Identification of a group of Mus dunni endogenous virus-like endogenous retroviruses from the C57BL/6J mouse genome: pro
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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 Kang-Hoon Lee & Ri-Na You & David G. Greenhalgh & Kiho Cho
Received: 30 July 2012 / Revised: 24 October 2012 / Accepted: 29 October 2012 / Published online: 30 November 2012 # Springer Science+Business Media Dordrecht 2012
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 Responsible Editor: Conly Rieder Electronic supplementary material The online version of this article (doi:10.1007/s10577-012-9322-z) contains supplementary material, which is available to authorized users. K.-H. Lee : D. G. Greenhalgh : K. Cho (*) Department of Surgery, University of California, Davis and Shriners Hospitals for Children Northern California, 2425 Stockton Blvd., Sacramento, CA 95817, USA e-mail: [email protected] R.-N. You Division of Electrical Engineering, School of Electrical Engineering and Computer Science, Korea Advanced Institute of Science and Technology, Daejeon 305-701, South Korea
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
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LTR MaLR MDEV MDL-ERV MLV MmERV MMTV MuERV MuRRS NCBI ORF PBS PERV RLV SERV SINE TRE UA UB
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