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Transcript
Brain & Development 23 (2001) S147–S151
www.elsevier.com/locate/braindev
Original article
Mutations in the gene encoding methyl-CpG-binding protein 2
cause Rett syndrome
Ignatia B. Van den Veyver a,b,*, Huda Y. Zoghbi a,c,d
a
Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
b
Department of Obstetrics and Gynecology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
c
Department of Pediatrics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
d
Howard Hughes Medical Institute, Houston, TX, USA
Abstract
Rett syndrome is an X-linked dominant neurodevelopmental disorder primarily affecting girls. About 80% of classic Rett syndrome is
caused by mutations in the gene for methyl-CpG-binding protein (MeCP2) in Xq28. MeCP2 links DNA methylation to transcriptional
repression, and MECP2 mutations likely cause partial or complete loss of function of the protein, leading to inappropriate transcription of
downstream genes at critical times in brain development. More severe and milder variant forms can all be caused by similar mutations. Most
classic Rett syndrome patients have random X-chromosome inactivation (XCI), but skewed patterns are present in a few. All asymptomatic
or mildly mentally delayed female carriers studied to date have non-random XCI patterns, suggesting that this attenuates the deleterious
effects of the MECP2 mutations in these women. The finding of non-random XCI patterns in some patients with very early truncations is
consistent with this observation and supports that many mutations could cause partial and not complete loss of function. Our observation that
the mutant mRNA is stable in three patients with truncating mutations supports this possibility. Further studies will have to be performed to
better understand the functional consequences of MECP2 mutations in RTT. q 2001 Elsevier Science B.V. All rights reserved.
Keywords: -Rett syndrome; MECP2; Methyl-CpG-binding domain; Transcription repression domain; Xq28; X-linked dominant; Mutations
1. Introduction
Rett syndrome (RTT) is an X-linked dominant neurodevelopmental disorder that affects about 1/10,000 to 1/15,000
females. RTT is characterized by apparently normal development for 6–18 months [1], followed by a period of regression with loss of purposeful hand use, deceleration of head
growth, and onset of repetitive, stereotyped hand movements. Affected girls develop gait ataxia and apraxia, autistic features, seizures, respiratory dysfunction (episodic
apnea and/or hyperpnea), autonomic dysfunction and have
decreased somatic growth [2]. This period of rapid deterioration is followed in puberty by a stabilization phase
that lasts through adulthood. Some girls have variant
forms of Rett syndrome: some may have a milder phenotype
and retain the ability to walk or speak and others a more
severe disease with an earlier onset (congenital form) [3,4].
* Corresponding author. Tel.: 11-713-798-4914; fax: 11-713-798-8728.
E-mail address: [email protected] (I.B. Van den Veyver).
2. The X-linked inheritance of Rett syndrome and
discovery of MECP2 mutations in Rett syndrome
The exact origin of RTT has long been debated [2,5,6],
but several observations suggested that it is an X-linked
dominant disorder. Although 99% of RTT occurrences are
sporadic, a few familial cases were reported in which the
disease was inherited through maternal lines [7,8]. X-linked
dominant inheritance was also supported by the observation,
in three families, of a non-random pattern of X-chromosome
inactivation in obligate carrier females without a RTT
phenotype [9–11] and the presence in two of these of a
male sibling who presented with a severe neonatal encephalopathy and died as an infant [11,12]. Based on these observations, a series of exclusion mapping studies aimed at
defining the smallest regions shared amongst affected individuals in familial RTT was used and mapped the Rett
syndrome gene to a 10 Mb region telomeric to DXS998
[10–15]. Mutational analysis of candidate genes in the
included region was then focused on those with known or
potential functions in the development of the CNS [16,17].
The unexpected observation of biallelic methylation of a
putative imprinted gene (PEG3) in three patients with Rett
0387-7604/01/$ - see front matter q 2001 Elsevier Science B.V. All rights reserved.
PII: S 0387-760 4(01)00376-X
S148
I.B. Van den Veyver, H.Y. Zoghbi / Brain & Development 23 (2001) S147–S151
syndrome (Van den Veyver and Zoghbi, unpublished
results) drew our attention to the gene encoding methylCpG-binding protein 2 (MeCP2) in Xq28. Using heteroduplex analysis and direct sequencing of the coding sequence
of the MECP2 gene, we identified mutations in patients with
classic Rett syndrome.
3. Function of MeCP2
MECP2 maps between L1CAM and the RCP/GCP loci in
Xq28 and undergoes X-inactivation [18]. The gene is very
conserved between species, not only in its coding region,
but also in the 3 0 and 5 0 untranslated regions (UTR) [19];
this has led to the recent identification in human and mouse
of a fourth MECP2 exon that encodes 5 0 UTR sequence [20].
MeCP2 was found to be the molecular link between DNA
methylation and transcriptional repression [21,22]. It binds
to symmetrically positioned CpG dinucleotides, methylated
at position 5 of cytosine (m 5CpG). MeCP2 can bind
throughout the chromosome, but it preferentially associates
with dense heterochromatin, rich in m 5CpG [23]. Methylation of CpG dinucleotides in the mammalian genome is
important to silence transcription of imprinted genes and
genes on the inactive X chromosome, in the immobilization
of endogenous transposon sequences and possibly in the
control of tissue-specific gene expression [24]. When
MeCP2 binds to the methylated CpG islands it recruits a
complex containing histone deacetylases (HDAC1 and
HDAC2) and the co-repressor Sin3A [21,22]. The tails of
core histones in the nucleosomes are deacetylated by
HDACs, which leads to compaction of heterochromatin,
making it inaccessible to the transcriptional activators and
components of the transcriptional machinery, resulting in
stable repression of downstream genes [24] (Fig. 1).
MeCP2 belongs to a family of methyl-CpG-binding
Fig. 1. Mutations in MECP2. Exons 2 through 4 of the MECP2 gene are
shown as gray boxes, non-coding regions in dark grey, the MBD in vertical
lines and the TRD in diagonal lines. Circles above the gene represent
missense mutations; truncating mutations are shown below the gene;
squares are nonsense mutations; triangles are frameshift mutations; S is
the splicing mutation. Recurrent mutations are indicated by the number
in parenthesis. Mutations at CpG dinucleotides are in filled circles or
squares. (*indicates an insertion of 3 bp in the frameshift mutation
1147del170bp).
domain-containing proteins [25], of which at least three
(MBD1, MBD2a, MBD3) are members of different transcriptional repressor complexes. These may have distinct
or overlapping functions with MeCP2 during methylationdependent epigenetic regulation of transcription [24]. In
addition there are at least four different DNA methyltransferases, one of which (DNMT1) plays a role in the stable
transmission of DNA methylation during cell division
[26,27], and two are de novo methylases (DNMT3a and
DNMT3b) [28]. The embryonic lethality seen after gastrulation in mice with null mutations for the DNA methyltransferases, supports the importance of DNA methylation in
development [27,28].
4. Mutations in MECP2
To date, we have identified mutations in the coding region
of MECP2 in 74 of 92 sporadic patients with classic RTT
(81%) and in four of nine RTT families [29,30]. We found
30 missense (MS) mutations, 22 of which are in the methylCpG-binding domain (MBD) of MeCP2, 35 nonsense (NS),
12 frameshift (FS) and 1 splice-site mutation. Forty-six of
48 truncating mutations are beyond the MBD, 41 of which
affect the transcription repression domain (TRD). Consistent with the sporadic occurrence of RTT, most of the mutations occurred de novo and the majority of nucleotide
substitutions are C to T transitions at CpG mutation hotspots
(Fig. 1).
We found two mutations that are predicted to truncate the
MBD. One is the splice-site mutation at the acceptor splice
site of exon 4; we could only detect the wild-type transcript
in lymphoblast mRNA from this patient, suggesting that she
either has a non-random XCI pattern, or that the mutant
RNA is unstable. Unfortunately, the patient was uninformative for the androgen receptor assay used to determine XCI
[30]. The other mutation (Y141X), as well as one reported
by Wan et al. (411delG) [31], is distal to the DNA-binding
surface of the MBD. Both of these Rett patients show a
tendency to non-random XCI in genomic DNA from peripheral blood leukocytes or from lymphoblastoid cell lines
[30,31]. Interestingly, there were also three larger deletions
of 41–170 base pairs distal to the TRD, in the C-terminal
region of the coding sequence. This area contains a number
of (quasi)-palindromic repeats that may make the region
vulnerable to such deletions [32]. Even though systematic
screening of the 5 0 UTR and 3 0 UTR and a search for larger
deletions has not been completed, we found mutations in
81% of sporadic classic RTT patients. Therefore we think
that this is most likely the major locus for Rett syndrome.
However, one can speculate that rare cases of RTT and other
similar disorders may be caused by mutations in other
MBD-containing proteins or in additional factors involved
in methylation-dependent transcriptional repression. It is
interesting that some authors have reported lower incidences of MECP2 mutations in sporadic RTT patients
I.B. Van den Veyver, H.Y. Zoghbi / Brain & Development 23 (2001) S147–S151
[31,33]; these studies may have included patients with
milder forms of RTT (such as preserved speech variant)
and have used different mutation screening methods, such
as denaturing gradient gel electrophoresis (DGGE) or denaturing high performance liquid chromatography (DHPLC).
It also remains to be investigated whether those could have
mutations in non-coding regions, in other genes with related
functions or in MeCP2 target genes (see below).
5. Genotype–phenotype correlation
In order to better understand the pathogenesis of RTT and
the role of the different mutations in the phenotype of RTT,
we undertook a detailed genotype–phenotype correlation
study on 48 RTT patients, 47 of whom fit all the diagnostic
criteria for classic Rett syndrome, while one was considered
to have a variant type of RTT, because of some preserved
speech and gait [30]. We analyzed 13 clinical variables (age
of onset, seizures, ambulatory function, respiratory function, head growth, motor function, hand movements,
somatic growth, communication, autonomic dysfunction,
screaming, self-abuse, scoliosis) as well as typical EEG
characteristics, the length of the QTc interval on EKG,
and CSF levels of biogenic amines and b-endorphins.
Each variable and an overall composite clinical severity
score (CCSS) were compared between patients with
missense mutations and those with nonsense mutations.
The most striking result of this study was that the CCSS
as well as most individual variables were similar in the two
groups of patients. We only found statistically significant
differences in respiratory dysfunction, levels of HVA (both
occurred more frequently in nonsense mutations), and
scoliosis (more in missense mutations) [30]. Since our
report, additional genotype-phenotype correlation studies
have been performed and investigators have reported both
similar and different results compared to ours. Cheadle et al.
[34] describe mutations in 44/55 (80%) of classic Rett
syndrome girls and scored for hand use, speech and capacity
to walk. These authors found a more severe phenotype associated with truncating mutations compared to missense
mutations, as well as with early truncations compared to
late truncations. Huppke and colleagues found mutations
in 24 of the 31 patients they studied (77.4%). In their
comparison of truncating and non-truncating mutations,
they did not find statistically significant differences using
a similar clinical severity score, but they suggest that there is
a trend towards a more severe phenotype with truncating
mutations [35]. Bienvenu and colleagues [33] found mutations in 30/46 typical RTT patients (65%) using DGGE and
direct sequencing. They did not report any correlation
between the mutation type and the phenotypic features
within the group of patients with mutations. They did report
that girls with known MECP2 mutations more frequently
lost purposeful hand skills, had more peripheral vasomotor
disturbances and seizures but had less problems with walk-
S149
ing. However, the P values for these features were above
0.05, and significance of this finding is therefore questionable [33]. Additional studies reported by Hoffbuhr et al.,
Gill et al., Yamakawa et al., Amano et al., Yamashita et
al., and Raffaelle et al. at the 2000 World Congress for
Rett syndrome (Karuizawa, Nagano, Japan) yielded different results: some groups report more severe phenotypes with
truncating mutations compared to missense mutations,
while others found the exact opposite, but overall, most
studies did not detect an unequivocal genotype–phenotype
correlation.
6. Role of X-chromosome inactivation
We studied XCI patterns in leucocyte-derived DNA
samples from 34 Rett syndrome patients, informative for
the XCI assay at the polymorphic human androgen receptor
locus and found that 91% of patients had random patterns of
XCI in these samples [30]. We found a skewed pattern of
XCI in a patient with a putative early truncation and in an
asymptomatic carrier mother [30]. Several other authors
have also found that in general, non-random patterns of
XCI are associated with milder (variant) phenotypes,
asymptomatic carriers and with early more severe mutations
[31,36] (Hoffbuhr, et al, 2000; presented at the 2000 World
Congers of Rett syndrome; Karuizawa, Nagano, Japan).
However some discrepancies exist: while we and others
have observed only very skewed XCI patterns in asymptomatic mutation carriers [30,31,33], the data on classic Rett
and variant forms with milder or more severe phenotypes
are not as clear. Both skewed and random XCI have been
observed in each of these groups, even associated with the
same mutations [36]. In addition, Hoffbuhr and colleagues
reported patients with early truncating mutations and
random XCI that have classic RTT, suggesting that this
XCI pattern can be associated with near total loss of function of MeCP2.
7. Role of MeCP2 in the pathogenesis of Rett syndrome
The currently favored hypothesis is that the mutated
MeCP2 cannot perform its function as a transcriptional
repressor, which may lead to inappropriate activation of a
number of genes during development. This idea is consistent with the in vitro and cell culture assays that demonstrate
that MeCP2 can bind double stranded DNA methylated at
cytosine and thereby suppress transcription of specific
reporter genes [21,22]. The available evidence to date points
towards such a loss of function of MeCP2 as the underlying
mechanism leading to the phenotype of Rett syndrome.
Most missense mutations seem to interfere with normal
function of the MBD or the TRD, while the majority, but
not all, of truncating mutations delete at least part of the
TRD. The methyl-CpG-binding capacity of four missense
mutations (R106W, R133C, F155S, T158M) was studied in
S150
I.B. Van den Veyver, H.Y. Zoghbi / Brain & Development 23 (2001) S147–S151
vitro and revealed that the first three reduced binding by
over 100-fold, while the T158M mutation only resulted in
a 2-fold reduction [37]. Moreover, because of XCI, each cell
has either the wild-type or the mutant MECP2active. This
excludes a possible dominant-negative mechanism in which
the protein produced from the mutant allele would interfere
with the function of its wild-type counterpart. However, it
does not exclude the less likely alternative of dominant–
negative interference of the mutant MeCP2 with the function of other methyl-CpG-binding complexes. Genes regulated by allele-specific methylation of CpG islands or other
regulatory regions usually belong to the class of imprinted
genes or of genes that undergo X-inactivation [24]. Within
these groups, those that could affect CNS development are
good candidates. It is incompletely understood whether
CpG island methylation plays a role in the developmental
regulation of expression of other genes. Even though this
has not been proven in mammalian systems [38], the
abnormalities observed in hypomethylated developing
Xenopus embryos suggest that methylation plays an important role in very early differentiation and development [39].
The affected target genes are most likely important in
normal development of the central nervous system, since
neuroimaging, neuropathological and neurochemical data
all suggest an arrest in CNS development [40]. Genes that
play a role in development and function of specific neuronal
systems, such as the serotonergic connections in the brainstem are likely to be important players and could be primarily or secondarily disrupted. An alternative possibility is that
the target genes are not neuronal specific, but that the developing brain is more dependent on MeCP2 function than any
other tissue. The elevated expression levels of longer forms
of the MECP2 mRNA in developing brain supports this
possibility [19].
The low percentage of early truncating mutations that
affect most or all of the MBD, is interesting and together
with our observation that there is a tendency for skewing of
XCI in patients with such a mutation suggests that the
common mutations seen in classic RTT may cause partial
and not complete loss of function. It remains to be determined whether all truncated proteins will enter the nucleus,
as the nuclear localization signal is located within the TRD
[41]. To support the ‘partial’ loss of function hypothesis, it
will be important to determine that the mutant protein is
expressed. Towards this goal, we have recently performed
RT-PCR on RNA from lymphoblast cell lines from three
RTT patients with missense mutations (R168X) and demonstrated by allele-specific restriction enzyme digestion and
direct sequencing of the RT-PCR product that the mutant
allele is expressed in these cells (Van den Veyver and
Zoghbi, unpublished results) (Fig. 2). This mutation is in
the last exon of the gene, and the absence of a downstream
intron is consistent with the absence of nonsense mediated
mRNA decay in the presence of this truncating mutation
[42]. We are further evaluating whether mutant truncated
protein is being produced.
Fig. 2. Expression of mutant mRNA in three patients with the R168X
mutation. Reverse-transcription polymerase chain reaction (RT-PCR)
amplification of lymphoblast derived total RNA was performed from
three patients with a R168X mutation and one control sample using primers
2bF and 3bR [29]. The C to T change at position 502 creates a HphI
restriction enzyme (RE) site. The undigested RT-PCR product is 761 bp
(lane ND). RE digestion of the control sample (WT lane) with HphI generates a 505 bp, a 142 bp and a 114 bp fragment. As can be seen in lanes 1,2
and 3 (patient samples), digestion with this enzyme generates additional
371 bp and 134 bp fragments, resulting from the mutant allele. Even though
this is a non-quantitative assay, samples 1 and 3 appear to have generated
more mutant PCR than WT product.
8. Conclusions
It has been well established that mutations in the X-linked
MECP2 gene are the cause for the majority (as much as 80%)
of classic RTT. Most mutations are de novo and occur at CpG
hotspots. For patients who fit the major and minor diagnostic
criteria for classic RTT, the combined published data do not
support a clear correlation between the severity of the phenotype and the type and position of the different mutations. The
phenotypic spectrum of MECP2 mutations will likely be
expanded in the future since affected males as well as
women with mild mental delay and asymptomatic carriers
who have skewed XCI have been described [31]. The
MECP2 mutations most likely lead to partial or complete
loss of function of the protein. This is thought to result in
inappropriate expression of a number of genes that are crucial
for normal CNS development. Further studies in RTT
patients and in mouse models will be needed to better understand the functional consequences of the MECP2 mutations.
This will hopefully lead to the design of targeted preventive
and therapeutic strategies.
Acknowledgements
We thank the Rett families who participated in our studies
through the years. The work was supported by the Baylor
Mental Retardation Research Center (NIH HD24064), the
Howard Hughes Medical Institute (HYZ) and NIH grants
HD24234 (HYZ) and HD01171 (IBV), the Blue Bird Circle
Rett Center and the International Rett Syndrome Association.
I.B. Van den Veyver, H.Y. Zoghbi / Brain & Development 23 (2001) S147–S151
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