Transposable elements, immune-related genes and epigenetic context in teleost fish: insights from a systematic review...

Transposable elements (TEs) are dispersed repetitive DNA sequences that constitute a major component of vertebrate genomes. TEs can influence genome organisation by inserting into new sites and by promoting rearrangements through recombination between repeat copies, which can contribute to gene innovation and chromosomal rearrangements. However, such changes may compromise genomic integrity and promote immune-related diseases through persistent activation of inflammatory and carcinogenic pathways. In this context, epigenetic control and immune surveillance are key mechanisms that restrain TE activity in vertebrates. Teleosts represent an early vertebrate lineage in which immune architecture is largely conserved relative to mammals. To date, however, data concerning fish TEs still remain largely unexplored. In this study, we combined a literature review with an extensive BLASTn screening of TE consensus sequences against Actinopterygii entries in GenBank to explore TE sequence matches with immune-related genes in teleost fish. Results revealed frequent TE sequence matches to immune-related loci, including inflammatory molecules, cell-surface and signalling receptors, and antiviral genes. EggNOG annotation and enrichment analysis supported a recurrent association between TE sequences and immune-related annotations, with significant enrichment of immune-related TE-gene associations in six of the eight species analysed. Furthermore, we discuss future directions integrating TE annotation with genomic mapping, epigenetic analyses, TE transcription and immune gene expression to clarify the biological relevance of TE-immune associations in fish. Overall, this systematic review provides a comprehensive perspective on the intricate relationship between TEs, epigenetic regulation, and immune system dynamics in teleost fish, supporting their inclusion in future studies of fish immune regulation, health and aquaculture.