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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

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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.

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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

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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).

Author information

Authors and Affiliations

  1. Department of Surgery, University of California, Davis and Shriners Hospitals for Children Northern California, 2425 Stockton Blvd., Sacramento, CA, 95817, USA

    Kang-Hoon Lee, David G. Greenhalgh & Kiho Cho

  2. Division of Electrical Engineering, School of Electrical Engineering and Computer Science, Korea Advanced Institute of Science and Technology, Daejeon, 305-701, South Korea

    Ri-Na You

Authors
  1. Kang-Hoon Lee
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  2. Ri-Na You
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  3. David G. Greenhalgh
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  4. Kiho Cho
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Corresponding author

Correspondence to Kiho Cho.

Additional information

Responsible Editor: Conly Rieder

Electronic supplementary material

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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)

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)

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)

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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Lee, KH., You, RN., Greenhalgh, D.G. et al. 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. Chromosome Res 20, 859–874 (2012). https://doi.org/10.1007/s10577-012-9322-z

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  • DOI: https://doi.org/10.1007/s10577-012-9322-z

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