Volume 41 Issue 4
Jul.  2020
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Yun-Fei Ma, Cui-Ping Huang, Fang-Ru Lu, Jin-Xiu Li, Xu-Man Han, Adeniyi C. Adeola, Yun Gao, Jia-Kun Deng, Hai-Bing Xie, Ya-Ping Zhang. OrthReg: a tool to predict cis-regulatory elements based on cross-species orthologous sequence conservation. Zoological Research, 2020, 41(4): 471-475. doi: 10.24272/j.issn.2095-8137.2020.099
Citation: Yun-Fei Ma, Cui-Ping Huang, Fang-Ru Lu, Jin-Xiu Li, Xu-Man Han, Adeniyi C. Adeola, Yun Gao, Jia-Kun Deng, Hai-Bing Xie, Ya-Ping Zhang. OrthReg: a tool to predict cis-regulatory elements based on cross-species orthologous sequence conservation. Zoological Research, 2020, 41(4): 471-475. doi: 10.24272/j.issn.2095-8137.2020.099

OrthReg: a tool to predict cis-regulatory elements based on cross-species orthologous sequence conservation

doi: 10.24272/j.issn.2095-8137.2020.099
#Authors contributed equally to this work
Funds:  This work was supported by the Chinese Academy of Sciences (XDA24010107), Ministry of Agriculture of China (2016ZX08009003-006), National Natural Science Foundation of China (31621062), Funding for Open Access Charge: Ministry of Agriculture of China (2016ZX08009003-006), and Animal Branch of the Germplasm Bank of Wild Species, Chinese Academy of Sciences (Large Research Infrastructure Funding)
More Information
  • Cis-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 cis-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.

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