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SHORT COM M UNICATION
The Werner Syndrome Gene and Global Sequence Variation
G. Passarino,* , † ,1 P. Shen,‡ J. B. Van Kirk,* A. A. Lin,* G. De Benedict is,† L. L. Cavalli Sf orza,*
P. J. Oef ner,‡ and P. A. Underhill *
* Department of Genetics, Stanford University School of M edicine, 300 Pasteur Drive, Stanford, California 94305; ‡ Stanford Genome
Technology Center, 855 California Avenue, Palo Alto, California 94304; and † Department of Cell Biology, University of Calabria,
Arcavacata, 87030, Rende, Italy
Received August 15, 2000; accepted September 29, 2000
We have identified a dense set of markers useful in
association studies involving the Werner syndrome
(WRN) gene. The homozygotic disruption of the WRN
gene is the cause of Werner disease. In addition, this
gene is likely to be involved in many complex traits,
such as aging, or at least some of the traits and diseases related to age. To investigate the genetic variation associated with the WRN gene, a sample of 93
individuals representing all the continents was analyzed by denaturing high-performance liquid chromatography. A systematic survey of all 35 exons and
flanking regions identified 58 single-nucleotide polymorphisms, 15 of which fall in the coding region and
cause 11 missense mutations. The resulting global nucleotide diversity was 5.226 3 10 24, with a slight difference between coding and noncoding regions. © 2001
Academic Press
Werner syndrome (WRN) is an autosomal recessive
progeroid disorder (3, 13). Patients prematurely display age-related conditions, such atherosclerosis, cancer, and osteoporosis. The median life span of patients
is 47 years (3). This disorder is caused by homozygotic
null mutations in the WRN gene (15). This gene lies on
the short arm of chromosome 8 and is composed of 35
exons. The gene encodes a 1432-amino-acid protein
with a central domain homologous to the RecQ family
of DNA helicases (15). In contrast to other known
RecQ-like helicases, the WRN protein displays both
exonuclease and helicase activities in vitro (5). All the
Werner syndrome mutations implicated in disease involve a truncation of the protein or a shift of the reading frame. Different mutations have been found to
cause the disease in Caucasian and Japanese patients
(10, 15, 16).
Beyond its role in Werner syndrome, the WRN pro1
To whom correspondence should be addressed at Department of
Genetics, Room M304, Stanford University School of Medicine, 300
Pasteur Drive, Stanford, CA 94305. Telephone: (650) 723-6506. Fax:
(650) 725-1534. E-mail: g.passarino@stanford.edu.
Genomics 71, 118 –122 (2001)
doi:10.1006/geno.2000.6405
0888-7543/01 $35.00
Copyright © 2001 by Academic Press
All rights of reproduction in any form reserved.
tein is likely to be a risk factor involved in common
diseases (2). For example, it has been proposed that the
1367Cys/Arg mutation could cause susceptibility to
myocardial infarction (17). B lymphocyte cell lines from
clinically normal heterozygous carriers exhibit in vitro
features intermediate between those of null and normal homozygotes (9). It is possible that the WRN protein is involved in normal aging (15, 16). This inference
is suggested by symptoms of Werner syndrome patients and also by the finding that the yeast sgs1 protein, which is homologous to WRN helicases, influences
aging (12). An intriguing cooperation has been found
between telomerase and the WRN protein: cooperation
to prevent the aging of Werner syndrome fibroblasts
(14).
We have screened the WRN gene and the surrounding genome region for single-nucleotide polymorphisms
(SNPs). SNPs have proven valuable in the study of
sequence variation in human genes (1, 4, 11). For example, SNPs facilitate the construction of dense, stable
haplotypes for association and population affinity studies. They may also contribute directly to genetic risk
for common diseases as indicated by the common disease– common variant hypothesis (4). Thus, understanding WRN gene variability might be useful in determining whether or not this gene plays a role in other
complex traits. To that end, we have performed a SNP
search across the WRN gene region. All 35 exons and
their respective flanking regions have been screened by
denaturing high-performance liquid chromatography
(DHPLC) (8) in a worldwide sample of 93 individuals.
To determine correctly the ancestral allele, and to understand better the evolution of the gene, we have
sequenced the equivalent regions in one chimpanzee. A
total of 58 SNPs were identified over the 12,839 bp
surveyed, encompassing 3558 bp of coding sequence.
All of the polymorphisms that we have found are listed
in Table 1. Thirty-four nucleotide changes are transitions, and 20 are transversions; of the remaining 4, 3
are single-nucleotide deletions while 1 is an insertion.
Among the 15 nucleotide changes that occurred in the
118
119
SHORT COMMUNICATION
TABLE 1
Fifty-eight Germline Sequence Variations Found in the WRN Gene in 93 Representatives
of Worldwide Populations
Position a
Ex 1
20
70
EX 2
326
126
156
EX 4
2161
253
252
571
120
EX 5
285
281
EX 6
744
745
158
EX 7
245
223
951
EX 8
146
EX 9
1379
1386
1392
EX 10
122
EX 11
248
25
125
EX 12
160
EX 13
23
EX 14
2130
124
EX 16
298
EX 19
219
2402
EX 20
230
2592
151
EX 21
283
263
242
EX 22
295
267
164
EX 23
136
Nucleotide
change
Amino acid change
A/G
C/G
Global
heterozygosity
Geographic distribution
0.107
0.043
Africa 1 Asia
Africa 1 Asia
0.010
0.010
0.010
Asia
Asia
Asia
0.053
0.043
0.172
0.172
0.107
Africa 1 Asia
Africa 1 Asia
Africa 1 Asia
Every continent
Europe 1 Asia 1 Africa
0.010
0.043
Africa
Europe 1 Africa
0.333
0.010
0.010
Every continent
Asia
Asia
0.010
0.086
0.010
Asia
Africa 1 Asia 1 Europe
Africa
0.053
Asia
0.107
0.032
0.130
Africa 1 Asia
Asia
Africa 1 Asia 1 Oceania 1 Europe
T/C
0.333
Every continent
T/C
Ins T
T/A
0.010
0.010
0.064
Asia
Africa
Africa
T/G
0.010
Asia
C/A
0.182
Africa 1 Asia 1 Oceania 1 Europe
Del G
A/T
0.043
0.150
Africa
Asia 1 Oceania 1 America 1 Europe
T/A
0.010
Europe
0.010
0.021
Asia
Asia 1 Europe
0.032
0.344
0.032
Africa
Every continent
Africa
A/G
A/G
C/T
0.021
0.172
0.333
Africa
Every continent
Every continent
A/G
G/T
A/G
0.010
0.419
0.010
Africa
Every continent
Asia
G/T
0.096
Europe 1 Asia 1 Africa
A/G
C/T
C/T
A/C
C/T
A/G
A/G
A/T
Lys32Arg b
Val114Ile b
T/C
T/C
T/C
A/C
G/T
C/T
T/A
T/G
Syn c
Thr172Pro
Asn240Lys
A/T
T/G
A/G
A/G
C/T
A/T
G/A
T/G
A/G
Leu383Trp
Syn
Met387Ile b,c
Gln724Leu
Syn c
120
SHORT COMMUNICATION
TABLE 1—Continued
Position a
EX 24
2205
2191
EX 25
274
16
17
EX 26
3453
EX 27
126
EX 29
23
EX 30
126
EX 32
4036
EX 33
234
EX 34
4314
4330
EX 35
4447
4544
Nucleotide
change
Amino acid change
Global
heterozygosity
Geographic distribution
T/G
C/T
0.247
0.483
Every continent
Every continent
Del G
C/T
A/G
0.129
0.397
0.354
Every continent
Every continent
Every continent
0.387
Every continent
C/T
0.311
Every continent
T/C
0.010
Africa
Del C
0.010
Africa
0.010
Africa
0.032
Africa
T/G
A/G
Phe1074Leu c
Gly1269Glu
C/T
C/T
C/T
Syn c
Cys1367Arg d
0.290
0.118
Every continent
Asia 1 Oceania 1 America 1 Europe
C/T
A/G
Arg1406Stop
0.021
0.010
Asia
Africa
Note. Primers and PCR and DHPLC conditions are available upon request.
a
Polymorphic sites inside the exons are given according to the GenBank Accession No. L76937. Intronic polymorphic sites are reported
with respect to their upstream (1) or downstream (2) position to the closest exon.
b
Conservative amino acid changes.
c
Observed by Castro et al. (2).
d
Observed by Ye et al. (17).
e
93 individuals from five continents were examined. The ethnic affiliations of these subjects were as follows: Africa (18): 2 Pygmies from
the Central African Republic, 5 Pygmies from Congo-Kinshasa, 4 Lissongo, 3 San from Namibia, 2 Ethiopians, 1 Sudanese, 1 Mandenka from
Senegal. Asia (41): 2 Bedouine, 2 Druze, 2 Palestinian, 2 Sephardic Jews, 1 Iranian, 1 Iraqi, 10 Pakistani, 1 Tamil, 1 Laotian, 3 Cambodian,
1 Jakut, 8 Chinese, 2 aboriginal Taiwanese, 4 Japanese, 1 Korean. Europe (16): 1 Adigey, 1 Russian, 2 Georgian, 7 Caucasian Americans of
central European ancestry, 2 French, 2 Italian, 1 Dane. America (10): 2 Amerindians from Brazil, 2 Amerindians from Colombia, 2 Mayans,
1 Quechua, 1 Muskogee from Oklahoma, 1 Pima from New Mexico, 1 Navaho from Arizona. Oceania (8): 2 New Guinean, 2 Australian, 1
Micronesian, 2 Melanesian, 1 Samoan.
coding region, 10 caused amino acid substitutions, 1
caused premature termination of the protein, and 4
were synonymous.
Four mutations, three of which result in an amino
acid change, occur in the exonuclease region (472–951,
corresponding to amino acids 80 –249). Of the three
nonsynonymous mutations, two are extremely rare,
while one (A571G) is common worldwide. By contrast,
in the helicase motifs, only one synonymous variation
(T2592G, corresponding to Leu 787) was found in helicase motif IV. A nonsynonymous polymorphism,
A2402T (Gln724Leu), is located close to motif III. A
comparison of human with chimpanzee WRN protein
confirms the functional constraints on these motifs
(Table 2).
Another important region of the WRN protein comprises amino acids 1370 –1375. This region is essential
for the correct cellular localization of the protein (7). No
mutations were detected in this region of the gene, but
several interesting polymorphisms were observed in its
vicinity. These include the Cys1367Arg polymorphism,
which has been reported to be associated with resistance to myocardial infarction (17) and is proposed to
interfere with the nuclear localization signal (2). In our
ascertainment set, this mutation has been found in
every continent but Africa, where only the ancestral
cysteine allele is present. The nonsense mutation at
nucleotide position 4447 that results in a truncated
protein of 1405 amino acids (27 amino acids shorter
than normal) was found in one individual each from
Iran and Pakistan. Analysis of 30 additional individuals from Pakistan yielded one more heterozygous individual.
The total nucleotide diversity estimate was 5.226 3
10 24, and, as previously reported (1, 4), it is the highest
in Africa. No difference was noticed between the nucleotide diversity estimates obtained for coding and
noncoding regions. As to the polymorphisms falling in
the coding sequence, 11 of 15 were nonsynonymous, 3
of which involved conservative amino acid changes
(326A . G, 571A . G, and 1392A . G). These results
are in good agreement with those obtained by Cargill et
121
SHORT COMMUNICATION
TABLE 2
Exonic Sequence Differences between the Werner
Gene in Human and That in Chimpanzee
Nucleotide
Position
4/5
88/89
337
423
447
571
762
1259
1313
1456
1481
1680
1743
1817
2275
2301
2355
2592
2633
2918
3188
3317
3355–56
3367
3468
3527
3655
3661
3771
4083
4359
4544
Human
Chimp
C
C
T
G
T
A
A
T
T
T
C
G
G
A
T
T
G
T
T
T
GC
A
G
G
C
G
A
C
G
A
TG insertion
G insertion
T
G
G
A
C
C
G
G
C
C
T
T
A
G
C
G
A
C
C
A
AT
G
A
C
G
A
C
T
A
G
Amino acid
Human
Chimp
Not coding
Not coding
Arg
Trp
Phe
Leu
Ser
Arg
Val
Ile
Leu
Leu
Glu
Ala
Asp
Gly
Ser
Ala
Ile
Thr
Asn
Asn
Pro
Leu
Trp
Leu
Asp
Asn
Leu
Leu
Ser
Ser
Leu
Leu
Ser
Asn
Met
Thr
Leu
Pro
Val
Glu
Ala
Ile
Lys
Glu
Ser
Ser
Ser
Thr
Gln
Gln
Val
Ile
Thr
Thr
Leu
Leu
Gly
Ser
Not coding
plest explanation is that these two alleles survived a
bottleneck that reduced the variability of our species.
This interpretation is bolstered by the fact that the
constant population infinite sites model does not fit the
data and by the Tajima test. The latter gave a negative
value (21.1), suggesting population expansion as the
HKA test (P 5 0.1) failed to reject neutrality (details on
these statistical methods are in Ref. 11). Intriguingly,
BRCA1, which codes for another helicase (the impairment of which causes breast cancer), does not comply
with the Luria and Delbrück/Lea and Coulson expectation either (unpublished data).
The polymorphisms that we have discovered are
valuable for constructing a dense SNP map of this
region of the genome. In addition, these polymorphisms will be helpful in constructing haplotypes and
studying associations between different alleles of the
WRN gene and complex traits. In particular, it would
be useful to test in diverse populations whether the
WRN gene is involved in the normal aging process or
does Werner syndrome merely mimic aging by affecting age-related traits and diseases? In this case, it
would be useful to see which functions or pathways are
involved in specific aging features or in overall aging
(6).
ACKNOWLEDGMENTS
We thank the DNA donors and the investigators who provided the
samples: L. Excoffier, M. E. Ibrahim, T. Jenkins, J. Kidd, A. Langaney, S. Q. Mehdi, and P. Parham. We are grateful to R. Hyman for
his helpful comments. The study was funded by an Ellison Medical
Foundation grant and by NIH Grant 1R01-HG01932.
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Note. Position refers to sequence deposited under GenBank Accession No. L76937.
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