CAN—a pan-carnivore SINE family
Nikita S. Vassetzky, Dmitri A. Kramerov
Laboratory of Eukaryotic Genomes Evolution, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov St.,
Moscow, 119991 Russia
Received: 13 July 2001 / Accepted: 18 September 2001
Abstract. Short retroposons or short interspersed elements
(SINEs) constituting 5–10% genome have been isolated from vari-
ous organisms. CAN SINEs initially found in American mink were
named after dogs (Canis), and the range of their distribution in the
genomes of carnivores and mammals in general remained topical.
Here we demonstrate CAN sequences in representatives of all
carnivore families, but not beyond carnivores, on the basis of
sequence bank search and genomic PCR. Analysis of their distri-
bution supports division of carnivores into caniform (dogs, mus-
telids, raccoons, bears, and pinnipeds) and feliform (cats, civets,
and hyenas) lineages. CAN structure is considered in the context of
their function and evolution.
A significant portion of the eukaryotic genome is composed of
mobile elements propagated by retroposition, a process involving
transcription and reverse transcription (Rogers 1985). Long retro-
posons (LINEs) code for the activities required for retroposition
(reverse transcriptase and endonuclease), while short retroposons
(SINEs) lack these.
SINEs are genomic repeats 80–400 bp long, apparently origi-
nating from RNA (more commonly tRNA); a typical SINE con-
sists of three regions; a tRNA-related region, a tRNA-unrelated
region, and an A-rich region. The tRNA-related region contains an
internal promoter of RNA polymerase III and provides for its
transcription (Daniels and Deininger 1985; Jagadeeswaran et al.
1981). Owing to the mechanism of amplification, the 3Ј-part of
SINEs is A-rich, and the genomic elements are flanked by short
SINEs can be classified as members of several superfamilies
sharing structural similarity, apparently inherited from a common
ancestor [e.g., members of Alu/B1 superfamily originate from an
ancient element FAM (Quentin 1992)]. The vast majority of SINE
copies in the genome are incapable of active amplification, and the
process is due to a few master sequences as indicated by the
presence of distinct subfamilies and the activity of one or a few at
any given time.
The process of SINE amplification in the genome goes within
a certain period of evolution; for instance, SINEs of CORE super-
family amplified in the earliest days of vertebrate evolution and are
inactive now (Gilbert and Labuda 2000), while Alu amplification
is still going (Leeflang et al. 1992). No mechanism of specific
SINE elimination from the genome is known, and SINEs remain in
the genomes of successors: MIR is found in all mammals, while
Alu is specific for primates, which allows their use as independent
phylogenetic markers (Kramerov et al. 1999; Murata et al. 1993;
Shimamura et al. 1997).
SINEs were initially found in primates and rodents (Krayev et
al. 1980; Rubin et al. 1980); now it is generally accepted that
several SINE families are present in most (probably all) higher
eukaryotes. Usually, one SINE family has over 100,000 copies per
haploid genome, while others are less abundant [e.g., the mouse
genome contains ∼100,000 B1s and B2s each (Kramerov et al.
1979) and ∼40,000 IDs (Kass et al. 1996)].
In carnivores CAN short retroposons were first found in
American mink (Lavrent’eva et al. 1989), then in the dog (Minnick
et al. 1992) and harbor seal (Coltman and Wright 1994). This was
a typical tRNA-related SINE family highly repeated in the ge-
nomes [∼400,000 per dog haploid genome (Bentolita et al. 1999)].
For over a decade the taxonomic range of this SINE distribution
remained controversial: most groups limited it to Canoidea (cani-
form carnivores including dogs, bears, raccoons, mustelids,
skunks, seals, and walruses, while feliform carnivores include cats,
civets, and hyenas) (Bentolila et al. 1999; Coltman and Wright
1994; Das et al. 1998; Zehr et al. 2001), whereas van der Vlugt and
Lenstra (1995) and Precon Slattery et al. (2000) detected this SINE
in the cat.
Here we resolve this dispute and demonstrate the presence of
CAN SINEs in the genomes of all carnivore lineages, but not
beyond carnivores. We also analyze the fine structure and arrange
variants of CANs. Since this SINE family is now known in an
unusually wide range of species, we consider phylogenetic rela-
tions of this short retroposon as well as the evolution of carnivores.
Materials and methods
We studied DNA of the following species. Carnivores: cat Felis
catus, dog Canis familiaris, walrus Odobenus rosmarus, civet
Viverra zibetha; non-carnivores: human Homo sapiens, mouse
Mus musculus, Daurian hedgehog Mesechinus (Hemiechinus)
dauuricus, water bat Myotis daubentoni, rabbit Oryctolagus cu-
niculus, short-eared elephant shrew Macroscelides proboscideus,
cow Bos taurus, nine-banded armadillo Dasypus novemcinctus,
Bennett’s tree kangaroo Dendrolagus bennettianus, tree shrew
Tupaia glis; and birds: gull Larus cachinans, white-naped crane
Grus vipio, and chicken Gallus gallus.
The walrus, kangaroo, and elephant shrew tissues were pro-
vided by S. Popov (Moscow Zoo); the civet and tree shrew tissues
were provided by O. Likhnova (Institute of Ecology and Evolu-
tion, Moscow), and the armadillo tissue was provided by R. DeBry
(University of Cincinnati). For other DNA sources and isolation
technique, see Borodulina and Kramerov (1999).
PCR conditions were described elsewhere (Kramerov et al.
1999; Serdobova and Kramerov 1998). The amplification products
were analyzed by electrophoresis in 4% NuSieve (FMC) agarose
gel. We used the following primers corresponding to the polymer-
ase III promoter box A and the extension of tRNA-related region
in CAN SINE: 5Ј-CTGGGTGGCTCAGTCRGT-3Ј and 5Ј-
AGCACAGAGCCYGAYGYG-3Ј. Under these PCR conditions,
100 ng genomic DNA sufficed to reveal single genomic copies;
Correspondence to: N.S. Vassetzky; E-mail: email@example.com
Mammalian Genome 13, 50–57 (2002).
© Springer-Verlag New York Inc. 2002
Incorporating Mouse Genome