Functional validation of transposable element–derived cis-regulatory elements in Atlantic salmon

• Published in: G3 Genes|Genomes|Genetics
• Main Authors: Sahlström, Hanna M, Datsomor, Alex K, Monsen, Øystein, Hvidsten, Torgeir R, Sandve, Simen Rød
• Format: Text
• Language: English
• Published: Oxford University Press 2023
• Subjects: Investigation; Atlantic salmon; Salmo salar
• Online Access: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10085797/; http://www.ncbi.nlm.nih.gov/pubmed/36753570; https://doi.org/10.1093/g3journal/jkad034

Transposable elements (TEs) are hypothesized to play important roles in shaping genome evolution following whole-genome duplications (WGDs), including rewiring of gene regulation. In a recent analysis, duplicate gene copies that had evolved higher expression in liver following the salmonid WGD ∼100 million years ago were associated with higher numbers of predicted TE-derived cis-regulatory elements (TE-CREs). Yet, the ability of these TE-CREs to recruit transcription factors (TFs) in vivo and impact gene expression remains unknown. Here, we evaluated the gene-regulatory functions of 11 TEs using luciferase promoter reporter assays in Atlantic salmon (Salmo salar) primary liver cells. Canonical Tc1-Mariner elements from intronic regions showed no or small repressive effects on transcription. However, other TE-CREs upstream of transcriptional start sites increased expression significantly. Our results question the hypothesis that TEs in the Tc1-Mariner superfamily, which were extremely active following WGD in salmonids, had a major impact on regulatory rewiring of gene duplicates, but highlights the potential of other TEs in post-WGD rewiring of gene regulation in the Atlantic salmon genome.