Epigenetic motifs distinguishing endogenous from exogenous retroviral integrants

Abstract Retroviruses are subject to epigenetic regulation by the host genome after integrating, similar to vertebrate genes. However, their patterns of integration, and therefore their likely epigenetic regulation, differ between genera. Beta- and gammaretroviruses are two types of simple retroviruses that have a strong tendency to infect germ cells and endogenize. While ancient endogenous retroviruses are often easy to spot due to mutations rendering them non-functional, more recent integrants can maintain the capacity for full viral production, making it sometimes difficult to discern which integrants are exogenous and likely more clinically relevant. Because endogenous retroviruses generally spend a longer time integrated and subject to host epigenetic regulation as proviral DNA, we hypothesized we could show these integrants exhibit sequence differences from their exogenous counterparts, likely resulting from DNA methylation and histone modifications, and that endogenous retroviruses would generally show habituation to host promoters. Therefore, we have used statistical analyses of publicly available sequence data to demonstrate that endogenous retroviral variants exhibit decreased CpG dinucleotide and trinucleotide frequencies over time, and that they will show evidence for loss of motifs associated with ’active’ histone modifications. Close examination of these patterns provides further clues for distinguishing endogenous and exogenous retroviral variants, potentially aiding in the study of retroviruses in less well-characterized wildlife species. Importance Expression of vertebrate genes is regulated by chemical modifications made directly to the DNA or to the proteins associated with it, termed epigenetics. Because retroviruses integrate into DNA, they are subject to the same epigenetic modifications as regular genes. Retroviruses will tend to endogenize, meaning they will become a permanent part of a species’ genome when their hidden DNA is passed down to progeny during reproduction. However, sometimes it is difficult to discern whether a retroviral sequence is endogenous (permanently fixed) or exogenous (an infectious entity). We hypothesized that changes to the retroviral sequences over time after endogenization would result from epigenetic modifications, and that these changes could help distinguish an endogenous retrovirus from an exogenous one. In this paper, we show that changes to the viral sequences associated with epigenetics indeed take place after endogenization.