Alu-Mediated Acquisition of Unstable ATTCT Pentanucleotide Repeats in the
Human ATXN10 Gene
Tatsuaki Kurosaki,* Tohru Matsuura, Kinji Ohno, and Shintaroh Ueda*
*Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan; and Division of
Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan
Spinocerebellar ataxia type 10 is caused by ATTCT repeat expansion in the ATXN10 gene in humans. We studied the
evolutionary history of the human genome to determine the time and mechanism of the acquisition of unstable ATTCT
repeats in the genome. We found that long interspersed element-1 (LINE-1) was inserted into ATXN10 intron 9; Alu was
then inserted in the middle of LINE-1; and endogenous retrovilcus K was lastly retrotransposed in the middle of Alu. The
ATTCT repeat was located on the boundary between the 3#-end of the Alu element and the direct repeat arising from
LINE-1. We determined nucleotide sequences of the orthologous region of 50 individuals representing 33 primate
species and compared them with the human sequence. The analysis revealed that the ATTCT repeat is present only in
human and apes. Old World monkeys also possess pentanucleotide repeats, but their motifs are TGTCT and GGTCT.
New World monkeys and prosimians are not informative because they lack the corresponding region in ATXN10 intron
9. Our studies dictate two parsimonious scenarios of evolution. First, a TTTCT motif arose from a TTTTT motif at the
junction of Alu and LINE-1, which was followed by introduction of A to make an ATTCT motif in hominoids. Second,
an ATTCT motif was directly generated from an ancestral ATTTT motif in the common ancestor of catarrhines. We also
demonstrate that orangutan uniquely introduced G to make a GTTCT motif and later C to make a GTTCC motif, where
newly introduced nucleotides are underlined. Our studies reveal that nucleotide substitutions in a poly(A) tail of the Alu
element and the following amplification of pentanucleotides occurred in the lineages of Old World monkeys and
hominoids and that unstable ATTCT pentanucleotide repeats originated in the common ancestor of hominoids. These
findings also highlight a new aspect of the role of retrotransposons in human disease and evolution, which might be
useful in investigating the mystery of human uniqueness.
Introduction
Spinocerebellar ataxia type 10 (SCA10) is an autosomal dominant neurodegenerative disorder characterized
by progressive ataxia and seizure (Grewal et al. 1998;
Rasmussen et al. 2001). It is caused by unstable and massive expansion of the ATTCT pentanucleotide repeat in intron 9 of the ATXN10 gene, which is mapped on 22q13.3
(Matsuura et al. 1999, 2000; Zu et al. 1999). SCA10 is the
only genetic disease known to be caused by an expansion of
a pentanucleotide repeat. A recent study has shown that mutant ATXN10 allele containing the expanded repeat is transcribed at the same level as the wild-type allele and that its
transcript is normally spliced, suggesting that the expanded
AUUCU repeats potentially exert a gain-of-function
disease mechanism (Wakamiya et al. 2006). The SCA10
expansion has unique characteristics of instability in both
somatic and germline tissues, which are distinct from other
repeat expansions (Matsuura et al. 2004). There is great
difference in the ATTCT repeat length between the alleles
of normal and affected individuals: Wild-type alleles have
10–29 repeats, whereas mutant alleles have 280–4,500 repeats (Matsuura et al. 2000, 2006). The size of the expanded
segment is among the largest found to date in human microsatellite mutations (Matsuura et al. 2000). In other types of
repeat expansion disorders, the difference is moderate, and
some of their repeat ranges are partially overlapped
between the wild-type and mutant alleles, suggesting the
presence of an intermediated ‘‘premutation’’ state of the
wild-type alleles. It is considered that the premutation repeats are unstable and may expand during transmission
Key words: spinocerebellar ataxia, SCA10, pentanucleotide repeat,
neurodegenerative disease, Alu.
E-mail: [email protected].
Mol. Biol. Evol. 26(11):2573–2579. 2009
doi:10.1093/molbev/msp172
Advance Access publication August 3, 2009
Ó The Author 2009. Published by Oxford University Press on behalf of
the Society for Molecular Biology and Evolution. All rights reserved.
For permissions, please e-mail: [email protected]
from parents to offspring. Repeat interruption is popularly
observed in the wild-type alleles of repeat expansion disease genes such as those of spinocerebellar ataxia type
1, spinocerebellar ataxia type 2, fragile X syndrome, and
Friedreich ataxia (FRDA) (Chung et al. 1993; Kunst and
Warren 1994; Imbert et al. 1996; Pulst et al. 1996; Sanpei
et al. 1996; Montermini et al. 1997; Kurosaki et al. 2006).
These interruptions are supposed to stabilize the repeat itself or prevent repeat expansion (Sobczak and Krzyzosiak
2004, 2005). However, the role of repeat interruptions in
SCA10 is controversial in that multiple interruptions have
been recently observed in the expanded ATTCT repeat of
SCA10 as well as large normal alleles and they may also
influence a disease presentation (Matsuura et al. 2006).
To better understand the role of interruptions in SCA10 expansion and disease, we addressed the evolutionary process
of the repeat configuration with interruption. Our analyses
reveal that Alu and long interspersed element-1 (LINE-1)
were retrotransposed into a common ancestor before the
divergence of Old World monkeys and the ATTCT motif
appeared at the junction of the Alu and LINE-1.
Materials and Methods
Samples
We examined the orthologous region of 14 individuals
of 5 species of apes, 28 individuals of 21 species of Old
World monkeys, 6 individuals of 6 species of New World
monkeys, and 2 individuals of 1 species of prosimians
(table 1).
Comparative In Silico Analysis of Mammalian ATXN10
Genes
The homologous regions of mammalian ATXN10
genes corresponding to the human ATXN10 ATTCT repeats
2574 Kurosaki et al.
Table 1
Repeat Configurations of ATXN10 Gene in Primates
Species
Num.
Repeat Configuration
Human
Apes
Chimpanzee
Gorilla
—
(ATTCT)10–29
8
1
Orangutan
2
White-handed gibbon
Agile gibbon
1
2
(ATTCT)4ATTTA
ATTCC(ATTCT)15/17ATCCT
ATTCTTTTAT
ATTCTATTCT(GTTCT)2
(GTTCTGTTCC)3ATTCT
ATTCT(GTTCT)3(GTTCT
GTTCC)3ATTCT
(ATTCT)4ATTTA
(ATTCT)11/14/15ATTCA
Old World monkeys
Green monkey
Patas monkey
Hamadryas baboon
Anubis baboon
Mandrill
Black mangabey
Blue monkey
1
1
1
1
1
Barbary macaque
Crab-eating macaque
Lion-tailed macaque
Stump-tailed macaque
Pig-tailed macaque
Rhesus macaque
Bonnet macaque
Assam macaque
Tibetan macaque
Taiwan macaque
Japanese macaque
Colobus
Hanuman langur
Guenon
1
1
1
1
1
1
1
1
1
1
6
1
1
1
AGTCT(TGTCT)4GGTCTTGTCT
AGTCT(TGTCT)10(GGTCT)2
TGTCT(GGTCT)2TGTCT
AGTCT(TGTCT)9(TGTCC)8
GTCTTTTCTTTTGTCT
AGTCT(TGTCT)5(TGTCC)9
GTCTTTTCTTTTGTCT
AGTCT(TGTCT)4GGTCTTGTCT
AGTCT(TGTCT)4GGTCTTGTCT
AGTCT(TGTCT)3(GGTCT)2TGTCT
AGTCT(TGTCT)3GGTCTTGTCT
AGTCTTATCT(TGTCT)3GGTC
TTGTCT
AGTAT(TGTCT)3(GGTCT)2TGTCT
AGTAT(TGTCT)2(GGTCT)3TGTCT
AGTAT(TGTCT)3(GGTCT)2TGTCT
AGTAT(TGTCT)2(GGTCT)3TGTCT
AGTAT(TGTCT)3(GGTCT)2TGTCT
AGTAT(TGTCT)3(GGTCT)2TGTCT
AGTAT(TGTCT)2(GGTCT)3TGTCT
AGTAT(TGTCT)2(GGTCT)3TGTCT
AGTAT(TGTCT)2(GGTCT)3TGTCT
AGTAT(TGTCT)3(GGTCT)2TGTCT
AGTAT(TGTCT)3(GGTCT)2TGTCT
AGTCT(TGTCT)3GGTCT
AGTCT(TGTCT)2(GGTCT)2
AGTCT(TGTCT)3GGTCTTGTCT
1
—
1
1
—
—
1
1
1
—
—
—
2
—
New World monkeys
White-throated
capuchin
Tafted capuchin
Long-haired
spider monkey
Cotton-top tamarin
Common marmoset
Owl monkey
Prosimians
Greater galago
1
3
were obtained from the University of California at Santa
Cruz Genome Browser. Retrotransposable elements were
identified using the RepeatMasker program (http://www.
repeatmasker.org) by using the data obtained from the
RepBase library of repeats (Jurka et al. 2005). Simple tandem repeats were surveyed using the Tandem Repeats
Finder program (Benson 1999). Their sequences were mechanically aligned with ClustalX version 1.83 (Thompson
et al. 1997) and further edited manually using BioEdit
version 7.0.5 to verify the insertions and deletions. The
Alu subfamily was identified using both the RepeatMasker
and CENSOR (http://www.girinst.org/censor/index.php)
programs.
Genomic Polymeric Chain Reaction (PCR) and
Sequencing of Nonhuman Primate ATXN10 Genes
DNA samples were prepared from blood specimens by
the conventional phenol–chloroform methods. The PCR
primers and conditions are summarized in supplementary
table 1, Supplementary Material online. For direct sequencing of fragments A–D in supplementary table 1, Supplementary Material online, we used KOD-plus-DNA
polymerase (Toyobo, Japan). We fractionated the PCR
products on an agarose gel, purified the excised fragments
using NucleoSpin Extract II (Macherey-Nagel, Germany),
and directly sequenced them on an ABI prism 3100 Genetic
Analyzer (Applied Biosystems, United States). For samples
showing ambiguous sequences of fragments A and B, the
PCR products were cloned and sequenced using TArget
Clone-plus-cloning system (Toyobo). For cloning and sequencing of fragments C and D, we employed KOD Dash
DNA polymerase (Toyobo) and the TOPO TA Cloning Kit
(Invitrogen, United States). For direct sequencing of prosimian fragment D, we used the Phusion high-fidelity
DNA polymerase (Finnzymes, Finland). The nucleotide
sequences were deposited in DDBJ/EMBL/GenBank (accession numbers AB449112–AB449143 and AB450921–
AB450926).
Results
To investigate the evolutionary origin of the unstable
ATTCT repeat in human ATXN10, comparative analysis
was first performed using the known mammalian ATXN10
!
FIG. 1.—Genomic structure of the human ATXN10 gene and ATTCT repeat surrounding region. (a) Genomic alignment of intron 9 corresponding to
the human ATXN10 ATTCT repeats among mammalian ATXN10 genes. The broken square denotes a 7.4-kb block that is absent in nonprimate species.
Repetitive sequences are also shown, classified into short interspersed elements (SINEs), LINEs, LTRs, and simple tandem repeats. pTRNT1 is a processed
pseudogene of TRNT1. (b) Nucleotide sequence surrounding the ATTCT pentanucleotide repeats in the human ATXN10 gene. SINEs, LINEs, LTRs, and
simple tandem repeats are indicated by blue, green, gray, and red colors, respectively. The black-shaded and yellow-shaded nucleotides represent the direct
repeats and poly(A) tail as a signature of the blue-shaded Alu insertion into the green-shaded LINE-1 sequence, respectively (due to the reversed direction,
the poly(A) tail is designated as poly(T) tail in the coding direction of the ATXN10 gene). The dark gray-shaded nucleotides represent the direct repeats as
a signature of the LTR-type transposable element, endogenous retrovilcus K (ERVK) (light gray shaded), insertion into the Alu sequence. The Alu element
is separated into two parts by insertion of the ERVK element. The retrotransposons found in the 7.4-kb block absent in nonprimate species are as follows:
1, Alu element (286–112); 2, Alu element (111–1); 3, Alu element (305–139); 4, LINE-1 (3443–3144); 5, LINE-1 (1585–2380); 6, LINE-1 (2368–4773); 7,
LINE-1 (4774–4852); 8, LINE-1 (4853–6235); 9, ERV1 (486–27); 10, ERVK (1–1236); and 11, MaLR (1–467). The numbers in parentheses are the
nucleotide positions of each retrotransposon (in the direction of the reading frame of the ATXN10 gene), which are according to the notation of each
reference sequence in RepeatMasker version open 3.2.5. The putative LINE-1 endonuclease cleavage site is indicated by a vertical black arrow.
Origin of ATXN10 ATTCT Pentanucleotide Repeats 2575
2576 Kurosaki et al.
genes, including human, chimpanzee, macaque, mouse, rat,
rabbit, dog, cow, elephant, and opossum. As shown in
figure 1a, the ATXN10 ATTCT repeat is present in human,
chimpanzee, and macaque, whereas an approximately
7.4-kb region containing the repeat is absent in the nonprimate mammals. Most—in fact nearly all—of the sequences
in this region were positively screened by the RepeatMasker program and the ATTCT repeat was located on
a fragment rich in interspersed repeats. Analysis of individual sequences revealed that three retrotransposons are
nested in the repeat flanking region (fig. 1b).
First, a LINE-1 (green in fig. 1b) was retrotransposed
in intron 9 of ATXN10. The subtype of LINE-1 was identified as L1ME2, which belongs to an old LINE-1 subfamily inserted into mammalian lineage before the primate
radiation (Smit et al. 1995).
Second, an Alu element (blue in fig. 1b) was inserted in
the middle of LINE-1. The Alu element was flanked by
a 13-bp stretch of direct repeats of 5#-TAKAMTGGATTYT-3# (black in fig. 1b) that originated from LINE-1.
The downstream repeat was exactly located at the LINE-1
endonuclease cleavage site of 5#-TTTT/GA-3# (arrow in
fig. 1b). Chimpanzee carried the same cleavage site of
5#-TTTT/GA-3#, whereas orangutan and rhesus macaque
harbored another well-known LINE-1 cleavage site of
5#-TTTT/AA-3# (Feng et al. 1996; Jurka 1997; Cost and
Boeke 1998), indicating that the Alu insertion is likely to
have occurred at 5#-TTTT/AA-3#. In addition, poly(A) tail
(yellow in fig. 1b) was preserved at the 3# end of the Alu.
The Alu element subtype was classified into AluSz or
AluSx. AluS is an intermediate-age Alu subfamily and
is considered to have explosively expanded 35–50 Ma
(Britten 1994; Kapitonov and Jurka 1996; Roy-Engel
et al. 2002). We calculated the approximate age of the
Alu element by the Kimura-2-parameter model with a mutation rate of 0.0015 substitutions/site/My at non-CpG substitution sites (Labuda and Striker 1989; Batzer et al. 1990;
Xing et al. 2004) and estimated that the retrotransposition
occurred 50 ± 3.9 (age ± standard deviation) Ma. This age
is compatible with the evolutionary divergence of species
between platyrrhines (New World monkeys) and catarrhines (Old World monkeys, apes, and human) that occurred around 40–50 Ma (Goodman et al. 1998; Kumar
and Hedges 1998).
Third, an LTR (long terminal repeat)–type transposable
element, endogenous retrovilcus K (ERVK) (light gray in fig.
1b), was inserted in the middle of Alu. The ERVK is flanked
by direct repeats (dark gray in fig. 1b) originating from
the Alu element. Explosive expansion of the ERVK element
is estimated to have occurred 30–45 Ma almost exclusively
in catarrhines (Mariani-Costantini et al. 1989; Steinhuber
et al. 1995; Sverdlov 2000). The insertion is thus likely to
have occurred in the common ancestor of catarrhines after
divergence between platyrrhines and catarrhines.
The ATTCT repeat was flanked by the 13-bp direct repeat (black in fig. 1b) originating from LINE-1 and by the
poly(A) tail (yellow in fig. 1b) of Alu, indicating that
the repeat arose from either element. To further dissect
the evolutionary origin of the unstable ATTCT repeat,
we determined nucleotide sequences of 5 species of apes,
21 of Old World monkeys, 6 of New World monkeys, and 1
of prosimians (supplementary fig. 1, Supplementary Material online). All catarrhine primates (apes and Old World
monkeys) carried the orthologous region, whereas New
World monkeys and prosimians lacked the region. The orthologous region in catarrhines harbored both Alu and
ERVK as in human, but the pentanucleotide repeats widely
varied in motif and length. In apes, except for orangutan,
the repeat configuration was of ATTCT pentanucleotide
as in human (table 1). Orangutan had repeat configurations
of GTTCT and GTTCC, flanked by ATTCT at both ends.
These results indicated that the ancestral configuration of
the repeat was ATTCT in hominoids. In Old World monkeys, the repeat configurations were not of ATTCT pentanucleotide but of TGTCT and GGTCT pentanucleotides.
To gain an insight into intraspecific variation, we examined
multiple individuals of each of the following species: chimpanzee (N 5 8), orangutan (N 5 2), agile gibbon (N 5 2),
patas monkey (N 5 3), and Japanese macaque (N 5 6). We
observed a single unique allele in chimpanzee and Japanese
macaque, whereas we detected two to three different alleles
in orangutan, agile gibbon, and patas monkey (table 1). It is
interesting to note that shorter repeat numbers resulted in
a unique allele, whereas longer repeats tended to give rise
to variable alleles.
We also determined nucleotide sequences of six species of New World monkeys (supplementary fig. 1, Supplementary Material online). The missing region in New
World monkeys corresponded to a region shown in nucleotide sequences in supplementary fig. 2, Supplementary
Material online, which included the ATTCT repeats, Alu,
ERVK, and the flanking regions of LINE-1. As the flanking
sequences were well conserved among New World monkeys and as the junction did not coincide with the end of
LINE-1, partial–complete deletion of the retrotransposons
is likely to have occurred in the common ancestor of New
World monkeys. In a prosimian, the 7.4-kb region, which
was absent in nonprimate mammals, was mostly deleted,
but the evolutionary origin of the lack of the retrotransposons remain unelucidated (supplementary fig. 3, Supplementary Material online).
Discussion
Transposable elements abundantly exist in the human
genome, occupying up to 44% of the whole genome
(Lander et al. 2001). Although most of the transposable elements have lost their transposition ability long ago, some
elements such as LINE-1 and Alu have been observed to
sustain this ability in the recent history of primate evolution
(Deininger and Batzer 2002). It is known that Alu causes
various inherited disorders such as Lesch–Nyhan syndrome
and Tay–Sachs disease. In addition, several types of cancer
are also associated with Alu-mediated recombination
(Deininger and Batzer 1999). The time and order of
LINE-1, Alu, and ERVK insertions into ATXN10 intron
9 that we estimated in the current studies well support
previous reports indicating when the retrotransposons
expanded in primate lineage.
Our current studies indicate that a T stretch at the
junction of Alu and LINE-1 has gradually evolved to
Origin of ATXN10 ATTCT Pentanucleotide Repeats 2577
FIG. 2.—Two parsimonious scenarios for acquisition of ATTCT pentanucleotide repeats in human ATXN10 gene. The LINE-1, Alu, and ERVK
retrotransposition events are shown as dark bars on the evolutionary tree with the putative time of each event. The number at each node represents
divergence time according to TimeTree (Hedges et al. 2006) in Ma. Repeat motifs are indicated by pentanucleotides and shaded in black. Newly
introduced nucleotides are underlined.
a pentanucleotide repeat during primate (simian) evolution.
One of the most parsimonious scenarios of evolution is as
follows (fig. 2a): First, an Alu insertion either before or after
divergence of platyrrhines and catarrhines generated
a TTTTT motif at the junction with LINE-1. Second, a polymorphic C was introduced into TTTTT to make a TTTCT
motif, where a newly introduced nucleotide is underlined.
We observe TTTCT only at the 3# end of the pentanucleotide repeats in all the species except chimpanzee and gib-
bons. Third, a clade of Old World monkeys introduced G at
the second nucleotide to make a TGTCT motif and thereafter another G at the first nucleotide to make a GGTCT
motif. Fourth, hominoids introduced A at the first nucleotide to make an ATTCT motif. Fifth, orangutan uniquely
introduced G at the first nucleotide to make a GTTCT motif
and later C at the fifth nucleotide to make a GTTCC motif.
This scenario indicates that ATTCT appeared after divergence of Old World monkeys. An alternative scenario of
2578 Kurosaki et al.
evolution is that ATTTT instead of TTTTT has evolved to
the unstable ATTCT pentanucleotide (fig. 2b). In the alternative scenario, ATTCT appeared before divergence of Old
World monkeys, and Old World monkeys introduced three
polymorphic nucleotides to the ATTCT motif. Although
three polymorphic nucleotide substitutions in a single clade
are less likely, conservation of AGTCT in the first unit of
the pentanucleotide repeat in all Old World monkeys except
for genus macaca supports the alternative scenario (table 1).
A previous study suggested that Alu elements are
a source for the genesis of microsatellite repeats (Arcot et al.
1995), and 5.7% of Alu poly(A) tail consists of patterned
A-rich repeat sequence (Economou et al. 1990). However,
there are few examples that show that the microsatellite repeat derived from an Alu element is responsible for a genetic
disorder in human. FRDA is caused by the expansion of
GAA triplet repeats in intron 1 of the FXN gene. Normal
alleles have 6–36 repeats, whereas mutant alleles have
66–1,700 repeats (Campuzano et al. 1996; Dürr et al.
1996; Epplen et al. 1997; Montermini et al. 1997). Justice
et al. (2001) report that the triplet repeats are introduced by
retrotransposition of an Alu element into the FXN gene during primate evolution, which is analogous to Alu that we
identify in intron 9 of ATXN10. Unlike ATXN10, the triplet
repeats in FXN lie in the middle A-rich region of the Alu
element (Montermini et al. 1997). To our knowledge,
our current studies first demonstrate that the unstable repeats in repeat expansion disease genes have originated
from a poly(A) tail of an Alu element and its junction.
The human ATXN10 gene acquired pathogenicity due to
subsequent mutations, namely, nucleotide substitutions
and configuration as repeats, in the poly(A) tract after retrotransposition during primate evolution. This might imply
that retrotransposon-mediated mutations could contribute
to the diversification of species and possibly to human
uniqueness.
Supplementary Material
Supplementary table 1 and supplementary figures 1–3
are available at Molecular Biology and Evolution online
(http://www.mbe.oxfordjournals.org/).
Acknowledgments
This study was supported by grants from the Ministry
of Education, Science, Sports, and Culture of Japan. No
conflict of interest is associated with the manuscript. We
thank anonymous reviewers for valuable advice.
Literature Cited
Arcot SS, Wang Z, Weber JL, Deininger PL, Batzer MA. 1995.
Alu repeats: a source for the genesis of primate microsatellites.
Genomics. 29:136–144.
Batzer MA, Kilroy GE, Richard PE, Shaikh TH, Desselle TD,
Hoppens CL, Deininger PL. 1990. Structure and variability
of recent inserted Alu family members. Nucleic Acids Res.
18:6793–6798.
Benson G. 1999. Tandem repeats finder: a program to analyze
DNA sequences. Nucleic Acids Res. 27:573–580.
Britten RJ. 1994. Evidence that most human Alu sequences were
inserted in a process that ceased about 30 million years ago.
Proc Natl Acad Sci USA. 91:6148–6150.
Campuzano V, Montermini L, Molto MD, et al. (31 co-authors).
1996. Friedreich’s ataxia: autosomal recessive disease caused
by an intronic GAA triplet repeat expansion. Science. 271:
1423–1427.
Chung MY, Ranum LP, Duvick LA, Servadio A, Zoghbi HY,
Orr HT. 1993. Evidence for a mechanism predisposing to
intergenerational CAG repeat instability in spinocerebellar
ataxia type I. Nat Genet. 5:254–258.
Cost GJ, Boeke JD. 1998. Targeting of human retrotransposon
integration is directed by the specificity of the L1 endonuclease for regions of unusual DNA structure. Biochemistry.
37:18081–18093.
Deininger PL, Batzer MA. 1999. Alu repeats and human disease.
Mol Genet Metab. 67:183–193.
Deininger PL, Batzer MA. 2002. Mammalian retroelements.
Genome Res. 12:1455–1465.
Dürr A, Cossee M, Agid Y, Campuzano V, Mignard C, Penet C,
Mandel JL, Brice A, Koenig M. 1996. Clinical and genetic
abnormalities in patients with Friedreich’s ataxia. N Engl J
Med. 335:1169–1175.
Economou EP, Bergen AW, Warren AC, Antonarakis SE. 1990.
The polydeoxyadenylate tract of Alu repetitive elements is
polymorphic in the human genome. Proc Natl Acad Sci USA.
87:2951–2954.
Epplen C, Epplen JT, Frank G, Miterski B, Santos EJ, Schols L.
1997. Differential stability of the (GAA)n tract in the
Friedreich ataxia (STM7) gene. Hum Genet. 99:834–836.
Feng Q, Moran JV, Kazazian HH Jr, Boeke JD. 1996. Human L1
retrotransposon encodes a conserved endonuclease required
for retrotransposition. Cell. 87:905–916.
Goodman M, Porter CA, Czelusniak J, Page SL, Schneider H,
Shoshani J, Gunnell G, Groves CP. 1998. Toward a phylogenetic classification of Primates based on DNA evidence
complemented by fossil evidence. Mol Phylogenet Evol. 9:
585–598.
Grewal RP, Tayag E, Figueroa KP, Zu L, Durazo A, Nunez C,
Pulst SM. 1998. Clinical and genetic analysis of a distinct
autosomal dominant spinocerebellar ataxia. Neurology. 51:
1423–1426.
Hedges SB, Dudley J, Kumar S. 2006. TimeTree: a public
knowledge-base of divergence times among organisms.
Bioinformatics. 22:2971–2972.
Imbert G, Saudou F, Yvert G, et al. (15 co-authors). 1996.
Cloning of the gene for spinocerebellar ataxia 2 reveals
a locus with high sensitivity to expanded CAG/glutamine
repeats. Nat Genet. 14:285–291.
Jurka J. 1997. Sequence patterns indicate an enzymatic
involvement in integration of mammalian retrotransposons.
Proc Natl Acad Sci USA. 94:1872–1877.
Jurka J, Kapitonov VV, Pavlicek A, Klonowski P, Kohany O,
Walichiewicz J. 2005. Repbase update, a database of
eukaryotic repetitive elements. Cytogenet Genome Res. 110:
462–467.
Justice CM, Den Z, Nguyen SV, Stoneking M, Deininger PL,
Batzer MA, Keats BJ. 2001. Phylogenetic analysis of the
Friedreich ataxia GAA trinucleotide repeat. J Mol Evol. 52:
232–238.
Kapitonov V, Jurka J. 1996. The age of Alu subfamilies. J Mol
Evol. 42:59–65.
Kumar S, Hedges SB. 1998. A molecular timescale for vertebrate
evolution. Nature. 392:917–920.
Kunst CB, Warren ST. 1994. Cryptic and polar variation of the
fragile X repeat could result in predisposing normal alleles.
Cell. 77:853–861.
Origin of ATXN10 ATTCT Pentanucleotide Repeats 2579
Kurosaki T, Ninokata A, Wang L, Ueda S. 2006. Evolutionary
scenario for acquisition of CAG repeats in human SCA1 gene.
Gene. 373:23–27.
Labuda D, Striker G. 1989. Sequence conservation in Alu
evolution. Nucleic Acids Res. 17:2477–2491.
Lander ES, Linton LM, Birren B, et al. (256 co-authors). 2001.
Initial sequencing and analysis of the human genome. Nature.
409:860–921.
Mariani-Costantini R, Horn TM, Callahan R. 1989. Ansestry of a
human endogenous retrovirus family. J Virol. 63:4982–4985.
Matsuura T, Achari M, Khajavi M, Bachinski LL, Zoghbi HY,
Ashizawa T. 1999. Mapping of the gene for a novel
spinocerebellar ataxia with pure cerebellar signs and epilepsy.
Ann Neurol. 45:407–411.
Matsuura T, Fang P, Lin X, et al. (14 co-authors). 2004. Somatic
and germline instability of the ATTCT repeat in spinocerebellar ataxia type 10. Am J Hum Genet. 74:1216–1224.
Matsuura T, Fang P, Pearson CE, Jayakar P, Ashizawa T,
Roa BB, Nelson DL. 2006. Interruptions in the expanded
ATTCT repeat of spinocerebellar ataxia type 10: repeat purity
as a disease modifier? Am J Hum Genet. 78:125–129.
Matsuura T, Yamagata T, Burgess DL, et al. (17 co-authors).
2000. Large expansion of the ATTCT pentanucleotide repeat
in spinocerebellar ataxia type 10. Nat Genet. 26:191–194.
Montermini L, Andermann E, Labuda M, et al. (14 co-authors).
1997. The Friedreich ataxia GAA triplet repeat: premutation
and normal alleles. Hum Mol Genet. 6:1261–1266.
Pulst SM, Nechiporuk A, Nechiporuk T, et al. (16 co-authors).
1996. Moderate expansion of a normally biallelic trinucleotide repeat in spinocerebellar ataxia type 2. Nat Genet. 14:
269–276.
Rasmussen A, Matsuura T, Ruano L, Yescas P, Ochoa A,
Ashizawa T, Alonso E. 2001. Clinical and genetic analysis of
four Mexican families with spinocerebellar ataxia type 10.
Ann Neurol. 50:234–239.
Roy-Engel AM, Carroll ML, El-Sawy M, Salem AH, Garber RK,
Nguyen SV, Deininger PL, Batzer MA. 2002. Non-traditional
Alu evolution and primate genomic diversity. J Mol Biol.
316:1033–1040.
Sanpei K, Takano H, Igarashi S, et al. (25 co-authors). 1996.
Identification of the spinocerebellar ataxia type 2 gene using
a direct identification of repeat expansion and cloning
technique, DIRECT. Nat Genet. 14:277–284.
Smit AF, Toth G, Riggs AD, Jurka J. 1995. Ancestral,
mammalian-wide subfamilies of LINE-1 repetitive sequences.
J Mol Biol. 246:401–417.
Sobczak K, Krzyzosiak WJ. 2004. Imperfect CAG repeats form
diverse structures in SCA1 transcripts. J Biol Chem. 279:
41563–41572.
Sobczak K, Krzyzosiak WJ. 2005. CAG repeats containing CAA
interruptions form branched hairpin structures in spinocerebellar ataxia type 2 transcripts. J Biol Chem. 280:
3898–3910.
Steinhuber S, Brack M, Hunsmann G, Schwelberger H,
Dierich MP, Vogetseder W. 1995. Distribution of human
endogenous retrovirus HERV-K genomes in humans and
different primates. Hum Genet. 96:188–192.
Sverdlov ED. 2000. Retroviruses and primate evolution.
BioEssays. 22:161–171.
Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F,
Higgins DG. 1997. The CLUSTAL_X windows interface:
flexible strategies for multiple sequence alignment aided by
quality analysis tools. Nucleic Acids Res. 25:4876–4882.
Wakamiya M, Matsuura T, Liu Y, Schuster GC, Gao R, Xu W,
Sarkar PS, Lin X, Ashizawa T. 2006. The role of ataxin 10 in
the pathogenesis of spinocerebellar ataxia type 10. Neurology.
67:607–613.
Xing J, Hedges DJ, Han K, Wang H, Cordaux R, Batzer MA.
2004. Alu element mutation spectra: molecular clocks and the
effect of DNA methylation. J Mol Biol. 344:675–682.
Zu L, Figueroa KP, Grewal R, Pulst SM. 1999. Mapping of
a new autosomal dominant spinocerebellar ataxia to chromosome 22. Am J Hum Genet. 64:594–599.
Norihiro Okada, Associate Editor
Accepted July 28, 2009