Transposable Elements as a Source of Novel Gene Regulation in Atlantic Salmon (Salmo salar)

Abstract

It has become evident over the last decade that transposable elements play an extensive role in gene regulatory evolution. Their ability to transpose close to genes, while also acting as cis-regulatory elements, permits TEs to insert novel transcription factor binding sites into promoter regions. In this way, TEs may ultimately change the regulatory control of genes and inadvertently rewire entire regulatory networks. However, the majority of TEs found to contain cis-regulatory elements have not proven to be functional. Recently, an analysis of salmonid gene expression evolution discovered that five Tc1/mariner TEs were correlated with genes that had evolved liver-specific increases in expression following a WGD event. In this thesis, we experimentally tested the individual impact of these five TEs on gene regulation by designing and performing reporter assays. We conducted experiments using whole TEs, open chromatin regions of each TE, and motif regions from each TE predicted to be bound by transcription factors. These three potential cis-regulatory elements were cloned into reporter vectors and transfected into Atlantic salmon primary liver cells (Salmo salar). The expression of the reporter gene, firefly luciferase, was then measured and quantified.

Our results clearly showed that none of the tested Tc1/mariners increased the expression of firefly luciferase. It also appears that some of the open chromatin regions within the TEs act as repressors, as they reduced the transcription of the reporter gene. We conclude that these TEs do not directly contribute to the observed liver-specific up-regulation of genes in the Atlantic salmon genome. However, we cannot eliminate the possibility of indirect effects such as epigenetic mechanisms.