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Comparative analysis reveals epigenomic evolution related to species traits and genomic imprinting in mammals
DNA methylation is an epigenetic modification that plays a crucial role in various regulatory processes, including gene expression regulation, transposable element repression, and genomic imprinting. However, most studies on DNA methylation have been conducted in humans and other model species, wher...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Elsevier
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10196708/ https://www.ncbi.nlm.nih.gov/pubmed/37215528 http://dx.doi.org/10.1016/j.xinn.2023.100434 |
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author | Hu, Yisi Yuan, Shenli Du, Xin Liu, Jiang Zhou, Wenliang Wei, Fuwen |
author_facet | Hu, Yisi Yuan, Shenli Du, Xin Liu, Jiang Zhou, Wenliang Wei, Fuwen |
author_sort | Hu, Yisi |
collection | PubMed |
description | DNA methylation is an epigenetic modification that plays a crucial role in various regulatory processes, including gene expression regulation, transposable element repression, and genomic imprinting. However, most studies on DNA methylation have been conducted in humans and other model species, whereas the dynamics of DNA methylation across mammals remain poorly explored, limiting our understanding of epigenomic evolution in mammals and the evolutionary impacts of conserved and lineage-specific DNA methylation. Here, we generated and gathered comparative epigenomic data from 13 mammalian species, including two marsupial species, to demonstrate that DNA methylation plays critical roles in several aspects of gene evolution and species trait evolution. We found that the species-specific DNA methylation of promoters and noncoding elements correlates with species-specific traits such as body patterning, indicating that DNA methylation might help establish or maintain interspecies differences in gene regulation that shape phenotypes. For a broader view, we investigated the evolutionary histories of 88 known imprinting control regions across mammals to identify their evolutionary origins. By analyzing the features of known and newly identified potential imprints in all studied mammals, we found that genomic imprinting may function in embryonic development through the binding of specific transcription factors. Our findings show that DNA methylation and the complex interaction between the genome and epigenome have a significant impact on mammalian evolution, suggesting that evolutionary epigenomics should be incorporated to develop a unified evolutionary theory. |
format | Online Article Text |
id | pubmed-10196708 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Elsevier |
record_format | MEDLINE/PubMed |
spelling | pubmed-101967082023-05-20 Comparative analysis reveals epigenomic evolution related to species traits and genomic imprinting in mammals Hu, Yisi Yuan, Shenli Du, Xin Liu, Jiang Zhou, Wenliang Wei, Fuwen Innovation (Camb) Article DNA methylation is an epigenetic modification that plays a crucial role in various regulatory processes, including gene expression regulation, transposable element repression, and genomic imprinting. However, most studies on DNA methylation have been conducted in humans and other model species, whereas the dynamics of DNA methylation across mammals remain poorly explored, limiting our understanding of epigenomic evolution in mammals and the evolutionary impacts of conserved and lineage-specific DNA methylation. Here, we generated and gathered comparative epigenomic data from 13 mammalian species, including two marsupial species, to demonstrate that DNA methylation plays critical roles in several aspects of gene evolution and species trait evolution. We found that the species-specific DNA methylation of promoters and noncoding elements correlates with species-specific traits such as body patterning, indicating that DNA methylation might help establish or maintain interspecies differences in gene regulation that shape phenotypes. For a broader view, we investigated the evolutionary histories of 88 known imprinting control regions across mammals to identify their evolutionary origins. By analyzing the features of known and newly identified potential imprints in all studied mammals, we found that genomic imprinting may function in embryonic development through the binding of specific transcription factors. Our findings show that DNA methylation and the complex interaction between the genome and epigenome have a significant impact on mammalian evolution, suggesting that evolutionary epigenomics should be incorporated to develop a unified evolutionary theory. Elsevier 2023-04-28 /pmc/articles/PMC10196708/ /pubmed/37215528 http://dx.doi.org/10.1016/j.xinn.2023.100434 Text en © 2023 The Author(s) https://creativecommons.org/licenses/by-nc-nd/4.0/This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). |
spellingShingle | Article Hu, Yisi Yuan, Shenli Du, Xin Liu, Jiang Zhou, Wenliang Wei, Fuwen Comparative analysis reveals epigenomic evolution related to species traits and genomic imprinting in mammals |
title | Comparative analysis reveals epigenomic evolution related to species traits and genomic imprinting in mammals |
title_full | Comparative analysis reveals epigenomic evolution related to species traits and genomic imprinting in mammals |
title_fullStr | Comparative analysis reveals epigenomic evolution related to species traits and genomic imprinting in mammals |
title_full_unstemmed | Comparative analysis reveals epigenomic evolution related to species traits and genomic imprinting in mammals |
title_short | Comparative analysis reveals epigenomic evolution related to species traits and genomic imprinting in mammals |
title_sort | comparative analysis reveals epigenomic evolution related to species traits and genomic imprinting in mammals |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10196708/ https://www.ncbi.nlm.nih.gov/pubmed/37215528 http://dx.doi.org/10.1016/j.xinn.2023.100434 |
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