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DNA methylation dynamics and dysregulation delineated by high-throughput profiling in the mouse
We have developed a mouse DNA methylation array that contains 296,070 probes representing the diversity of mouse DNA methylation biology. We present a mouse methylation atlas as a rich reference resource of 1,239 DNA samples encompassing distinct tissues, strains, ages, sexes, and pathologies. We de...
Autores principales: | , , , , , , , , , , , , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Elsevier
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9306256/ https://www.ncbi.nlm.nih.gov/pubmed/35873672 http://dx.doi.org/10.1016/j.xgen.2022.100144 |
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author | Zhou, Wanding Hinoue, Toshinori Barnes, Bret Mitchell, Owen Iqbal, Waleed Lee, Sol Moe Foy, Kelly K. Lee, Kwang-Ho Moyer, Ethan J. VanderArk, Alexandra Koeman, Julie M. Ding, Wubin Kalkat, Manpreet Spix, Nathan J. Eagleson, Bryn Pospisilik, John Andrew Szabó, Piroska E. Bartolomei, Marisa S. Vander Schaaf, Nicole A. Kang, Liang Wiseman, Ashley K. Jones, Peter A. Krawczyk, Connie M. Adams, Marie Porecha, Rishi Chen, Brian H. Shen, Hui Laird, Peter W. |
author_facet | Zhou, Wanding Hinoue, Toshinori Barnes, Bret Mitchell, Owen Iqbal, Waleed Lee, Sol Moe Foy, Kelly K. Lee, Kwang-Ho Moyer, Ethan J. VanderArk, Alexandra Koeman, Julie M. Ding, Wubin Kalkat, Manpreet Spix, Nathan J. Eagleson, Bryn Pospisilik, John Andrew Szabó, Piroska E. Bartolomei, Marisa S. Vander Schaaf, Nicole A. Kang, Liang Wiseman, Ashley K. Jones, Peter A. Krawczyk, Connie M. Adams, Marie Porecha, Rishi Chen, Brian H. Shen, Hui Laird, Peter W. |
author_sort | Zhou, Wanding |
collection | PubMed |
description | We have developed a mouse DNA methylation array that contains 296,070 probes representing the diversity of mouse DNA methylation biology. We present a mouse methylation atlas as a rich reference resource of 1,239 DNA samples encompassing distinct tissues, strains, ages, sexes, and pathologies. We describe applications for comparative epigenomics, genomic imprinting, epigenetic inhibitors, patient-derived xenograft assessment, backcross tracing, and epigenetic clocks. We dissect DNA methylation processes associated with differentiation, aging, and tumorigenesis. Notably, we find that tissue-specific methylation signatures localize to binding sites for transcription factors controlling the corresponding tissue development. Age-associated hypermethylation is enriched at regions of Polycomb repression, while hypomethylation is enhanced at regions bound by cohesin complex members. Apc(Min/+) polyp-associated hypermethylation affects enhancers regulating intestinal differentiation, while hypomethylation targets AP-1 binding sites. This Infinium Mouse Methylation BeadChip (version MM285) is widely accessible to the research community and will accelerate high-sample-throughput studies in this important model organism. |
format | Online Article Text |
id | pubmed-9306256 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Elsevier |
record_format | MEDLINE/PubMed |
spelling | pubmed-93062562022-07-22 DNA methylation dynamics and dysregulation delineated by high-throughput profiling in the mouse Zhou, Wanding Hinoue, Toshinori Barnes, Bret Mitchell, Owen Iqbal, Waleed Lee, Sol Moe Foy, Kelly K. Lee, Kwang-Ho Moyer, Ethan J. VanderArk, Alexandra Koeman, Julie M. Ding, Wubin Kalkat, Manpreet Spix, Nathan J. Eagleson, Bryn Pospisilik, John Andrew Szabó, Piroska E. Bartolomei, Marisa S. Vander Schaaf, Nicole A. Kang, Liang Wiseman, Ashley K. Jones, Peter A. Krawczyk, Connie M. Adams, Marie Porecha, Rishi Chen, Brian H. Shen, Hui Laird, Peter W. Cell Genom Resource We have developed a mouse DNA methylation array that contains 296,070 probes representing the diversity of mouse DNA methylation biology. We present a mouse methylation atlas as a rich reference resource of 1,239 DNA samples encompassing distinct tissues, strains, ages, sexes, and pathologies. We describe applications for comparative epigenomics, genomic imprinting, epigenetic inhibitors, patient-derived xenograft assessment, backcross tracing, and epigenetic clocks. We dissect DNA methylation processes associated with differentiation, aging, and tumorigenesis. Notably, we find that tissue-specific methylation signatures localize to binding sites for transcription factors controlling the corresponding tissue development. Age-associated hypermethylation is enriched at regions of Polycomb repression, while hypomethylation is enhanced at regions bound by cohesin complex members. Apc(Min/+) polyp-associated hypermethylation affects enhancers regulating intestinal differentiation, while hypomethylation targets AP-1 binding sites. This Infinium Mouse Methylation BeadChip (version MM285) is widely accessible to the research community and will accelerate high-sample-throughput studies in this important model organism. Elsevier 2022-07-13 /pmc/articles/PMC9306256/ /pubmed/35873672 http://dx.doi.org/10.1016/j.xgen.2022.100144 Text en © 2022 The Author(s) https://creativecommons.org/licenses/by/4.0/This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Resource Zhou, Wanding Hinoue, Toshinori Barnes, Bret Mitchell, Owen Iqbal, Waleed Lee, Sol Moe Foy, Kelly K. Lee, Kwang-Ho Moyer, Ethan J. VanderArk, Alexandra Koeman, Julie M. Ding, Wubin Kalkat, Manpreet Spix, Nathan J. Eagleson, Bryn Pospisilik, John Andrew Szabó, Piroska E. Bartolomei, Marisa S. Vander Schaaf, Nicole A. Kang, Liang Wiseman, Ashley K. Jones, Peter A. Krawczyk, Connie M. Adams, Marie Porecha, Rishi Chen, Brian H. Shen, Hui Laird, Peter W. DNA methylation dynamics and dysregulation delineated by high-throughput profiling in the mouse |
title | DNA methylation dynamics and dysregulation delineated by high-throughput profiling in the mouse |
title_full | DNA methylation dynamics and dysregulation delineated by high-throughput profiling in the mouse |
title_fullStr | DNA methylation dynamics and dysregulation delineated by high-throughput profiling in the mouse |
title_full_unstemmed | DNA methylation dynamics and dysregulation delineated by high-throughput profiling in the mouse |
title_short | DNA methylation dynamics and dysregulation delineated by high-throughput profiling in the mouse |
title_sort | dna methylation dynamics and dysregulation delineated by high-throughput profiling in the mouse |
topic | Resource |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9306256/ https://www.ncbi.nlm.nih.gov/pubmed/35873672 http://dx.doi.org/10.1016/j.xgen.2022.100144 |
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