Journal
NATURE COMMUNICATIONS
Volume 12, Issue 1, Pages -Publisher
NATURE PORTFOLIO
DOI: 10.1038/s41467-021-26153-7
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Funding
- Agriculture and Food Research Initiative Competitive from the USDA National Institute of Food and Agriculture [2018-67015-27501, 2015-67015-22940]
- Multistate Research Project [NRSP8, NC1170]
- California Agricultural Experimental Station
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This study provides a comprehensive catalogue of regulatory elements in the pig genome, highlighting the enrichment of genomic variants associated with complex traits and adaptive evolution in active promoters and enhancers. Tissue-specific regulatory selection differs between Asian and European pig domestication processes, with porcine regulatory elements showing greater conservation in DNA sequence compared to human and mouse genomes. Integrating human genome-wide association studies reveals that mice or pigs may be more suitable biomedical models for different complex traits and diseases, based on tissue-specific regulatory conservation.
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. Annotating functional elements of the genome helps the interpretation of genetic variation. Here, the authors compile functional genomics data for the pig genome over 14 tissues with 15 different chromatin states, integrate the data with WGS and GWAS data, and compare conservation of regulatory elements across mouse and human tissues.
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