Identification and classification of endogenous retroviruses in the canine genome using degenerative PCR and in-silico data analysis

Haiin Jo, Hojun Choi, Min Kyeung Choi, Ning Song, Jin Hoi Kim, Jae Wook Oh, Kunho Seo, Han Geuk Seo, Taehoon Chun, Tae Hun Kim, Chankyu Park

Research output: Contribution to journalArticle

10 Citations (Scopus)

Abstract

Pooled genomic DNA from 10 dogs was subjected to polymerase chain reaction with primers targeting the retroviral pro/pol region. Sequence analysis of 120 clones obtained by PCR revealed 81 of retroviral origin. Subsequent analysis of the dog genome (CanFam 2.0) by BLAST investigation using degenerate PCR products and previously identified retroviral sequences permitted the identification of additional retroviral γ and β sequences. A phylogenetic analysis using the retroviral protease (PR) and reverse transcriptase (RT) sequences in the dog genome resulted in identification of 17 γ and 7 β families. In addition, we also identified 167 spuma-like ERV elements from CanFam 2.0 based on sequence homology to murine (Mu)ERV-L and human (H)ERV-L. Our results could contribute to the understanding of the influence of retroviruses in shaping the genome structure and altering gene expression by providing quantitative and locational information of ERV loci and their diversity in the dog genome.

Original languageEnglish
Pages (from-to)195-204
Number of pages10
JournalVirology
Volume422
Issue number2
DOIs
Publication statusPublished - 2012 Jan 20

Fingerprint

Endogenous Retroviruses
Computer Simulation
Canidae
Genome
Dogs
Polymerase Chain Reaction
RNA-Directed DNA Polymerase
Retroviridae
Sequence Homology
Sequence Analysis
Peptide Hydrolases
Clone Cells
Gene Expression
DNA

Keywords

  • Canine
  • Endogenous retrovirus
  • ERV
  • Genome
  • Pol
  • Pro

ASJC Scopus subject areas

  • Virology

Cite this

Identification and classification of endogenous retroviruses in the canine genome using degenerative PCR and in-silico data analysis. / Jo, Haiin; Choi, Hojun; Choi, Min Kyeung; Song, Ning; Kim, Jin Hoi; Oh, Jae Wook; Seo, Kunho; Seo, Han Geuk; Chun, Taehoon; Kim, Tae Hun; Park, Chankyu.

In: Virology, Vol. 422, No. 2, 20.01.2012, p. 195-204.

Research output: Contribution to journalArticle

Jo, H, Choi, H, Choi, MK, Song, N, Kim, JH, Oh, JW, Seo, K, Seo, HG, Chun, T, Kim, TH & Park, C 2012, 'Identification and classification of endogenous retroviruses in the canine genome using degenerative PCR and in-silico data analysis', Virology, vol. 422, no. 2, pp. 195-204. https://doi.org/10.1016/j.virol.2011.10.010
Jo, Haiin ; Choi, Hojun ; Choi, Min Kyeung ; Song, Ning ; Kim, Jin Hoi ; Oh, Jae Wook ; Seo, Kunho ; Seo, Han Geuk ; Chun, Taehoon ; Kim, Tae Hun ; Park, Chankyu. / Identification and classification of endogenous retroviruses in the canine genome using degenerative PCR and in-silico data analysis. In: Virology. 2012 ; Vol. 422, No. 2. pp. 195-204.
@article{c1d8f242a6884ac59f06f67ff9b6b2f1,
title = "Identification and classification of endogenous retroviruses in the canine genome using degenerative PCR and in-silico data analysis",
abstract = "Pooled genomic DNA from 10 dogs was subjected to polymerase chain reaction with primers targeting the retroviral pro/pol region. Sequence analysis of 120 clones obtained by PCR revealed 81 of retroviral origin. Subsequent analysis of the dog genome (CanFam 2.0) by BLAST investigation using degenerate PCR products and previously identified retroviral sequences permitted the identification of additional retroviral γ and β sequences. A phylogenetic analysis using the retroviral protease (PR) and reverse transcriptase (RT) sequences in the dog genome resulted in identification of 17 γ and 7 β families. In addition, we also identified 167 spuma-like ERV elements from CanFam 2.0 based on sequence homology to murine (Mu)ERV-L and human (H)ERV-L. Our results could contribute to the understanding of the influence of retroviruses in shaping the genome structure and altering gene expression by providing quantitative and locational information of ERV loci and their diversity in the dog genome.",
keywords = "Canine, Endogenous retrovirus, ERV, Genome, Pol, Pro",
author = "Haiin Jo and Hojun Choi and Choi, {Min Kyeung} and Ning Song and Kim, {Jin Hoi} and Oh, {Jae Wook} and Kunho Seo and Seo, {Han Geuk} and Taehoon Chun and Kim, {Tae Hun} and Chankyu Park",
year = "2012",
month = "1",
day = "20",
doi = "10.1016/j.virol.2011.10.010",
language = "English",
volume = "422",
pages = "195--204",
journal = "Virology",
issn = "0042-6822",
publisher = "Academic Press Inc.",
number = "2",

}

TY - JOUR

T1 - Identification and classification of endogenous retroviruses in the canine genome using degenerative PCR and in-silico data analysis

AU - Jo, Haiin

AU - Choi, Hojun

AU - Choi, Min Kyeung

AU - Song, Ning

AU - Kim, Jin Hoi

AU - Oh, Jae Wook

AU - Seo, Kunho

AU - Seo, Han Geuk

AU - Chun, Taehoon

AU - Kim, Tae Hun

AU - Park, Chankyu

PY - 2012/1/20

Y1 - 2012/1/20

N2 - Pooled genomic DNA from 10 dogs was subjected to polymerase chain reaction with primers targeting the retroviral pro/pol region. Sequence analysis of 120 clones obtained by PCR revealed 81 of retroviral origin. Subsequent analysis of the dog genome (CanFam 2.0) by BLAST investigation using degenerate PCR products and previously identified retroviral sequences permitted the identification of additional retroviral γ and β sequences. A phylogenetic analysis using the retroviral protease (PR) and reverse transcriptase (RT) sequences in the dog genome resulted in identification of 17 γ and 7 β families. In addition, we also identified 167 spuma-like ERV elements from CanFam 2.0 based on sequence homology to murine (Mu)ERV-L and human (H)ERV-L. Our results could contribute to the understanding of the influence of retroviruses in shaping the genome structure and altering gene expression by providing quantitative and locational information of ERV loci and their diversity in the dog genome.

AB - Pooled genomic DNA from 10 dogs was subjected to polymerase chain reaction with primers targeting the retroviral pro/pol region. Sequence analysis of 120 clones obtained by PCR revealed 81 of retroviral origin. Subsequent analysis of the dog genome (CanFam 2.0) by BLAST investigation using degenerate PCR products and previously identified retroviral sequences permitted the identification of additional retroviral γ and β sequences. A phylogenetic analysis using the retroviral protease (PR) and reverse transcriptase (RT) sequences in the dog genome resulted in identification of 17 γ and 7 β families. In addition, we also identified 167 spuma-like ERV elements from CanFam 2.0 based on sequence homology to murine (Mu)ERV-L and human (H)ERV-L. Our results could contribute to the understanding of the influence of retroviruses in shaping the genome structure and altering gene expression by providing quantitative and locational information of ERV loci and their diversity in the dog genome.

KW - Canine

KW - Endogenous retrovirus

KW - ERV

KW - Genome

KW - Pol

KW - Pro

UR - http://www.scopus.com/inward/record.url?scp=84855201422&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84855201422&partnerID=8YFLogxK

U2 - 10.1016/j.virol.2011.10.010

DO - 10.1016/j.virol.2011.10.010

M3 - Article

VL - 422

SP - 195

EP - 204

JO - Virology

JF - Virology

SN - 0042-6822

IS - 2

ER -