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

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-g...

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Autores principales: Son, Keun Hong, Aldonza, Mark Borris D., Nam, A-Reum, Lee, Kang-Hoon, Lee, Jeong-Woon, Shin, Kyung-Ju, Kang, Keunsoo, Cho, Je-Yoel
Formato: Online Artículo Texto
Lenguaje:English
Publicado: American Association for the Advancement of Science 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10321747/
https://www.ncbi.nlm.nih.gov/pubmed/37406108
http://dx.doi.org/10.1126/sciadv.ade3399
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author Son, Keun Hong
Aldonza, Mark Borris D.
Nam, A-Reum
Lee, Kang-Hoon
Lee, Jeong-Woon
Shin, Kyung-Ju
Kang, Keunsoo
Cho, Je-Yoel
author_facet Son, Keun Hong
Aldonza, Mark Borris D.
Nam, A-Reum
Lee, Kang-Hoon
Lee, Jeong-Woon
Shin, Kyung-Ju
Kang, Keunsoo
Cho, Je-Yoel
author_sort Son, Keun Hong
collection PubMed
description 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.
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spelling pubmed-103217472023-07-06 Integrative mapping of the dog epigenome: Reference annotation for comparative intertissue and cross-species studies Son, Keun Hong Aldonza, Mark Borris D. Nam, A-Reum Lee, Kang-Hoon Lee, Jeong-Woon Shin, Kyung-Ju Kang, Keunsoo Cho, Je-Yoel Sci Adv Biomedicine and Life Sciences 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. American Association for the Advancement of Science 2023-07-05 /pmc/articles/PMC10321747/ /pubmed/37406108 http://dx.doi.org/10.1126/sciadv.ade3399 Text en Copyright © 2023 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution NonCommercial License 4.0 (CC BY-NC). https://creativecommons.org/licenses/by-nc/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution-NonCommercial license (https://creativecommons.org/licenses/by-nc/4.0/) , which permits use, distribution, and reproduction in any medium, so long as the resultant use is not for commercial advantage and provided the original work is properly cited.
spellingShingle Biomedicine and Life Sciences
Son, Keun Hong
Aldonza, Mark Borris D.
Nam, A-Reum
Lee, Kang-Hoon
Lee, Jeong-Woon
Shin, Kyung-Ju
Kang, Keunsoo
Cho, Je-Yoel
Integrative mapping of the dog epigenome: Reference annotation for comparative intertissue and cross-species studies
title Integrative mapping of the dog epigenome: Reference annotation for comparative intertissue and cross-species studies
title_full Integrative mapping of the dog epigenome: Reference annotation for comparative intertissue and cross-species studies
title_fullStr Integrative mapping of the dog epigenome: Reference annotation for comparative intertissue and cross-species studies
title_full_unstemmed Integrative mapping of the dog epigenome: Reference annotation for comparative intertissue and cross-species studies
title_short Integrative mapping of the dog epigenome: Reference annotation for comparative intertissue and cross-species studies
title_sort integrative mapping of the dog epigenome: reference annotation for comparative intertissue and cross-species studies
topic Biomedicine and Life Sciences
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10321747/
https://www.ncbi.nlm.nih.gov/pubmed/37406108
http://dx.doi.org/10.1126/sciadv.ade3399
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