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可变剪接有助于美洲本地适应的家鼠的可塑性和调控差异。

Alternative splicing contributes to plasticity and regulatory divergence in locally adapted house mice from the Americas.

作者信息

Phifer-Rixey Megan, Ward Joseph R, Mack Katya L

机构信息

Department of Biology, Drexel University, Philadelphia, PA, USA.

Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA.

出版信息

bioRxiv. 2025 Jul 7:2025.07.03.662996. doi: 10.1101/2025.07.03.662996.

Abstract

Alternative splicing is a major driver of transcriptome and proteome variation, but the role of alternative splicing in regulatory evolution remains understudied. Alternative splicing can also contribute to phenotypic plasticity, which may be critical when taxa colonize new environments. Here, we investigate variation in alternative splicing among new wild-derived strains of mice from different climates in the Americas on both a standard and high-fat diet. We show that alternative splicing is widespread and highly context-dependent. Comparisons between strains on different diets revealed abundant gene-by-environment interactions affecting alternative splicing, with most genes showing strain- and sex-specific diet responses. More often than not, genes that were differentially spliced between strains were not differentially expressed, adding to evidence that the two regulatory mechanisms often act independently. Moreover, differentially spliced genes were more widely expressed across tissues but also less central to biological networks than differentially expressed genes, suggesting differences in pleiotropic constraint. Importantly, divergence in alternative splicing was found to be predominantly driven by regulatory changes. However, changes affecting splicing make be central to plasticity as they were impacted more by environmental variation. Finally, we performed scans for selection and found that, while genes with splicing divergence more often co-localized with genomic outliers associated with metabolic traits, they were not enriched for genomic outliers. Overall, our results provide evidence that alternative splicing plays an important role in gene regulation in house mice, contributing to adaptation and plasticity.

摘要

可变剪接是转录组和蛋白质组变异的主要驱动因素,但可变剪接在调控进化中的作用仍未得到充分研究。可变剪接也可能导致表型可塑性,这在物种定殖新环境时可能至关重要。在此,我们研究了来自美洲不同气候地区的新野生小鼠品系在标准饮食和高脂饮食条件下的可变剪接变异情况。我们发现可变剪接广泛存在且高度依赖于环境背景。不同饮食条件下品系间的比较揭示了大量影响可变剪接的基因与环境的相互作用,大多数基因表现出品系和性别特异性的饮食反应。通常情况下,品系间差异剪接的基因并不差异表达,这进一步证明了这两种调控机制常常独立发挥作用。此外,差异剪接基因在各组织中的表达更为广泛,但在生物网络中的核心程度低于差异表达基因,这表明在多效性限制方面存在差异。重要的是,发现可变剪接的差异主要由调控变化驱动。然而,影响剪接的变化可能对可塑性至关重要,因为它们受环境变异的影响更大。最后,我们进行了选择扫描,发现虽然剪接差异的基因更常与代谢性状相关联的基因组异常位点共定位,但它们并未在基因组异常位点中富集。总体而言,我们的结果证明可变剪接在家鼠基因调控中发挥重要作用,有助于适应和可塑性。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/bef8/12265563/7e78c8c32473/nihpp-2025.07.03.662996v1-f0001.jpg

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