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ASMdb: a comprehensive database for allele-specific DNA methylation in diverse organisms
DNA methylation is known to be the most stable epigenetic modification and has been extensively studied in relation to cell differentiation, development, X chromosome inactivation and disease. Allele-specific DNA methylation (ASM) is a well-established mechanism for genomic imprinting and regulates...
Autores principales: | , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8728259/ https://www.ncbi.nlm.nih.gov/pubmed/34664666 http://dx.doi.org/10.1093/nar/gkab937 |
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author | Zhou, Qiangwei Guan, Pengpeng Zhu, Zhixian Cheng, Sheng Zhou, Cong Wang, Huanhuan Xu, Qian Sung, Wing-kin Li, Guoliang |
author_facet | Zhou, Qiangwei Guan, Pengpeng Zhu, Zhixian Cheng, Sheng Zhou, Cong Wang, Huanhuan Xu, Qian Sung, Wing-kin Li, Guoliang |
author_sort | Zhou, Qiangwei |
collection | PubMed |
description | DNA methylation is known to be the most stable epigenetic modification and has been extensively studied in relation to cell differentiation, development, X chromosome inactivation and disease. Allele-specific DNA methylation (ASM) is a well-established mechanism for genomic imprinting and regulates imprinted gene expression. Previous studies have confirmed that certain special regions with ASM are susceptible and closely related to human carcinogenesis and plant development. In addition, recent studies have proven ASM to be an effective tumour marker. However, research on the functions of ASM in diseases and development is still extremely scarce. Here, we collected 4400 BS-Seq datasets and 1598 corresponding RNA-Seq datasets from 47 species, including human and mouse, to establish a comprehensive ASM database. We obtained the data on DNA methylation level, ASM and allele-specific expressed genes (ASEGs) and further analysed the ASM/ASEG distribution patterns of these species. In-depth ASM distribution analysis and differential methylation analysis conducted in nine cancer types showed results consistent with the reported changes in ASM in key tumour genes and revealed several potential ASM tumour-related genes. Finally, integrating these results, we constructed the first well-resourced and comprehensive ASM database for 47 species (ASMdb, www.dna-asmdb.com). |
format | Online Article Text |
id | pubmed-8728259 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-87282592022-01-05 ASMdb: a comprehensive database for allele-specific DNA methylation in diverse organisms Zhou, Qiangwei Guan, Pengpeng Zhu, Zhixian Cheng, Sheng Zhou, Cong Wang, Huanhuan Xu, Qian Sung, Wing-kin Li, Guoliang Nucleic Acids Res Database Issue DNA methylation is known to be the most stable epigenetic modification and has been extensively studied in relation to cell differentiation, development, X chromosome inactivation and disease. Allele-specific DNA methylation (ASM) is a well-established mechanism for genomic imprinting and regulates imprinted gene expression. Previous studies have confirmed that certain special regions with ASM are susceptible and closely related to human carcinogenesis and plant development. In addition, recent studies have proven ASM to be an effective tumour marker. However, research on the functions of ASM in diseases and development is still extremely scarce. Here, we collected 4400 BS-Seq datasets and 1598 corresponding RNA-Seq datasets from 47 species, including human and mouse, to establish a comprehensive ASM database. We obtained the data on DNA methylation level, ASM and allele-specific expressed genes (ASEGs) and further analysed the ASM/ASEG distribution patterns of these species. In-depth ASM distribution analysis and differential methylation analysis conducted in nine cancer types showed results consistent with the reported changes in ASM in key tumour genes and revealed several potential ASM tumour-related genes. Finally, integrating these results, we constructed the first well-resourced and comprehensive ASM database for 47 species (ASMdb, www.dna-asmdb.com). Oxford University Press 2021-10-19 /pmc/articles/PMC8728259/ /pubmed/34664666 http://dx.doi.org/10.1093/nar/gkab937 Text en © The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research. 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 non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com |
spellingShingle | Database Issue Zhou, Qiangwei Guan, Pengpeng Zhu, Zhixian Cheng, Sheng Zhou, Cong Wang, Huanhuan Xu, Qian Sung, Wing-kin Li, Guoliang ASMdb: a comprehensive database for allele-specific DNA methylation in diverse organisms |
title | ASMdb: a comprehensive database for allele-specific DNA methylation in diverse organisms |
title_full | ASMdb: a comprehensive database for allele-specific DNA methylation in diverse organisms |
title_fullStr | ASMdb: a comprehensive database for allele-specific DNA methylation in diverse organisms |
title_full_unstemmed | ASMdb: a comprehensive database for allele-specific DNA methylation in diverse organisms |
title_short | ASMdb: a comprehensive database for allele-specific DNA methylation in diverse organisms |
title_sort | asmdb: a comprehensive database for allele-specific dna methylation in diverse organisms |
topic | Database Issue |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8728259/ https://www.ncbi.nlm.nih.gov/pubmed/34664666 http://dx.doi.org/10.1093/nar/gkab937 |
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