IAP retrotransposons contribute to the transcriptional diversity of the murine placenta

Abstract Transposable elements (TEs) have made important contributions to the evolution of the placenta, and are argued to have played a role in the wide inter-species diversification of this critical developmental organ. Co-option of TEs by host genomes has led to the genesis of important placental genes, as well as trophoblast-specific gene regulatory elements. In mice, past work has demonstrated how multiple species-specific TE subfamilies are used as transcriptional enhancers in trophoblast stem cells. However, the involvement of TEs in the regulation of mouse placental gene expression in vivo remains unclear. Here, we characterised the TE regulatory and transcriptional landscape in mouse placenta and gauged their evolutionary dynamics through a comparative approach. We found that overall, TE cis-regulatory activity is greatly diminished in differentiated mouse trophoblast when compared to their stem cell counterpart. On the other hand, evolutionarily young intracisternal A particle (IAP) elements are highly expressed in the placenta and create several alternative, placenta-specific transcriptional start sites for protein-coding genes. Placenta-expressed IAP elements are genetically polymorphic between mouse strains and drive species-specific expression of associated genes. These putative co-option events are therefore recent and may represent a prime example of how TE activity can drive fast placental evolution.