IAP retrotransposons contribute to the transcriptional diversity of the murine placenta

Transposable elements (TEs) have made important contributions to the evolution of the placenta, being co-opted to form key placental genes, as well as trophoblast-specific gene regulatory elements. But although multiple TE subfamilies have been shown to act as transcriptional enhancers in early mouse trophoblast development, it remains unclear to what extent TEs regulate placental gene expression after the establishment of a functional foetal–maternal interface. Here, we characterised the TE regulatory and transcriptional landscape in mouse placenta and gauged their evolutionary dynamics. We found that the overall gene regulatory potential of TEs is greatly diminished in differentiated mouse trophoblasts when compared to their stem cell counterpart. However, evolutionarily young intracisternal A-particle elements are highly expressed in the placenta and create several alternative, placenta-specific transcriptional start sites for protein-coding genes. Intracisternal A-particle elements that are active in the placenta drive species-specific expression of associated genes and display wide genetic diversity between mouse strains. These putative co-option events are therefore evolutionarily recent and may represent a prime example of how TE activity can drive fast placental evolution.