Short interspersed elements (SINEs) from insectivores. Two classes of
mammalian SINEs distinguished by A-rich tail structure
Olga R. Borodulina, Dmitri A. Kramerov
Laboratory of Eukaryotic Genome Evolution, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov Str.,
Moscow, 119991 Russia
Received: 12 December 2000 / Accepted: 31 May 2001
Abstract. Four tRNA-related SINE families were isolated from
the genome of the shrew Sorex araneus (SOR element), mole
Mogera robusta (TAL element), and hedgehog Mesechinus
dauuricus (ERI-1 and ERI-2 elements). Each of these SINEs fami-
lies is specific for a single Insectivora family: SOR, for Soricidae
(shrews); TAL, for Talpidae (moles and desmans); ERI-1 and
ERI-2, for Erinaceidae (hedgehogs). There is a long polypyrimi-
dine region (TC-motif) in TAL, ERI-1, and ERI-2 elements lo-
cated immediately upstream of an A-rich tail with polyadenylation
signals (AATAAA) and an RNA polymerase III terminator (T
). Ten out of 14 analyzed mammalian tRNA-related
SINE families have an A-rich tail similar to that of TAL, ERI-1,
and ERI-2 elements. These elements were assigned to class T
The other four SINEs including SOR element have no polyade-
nylation signal and transcription terminator in their A-rich tail and
were assigned to class T
. Class T
SINEs occur only in mammals,
and most of them have a long polypyrimidine region. Possible
models of retroposition of class T
SINEs are discussed.
Short interspersed elements (SINEs) or short retroposons are 80–
400 bp repetitive DNA sequences that proliferate in eukaryotic
genomes via transcription followed by reverse transcription (Rog-
ers 1985; Okada 1991). There is one or a few SINE families in
each mammalian species analyses. Usually 10
copies of a
SINE family can be found in the genome, and such copies feature
significant sequence variability (5–20%). SINEs contain a bipartite
(A and B boxes) promoter for RNA polymerase III (pol III) and
can be transcribed with this enzyme. 5Ј-region of most SINEs
shows reasonable sequence similarity to certain tRNAs commonly
considered as their ancestor. Such tRNA-derived SINEs are not
just pseudogenes of tRNAs, but have a composite structure that
includes a tRNA-related region, a tRNA-unrelated region, and an
A-rich tail. Instead of the A-rich sequence, SINEs of some families
have a tail consisting of short repeats, for example TGG (Yoshioka
et al. 1993), G(T/A)TTCTAT or GAT(T/A)ATCTAT (Ogiwara et
al. 1999). About 25 SINE families are recognized as tRNA-derived
SINEs; they were found in vertebrates, invertebrates, and plants
(Okada and Ohshima 1995). In addition to tRNA-derived SINEs,
there are 7SL RNA-derived ones such as rodent B1 and primate
Alu elements (Labuda and Zietkiewicz 1994).
Recently SINEs were proposed as phylogenetic markers and
proved quite reliable for genotyping middle rank taxa—families
and orders. The species sharing the same SINE family (Serdobova
and Kramerov 1998) or a SINE inserted in the same locus (Shed-
lock and Okada 2000) are considered as related. For example, ID,
a SINE family specific to rat, mouse, and hamster, is present also
in the guinea pig genome (Martignetti and Brosius 1993; Kim et al.
1994). These data prove that guinea pig is a rodent, although some
authors (Graur et al. 1991) challenge the relationships between this
species and typical rodents. The finding of B1-dID SINE family in
the genome of both squirrels and dormice demonstrates that these
two rodent families are closely related and that dormice should not
be assigned to myomorph rodents owing to the absence of B1-dID
elements in their genomes (Kramerov et al. 1999). The presence or
absence of CHR-1 and CHR-2 SINEs at particular orthologous loci
prove that whales form a clade within even-toed ungulates (Shi-
mamura et al. 1997). Similar analysis of several copies of Alu
supports the African origin of humans (Stoneking et al. 1997).
Here we describe SINE families from the genomes of insectivores,
keeping in mind further phylogenetic analysis of these animals.
Insectivora is one of the most primitive orders of placental mam-
mals, and their relations with other orders are important for un-
derstanding the mammalian phylogeny. Order Insectivora include
six families: hedgehogs (Erinacidae), shrews (Soricidae), moles
(Talpidae), tenrecs (Tenrecidae), solenodons (Solenodontidae),
and golden moles (Chrysochloridae). The first three families are
best known and widespread; hence, SINEs were primarily isolated
from these families. These findings significantly increase the num-
ber of known tRNA-derived SINEs in mammals, which allowed us
to generalize the data on conservative structures in mammalian
SINEs and recognize two SINE classes with different organization
of the tail.
Materials and methods
Tissues of insectivores were provided by A. Bannikova (Bio-
logical Department, Moscow State University) and E. Lyapunova (Institute
of Developmental Biology, RAS, Moscow). Tissue samples from bats were
obtained by A. Borisenko (Zoological Museum, Moscow State University).
Liver samples from tree shrew and elephant shrew were donated by O.
Likhnova (Institute of Ecology and Evolution, RAS, Moscow) and S.
Popov (Moscow Zoo), respectively.
DNA was isolated from fresh or ethanol-fixed tissues (liver, kidney, or
muscle) by incubation with proteinase K followed by phenol/chloroform
A-B PCR method.
A-B PCR was carried out as described elsewhere
(Borodulina and Kramerov 1999). In brief, the reaction mixture (100 l)
contained 0.1 ng of genomic DNA and two 12-nucleotide primers specific
to A and B boxes of RNA pol III promoter consensus. After 27 PCR cycles
(95°C, 1 min; 34°C, 1 min; 72°C, 1 min) the amplified 30- to 40-bp DNA
fragments were isolated by electrophoresis in 5% NuSieve (FMC) agarose
gel. They were cloned and sequenced or radioactively labeled by PCR and
used for screening of the genomic libraries as described previously
(Borodulina and Kramerov 1999).
The nucleotide sequence data reported in this paper have been submitted to
GenBank and have been assigned the accession numbers AF195903–
Correspondence to: D.A. Kramerov; E-mail: email@example.com.
Mammalian Genome 12, 779–786 (2001).
© Springer-Verlag New York Inc. 2001