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

文献类型： 外文期刊

作者： Zhao, Pengju 1 ; Gu, Lihong 3 ; Gao, Yahui 4 ; Pan, Zhangyuan 5 ; Liu, Lei 6 ; Li, Xingzheng 6 ; Zhou, Huaijun 5 ; Yu, Dongyou 1 ; Han, Xinyan 1 ; Qian, Lichun 1 ; Liu, George E. 4 ; Fang, Lingzhao 7 ; Wang, Zhengguang 1 ;

作者机构： 1.Zhejiang Univ, Hainan Inst, Yongyou Ind Pk, Sanya 572000, Peoples R China

2.Zhejiang Univ, Coll Anim Sci, Hangzhou 310058, Zhejiang, Peoples R China

3.Hainan Acad Agr Sci, Inst Anim Sci & Vet Med, 14 Xingdan Rd, Haikou 571100, Peoples R China

4.ARS, Anim Genom & Improvement Lab, Beltsville Agr Res Ctr, USDA, Beltsville, MD 20705 USA

5.Univ Calif Davis, Dept Anim Sci, Davis, CA 95616 USA

6.Chinese Acad Agr Sci, Agr Genom Inst Shenzhen, Minist Agr & Rural Affairs, Shenzhen Branch,Guangdong Lab Lingnan Modern Agr,G, Shenzhen 518124, Peoples R China

7.Aarhus Univ, Ctr Quantitat Genet & Genom, DK-8000 Aarhus, Denmark

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

页码：

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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