Insertion of ERE elements in the horse genome and gene expression regulation

The most abundant SINE retrotransposons in the horse genome belong to the ERE family.   We observed that, in the horse population, ERE-1 containing loci are frequently characterized by insertion polymorphism (IP): the probability of IP is particularly high (up to 50%) for ERE-1 loci sharing more than 98% identity with the consensus. We then defined the position of ERE-1 elements relative to genes and found that 44% of them were inserted within introns of validated or putative genes, while 3% of them were located near genes.  To test whether the presence of an ERE-1 element within a promoter can affect gene expression, we carried out reporter gene assays both in human and in horse cell lines in culture. Expression of the eGFP reporter gene was greatly reduced when an ERE-1 element was inserted within a promoter.  In conclusion, these results suggest that the insertion of ERE-1 sequences next to genes may deeply shape the transcriptome of a lineage. In addition, given the high frequency of IP, ERE-1 loci represent a powerful tool for population genetics studies.