λ-carrageenan-induced inflammation modulates transposable element expression in skin and brain of gilthead seabream (Sparus aurata)

Transposable elements are major components of teleost genomes. However, their transcriptional regulation during inflammatory responses has not been investigated in vivo in teleosts. In this study, we used a λ-carrageenan model of sterile inflammation in gilthead seabream and analysed skin and brain RNA-seq data using a workflow that jointly quantified transcripts derived from TE families and host genes. This study aimed to determine whether λ-carrageenan alters TE family transcription as part of an integrated response to inflammation. Under basal conditions, we detected widespread transcription from Class I and Class II TE families in each tissue. Following λ-carrageenan injection, differential expression analysis identified a limited but consistent TE response. In skin, 19 TE families and 1035 genes were differentially expressed, whereas in the brain, 15 TE families and 874 genes changed expression. When grouping TEs at the class level, the skin response was characterised by a predominance of induced Class II elements, whereas the brain response was characterised by repressed Class I TE families. Differentially expressed TE families were distributed across all the chromosomes and frequently occurred in genomic regions that also contained differentially expressed genes. Functional enrichment analysis suggested that genes near the regulated TEs were mainly related to metabolic pathways in skin and adaptive immune functions in brain. These findings suggest that inflammation could be associated with differential transcription of a subset of TE families in these tissues. These results a new perspective on the relationship between TEs and the immune system of fish of interest in aquaculture.