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Zexi Cai

Pig genome functional annotation enhances the biological interpretation of complex traits and human disease

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  • Zhangyuan Pan, University of California at Davis
  • ,
  • Yuelin Yao, University of Edinburgh
  • ,
  • Hongwei Yin, Chinese Academy of Agricultural Sciences
  • ,
  • Zexi Cai
  • Ying Wang
  • Lijing Bai, Chinese Academy of Agricultural Sciences
  • ,
  • Colin Kern, University of California at Davis
  • ,
  • Michelle Halstead, University of California at Davis
  • ,
  • Ganrea Chanthavixay, University of California at Davis
  • ,
  • Nares Trakooljul, Leibniz Institute for Farm Animal Biology
  • ,
  • Klaus Wimmers, Leibniz Institute for Farm Animal Biology
  • ,
  • Goutam Sahana
  • Guosheng Su
  • Mogens Sandø Lund
  • Merete Fredholm, University of Copenhagen
  • ,
  • Peter Karlskov-Mortensen, University of Copenhagen
  • ,
  • Catherine W Ernst, Michigan State University
  • ,
  • Pablo Ross, University of California at Davis
  • ,
  • Christopher K Tuggle, Iowa State University
  • ,
  • Lingzhao Fang, University of Edinburgh
  • ,
  • Huaijun Zhou, University of California at Davis

The functional annotation of livestock genomes is crucial for understanding the molecular mechanisms that underpin complex traits of economic importance, adaptive evolution and comparative genomics. Here, we provide the most comprehensive catalogue to date of regulatory elements in the pig (Sus scrofa) by integrating 223 epigenomic and transcriptomic data sets, representing 14 biologically important tissues. We systematically describe the dynamic epigenetic landscape across tissues by functionally annotating 15 different chromatin states and defining their tissue-specific regulatory activities. We demonstrate that genomic variants associated with complex traits and adaptive evolution in pig are significantly enriched in active promoters and enhancers. Furthermore, we reveal distinct tissue-specific regulatory selection between Asian and European pig domestication processes. Compared with human and mouse epigenomes, we show that porcine regulatory elements are more conserved in DNA sequence, under both rapid and slow evolution, than those under neutral evolution across pig, mouse, and human. Finally, we provide biological insights on tissue-specific regulatory conservation, and by integrating 47 human genome-wide association studies, we demonstrate that, depending on the traits, mouse or pig might be more appropriate biomedical models for different complex traits and diseases.

Original languageEnglish
Article number5848
JournalNature Communications
Number of pages15
Publication statusPublished - Dec 2021

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Publisher Copyright: © 2021, The Author(s).

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