Integrative mapping of the dog epigenome: Reference annotation for comparative intertissue and cross-species studies

• Published in: Science advances Vol. 9; no. 27; p. eade3399
• Main Authors: Son, Keun Hong, Aldonza, Mark Borris D, Nam, A-Reum, Lee, Kang-Hoon, Lee, Jeong-Woon, Shin, Kyung-Ju, Kang, Keunsoo, Cho, Je-Yoel
• Format: Journal Article
• Language: English
• Published: United States American Association for the Advancement of Science 07.07.2023
• Subjects: Animals; Biomedicine and Life Sciences; Chromatin - genetics; Dogs; Epigenesis, Genetic; Epigenome; Epigenomics; Genetics; Genome; Histone Code; Regulatory Sequences, Nucleic Acid; SciAdv r-articles; Systems Biology
• ISSN: 2375-2548; 2375-2548
• DOI: 10.1126/sciadv.ade3399

Dogs have become a valuable model in exploring multifaceted diseases and biology relevant to human health. Despite large-scale dog genome projects producing high-quality draft references, a comprehensive annotation of functional elements is still lacking. We addressed this through integrative next-generation sequencing of transcriptomes paired with five histone marks and DNA methylome profiling across 11 tissue types, deciphering the dog's epigenetic code by defining distinct chromatin states, super-enhancer, and methylome landscapes, and thus showed that these regions are associated with a wide range of biological functions and cell/tissue identity. In addition, we confirmed that the phenotype-associated variants are enriched in tissue-specific regulatory regions and, therefore, the tissue of origin of the variants can be traced. Ultimately, we delineated conserved and dynamic epigenomic changes at the tissue- and species-specific resolutions. Our study provides an epigenomic blueprint of the dog that can be used for comparative biology and medical research.