OrthReg: a tool to predict <i>cis</i>-regulatory elements based on cross-species orthologous sequence conservation
Yunfei Ma, 中国科学院昆明动物研究所遗传资源与进化国家重点实验室, 云南 昆明 650223, 中国, Cuiping Huang, Fang-Ru Lu, Jinxiu Li, Xu-Man Han, Adeniyi C. Adeola, Yun Gao, Jia-Kun Deng, Hai‐Bing Xie, Ya‐Ping Zhang, 中国科学院大学昆明生命科学院, 云南 昆明 650204, 中国, 中国科学院大学, 北京 100049, 中国, 中国科学院动物进化与遗传前沿交叉卓越创新中心, 云南 昆明 650223, 中国, 云南大学云南生物资源保护与利用国家重点实验室, 云南 昆明 650091, 中国, 云南大学生命科学院云南省高校动物遗传多样性与进化重点实验室, 云南 昆明 650091, 中国
Abstract
<i>Cis</i>-regulatory elements play an important role in the development of traits and disease in organisms ( ; ) and their annotation could facilitate genetic studies. The Encyclopedia of DNA Elements (ENCODE) ( ) and Functional Annotation of Animal Genomes (FAANG) ( ) offer pioneering data on regulatory elements in several species. Currently, however, regulatory element annotation data remain limited for most organisms. In this study, we developed a tool (OrthReg) for annotating conserved orthologous <i>cis</i>-regulatory elements in targeted genomes using an annotated reference genome. Cross-species validation of this annotation tool using human and mouse ENCODE data confirmed the robustness of this strategy. To explore the efficiency of the tool, we annotated the pig genome and identified more than 28 million regulatory annotation records using the reference human ENCODE data. With this regulatory annotation, some putative regulatory non-coding variants were identified within domestication sweeps in European and East Asian pigs. Thus, this tool can utilize data produced by ENCODE, FAANG, and similar projects, and can be easily extended to customized experimental data. The extensive application of this tool will help to identify informative single nucleotide polymorphisms (SNPs) in post-genome-wide association studies and resequencing analysis of organisms with limited regulatory annotation data.