Department of Animal and Aquacultural Sciences, Faculty of Bioscience, Norwegian University of Life Sciences, 1430 Aas, Norway.
Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1430 Aas, Norway.
G3 (Bethesda). 2023 Apr 11;13(4). doi: 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.
转座元件（TEs）被认为在全基因组复制（WGD）后塑造基因组进化中发挥着重要作用，包括基因调控的重新布线。在最近的一项分析中，与鲑鱼科 WGD 约 1 亿年前在肝脏中进化出更高表达水平的重复基因拷贝相关的是，预测的 TE 衍生顺式调控元件（TE-CREs）数量更高。然而，这些 TE-CREs 在体内招募转录因子（TFs）并影响基因表达的能力仍然未知。在这里，我们使用大西洋鲑（Salmo salar）原代肝细胞中的荧光素酶启动子报告基因检测评估了 11 个 TE 的基因调控功能。来自内含子区域的典型 Tc1-Mariner 元件对转录没有或只有很小的抑制作用。然而，转录起始位点上游的其他 TE-CREs 则显著增加了表达。我们的结果质疑了 Tc1-Mariner 超家族中的 TEs 在鲑鱼科 WGD 后具有重大影响的假设，即它们对基因重复的调控重布线有重大影响，但强调了其他 TEs 在大西洋鲑基因组中 WGD 后基因调控重布线中的潜在作用。
