[张贴报告]Annotation and assessment of functional variants by regulatory regions from epigenomic data in farm animals

Annotation and assessment of functional variants by regulatory regions from epigenomic data in farm animals
编号:137 稿件编号:57 访问权限:仅限参会人 更新:2024-10-28 14:15:01 浏览:66次 张贴报告

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摘要
Single nucleotide polymorphisms (SNPs) and small insertions/deletions (2-50bp) in genomic regulatory regions may impact function, and although widespread, they are largely unexplored in livestock. Over 113 million candidate functional variants were annotated using data from nearly 900 epigenomic datasets across 10 species. The function of variants depends heavily on their influence on regulatory elements. We identified the primary tissues in which functional variants are active by analyzing regulatory signals co-located with these variants, leading to the construction of a comprehensive cis-regulatory element (CRE) map for the pig genomeacross ten spieces. We also identified topologically associating domains (TADs) and loops from 56 Hi-C datasets, using them to associate SNPs with genes. Further integration of single-cell RNA-seq data revealed that different trait-related variants were enriched in different cell types. Therefore, we developed the Integrated Functional Mutation (IFmut) platform(http://www.ifmutants.com:8212) for users to effortlessly navigate and uncover potential function of variants. Our work offers a powerful and flexible platform for the study of genomic variation in farm animals, setting a new benchmark in livestock research and breeding strategies.
 
关键字
SNP, cis-regulatory element, Hi-C,single-cell RNA-seq, database
报告人
孙嘉豪
学生 HZAU

稿件作者
孙嘉豪 HZAU
ZhaoYunxia Huazhong Agriculture University
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