Young SINEs in pig genomes impact gene regulation, genetic diversity, and complex traits

文献类型： 外文期刊

第一作者： Zhao, Pengju

作者： Zhao, Pengju;Yu, Dongyou;Han, Xinyan;Qian, Lichun;Wang, Zhengguang;Zhao, Pengju;Yu, Dongyou;Han, Xinyan;Qian, Lichun;Wang, Zhengguang;Gu, Lihong;Gao, Yahui;Liu, George E.;Pan, Zhangyuan;Zhou, Huaijun;Liu, Lei;Li, Xingzheng;Fang, Lingzhao

作者机构：

期刊名称：COMMUNICATIONS BIOLOGY （ 影响因子：5.9； 五年影响因子：6.3 ）

ISSN：

年卷期： 2023 年 6 卷 1 期

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收录情况： SCI

摘要： Transposable elements (TEs) are a major source of genetic polymorphisms and play a role in chromatin architecture, gene regulatory networks, and genomic evolution. However, their functional role in pigs and contributions to complex traits are largely unknown. We created a catalog of TEs (n = 3,087,929) in pigs and found that young SINEs were predominantly silenced by histone modifications, DNA methylation, and decreased accessibility. However, some transcripts from active young SINEs showed high tissue-specificity, as confirmed by analyzing 3570 RNA-seq samples. We also detected 211,067 dimorphic SINEs in 374 individuals, including 340 population-specific ones associated with local adaptation. Mapping these dimorphic SINEs to genome-wide associations of 97 complex traits in pigs, we found 54 candidate genes (e.g., ANK2 and VRTN) that might be mediated by TEs. Our findings highlight the important roles of young SINEs and provide a supplement for genotype-to-phenotype associations and modern breeding in pigs. A catalog of over 3 million transposable elements in pigs reveals that evolutionarily young SINEs are associated with increased epigenomic silencing, and may be related to expression of nearby genes.

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