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DOI: 10.1126/science.1194174
, 496 (2010); 330Science et al.Kimiko Inoue,
Transfer NuclearChromosome Improves Mouse Somatic Cell
Expression from the Active XXistImpeding
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Impeding Xist Expression from the
Active X Chromosome Improves
Mouse Somatic Cell Nuclear Transfer
Kimiko Inoue,
1,2
Takashi Kohda,
3
Michihiko Sugimoto,
1
Takashi Sado,
4
Narumi Ogonuki,
1
Shogo Matoba,
1
Hirosuke Shiura,
1
Rieko Ikeda,
1
Keiji Mochida,
1
Takashi Fujii,
5
Ken Sawai,
5
Arie P. Otte,
6
X. Cindy Tian,
7
Xiangzhong Yang,
7
Fumitoshi Ishino,
3
Kuniya Abe,
1,2
Atsuo Ogura
1,2,8
*
Cloning mammals by means of somatic cell nuclear transfer (SCNT) is highly inefficient because of
erroneous reprogramming of the donor genome. Reprogramming errors appear to arise randomly,
but the nature of nonrandom, SCNT-specific errors remains elusive. We found that Xist,a
noncoding RNA that inactivates one of the two X chromosomes in females, was ectopically
expressed from the active X (Xa) chromosome in cloned mouse embryos of both sexes. Deletion of
Xist on Xa showed normal global gene expression and resulted in about an eight- to ninefold
increase in cloning efficiency. We also identified an Xist-independent mechanism that specifically
down-regulated a subset of X-linked genes through somatic-type repressive histone blocks. Thus,
we have identified nonrandom reprogramming errors in mouse cloning that can be altered to
improve the efficiency of SCNT methods.
Cloned animals have been generated from
embryonic cells (blastomeres) or somatic
cells by nuclear transfer. The latter type of
cloning, somatic cell nuclear transfer (SCNT), has
more practical applications and has been applied
successfully to more than 20 animal species (1).
However, despite extensive efforts to improve the
technique, the efficiency in terms of normal birth
remains low. For example, screening for tissue-
specific stem cells that might provide a more effi-
cient donor cell has shown limited success (2,3).
The observation of many SCNT-specific pheno-
types in cloned animals, such as placental ab-
normalities (4) and immunodeficiency (5), led
us to hypothesize that SCNT might be associated
with some definable, nonrandom epigenetic er-
rors. By combining genetics, functional genomics,
and cloning technologies, we now identify non-
random reprogramming errors in cloned embryos
that provide promising clues for improving SCNT
cloning.
To define the gene expression patterns spe-
cific for SCNT, we generated mouse embryos from
cumulus cells and immature Sertoli cells under
standardized SCNT conditions (6). Single cloned
blastocysts were analyzed for their global gene
expression patterns by comparing them with
genotype-matched controls produced by means
of in vitro fertilization (IVF) at the same time (7).
When the relative expression levels of filtered
genes in cloned embryos taken from a 44,000
oligoDNAmicroarraywereplottedonthe20
chromosomes, genes on the X chromosome were
specifically down-regulated (Fig. 1A). This phe-
nomenon was sex- and genotype-independent be-
cause the average X:autosome (X:A) expression
ratio in the three types of cloned embryos (cumu-
lus and Sertoli clones with different genotypes)
was consistently lower than in the corresponding
control embryos (Fig. 1B). Detailed observations
on the entire X chromosome revealed that although
there seemed to be some gene-specific variations,
the X-linked genes were largely down-regulated
in most regions (Fig. 1C). We then performed a
statistical analysis using Student’sttest to iden-
tify the number of affected genes in cloned em-
bryos. In each clone group, 2560 to 5540 out of
1
BioResource Center, RIKEN, 305-0024 Tsukuba, Japan.
2
Graduate School of Life and Environmental Science, University
of Tsukuba, 305-8572 Tsukuba, Japan.
3
Medical Research
Institute, Tokyo Medical and Dental University, 113-8510 Tokyo,
Japan.
4
Medical Institute of Bioregulation, Kyushu University,
812-8582 Fukuoka, Japan.
5
Faculty of Agriculture, Iwate Uni-
versity, 020-8550 Iwate, Japan.
6
Swammerdam Institute for Life
Sciences, University of Amsterdam, 1018 TV Amsterdam, Nether-
lands.
7
Center for Regenerative Biology and Department of
Animal Science, University of Connecticut, Storrs, CT 06269,
USA.
8
The Center for Disease Biology and Integrative Medicine,
Faculty of Medicine, University of Tokyo, 113-0033 Tokyo, Japan.
*To whom correspondence should be addressed. E-mail:
ogura@rtc.riken.go.jp
Fig. 1. Large-scale down-regulation of
X-linked genes in SCNT embryos. (A)A
representative pattern of relative gene
expression levels of a B6D2F1 IVF em-
bryo,acumuluscellclonedembryo,and
a Sertoli cloned embryo, plotted on the
genomic positions from chromosomes
1 to X (except for Y). The red bar indi-
cates down-regulated X-linked genes
in a cloned embryo. (B)Theratioofthe
expression levels of X-linked genes to
autosomal genes. Wild-type cloned
embryos, including those treated with
TSA, showed lower X:A ratios as com-
pared with the corresponding IVF controls.
The data are represented as the mean T
SEM.
a, a′
P<0.01,
b, b′
P< 0.0001,
c, c′
P<
0.05 (one-way analysis of variance and
Student’sttest). (C) Relative gene ex-
pression levels of (red) cumulus cell
cloned embryos, (blue) cumulus cell
cloned embryos treated with TSA (n=
3 embryos), and (gray) IVF embryos
plotted on the positions of the X chromo-
some. Dotted lines represent a single
embryo, and solid lines indicate their
mean values. Arrowheads 1 and 2
indicate the position of the Xlr and
Magea clusters, respectively (Fig. 3B).
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39,448 gene probes were expressed differen-
tially as compared with that of the genotype-
matched IVF controls (fig. S1A). However, the
affected genes common to all the clone groups
represented only 129 genes (145 probes), with
90 being up-regulated and 39 down-regulated
(fig. S1B). Thus, SCNT caused dysregulation of
a large subset of genes, but most followed a pat-
tern specific to each donor cell type. Twenty-one
out of 39 (54%) of the commonly down-regulated
genes (“CDGs”)weremappedtotheXchro-
mosome (P< 1.0 × 10
−72
versus the expected
number from the X-linked gene population with
Pearson’sc
2
test) (table S1 and fig. S1C), com-
pared with a nonbiased population of genes in
the up-regulated genes (P> 0.05) (table S2 and
fig. S1C). For some CDGs, their clone-associated
down-regulation was confirmed by means of
quantitative real-time polymerase chain reaction
(RT-PCR) experiments (fig. S2). We also ana-
lyzed embryos cloned from fibroblasts and from
blastomeres of four-cell embryos and confirmed
that the X-linked down-regulation largely could
be attributed to SCNT cloning and not general-
ly to nuclear transfer cloning (fig. S3 and table
S1). Next, we tested whether the X-linked down-
regulation of cloned embryos could be amelio-
rated through treatment with trichostatin A (TSA),
which is a histone deacetylase inhibitor (HDACi)
known to improve mouse cloning efficiency
(8). However, this treatment produced no signif-
icant improvement in the X:A expression ratio
(P> 0.05) (Fig. 1B) or in the expression levels
of X-linked genes (Fig. 1C) as compared with
that of untreated cloned embryos.
The chromosome-wide gene down-regulation
on the X chromosome in cloned embryos was
reminiscent of X chromosome inactivation (XCI).
This process normally triggers inactivation of one
of the two X chromosomes in female embryos so
that the gene dosage is comparable with that in
males. XCI is initiated by Xist RNA coating in
cis, although it is completed and maintained by
many other molecules (Fig. 2D) (9). We then
examined whether Xist was expressed excessively
in our cloned embryos, as has been reported for
embryos cloned from cumulus cell nuclei (10,11).
In both female and male cloned embryos, the Xist
expression levels were significantly higher than
in control IVF embryos (P< 0.05), as confirmed
with microarray (Fig. 2A) and quantitative RT-
PCR analyses (fig. S4A). We postulate from
these findings that Xist was expressed ectopically
from the active X chromosome (Xa) in cloned
embryos. We then observed the number of Xist
domains within each blastomere nucleus at the
morula or early blastocyst stage by use of RNA
fluorescent in situ hybridization (FISH). As expected,
about half of the IVF embryos consistently
showed a single domain in each blastomere, and
the remaining half showed no domain, probably
representing female and male embryos, respec-
tively (Fig. 2, B and C). In female clones, all four
embryos contained blastomeres with unusual
biallelic Xist domains with a variable frequency
from 20.0 to 51.7% (Fig. 2, B and C). In male
clones, all seven embryos analyzed showed one
strong Xist RNAdomaininthemajorityofblas-
tomeres (Fig. 2, B and C), whereas their donors
had no Xist expression (12). We could exclude
the possibility of involvement of tetraploidy in
this excessive number of Xist RNA domains
because there were very few blastomeres with
duplicated X chromosomes in the cloned em-
bryos (fig. S5). We further confirmed the local-
ization of trimethylated histone H3 at lysine 27
(H3K27me3) and of Eed, which are responsible
for the repressive chromatin state in the inactive
X(9). In male and female cloned embryos, they
colocalized exclusively in one and two domains
in the nucleus, respectively, suggesting that the
ectopic Xist expression indeed leads to XCI (Fig.
2D). The ectopic expression of Xist first appeared
at the four-cell stage and increased up to the
blastocyst stage, as revealed through quantitative
RT-PCR and RNA FISH analysis by use of male
cloned embryos (fig. S6). These findings support
our hypothesis that Xist is ectopically expressed
and aberrantly inactivate Xa in both male and
female clones. At present, we do not know the
causes of the ectopic expression of Xist in cloned
embryos. However, because it is assumed that the
major mechanisms of genomic memory for Xi
(or conversely, Xa) in preimplantation embryos
and somatic cells are different (9,13,14), re-
establishment of the Xi (or Xa) memory in the
Fig. 2. Xist is ectopically expressed on the active X
chromosome in female and male cloned embryos.
(A) The expression levels of Xist in female and male
embryos. The expression levels are significantly
higher in cloned embryos of both sexes (P< 0.05,
Student’sttest). (B) Morula or early blastocyst stage
embryos with localizations for (red) Xist RNA and
(blue) nucleus. Ectopic expression of Xist is evident
from the existence of two domains in females (white
arrowheads) and one domain in males for Xist RNA
(black arrowheads). (C) The ratio of blastomeres
classified by the number of Xist RNA domains within
single embryos (0 to 2). Each bar represents one
embryo. (D) Immunostaining for H3K27me3 and
EedinIVFandclonedblastocysts.Thesignalsof
H3K27me3 and Eed are colocalized in single or
double domains within blastomere nuclei. There are
two localizations in embryos cloned from cumulus
cells (females) and one in embryos cloned from
Sertolicells(male),suggestingthattheXachromo-
some is inactivated aberrantly in cloned embryos
of both sexes.
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somatically derived genome in reconstructed
embryos might have been incomplete.
Because Xist has a chromosome-wide repres-
sive effect on X-linked genes in cis, next we
asked to what extent its ectopic expression might
be responsible for the aberrant gene expression
observed in cloned embryos. To this end, SCNT
was performed by using donor cells containing
an Xist-deficient (X
DXist
)Xchromosome(15)for
Xa and analyzed the embryos for their gene
expression patterns. In both female (cumulus
cell) and male (Sertoli cell) clones, the numbers
of down-regulated X-linked genes in wild-type
clones were considerably decreased in X
DXist
clones by 85% (80 →12) and 85% (141 →21)
in female and male embryos, respectively (Fig.
3A). This effect is clearly noted in the upper shift
of the gene expression levels plotted on the X
chromosome (Fig. 3, B and C) and A:X ratios
(Fig. 1B). This had a genome-wide effect, and the
numbers of down-regulated autosomal genes
also decreased by 85% (461 →71) and 73%
(340 →91) in female and male embryos, respec-
tively (Fig. 3A). These results indicate that the
ectopic Xist expression could have adversely af-
fected gene expression in cloned embryos in a
genome-wide manner, probably through com-
plex gene networks connecting autosomal genes
and X-linked genes that direct embryonic devel-
opment. However, two discrete groups of genes
remained down-regulated (Fig. 3, B and C). These
were the Magea and Xlr gene clusters localized
on XqF3 and XqA7.2–7.3, respectively (Fig.
1C). Twelve of the 21 X-linked CDGs were clas-
sified into one of these two clusters [table S1 and
supporting online material (SOM) text].
In the next series of experiments, we transferred
SCNT embryos containing an Xist-deficient Xa
into pseudopregnant recipient females. In both
cumulus and Sertoli cell–derived clones, their
development was greatly improved; the average
birth rates reached 12.7 and 14.4% per embryos
transferred (up to 19.2%), corresponding to eight-
to ninefold higher levels than wild-type controls,
respectively (Fig. 3, D and E, and table S3).
Mouse cloning from this standard genetic strain
background (B6D2F1) has not reached such high
efficiencies (1,16). Most clones grew into nor-
mal adults and showed no gross abnormalities
(table S3).
In this study, we identified two types of SCNT-
associated errors specifically affecting the X chro-
mosome in mice: (i) the ectopic Xist expression
from Xa and (ii) persistence of repressive histone
modifications (H3K9me2) in the Magea and Xlr
regions (SOM text). These errors were resistant to
TSA treatment, indicating that they cannot be
rescued by simply enhancing the accessibility of
the putative ooplasmic reprogramming factors.
Thus, we can broadly classify the epigenetic errors
in cloned mouse embryos into two categories: One
is random and can be overcome to some extent
by enhancing genomic reprogramming (such as
through HDACi treatment), whereas the other is
more specific and probably beyond the ability of
the putative ooplasmic factors that are to repro-
gram the germ cell genome (17). We found that
XIST expression was also elevated in female and
male bovine SCNT embryos (fig. S4B); there-
fore, this could have broad implications for im-
proving mammalian SCNT techniques. Indeed,
there is a clear association between the death of
bovine cloned embryos and aberrant X-linked gene
expression in the placenta (18). Because the data
presented in this study are still limited, it is neces-
sary to examine whether certain genetic or epige-
netic modifications for XIST might improve the
survival of SCNT embryos using other mamma-
lian species or mice from different strains.
A major goal of cloning research is to increase
the efficiency of mammalian SCNT to a practical
level (for example, >20% per embryos transferred)
because of the many potential applications in
biological drug manufacturing, regenerative med-
icine, and agriculture (19). To this end, we need to
overcome the fundamental differences between
somatic and germ cell genomes. We expect that
cloning will become more practical by specifi-
cally targeting nonrandom epigenetic errors asso-
ciated with SCNT.
Fig. 3. Deletion of Xist ontheactiveXchromo-
some (Xa) in SCNT embryos improves their gene
expression patterns and developmental ability in
vivo. (A) The numbers of down-regulated genes in
SCNT embryos compared with corresponding IVF
embryos. With deletion of Xist on the Xa, they are
reduced by 73 to 85% for both the X chromosomes
or autosomes in both female cumulus cell and male
Sertolicellclones.(Band C) The relative expression
levels of X-linked genes plotted on the X chromo-
some position in (B) cumulus and (C) Sertoli cell
cloned embryos. The majority of down-regulated
genes are increased in their expression levels, except
for genes within the Xlr (arrowheads 1) or Magea
(arrowheads 2) clusters, in Xist-knockout clones (n=
5 and 4 cumulus and Sertoli clones, respectively, in
green), compared with (red) wild-type cloned em-
bryos (SOM text). (D) The birth rates per embryos
transferred. Eight- to ninefold increases were ob-
served in Xist knockout clones. (E) Fetuses born after
nuclear transfer by using Sertoli cells (left) with or
(right) without the Xist gene on Xa. The birth rates
were 1.6 and 15.4% of embryos transferred, respec-
tively (table S2).
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References and Notes
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material on Science Online.
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340, 183 (2006).
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(2005).
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13. L. E. McDonald, C. A. Paterson, G. F. Kay, Genomics 54,
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R. Yanagimachi, Nature 394, 369 (1998).
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22, 25 (2004).
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19. X. Yang et al., Nat. Genet. 39, 295 (2007).
20. The mice in which Xist had been knocked out (RBRC
01260) were provided by the RIKEN BioResource Center.
This research was supported by grants from the Ministry
of Education, Culture, Sports, Science and Technology
and NOVARTIS Foundation (Japan) for the Promotion of
Science. The H3K9me2 antibody used for chromatin
immunoprecipitation on chip was a kind gift from
H. Kimura. We thank M. Tachibana, Y. Shinkai, H. Koseki,
T. H. Endo, and S. L. Marjani for their invaluable
suggestions. The microarray data have been deposited in
the Gene Expression Omnibus and given the series
accession number GSE23181.
Supporting Online Material
www.sciencemag.org/cgi/content/full/science.1194174/DC1
Materials and Methods
SOM Text
Figs. S1 to S8
Tables S1 to S3
References
24 June 2010; accepted 2 September 2010
Published online 16 September 2010;
10.1126/science.1194174
Include this information when citing this paper.
Two Pairs of Neurons
in the Central Brain Control
Drosophila Innate Light Preference
Zhefeng Gong,
1
*Jiangqu Liu,
1,2
Chao Guo,
1,2
Yanqiong Zhou,
1,2
Yan Teng,
3
Li Liu
1
*
Appropriate preferences for light or dark conditions can be crucial for an animal’s survival. Innate
light preferences are not static in some animals, including the fruit fly Drosophila melanogaster,
which prefers darkness in the feeding larval stage but prefers light in adulthood. To elucidate the
neural circuit underlying light preference, we examined the neurons involved in larval phototactic
behavior by regulating neuronal functions. Modulating activity of two pairs of isomorphic neurons
in the central brain switched the larval light preference between photophobic and photophilic. These
neurons were found to be immediately downstream of pdf-expressing lateral neurons, which are
innervated by larval photoreceptors. Our results revealed a neural mechanism that could enable the
adjustment of animals’response strategies to environmental stimuli according to biological needs.
Preference between light and darkness plays
an important role in animal life (1–4). The
fruit fly Drosophila melanogaster avoids
light at the first to mid-third instar larval stage,
but this photophobic behavior is thereafter re-
duced, before pupation (5–7). In addition to the
circadian photoreceptor cryptochrome (CRY),
the larval visual system includes two bilateral
groups of 12 photoreceptors (8,9): the Bolwig’s
organs (BO), which send out Bolwig’snerves
(BNs) to innervate the pace-making neurons, the
pigment-dispersing factor (Pdf)–expressing later-
al neurons (pdf neurons) in larval central brain
(6,10). Blocking either BO or pdf neurons causes
larval blindness, as measured by phototactic as-
say (6,11,12).
To investigate downstream neurons under-
lying larval phototactic behavior, we screened a
batch of up to 800 Gal4 lines [obtained from
Drosophila Genetic Resource Center (DGRC),
Kyoto] in a simple light-dark choice assay (6)
using the Gal4/UAS system to drive ectopic ex-
pression of the tetanus toxin light chain (TeTxLC;
UAS-TNTG), a neuron-specific toxin that pre-
vents presynaptic release of synaptic vesicles (13).
Whereas most Gal4 lines manifested photopho-
bia and several Gal4 lines exhibited loss of light
preference with ectopic TeTxLC expression at
early to mid-third instar larval stage, one Gal4
line, NP394-Gal4, demonstrated a preference for
light. This line showed positive larval phototaxis
when TeTxLC expression was driven by NP394-
Gal4 [Fig. 1A, performance index (PI) =−0.35 T
0.07, P< 0.001, n= 16; fig. S1]. Furthermore,
temporary TeTxLC expression in NP394-Gal4–
labeled neurons was able to confer positive pho-
totaxis at various larval stages (fig. S2). The
positive larval phototaxis was reproduced by ec-
topic expression of a mutated form of the open
rectifier potassium channel, dORK∆C(Fig.1A,
PI =−0.25 T0.09, P<0.05,n= 16), the over-
expression of which hyperpolarizes neurons and
subsequently inactivates neuronal function (14).
To find more phototaxis-positive Gal4 lines
sharing common labeling with the NP394-Gal4,
we rescreened all the Gal4 lines by overexpress-
ing dORK∆C. This method was chosen because
the overexpression of TeTxLC led to lethality or
defects in locomotion in a large number of Gal4
lines, meaning that behavioral assays could not
be conducted. Two lines, NP423-Gal4 and NP867-
Gal4, manifested positive larval phototaxis when
the labeled neurons were inhibited by dORK∆C
(Fig. 1A, PI = −0.22 T0.06 for NP423-Gal4 >
dORK∆Cand PI = −0.34 T0.07 for NP867-Gal4 >
dORK∆C,n= 16 for both lines). For further
confirmation at the behavioral level, we applied
the temperature-sensitive form of Dynamin (shi
ts
)
that instantly inhibits cell endocytosis at the re-
strictive temperature (15). In all three Gal4 lines,
ectopic expression of shi
ts
at the restrictive tem-
perature resulted in positive larval phototaxis
(Fig. 1B, PI = −0.22 T0.05 for NP394-Gal4 >
UAS-shi
ts
,PI=−0.22 T0.05 for NP423-Gal4 >
UAS-shi
ts
,andPI=−0.29 T0.05 for NP867-
Gal4 > UAS-shi
ts
,n= 16 for all lines). By contrast,
hyperactivation of NP394-Gal4–labeled neurons
by expressing the sodium channel NaChBac
(16) significantly enhanced light avoidance in late
third instar larvae, which generally exhibit re-
duced light avoidance compared with younger
larvae (figs. S3 and S4). Thus, we concluded that
regulation of activity in neurons labeled by these
Gal4 lines could switch larval phototaxis between
negative and positive, suggesting that these neu-
rons mediate the larval preference between light
and darkness.
In parallel with behavioral screening, we used
a membrane-tethered green fluorescent protein
(mCD8-GFP) to visualize the expression patterns
of the Gal4 lines at the larval stage. Outside the
central nervous system (CNS), common labeling
was found only in the salivary gland in all three
Gal4 lines (table S1). In the larval CNS, the NP394-
Gal4 expression pattern was most restricted of
the three Gal4 lines (Fig. 1, C to H, and fig. S5).
NP394-Gal4 labeling was most marked in two
pairs of mirror-symmetrically arranged neurons
in the supraesophageal ganglion from as early as
the first instar and throughout larval development
(fig. S6). For convenience, we refer to these cells
as NP394-neurons. In the other two Gal4 lines,
labeling of neurons with morphology and loca-
tion similar to those of the NP394-neurons was
also observed (Fig. 1, C to H). To confirm that the
same NP394-neurons were labeled in all three
Gal4 lines, we conducted combinatorial Gal4
labeling. In flies carrying combinations of two
1
State Key Laboratory of Brain and Cognitive Science, In-
stitute of Biophysics, Chinese Academy of Sciences, Beijing
100101, People’s Republic of China.
2
Graduate University
of the Chinese Academy of Sciences, Beijing 100039, People’s
Republic of China.
3
Protein Science Core Facility Center,
Institute of Biophysics, Chinese Academy of Sciences, Beijing
100101, People’s Republic of China.
*To whom correspondence should be addressed. E-mail:
zfgong@moon.ibp.ac.cn (Z.G.); liuli@sun5.ibp.ac.cn (L.L.)
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