基因组环境决定了 DNA 甲基化对大西洋鲑(Salmo salar)肠道上皮细胞基因表达的影响。

IF 2.9 3区 生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY
Epigenetics Pub Date : 2024-12-01 Epub Date: 2024-08-16 DOI:10.1080/15592294.2024.2392049
Aikaterini Katirtzoglou, Søren B Hansen, Harald Sveier, Michael D Martin, Jaelle C Brealey, Morten T Limborg
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引用次数: 0

摘要

DNA 甲基化是真核生物中一种关键的表观遗传调控机制,按照传统观点,它的作用是抑制基因活性,尤其是启动子区域内的基因活性。然而,这种观点正在受到挑战,因为越来越明显的是,DNA 甲基化与基因表达之间的联系因基因组位置而异,因此比最初想象的要复杂得多。我们利用全基因组亚硫酸氢盐测序技术研究了大西洋鲑(Salmo salar)肠道上皮细胞的 DNA 甲基化水平,并将其与同一肠道组织样本的 RNA 测序(RNA-seq)得出的基因表达数据进行了关联。假定表观遗传学信号在不同表型之间可能会有明显差异,我们对大鱼和小鱼进行了比较,发现 22 个不同甲基化区域和 21 个基因之间存在显著关联。我们没有在大鱼和小鱼之间发现明显的甲基化差异。但是,我们观察到转录起始位点(TSS)周围的甲基化水平与这些基因的表达水平呈负相关。我们发现甲基化水平与 TSS 上游或下游的基因表达既有负相关,也有正相关,这揭示了一种更难以预测的模式。甲基化与表达呈显著相关的 21 个基因参与了与鲑鱼健康有关的生物过程,如生长和免疫反应。解密 DNA 甲基化如何影响这些基因的表达为未来的应用提供了巨大的潜力。例如,我们的研究结果表明了基因组背景在针对表观遗传修饰以改善大西洋鲑等水产养殖物种的福利方面的重要性。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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 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.

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来源期刊
Epigenetics
Epigenetics 生物-生化与分子生物学
CiteScore
6.80
自引率
2.70%
发文量
82
审稿时长
3-8 weeks
期刊介绍: Epigenetics publishes peer-reviewed original research and review articles that provide an unprecedented forum where epigenetic mechanisms and their role in diverse biological processes can be revealed, shared, and discussed. Epigenetics research studies heritable changes in gene expression caused by mechanisms others than the modification of the DNA sequence. Epigenetics therefore plays critical roles in a variety of biological systems, diseases, and disciplines. Topics of interest include (but are not limited to): DNA methylation Nucleosome positioning and modification Gene silencing Imprinting Nuclear reprogramming Chromatin remodeling Non-coding RNA Non-histone chromosomal elements Dosage compensation Nuclear organization Epigenetic therapy and diagnostics Nutrition and environmental epigenetics Cancer epigenetics Neuroepigenetics
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