Identification of blacklist regions in cattle and pig genomes

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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Publication Details

Journal
Genomics
Published
2025-03-06
DOI
https://doi.org/10.1016/j.ygeno.2025.111027
Primary Topic
Genetic and phenotypic traits in livestock
Type
article
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article

Identification of blacklist regions in cattle and pig genomes

Jingwen Dou, Zhenshuang Tang, Xiaoyong Du, Yue Xiang et al.
Genomics
Genetic and phenotypic traits in livestock
article

Identification of blacklist regions in cattle and pig genomes

Jingwen Dou, Zhenshuang Tang, Xiaoyong Du, Yue Xiang, Jing Xu, Aishao Shangguan, Saixian Zhang, Zhonglin Tang, Liangliang Fu, Hong Liu, Mei Kong, Yuhua Fu, Xinyun Li, Xiaolong Qi, Zhuqing Zheng, Jingjin Li
article en

Abstract

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.

GenomicsVol. 117(3)
Huazhong Agricultural University (CN), Agricultural Genomics Institute at Shenzhen (CN), Ministry of Agriculture (ID), Chinese Academy of Agricultural Sciences (CN), Hubei Academy of Agricultural Sciences (CN)
Zero hunger
Openalex Percentile: Top 95%
Genetic and phenotypic traits in livestock
DOIOpen Access PDFOpenAlex
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