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Identification of blacklist regions in cattle and pig genomes

文献类型： 外文期刊

作者： Kong, Mei 1 ; Dou, Jingwen 2 ; Liu, Hong 2 ; Xu, Jing 2 ; Zheng, Zhuqing 2 ; Shangguan, Aishao 4 ; Tang, Zhenshuang 6 ; Qi, Xiaolong 1 ; Zhang, Saixian 1 ; Xiang, Yue 2 ; Fu, Yuhua 2 ; Du, Xiaoyong 5 ; Li, Xinyun 2 ; Fu, Liangliang 2 ; Tang, Zhonglin 1 ; Li, Jingjin 1 ;

作者机构： 1.Chinese Acad Agr Sci, Agr Genom Inst Shenzhen, Guangdong Lab Lingnan Modern Agr, Key Lab Livestock & Poultry Multi MARA, Shenzhen 518000, Peoples R China

2.Huazhong Agr Univ, Coll Anim Sci & Technol, Key Lab Agr Anim Genet Breeding & Reprod, Minist Educ, Wuhan 430070, Peoples R China

3.Huazhong Agr Univ, Coll Anim Sci & Technol, Key Lab Swine Genet & Breeding, Minist Agr, Wuhan 430070, Peoples R China

4.Hubei Acad Agr Sci, Inst Anim Sci & Vet Med, Hubei Key Lab Anim Embryo Engn & Mol Breeding, Wuhan 430064, Peoples R China

5.Huazhong Agr Univ, Coll Informat, Wuhan 430070, Peoples R China

6.Yazhouwan Natl Lab, Sanya 572024, Peoples R China

关键词： Cattle; Pigs; ChIP-seq; Blacklist; Genome; Peak calling

期刊名称：GENOMICS （ 影响因子：3.0； 五年影响因子：3.3 ）

ISSN： 0888-7543

年卷期： 2025 年 117 卷 3 期

页码：

收录情况： SCI

摘要： Cattle and pigs are important farm animals and biomedical models for studying human development and diseases. Accurate annotation of their cis-regulatory elements is essential for advancing breeding strategies and biological research. Identifying these elements typically relies on ChIP-seq data, which profiles histone modifications and transcription factors. Although some large-scale ChIP-seq projects have decoded functional genomes in cattle and pigs, no comprehensive blacklist identification has been performed. In this study, we systematically identified and evaluated blacklist regions in cattle and pig genomes using the ENCODE pipeline. We annotated 126.8 Mb and 99.9 Mb of blacklist regions in cattle and pigs, respectively. We found that removing these blacklist regions is a critical quality control measure that can enhance the reliability of ChIP-seq analysis. Overall, our results provide a valuable resource for farm animal research, and we propose eliminating these problematic regions to reduce abnormally high signals and improve downstream analyses.

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