Genomic context determines the effect of DNA methylation on gene expression in the gut epithelium of Atlantic salmon (Salmo salar)
The canonical view of DNA methylation, a pivotal epigenetic regulation mechanism in eukaryotes, dictates its role as a suppressor of gene activity, particularly within promoter regions. However, this view is being challenged as it is becoming increasingly evident that the connection between DNA meth...
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ftdoajarticles:oai:doaj.org/article:382872e064a9439eacf75226e7e4b3ac 2024-09-15T17:56:06+00:00 Genomic context determines the effect of DNA methylation on gene expression in the gut epithelium of Atlantic salmon (Salmo salar) Aikaterini Katirtzoglou Søren B. Hansen Harald Sveier Michael D. Martin Jaelle C. Brealey Morten T. Limborg 2024-12-01T00:00:00Z https://doi.org/10.1080/15592294.2024.2392049 https://doaj.org/article/382872e064a9439eacf75226e7e4b3ac EN eng Taylor & Francis Group https://www.tandfonline.com/doi/10.1080/15592294.2024.2392049 https://doaj.org/toc/1559-2294 https://doaj.org/toc/1559-2308 doi:10.1080/15592294.2024.2392049 1559-2308 1559-2294 https://doaj.org/article/382872e064a9439eacf75226e7e4b3ac Epigenetics, Vol 19, Iss 1 (2024) DNA methylation salmon WGBS RNA-seq gut epigenetics Genetics QH426-470 article 2024 ftdoajarticles https://doi.org/10.1080/15592294.2024.2392049 2024-08-26T15:21:16Z The canonical view of DNA methylation, a pivotal epigenetic regulation mechanism in eukaryotes, dictates its role as a suppressor of gene activity, particularly within promoter regions. However, this view is being challenged as it is becoming increasingly evident that the connection between DNA methylation and gene expression varies depending on the genomic location and is therefore more complex than initially thought. We examined DNA methylation levels in the gut epithelium of Atlantic salmon (Salmo salar) using whole-genome bisulfite sequencing, which we correlated with gene expression data from RNA sequencing of the same gut tissue sample (RNA-seq). Assuming epigenetic signals might be pronounced between distinctive phenotypes, we compared large and small fish, finding 22 significant associations between 22 differentially methylated regions and 21 genes. We did not detect significant methylation differences between large and small fish. However, we observed a consistent signal of methylation levels around the transcription start sites (TSS), being negatively correlated with the expression levels of those genes. We found both negative and positive associations of methylation levels with gene expression further upstream or downstream of the TSS, revealing a more unpredictable pattern. The 21 genes showing significant methylation-expression correlations were involved in biological processes related to salmon health, such as growth and immune responses. Deciphering how DNA methylation affects the expression of such genes holds great potential for future applications. For instance, our results suggest the importance of genomic context in targeting epigenetic modifications to improve the welfare of aquaculture species like Atlantic salmon. Article in Journal/Newspaper Atlantic salmon Salmo salar Directory of Open Access Journals: DOAJ Articles Epigenetics 19 1 |
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Open Polar |
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Directory of Open Access Journals: DOAJ Articles |
op_collection_id |
ftdoajarticles |
language |
English |
topic |
DNA methylation salmon WGBS RNA-seq gut epigenetics Genetics QH426-470 |
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DNA methylation salmon WGBS RNA-seq gut epigenetics Genetics QH426-470 Aikaterini Katirtzoglou Søren B. Hansen Harald Sveier Michael D. Martin Jaelle C. Brealey Morten T. Limborg Genomic context determines the effect of DNA methylation on gene expression in the gut epithelium of Atlantic salmon (Salmo salar) |
topic_facet |
DNA methylation salmon WGBS RNA-seq gut epigenetics Genetics QH426-470 |
description |
The canonical view of DNA methylation, a pivotal epigenetic regulation mechanism in eukaryotes, dictates its role as a suppressor of gene activity, particularly within promoter regions. However, this view is being challenged as it is becoming increasingly evident that the connection between DNA methylation and gene expression varies depending on the genomic location and is therefore more complex than initially thought. We examined DNA methylation levels in the gut epithelium of Atlantic salmon (Salmo salar) using whole-genome bisulfite sequencing, which we correlated with gene expression data from RNA sequencing of the same gut tissue sample (RNA-seq). Assuming epigenetic signals might be pronounced between distinctive phenotypes, we compared large and small fish, finding 22 significant associations between 22 differentially methylated regions and 21 genes. We did not detect significant methylation differences between large and small fish. However, we observed a consistent signal of methylation levels around the transcription start sites (TSS), being negatively correlated with the expression levels of those genes. We found both negative and positive associations of methylation levels with gene expression further upstream or downstream of the TSS, revealing a more unpredictable pattern. The 21 genes showing significant methylation-expression correlations were involved in biological processes related to salmon health, such as growth and immune responses. Deciphering how DNA methylation affects the expression of such genes holds great potential for future applications. For instance, our results suggest the importance of genomic context in targeting epigenetic modifications to improve the welfare of aquaculture species like Atlantic salmon. |
format |
Article in Journal/Newspaper |
author |
Aikaterini Katirtzoglou Søren B. Hansen Harald Sveier Michael D. Martin Jaelle C. Brealey Morten T. Limborg |
author_facet |
Aikaterini Katirtzoglou Søren B. Hansen Harald Sveier Michael D. Martin Jaelle C. Brealey Morten T. Limborg |
author_sort |
Aikaterini Katirtzoglou |
title |
Genomic context determines the effect of DNA methylation on gene expression in the gut epithelium of Atlantic salmon (Salmo salar) |
title_short |
Genomic context determines the effect of DNA methylation on gene expression in the gut epithelium of Atlantic salmon (Salmo salar) |
title_full |
Genomic context determines the effect of DNA methylation on gene expression in the gut epithelium of Atlantic salmon (Salmo salar) |
title_fullStr |
Genomic context determines the effect of DNA methylation on gene expression in the gut epithelium of Atlantic salmon (Salmo salar) |
title_full_unstemmed |
Genomic context determines the effect of DNA methylation on gene expression in the gut epithelium of Atlantic salmon (Salmo salar) |
title_sort |
genomic context determines the effect of dna methylation on gene expression in the gut epithelium of atlantic salmon (salmo salar) |
publisher |
Taylor & Francis Group |
publishDate |
2024 |
url |
https://doi.org/10.1080/15592294.2024.2392049 https://doaj.org/article/382872e064a9439eacf75226e7e4b3ac |
genre |
Atlantic salmon Salmo salar |
genre_facet |
Atlantic salmon Salmo salar |
op_source |
Epigenetics, Vol 19, Iss 1 (2024) |
op_relation |
https://www.tandfonline.com/doi/10.1080/15592294.2024.2392049 https://doaj.org/toc/1559-2294 https://doaj.org/toc/1559-2308 doi:10.1080/15592294.2024.2392049 1559-2308 1559-2294 https://doaj.org/article/382872e064a9439eacf75226e7e4b3ac |
op_doi |
https://doi.org/10.1080/15592294.2024.2392049 |
container_title |
Epigenetics |
container_volume |
19 |
container_issue |
1 |
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1810432319072239616 |