Transposable Elements: Epigenetic Silencing Mechanisms or Modulating Tools for Vertebrate Adaptations? Two Sides of the Same Coin

Transposable elements constitute one of the main components of eukaryotic genomes. Invertebrates, they differ in content, typology, and family diversity and played a crucial role in theevolution of this taxon. However, due to their transposition ability, TEs can be responsible for genomeinstability, and thus silencing mechanisms were evolved to allow the coexistence between TEs andeukaryotic host-coding genes. Several papers are highlighting in TEs the presence of regulatoryelements involved in regulating nearby genes in a tissue-specific fashion. This suggests that TEs arenot sequenced merely to silence; rather, they can be domesticated for the regulation of host-codinggene expression, permitting species adaptation and resilience as well as ensuring human health. Thisreview presents the main silencing mechanisms acting in vertebrates and the importance of exploitingthese mechanisms for TE control to rewire gene expression networks, challenging the general view ofTEs as threatening elements.