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Functional validation of transposable element–derived cis-regulatory elements in Atlantic salmon
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...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10085797/ https://www.ncbi.nlm.nih.gov/pubmed/36753570 http://dx.doi.org/10.1093/g3journal/jkad034 |
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author | Sahlström, Hanna M Datsomor, Alex K Monsen, Øystein Hvidsten, Torgeir R Sandve, Simen Rød |
author_facet | Sahlström, Hanna M Datsomor, Alex K Monsen, Øystein Hvidsten, Torgeir R Sandve, Simen Rød |
author_sort | Sahlström, Hanna M |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-10085797 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-100857972023-04-12 Functional validation of transposable element–derived cis-regulatory elements in Atlantic salmon Sahlström, Hanna M Datsomor, Alex K Monsen, Øystein Hvidsten, Torgeir R Sandve, Simen Rød G3 (Bethesda) Investigation 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. Oxford University Press 2023-02-08 /pmc/articles/PMC10085797/ /pubmed/36753570 http://dx.doi.org/10.1093/g3journal/jkad034 Text en © The Author(s) 2023. Published by Oxford University Press on behalf of the Genetics Society of America. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Investigation Sahlström, Hanna M Datsomor, Alex K Monsen, Øystein Hvidsten, Torgeir R Sandve, Simen Rød Functional validation of transposable element–derived cis-regulatory elements in Atlantic salmon |
title | Functional validation of transposable element–derived cis-regulatory elements in Atlantic salmon |
title_full | Functional validation of transposable element–derived cis-regulatory elements in Atlantic salmon |
title_fullStr | Functional validation of transposable element–derived cis-regulatory elements in Atlantic salmon |
title_full_unstemmed | Functional validation of transposable element–derived cis-regulatory elements in Atlantic salmon |
title_short | Functional validation of transposable element–derived cis-regulatory elements in Atlantic salmon |
title_sort | functional validation of transposable element–derived cis-regulatory elements in atlantic salmon |
topic | Investigation |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10085797/ https://www.ncbi.nlm.nih.gov/pubmed/36753570 http://dx.doi.org/10.1093/g3journal/jkad034 |
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