Endogenous feline leukemia virus long terminal repeat integration site diversity seeds functional genomic variation

Endogenous retroviruses (ERV) are indicators of vertebrate evolutionary history and play important roles as homeostatic regulators. ERV long terminal repeat (LTR) elements may act as cis-activating promoters or trans-activating enhancer elements modifying gene transcription distant from LTR insertion sites. We have previously documented a wide diversity of solo endogenous feline leukemia virus (FeLV) LTR copy number in individual cats, suggesting that activity among these retrotransposable elements may influence susceptibility to pathogens, risk of cancer, and other disease phenotypes. To determine FeLV-LTR variation in cats with differing levels of genetic diversity, we assessed enFeLV-LTR integration site diversity in 20 cats from three different populations with varying degrees of inbreeding. We used a targeted linker-mediated PCR approach to deep sequence LTR integration sites, mapped host gene segments within 1 Mb, and performed RNA-sequencing to examine differential gene expression. A total of 2,704 LTR integration sites were mapped representing 765 individual integration sites unequally represented among all 20 cats (range 34-304; average 135). We identified three commonly shared LTR integration sites among all 20 individuals (fixed sites), and 412 sites that were only found in one individual (unique sites). The remaining 353 integrations were shared by 2-19 cats (conserved sites). Each individual, with the exception of one cat from the most inbred colony, had at least two unique sites (range 0-85; average 20). When challenged with exogenous FeLV, we found significantly increased expression of both exogenous and endogenous FeLV orthologs, lending further support to previous findings of potential exFeLV-enFeLV interaction. This study assesses FeLV LTR integration sites in individual animals, providing unique transposome genotypes. Further, we document substantial individual variation in LTR integration site locations, even in a highly inbred population, and provide baseline evidence for endogenous retroviral element position influence on host gene transcription.