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Genomic landscapes of endogenous retroviruses unveil intricate genetics of conventional and genetically-engineered laboratory mouse strains.

Abstract Laboratory strains of mice, both conventional and genetically engineered, have been introduced as critical components of a broad range of studies investigating normal and disease biology. Currently, the genetic identity of laboratory mice is primarily confirmed by surveying polymorphisms in selected sets of "conventional" genes and/or microsatellites in the absence of a single completely sequenced mouse genome. First, we examined variations in the genomic landscapes of transposable repetitive elements, named the TREome, in conventional and genetically engineered mouse strains using murine leukemia virus-type endogenous retroviruses (MLV-ERVs) as a probe. A survey of the genomes from 56 conventional strains revealed strain-specific TREome landscapes, and certain families (e.g., C57BL) of strains were discernible with defined patterns. Interestingly, the TREome landscapes of C3H/HeJ (toll-like receptor-4 [TLR4] mutant) inbred mice were different from its control C3H/HeOuJ (TLR4 wild-type) strain. In addition, a CD14 knock-out strain had a distinct TREome landscape compared to its control/backcross C57BL/6J strain. Second, an examination of superantigen (SAg, a "TREome gene") coding sequences of mouse mammary tumor virus-type ERVs in the genomes of the 46 conventional strains revealed a high diversity, suggesting a potential role of SAgs in strain-specific immune phenotypes. The findings from this study indicate that unexplored and intricate genomic variations exist in laboratory mouse strains, both conventional and genetically engineered. The TREome-based high-resolution genetics surveillance system for laboratory mice would contribute to efficient study design with quality control and accurate data interpretation. This genetics system can be easily adapted to other species ranging from plants to humans.
PMID
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Authors

Mayor MeshTerms
Keywords

Genetic surveillance

Genome complexity

TREome gene profile

TREome landscape

Transposable repetitive elements (TREome)

Journal Title experimental and molecular pathology
Publication Year Start
%A Lee, Kang-Hoon; Lim, Debora; Chiu, Sophia; Greenhalgh, David; Cho, Kiho
%T Genomic landscapes of endogenous retroviruses unveil intricate genetics of conventional and genetically-engineered laboratory mouse strains.
%J Experimental and molecular pathology, vol. 100, no. 2, pp. 248-256
%D 04/2016
%V 100
%N 2
%M eng
%B Laboratory strains of mice, both conventional and genetically engineered, have been introduced as critical components of a broad range of studies investigating normal and disease biology. Currently, the genetic identity of laboratory mice is primarily confirmed by surveying polymorphisms in selected sets of "conventional" genes and/or microsatellites in the absence of a single completely sequenced mouse genome. First, we examined variations in the genomic landscapes of transposable repetitive elements, named the TREome, in conventional and genetically engineered mouse strains using murine leukemia virus-type endogenous retroviruses (MLV-ERVs) as a probe. A survey of the genomes from 56 conventional strains revealed strain-specific TREome landscapes, and certain families (e.g., C57BL) of strains were discernible with defined patterns. Interestingly, the TREome landscapes of C3H/HeJ (toll-like receptor-4 [TLR4] mutant) inbred mice were different from its control C3H/HeOuJ (TLR4 wild-type) strain. In addition, a CD14 knock-out strain had a distinct TREome landscape compared to its control/backcross C57BL/6J strain. Second, an examination of superantigen (SAg, a "TREome gene") coding sequences of mouse mammary tumor virus-type ERVs in the genomes of the 46 conventional strains revealed a high diversity, suggesting a potential role of SAgs in strain-specific immune phenotypes. The findings from this study indicate that unexplored and intricate genomic variations exist in laboratory mouse strains, both conventional and genetically engineered. The TREome-based high-resolution genetics surveillance system for laboratory mice would contribute to efficient study design with quality control and accurate data interpretation. This genetics system can be easily adapted to other species ranging from plants to humans.
%P 248
%L 256
%Y 10.1016/j.yexmp.2016.01.005
%W PHY
%G AUTHOR
%R 2016......100..248L

@Article{Lee2016,
author="Lee, Kang-Hoon
and Lim, Debora
and Chiu, Sophia
and Greenhalgh, David
and Cho, Kiho",
title="Genomic landscapes of endogenous retroviruses unveil intricate genetics of conventional and genetically-engineered laboratory mouse strains.",
journal="Experimental and molecular pathology",
year="2016",
month="Apr",
day="11",
volume="100",
number="2",
pages="248--256",
abstract="Laboratory strains of mice, both conventional and genetically engineered, have been introduced as critical components of a broad range of studies investigating normal and disease biology. Currently, the genetic identity of laboratory mice is primarily confirmed by surveying polymorphisms in selected sets of ``conventional'' genes and/or microsatellites in the absence of a single completely sequenced mouse genome. First, we examined variations in the genomic landscapes of transposable repetitive elements, named the TREome, in conventional and genetically engineered mouse strains using murine leukemia virus-type endogenous retroviruses (MLV-ERVs) as a probe. A survey of the genomes from 56 conventional strains revealed strain-specific TREome landscapes, and certain families (e.g., C57BL) of strains were discernible with defined patterns. Interestingly, the TREome landscapes of C3H/HeJ (toll-like receptor-4 [TLR4] mutant) inbred mice were different from its control C3H/HeOuJ (TLR4 wild-type) strain. In addition, a CD14 knock-out strain had a distinct TREome landscape compared to its control/backcross C57BL/6J strain. Second, an examination of superantigen (SAg, a ``TREome gene'') coding sequences of mouse mammary tumor virus-type ERVs in the genomes of the 46 conventional strains revealed a high diversity, suggesting a potential role of SAgs in strain-specific immune phenotypes. The findings from this study indicate that unexplored and intricate genomic variations exist in laboratory mouse strains, both conventional and genetically engineered. The TREome-based high-resolution genetics surveillance system for laboratory mice would contribute to efficient study design with quality control and accurate data interpretation. This genetics system can be easily adapted to other species ranging from plants to humans.",
issn="1096-0945",
doi="10.1016/j.yexmp.2016.01.005",
url="http://www.ncbi.nlm.nih.gov/pubmed/26779669",
language="eng"
}

%0 Journal Article
%T Genomic landscapes of endogenous retroviruses unveil intricate genetics of conventional and genetically-engineered laboratory mouse strains.
%A Lee, Kang-Hoon
%A Lim, Debora
%A Chiu, Sophia
%A Greenhalgh, David
%A Cho, Kiho
%J Experimental and molecular pathology
%D 2016
%8 Apr 11
%V 100
%N 2
%@ 1096-0945
%G eng
%F Lee2016
%X Laboratory strains of mice, both conventional and genetically engineered, have been introduced as critical components of a broad range of studies investigating normal and disease biology. Currently, the genetic identity of laboratory mice is primarily confirmed by surveying polymorphisms in selected sets of "conventional" genes and/or microsatellites in the absence of a single completely sequenced mouse genome. First, we examined variations in the genomic landscapes of transposable repetitive elements, named the TREome, in conventional and genetically engineered mouse strains using murine leukemia virus-type endogenous retroviruses (MLV-ERVs) as a probe. A survey of the genomes from 56 conventional strains revealed strain-specific TREome landscapes, and certain families (e.g., C57BL) of strains were discernible with defined patterns. Interestingly, the TREome landscapes of C3H/HeJ (toll-like receptor-4 [TLR4] mutant) inbred mice were different from its control C3H/HeOuJ (TLR4 wild-type) strain. In addition, a CD14 knock-out strain had a distinct TREome landscape compared to its control/backcross C57BL/6J strain. Second, an examination of superantigen (SAg, a "TREome gene") coding sequences of mouse mammary tumor virus-type ERVs in the genomes of the 46 conventional strains revealed a high diversity, suggesting a potential role of SAgs in strain-specific immune phenotypes. The findings from this study indicate that unexplored and intricate genomic variations exist in laboratory mouse strains, both conventional and genetically engineered. The TREome-based high-resolution genetics surveillance system for laboratory mice would contribute to efficient study design with quality control and accurate data interpretation. This genetics system can be easily adapted to other species ranging from plants to humans.
%U http://dx.doi.org/10.1016/j.yexmp.2016.01.005
%U http://www.ncbi.nlm.nih.gov/pubmed/26779669
%P 248-256

PT Journal
AU Lee, K
   Lim, D
   Chiu, S
   Greenhalgh, D
   Cho, K
TI Genomic landscapes of endogenous retroviruses unveil intricate genetics of conventional and genetically-engineered laboratory mouse strains.
SO Experimental and molecular pathology
JI Exp. Mol. Pathol.
PD Apr
PY 2016
BP 248
EP 256
VL 100
IS 2
DI 10.1016/j.yexmp.2016.01.005
LA eng
AB Laboratory strains of mice, both conventional and genetically engineered, have been introduced as critical components of a broad range of studies investigating normal and disease biology. Currently, the genetic identity of laboratory mice is primarily confirmed by surveying polymorphisms in selected sets of "conventional" genes and/or microsatellites in the absence of a single completely sequenced mouse genome. First, we examined variations in the genomic landscapes of transposable repetitive elements, named the TREome, in conventional and genetically engineered mouse strains using murine leukemia virus-type endogenous retroviruses (MLV-ERVs) as a probe. A survey of the genomes from 56 conventional strains revealed strain-specific TREome landscapes, and certain families (e.g., C57BL) of strains were discernible with defined patterns. Interestingly, the TREome landscapes of C3H/HeJ (toll-like receptor-4 [TLR4] mutant) inbred mice were different from its control C3H/HeOuJ (TLR4 wild-type) strain. In addition, a CD14 knock-out strain had a distinct TREome landscape compared to its control/backcross C57BL/6J strain. Second, an examination of superantigen (SAg, a "TREome gene") coding sequences of mouse mammary tumor virus-type ERVs in the genomes of the 46 conventional strains revealed a high diversity, suggesting a potential role of SAgs in strain-specific immune phenotypes. The findings from this study indicate that unexplored and intricate genomic variations exist in laboratory mouse strains, both conventional and genetically engineered. The TREome-based high-resolution genetics surveillance system for laboratory mice would contribute to efficient study design with quality control and accurate data interpretation. This genetics system can be easily adapted to other species ranging from plants to humans.
ER

PMID- 26779669
OWN - NLM
STAT- In-Process
DA  - 20160407
LR  - 20160407
IS  - 1096-0945 (Electronic)
IS  - 0014-4800 (Linking)
VI  - 100
IP  - 2
DP  - 2016 Apr
TI  - Genomic landscapes of endogenous retroviruses unveil intricate genetics of
      conventional and genetically-engineered laboratory mouse strains.
PG  - 248-56
LID - 10.1016/j.yexmp.2016.01.005 [doi]
LID - S0014-4800(16)00006-X [pii]
AB  - Laboratory strains of mice, both conventional and genetically engineered, have
      been introduced as critical components of a broad range of studies investigating 
      normal and disease biology. Currently, the genetic identity of laboratory mice is
      primarily confirmed by surveying polymorphisms in selected sets of "conventional"
      genes and/or microsatellites in the absence of a single completely sequenced
      mouse genome. First, we examined variations in the genomic landscapes of
      transposable repetitive elements, named the TREome, in conventional and
      genetically engineered mouse strains using murine leukemia virus-type endogenous 
      retroviruses (MLV-ERVs) as a probe. A survey of the genomes from 56 conventional 
      strains revealed strain-specific TREome landscapes, and certain families (e.g.,
      C57BL) of strains were discernible with defined patterns. Interestingly, the
      TREome landscapes of C3H/HeJ (toll-like receptor-4 [TLR4] mutant) inbred mice
      were different from its control C3H/HeOuJ (TLR4 wild-type) strain. In addition, a
      CD14 knock-out strain had a distinct TREome landscape compared to its
      control/backcross C57BL/6J strain. Second, an examination of superantigen (SAg, a
      "TREome gene") coding sequences of mouse mammary tumor virus-type ERVs in the
      genomes of the 46 conventional strains revealed a high diversity, suggesting a
      potential role of SAgs in strain-specific immune phenotypes. The findings from
      this study indicate that unexplored and intricate genomic variations exist in
      laboratory mouse strains, both conventional and genetically engineered. The
      TREome-based high-resolution genetics surveillance system for laboratory mice
      would contribute to efficient study design with quality control and accurate data
      interpretation. This genetics system can be easily adapted to other species
      ranging from plants to humans.
CI  - Copyright (c) 2016 Elsevier Inc. All rights reserved.
FAU - Lee, Kang-Hoon
AU  - Lee KH
AD  - Department of Surgery, University of California, Davis, and Shriners Hospitals
      for Children Northern California, Sacramento, CA 95817, United States.
FAU - Lim, Debora
AU  - Lim D
AD  - Department of Surgery, University of California, Davis, and Shriners Hospitals
      for Children Northern California, Sacramento, CA 95817, United States.
FAU - Chiu, Sophia
AU  - Chiu S
AD  - Department of Surgery, University of California, Davis, and Shriners Hospitals
      for Children Northern California, Sacramento, CA 95817, United States.
FAU - Greenhalgh, David
AU  - Greenhalgh D
AD  - Department of Surgery, University of California, Davis, and Shriners Hospitals
      for Children Northern California, Sacramento, CA 95817, United States.
FAU - Cho, Kiho
AU  - Cho K
AD  - Department of Surgery, University of California, Davis, and Shriners Hospitals
      for Children Northern California, Sacramento, CA 95817, United States. Electronic
      address: [email protected]
LA  - eng
GR  - R01 GM071360/GM/NIGMS NIH HHS/United States
GR  - R01 GM071360/GM/NIGMS NIH HHS/United States
PT  - Journal Article
PT  - Research Support, N.I.H., Extramural
PT  - Research Support, Non-U.S. Gov't
DEP - 20160111
PL  - United States
TA  - Exp Mol Pathol
JT  - Experimental and molecular pathology
JID - 0370711
SB  - IM
PMC - PMC4823159
MID - NIHMS757187
OID - NLM: NIHMS757187 [Available on 04/01/17]
OID - NLM: PMC4823159 [Available on 04/01/17]
OTO - NOTNLM
OT  - Genetic surveillance
OT  - Genome complexity
OT  - TREome gene profile
OT  - TREome landscape
OT  - Transposable repetitive elements (TREome)
EDAT- 2016/01/19 06:00
MHDA- 2016/01/19 06:00
CRDT- 2016/01/19 06:00
PMCR- 2017/04/01 00:00
PHST- 2015/09/24 [received]
PHST- 2016/01/09 [accepted]
PHST- 2016/01/11 [aheadofprint]
AID - S0014-4800(16)00006-X [pii]
AID - 10.1016/j.yexmp.2016.01.005 [doi]
PST - ppublish
SO  - Exp Mol Pathol. 2016 Apr;100(2):248-56. doi: 10.1016/j.yexmp.2016.01.005. Epub
      2016 Jan 11.
TY  - JOUR
AU  - Lee, Kang-Hoon
AU  - Lim, Debora
AU  - Chiu, Sophia
AU  - Greenhalgh, David
AU  - Cho, Kiho
PY  - 2016/Apr/11
TI  - Genomic landscapes of endogenous retroviruses unveil intricate genetics of conventional and genetically-engineered laboratory mouse strains.
T2  - Exp. Mol. Pathol.
JO  - Experimental and molecular pathology
SP  - 248
EP  - 256
VL  - 100
IS  - 2
N2  - Laboratory strains of mice, both conventional and genetically engineered, have been introduced as critical components of a broad range of studies investigating normal and disease biology. Currently, the genetic identity of laboratory mice is primarily confirmed by surveying polymorphisms in selected sets of "conventional" genes and/or microsatellites in the absence of a single completely sequenced mouse genome. First, we examined variations in the genomic landscapes of transposable repetitive elements, named the TREome, in conventional and genetically engineered mouse strains using murine leukemia virus-type endogenous retroviruses (MLV-ERVs) as a probe. A survey of the genomes from 56 conventional strains revealed strain-specific TREome landscapes, and certain families (e.g., C57BL) of strains were discernible with defined patterns. Interestingly, the TREome landscapes of C3H/HeJ (toll-like receptor-4 [TLR4] mutant) inbred mice were different from its control C3H/HeOuJ (TLR4 wild-type) strain. In addition, a CD14 knock-out strain had a distinct TREome landscape compared to its control/backcross C57BL/6J strain. Second, an examination of superantigen (SAg, a "TREome gene") coding sequences of mouse mammary tumor virus-type ERVs in the genomes of the 46 conventional strains revealed a high diversity, suggesting a potential role of SAgs in strain-specific immune phenotypes. The findings from this study indicate that unexplored and intricate genomic variations exist in laboratory mouse strains, both conventional and genetically engineered. The TREome-based high-resolution genetics surveillance system for laboratory mice would contribute to efficient study design with quality control and accurate data interpretation. This genetics system can be easily adapted to other species ranging from plants to humans.
SN  - 1096-0945
UR  - http://dx.doi.org/10.1016/j.yexmp.2016.01.005
UR  - http://www.ncbi.nlm.nih.gov/pubmed/26779669
ID  - Lee2016
ER  - 
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