Building an atlas of transposable elements reveals the extensive roles of young sine in gene regulation, genetic diversity and complex traits in pigs

Authors: ZHAO, PENGJU - Zhejiang University; GU, LIHONG - Hainan University; GAO, YAHUI - University Of Maryland; PAN, ZHANGYUAN - University Of California, Davis; LIU, LEI - Chinese Academy Of Agricultural Sciences; LI, XINGZHENG - Chinese Academy Of Agricultural Sciences; ZHOU, HUAIJUN - University Of California, Davis; HAN, XINYAN - Zhejiang University; QIAN, LICHUN - Zhejiang University; Liu, Ge - George; FANG, LINGZHAO - University Of Edinburgh; WANG, ZHENGGUANG - Zhejiang University

Submitted to: Communications Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/9/2023
Publication Date: 8/31/2023
Citation: Zhao, P., Gu, L., Gao, Y., Pan, Z., Liu, L., Li, X., Zhou, H., Han, X., Qian, L., Liu, G., Fang, L., Wang, Z. 2023. Building an atlas of transposable elements reveals the extensive roles of young sine in gene regulation, genetic diversity and complex traits in pigs. Communications Biology. 6(1):894. https://doi.org/10.1038/s42003-023-05234-x.
DOI: https://doi.org/10.1038/s42003-023-05234-x

Interpretive Summary: Transposable elements (TEs) are one type of genetic variations, contributing to gene regulation, genetic diversity and complex traits. We built a list of TEs in pigs and found that selected TEs, such as short interspersed nuclear elements (SINEs), were associated with genomic regions of distinct functions across tissues. These results fill our knowledge gaps and provide the foundation for incorporating new knowledge into the future animal breeding program. Farmers, scientist, and policy planners who need improve animal health and production based on genome-enabled animal selection will benefit from this study.

Technical Abstract: Transposable elements (TEs) are an extensive source of genetic polymorphisms and play an indispensable role in chromatin architecture, transcriptional regulatory networks, and DNA modifications. The pig is an important source of animal protein and serves as a biomedical model for humans, yet the functional role of TEs in pigs and their contributions to complex traits are largely unknown. Here, we built a comprehensive catalog of TEs (n = 3,087,929) in pigs by a newly developed pipeline. Through integrating multi-omics data from 21 tissues, we found that SINEs with different ages were significantly associated with genomic regions with distinct functions across tissues. The majority of young SINEs were predominantly silenced by histone modifications and DNA methylation and accessibility. While, the expression of transcripts that were derived from the remaining active young SINEs exhibited strong tissue specificity through cross-examining 3,570 RNA-seq from 79 tissues and cell types. Furthermore, we detected 211,067 polymorphic SINEs (polySINEs) in 374 individuals genome wide, and found that they clearly recapitulated known patterns of population admixture in pigs. Out of them, 340 population-specific polySINEs were associated with local adaptation. Mapping these polySINEs 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 in functional genomics and provide a supplement for genotype-to-phenotype associations and modern breeding in pigs.