 1 December
2003 10.1126/science.1092727 Include this information when
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Volume 303, Number 5658, Issue of 30 Jan 2004, pp. 644-649.
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