数字农科院2.0

Multi-omics analysis reveals critical cis-regulatory roles of transposable elements in livestock genomes

文献类型： 外文期刊

作者： Chao Wang;Bowen Lei;Yongzhou Bao;Zhen Wang;Choulin Chen;Yuanyuan Zhang;Shenghua Qin;Tao Sun;Zhonglin Tang;Yuwen Liu

作者机构：

关键词： （1-1-1）Animals;Genomic analysis;Molecular Genetics;Sequence analysis

期刊名称： iScience

ISSN： 2589-0042

年卷期： 2025 年 28 卷 3 期

页码：

收录情况： SCIE（2025版）

摘要： Transposable elements (TEs) are important sources of genetic and regulatory variation, yet their functional roles in domesticated animals remain insufficiently explored. To address this gap, we comprehensively annotated TE types, ages, and distributions in the genomes of pig (Sus scrofa), cattle (Bos taurus), and chicken (Gallus gallus). Our analysis revealed species-specific patterns in TE abundance, amplification, and activity in modern genomes. By integrating transcriptomic and epigenomic data, we explored the impact of specific TE types on cis-regulatory elements (CREs) and constructed a TE expression atlas across five tissues in all three species. Our findings underscored the critical roles of tissue-specific TE expression and chromatin accessibility in regulating tissue-specific biological processes. Most notably, we developed a computational framework to uncover TE-mediated gene regulatory networks (TE-GRNs). Our findings provide valuable insights into the regulatory functions of TEs in livestock and offer a robust approach for studying TE-GRNs in diverse biological contexts.

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