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

Area of Science:

• Genomics
• Evolutionary Biology
• Molecular Biology

Background:

• Transposable elements (TEs) are key drivers of genome evolution.
• Whole-genome duplication (WGD) events can lead to significant genomic changes.
• TEs are hypothesized to rewire gene regulation following WGDs.

Purpose of the Study:

• To investigate the gene-regulatory functions of 11 TEs in Atlantic salmon.
• To assess the impact of TE-derived cis-regulatory elements (TE-CREs) on gene expression.
• To evaluate the role of TEs in post-WGD regulatory rewiring.

Main Methods:

• Luciferase reporter assays were performed in primary liver cells of Atlantic salmon (Salmo salar).
• The study analyzed the effects of TE-CREs located in intronic and upstream regions.
• Gene expression changes were measured to determine regulatory functions.

Main Results:

• Canonical Tc1-Mariner elements from intronic regions exhibited no or minor repressive effects on transcription.
• TE-CREs located upstream of transcriptional start sites significantly increased gene expression.
• The findings challenge the extensive role of Tc1-Mariner elements in post-salmonid WGD regulatory rewiring.

Conclusions:

• Specific TE-CREs possess significant gene-regulatory functions in Atlantic salmon.
• The study highlights the potential of certain TEs, beyond Tc1-Mariner, in post-WGD gene regulation.
• TEs contribute to genome evolution by influencing gene expression patterns after WGD events.