Influence of Endogenous Viral Sequences on Gene Expression

Endogenous viral elements (EVEs) are the heritable sequences present in eukaryotic genomes that have originated from viral nucleotide sequences. EVEs are subdivided into two groups, according to the presence or absence of long terminal repeats (LTRs). EVEs with LTRs are called endogenous retroviruses (ERVs), and they account for approximately 8% of the human genome. EVEs without LTRs seem to be related to non-reverse-transcribing RNA and DNA viruses, and recent studies have revealed that numerous vertebrate genomes contain these non-LTR EVEs. Such EVEs are proposed to play essential roles in gene expression. EVEs can regulate gene expression as cis-regulatory DNA and RNA elements. EVE-derived non-coding RNAs and/or proteins can also influence cell transcriptomes in trans. To maintain cell integrity, cells epigenetically silence the expression of most EVEs, making these elements generally biochemically inert. These epigenetic alterations around the EVE loci can also affect host transcriptomes. Here, we highlight the current knowledge available on the regulatory activities of ERVs and non-retroviral EVEs, especially the EVEs derived from bornaviruses, which are known as endogenous bornavirus-like elements (EBLs). Better knowledge of this area will improve our understanding of gene regulation and also the co-evolution of viruses and their hosts