9 Springer-Verlag New York Inc. 1995. SINE elements of carnivores. H.H.J. van der Vlugt, J.A. Lenstra. Institute of Infectious Diseases and Immunology, Faculty ...
Mammalian Genome 6, 49-51 (1995).
"~enome 9 Springer-Verlag New York Inc. 1995
SINE elements of carnivores H.H.J. van der Vlugt, J.A. Lenstra Institute of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, P.O. Box 80.165, 3508 TD Utrecht, The Netherlands Received 13 December 1993 / Accepted 31 August 1994 Studying the genomes of carnivores on the molecular level may be useful in several respects. For example, the level of inbreeding of endangered carnivore species can be monitored via a moleculargenetic approach (Wayne 1993; Menotti-Raymond and O'Brien 1993; O'Brien 1994). Further, the prevalence of several genetically determined diseases in many dog breeds may allow studies of the function and pathology of many mammalian genes and also provide animal models of human genetic disorders. Five to ten percent of the mammalian genome is occupied by SINEs (short interspersed repeats), which do not have any known function. Since SINEs are specific for the order (Weiner et al. 1986; Lenstra et al. 1993), they serve as tags for a species-specific hybridization or amplification. For instance, the A l u - P C R (Nelson et al. 1989) is widely used to amplify human DNA from YAC clones, somatic cell hybrids, or cell-sorted chromosome material. Here we investigated the major SINE sequences from the dog and the mink. Oligonucleotides were designed on the basis of alignments of database entries. By hybridization and PCR we found that the cat genome contains a related SINE.
SINE elements from the American mink (EMBL entry MVB2RPT) and from the domestic dog (entry CFREPDNA) have been reported previously (Lavrentiera et al. 1989; Minnick et al. 1992). Recently, a similar SINE element has been identified in the harbor seal (entry PVSINEC; Coltman and Wright 1994). A FASTA database search (Pearson and Lipman 1988) of the EMBL library (release 34) with MVB2RPT revealed similarities to several segments of genes from the mink and the dog. Alignments were produced and edited by the PC program MULTALIN (Corpet 1988). The regions of similarity (Fig. 1) were found to be flanked by short direct repeats typical for other SINEs (Weiner et al. 1986). This indicates that the actual S1NE repeats correspond to the 180 to 210 bp between the direct repeats (positions 32-227 of MVB2RPT). Like several other SINEs (Lenstra et al. 1993; Sakagami et al. 1994), the 5' part of the SINE consists of a tRNA-like sequence with the A-box and B-box of the split RNA polymerase III promoter. Coltman and Wright (1994) reported a relatively high similarity to tRNA Ala. A rather G/C-rich inverted repeat of nine to ten nucleotides is located immediately upstream of the B box. The 3' part consists of a degenerated (TC) tandem repeat and an A-rich region.
Correspondence to." J.A. Lenstra
[ MVB2RPT
CDCOLIPB CDCOLIP
MVSAAIA
19494-
A G A A C A G A T A A C T T G . . A . C. . . . . . . . . .
4752-
CFREPDNA
1-
PVSIBEC
11-
- ....
G...C..T...-..GC.-
A A A G G ~ G
..... ....
.......
T ................ CA . . . . .
A ....
-..G.C....
G...CA .....
.....
T ...........
. ....
G. . . .
T .......
9 .A.C .......... T A A T G A. . . . . .
'CA~SI ~E~
-..G...AT..A T.C .......
.... .......
C ....
G.GC-....CT..A.AC.C G...-
G..T ........ TG..T .... G, .T..T
- ....
G........
TG..T .....
G.TT..A
.... - ....
A..-T
TG.AT ........ TG..C ....
TG . . . . . . . . .
....
A....C
T ....
.......
C.....
......
A....CTC
....
A ..........
........
.....
C.,- ....
A ....
A....A C...A
..........
-A ....
TC..- ....
..A...G
.....
CT.C..G...A
-A ....... -A .....
-,..TC.
..........
. .A--.
- ....
....... ......
.....
I -...TC.
..AT .........
T..A..A C.C .....
T ....
--
-...TCT -...TC. -...TCT
CA,.---.A.T..TGAGA.-...T.. C..- ....
, .A..AT .....
....
- ......
C.G.T---.
....
T ......
C ......
T .......
.........
......
T.TC...G-.
C...........
C.G.T---..AT
- .......... T..G..-
T ............
C......
CT.ATA.C .... C.T ....
-A .....
A.G..-A
T ........
A.A..C...A.T.G...C..TA
GAGC-....CT..A.AC.C .....
....
............
.....
C.A.C..C CTA . . . .
A..,.A
....................
C.A....C
.....
- ....
........
AT..A.AC.CA
- ......
AG..T ........
T ....
TGA.......
G.. -C..T..G-..GC
GCCT . . . . . . . . .
G....
AT .......
T ........
TGATATTCGG...CA ...............
,AT ......... A..A.AA
- .............
-...TC.
.......
A..A ..........
-T.---- ......
11-
MVB2LE
1-
MVB2LA
1-
MVB2LA
61-
MVB2RPT
C T C C T T C T C T C T C T G C C T G C C.T. . .
CDCOLIPB
...TGC..G.G...--.
CDCOLIP
.C.TGC..G.G.,
MVTI1
--.T.C
CFCOMCSA
G..TGC..G.G...--...
CFFIXA
9. . T G C T . A . G . . . - - . . . . T . - - C T . . G . . T G . G T G
MVSAAIA
GC.TGC ......
M28626
TC..C..CT ..... - ................... ...TGC..G.G...--....G
PVSINEC MVB2LB MVB2LD MVB2LF MVB2LE MVB2LA MVB2LA
....
TG..C ....
A ........
----.
MVB2LF
CFREPDNA
.......
G...C ..........................
564-
CFARGES
hairpin
[ CANSINE21
G...C,.T..G-..GC
T C T A A C C T T G. . . . . . . . . . . . . . . . .
24772417-
I
CANSIN~I~
1355-AAAAAGTCCCCACCTGGG.CAGC .....
M28626
MVB2LB MVB2LD
[
I ] I I ] I AGAA~AA~C~G~C~G~G~GG~CAG~GGG~AAG~CG~G~C~CAG~-~AGGTCAT-GA~C~G~G~A~GGGAICGAGICCcG~A~-GGGC~CT~C~CGG~GGGGA~C~TGc~C~
MVTI1 1612CFCOMCSA 1 3 8 9 CFFIXA
