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

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.