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Chromosome Research

, Volume 20, Issue 7, pp 859–874 | Cite as

Identification of a group of Mus dunni endogenous virus-like endogenous retroviruses from the C57BL/6J mouse genome: proviral genomes, strain distribution, expression characteristics, and genomic integration profile

  • Kang-Hoon Lee
  • Ri-Na You
  • David G. Greenhalgh
  • Kiho Cho
Article

Abstract

About 10 % of the mouse genome is occupied by sequences associated with endogenous retroviruses (ERVs). However, a comprehensive profile of the mouse ERVs and related elements has not been established yet. In this study, we identified a group of ERVs from the mouse genome and characterized their biological properties. Using a custom ERV mining protocol, 191 ERVs (159 loci reported previously and 32 new loci), tentatively named Mus dunni endogenous virus (MDEV)-like ERVs (MDL-ERVs), were mapped on the C57BL/6J mouse genome. Seven of them retained putative full coding potentials for three retroviral polypeptides (gag, pol, and env). Among the 57 mouse strains examined, all but the Mus pahari/Ei strain had PCR amplicons corresponding to a conserved MDL-ERV region. Interestingly, the Mus caroli/EiJ’s amplicon was somewhat larger than the others, coinciding with a substantial phylogenetic distance between the MDL-ERV populations of M. caroli/EiJ and C57BL/6J strains. MDL-ERVs were highly expressed in the lung, spleen, and thymus of C57BL/6J mice compared to the brain, heart, kidney, and liver. Seven MDL-ERVs were mapped in the introns of six annotated genes. Of interest, some MDL-ERVs were mapped periodically on three clusters in chromosome X. The finding that these MDL-ERVs were one of several types of retroelements, which form mosaic-repeat units of tandem arrays, suggests that the formation of the mosaic-repeat unit preceded the tandem arrangement event. Further studies are warranted to understand the biological roles of MDL-ERVs in both normal and pathologic conditions.

Keywords

MDEV-like ERVs Expression Genome organization Gammaretrovirus-like ERVs 

List of abbreviations

ERV

Endogenous retrovirus

ETn

Early transposon

FeLV

Feline leukemia virus

GALV

Gibbon ape leukemia virus

IAP

Intracisternal A-type particle

KoRV

Koala retrovirus

LINE

Long interspersed nuclear element

LTR

Long terminal repeat

MaLR

Mammalian apparent long terminal repeat retrotransposon

MDEV

Mus dunni endogenous virus

MDL-ERV

Mus dunni endogenous virus-like endogenous retrovirus

MLV

Murine leukemia virus

MmERV

Mus musculus retrovirus

MMTV

Mouse mammary tumor virus

MuERV

Murine endogenous retrovirus

MuRRS

Murine retrovirus-related DNA sequence

NCBI

National Center for Biotechnology Information

ORF

Open reading frame

PBS

Primer binding site

PERV

Porcine endogenous retrovirus

RLV

Rat leukemia virus

SERV

Sus scrofa endogenous retrovirus

SINE

Short interspersed nuclear element

TRE

Transcription regulatory element

UA

Unit of cluster-A

UB

Unit of cluster-B

UC

Unit of cluster-C

VL30

Retrovirus-like 30

Notes

Acknowledgments

This study was supported by grants from Shriners of North America [no. 86800 to KC, no. 84302 to KHL (postdoctoral fellowship)] and the National Institutes of Health (R01 GM071360 to KC).

Supplementary material

10577_2012_9322_MOESM1_ESM.xls (78 kb)
Supplementary Table S1 Characteristics of a group of 191 MDL-ERVs identified from the C57BL/6J mouse genome. The gray highlighted rows indicate the MDL-ERVs which are newly identified in this study. Putative full-length MDL-ERVs are identified with a number sign. Chr chromosome, ORF open reading frame, +/− (strand orientation). ERVs reported in previous studies: *Elfaitouri et al. 2011, **Bromham et al. 2001 (XLS 77 kb)
10577_2012_9322_MOESM2_ESM.xls (58 kb)
Supplementary Table S2 Transcription regulatory element profiles within the MDL-ERV promoter sequences isolated from C57BL/6J and Mus caroli/EiJ mice. Transcription regulatory elements, which are ubiquitous and/or unique for each strain/branch, are presented in separate sections. Two branches (i/ii and iii/iv) from each strain correspond to the ones in Fig. 3a (XLS 58 kb)
10577_2012_9322_MOESM3_ESM.xls (48 kb)
Supplementary Table S3 Annotated genes neighboring (100 kb upstream and downstream) the 80 MDL-ERVs identified in the C57BL/6J mouse genome. The MDL-ERVs, which share the same genomic loci as the previously reported MmERVs, are indicated. The annotated genes harboring the MDL-ERVs in their introns are highlighted in red. Chr chromosome (XLS 48 kb)
10577_2012_9322_MOESM4_ESM.xls (24 kb)
Supplementary Table S 4 Subgroups of the 191 MDL-ERVs. Various subgroups of the 191 MDL-ERVs, which were identified from the C57BL/6J mouse genome, are summarized. All subgroupings were performed based on whether the MDL-ERVs are present in chromosome X or not (XLS 23 kb)

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Copyright information

© Springer Science+Business Media Dordrecht 2012

Authors and Affiliations

  • Kang-Hoon Lee
    • 1
  • Ri-Na You
    • 2
  • David G. Greenhalgh
    • 1
  • Kiho Cho
    • 1
  1. 1.Department of SurgeryUniversity of California, Davis and Shriners Hospitals for Children Northern CaliforniaSacramentoUSA
  2. 2.Division of Electrical Engineering, School of Electrical Engineering and Computer ScienceKorea Advanced Institute of Science and TechnologyDaejeonSouth Korea

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