Genomic environment and digital expression of bovine endogenous retroviruses

In this work, we attempt to identify the location and expression of bovine ERVs and the nature of nearby genes. As many as 1610 bovine genes contain a bovine ERV (BoERV) inserted into their introns. Most of these BoERVs present an antisense orientation, which could be a consequence of the detrimental effects of the sense insertion. Based on the overrepresentation of Gene Ontology terms, we determined that some genes located in the vicinity of BoERVs are related to viral response and chromatin assembly. In addition, we identified some genes that belonged to IFNs that are inserted in or between BoERVs, pointing out a possible role of BoERVs in some gene duplication. Based on EST database mining, significant expression was detected for BoERV genes in the thyroid and in embryos only. Transcription factor binding sites for Rxra, a steroid and thyroid hormone receptor, were detected in three of the most expressed BoERVs in the thyroid glands.