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Spatiotemporal DNA methylome dynamics of the developing mouse fetus
Cytosine DNA methylation is essential for mammalian development but understanding of its spatiotemporal distribution in the developing embryo remains limited(1,2). Here, as part of the mouse Encyclopedia of DNA Elements (ENCODE) project, we profiled 168 methylomes from 12 mouse tissues or organs at...
Autores principales: | , , , , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7398276/ https://www.ncbi.nlm.nih.gov/pubmed/32728242 http://dx.doi.org/10.1038/s41586-020-2119-x |
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author | He, Yupeng Hariharan, Manoj Gorkin, David U. Dickel, Diane E. Luo, Chongyuan Castanon, Rosa G. Nery, Joseph R. Lee, Ah Young Zhao, Yuan Huang, Hui Williams, Brian A. Trout, Diane Amrhein, Henry Fang, Rongxin Chen, Huaming Li, Bin Visel, Axel Pennacchio, Len A. Ren, Bing Ecker, Joseph R. |
author_facet | He, Yupeng Hariharan, Manoj Gorkin, David U. Dickel, Diane E. Luo, Chongyuan Castanon, Rosa G. Nery, Joseph R. Lee, Ah Young Zhao, Yuan Huang, Hui Williams, Brian A. Trout, Diane Amrhein, Henry Fang, Rongxin Chen, Huaming Li, Bin Visel, Axel Pennacchio, Len A. Ren, Bing Ecker, Joseph R. |
author_sort | He, Yupeng |
collection | PubMed |
description | Cytosine DNA methylation is essential for mammalian development but understanding of its spatiotemporal distribution in the developing embryo remains limited(1,2). Here, as part of the mouse Encyclopedia of DNA Elements (ENCODE) project, we profiled 168 methylomes from 12 mouse tissues or organs at 9 developmental stages from embryogenesis to adulthood. We identified 1,808,810 genomic regions that showed variations in CG methylation by comparing the methylomes of different tissues or organs from different developmental stages. These DNA elements predominantly lose CG methylation during fetal development, whereas the trend is reversed after birth. During late stages of fetal development, non-CG methylation accumulated within the bodies of key developmental transcription factor genes, coinciding with their transcriptional repression. Integration of genome-wide DNA methylation, histone modification and chromatin accessibility data enabled us to predict 461,141 putative developmental tissue-specific enhancers, the human orthologues of which were enriched for disease-associated genetic variants. These spatiotemporal epigenome maps provide a resource for studies of gene regulation during tissue or organ progression, and a starting point for investigating regulatory elements that are involved in human developmental disorders. |
format | Online Article Text |
id | pubmed-7398276 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-73982762020-08-17 Spatiotemporal DNA methylome dynamics of the developing mouse fetus He, Yupeng Hariharan, Manoj Gorkin, David U. Dickel, Diane E. Luo, Chongyuan Castanon, Rosa G. Nery, Joseph R. Lee, Ah Young Zhao, Yuan Huang, Hui Williams, Brian A. Trout, Diane Amrhein, Henry Fang, Rongxin Chen, Huaming Li, Bin Visel, Axel Pennacchio, Len A. Ren, Bing Ecker, Joseph R. Nature Article Cytosine DNA methylation is essential for mammalian development but understanding of its spatiotemporal distribution in the developing embryo remains limited(1,2). Here, as part of the mouse Encyclopedia of DNA Elements (ENCODE) project, we profiled 168 methylomes from 12 mouse tissues or organs at 9 developmental stages from embryogenesis to adulthood. We identified 1,808,810 genomic regions that showed variations in CG methylation by comparing the methylomes of different tissues or organs from different developmental stages. These DNA elements predominantly lose CG methylation during fetal development, whereas the trend is reversed after birth. During late stages of fetal development, non-CG methylation accumulated within the bodies of key developmental transcription factor genes, coinciding with their transcriptional repression. Integration of genome-wide DNA methylation, histone modification and chromatin accessibility data enabled us to predict 461,141 putative developmental tissue-specific enhancers, the human orthologues of which were enriched for disease-associated genetic variants. These spatiotemporal epigenome maps provide a resource for studies of gene regulation during tissue or organ progression, and a starting point for investigating regulatory elements that are involved in human developmental disorders. Nature Publishing Group UK 2020-07-29 2020 /pmc/articles/PMC7398276/ /pubmed/32728242 http://dx.doi.org/10.1038/s41586-020-2119-x Text en © The Author(s) 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. |
spellingShingle | Article He, Yupeng Hariharan, Manoj Gorkin, David U. Dickel, Diane E. Luo, Chongyuan Castanon, Rosa G. Nery, Joseph R. Lee, Ah Young Zhao, Yuan Huang, Hui Williams, Brian A. Trout, Diane Amrhein, Henry Fang, Rongxin Chen, Huaming Li, Bin Visel, Axel Pennacchio, Len A. Ren, Bing Ecker, Joseph R. Spatiotemporal DNA methylome dynamics of the developing mouse fetus |
title | Spatiotemporal DNA methylome dynamics of the developing mouse fetus |
title_full | Spatiotemporal DNA methylome dynamics of the developing mouse fetus |
title_fullStr | Spatiotemporal DNA methylome dynamics of the developing mouse fetus |
title_full_unstemmed | Spatiotemporal DNA methylome dynamics of the developing mouse fetus |
title_short | Spatiotemporal DNA methylome dynamics of the developing mouse fetus |
title_sort | spatiotemporal dna methylome dynamics of the developing mouse fetus |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7398276/ https://www.ncbi.nlm.nih.gov/pubmed/32728242 http://dx.doi.org/10.1038/s41586-020-2119-x |
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