Long terminal repeats of porcine endogenous retroviruses

1
Long terminal repeats of porcine endogenous
retroviruses in Sus scrofa
Yun-Ji Kim1 Jae-Won Huh1, Byung-Wook Cho2,
Dae-Soo Kim3, Hong-Seok Ha1, Ja-Rang Lee1, Kung
Ahn1, and Heui-Soo Kim1,3 1 Division of
Biological Sciences, College of Natural Sciences,
Pusan National University, Busan 609-735,
Republic of Korea 2 Department of Animal Science,
College of Life Sciences, Pusan National
University,Miryang 627-706, Republic of Korea 3
PBBRC, Interdisciplinary Research Program of
Bioinformatics, College of Natural Sciences,
Pusan National University, Busan 609-735,
Republic of Korea http//www..primate.or.kr
Using PCR, sequencing, and bioinformatic
approaches with the genomic DNAs of Korean pigs
(domestic, wild, and hybrid with Yorkshire),
twelve solitary PERV long terminal repeat
elements were identified and analyzed. Structure
analysis of the LTR elements indicated that they
have different repeat sequences in the U3 region.
The PERV-A6-KWP1 and KWP2 elements bear seven
and eight 39 bp repeats, respectively. The R
region of the PERV LTR elements was highly
conserved in pig and mouse genomes, suggesting
that they seem to have originated from a common
exogenous viral element, and then independently
evolved throughout the course of mammalian
evolution.
KWP,KDP,KDPKYP
QIAEX II gel extraction kit(Qiagen) High Pure
plasmid isolation kit
BLAST,MEGA2
Fig. 1. Schematic representation of various PERV
LTR elements (A) and consensus sequences of
figured boxes (B). Open boxes indicate the
conserved regions, and figured boxes indicate the
specific sequences. Closed boxes indicate the
different consensus sequences. Different boxes in
tandem repeated region indicate the repeat number
of tandem repeat sequences. Numbers indicate the
specific position in individual LTR sequences.
The underlined nucleotide sequences indicate the
binding site for the transcription factor, NF-Y.
The structures of solitary PERV LTR elements
(PERV-A5, -A6, -A7, -A8, -X9, -X10) are derived
from Korean pigs, KYP-hybrid of Korean domestic
pig Yorkshire, KDP-Korean domestic pig, and
KWP-Korean wild pig (see also Table 2). KWP1 and
KWP2 indicate the allele difference in the same
individual. Group 2 is PERV-C LTR element and
Group 1a is defined by the different copy number
of tandem repeated sequences in our sequencing
analysis. In the case of the mouse LTR-IS
element, only the conserved region (open gray
box) has high homology with PERV LTR
elements....

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