Longitudinal DNA methylation dynamics as a practical indicator in clinical epigenetics.

DNA Methylation / genetics Epigenomics / methods Humans
Blood DNA methylation EWAS marker likelihood Illumina 450 K beadchip Temporal stability

Journal

Clinical epigenetics
ISSN: 1868-7083
Titre abrégé: Clin Epigenetics
Pays: Germany
ID NLM: 101516977

Informations de publication

Date de publication:
13 12 2021
Historique:
received: 13 07 2021
accepted: 24 11 2021
entrez: 14 12 2021
pubmed: 15 12 2021
medline: 1 2 2022
Statut: epublish

Résumé

One of the fundamental assumptions of DNA methylation in clinical epigenetics is that DNA methylation status can change over time with or without interplay with environmental and clinical conditions. However, little is known about how DNA methylation status changes over time under ordinary environmental and clinical conditions. In this study, we revisited the high frequency longitudinal DNA methylation data of two Japanese males (24 time-points within three months) and characterized the longitudinal dynamics. The results showed that the majority of CpGs on Illumina HumanMethylation450 BeadChip probe set were longitudinally stable over the time period of three months. Focusing on dynamic and stable CpGs extracted from datasets, dynamic CpGs were more likely to be reported as epigenome-wide association study (EWAS) markers of various traits, especially those of immune- and inflammatory-related traits; meanwhile, the stable CpGs were enriched in metabolism-related genes and were less likely to be EWAS markers, indicating that the stable CpGs are stable both in the short-term within individuals and under various environmental and clinical conditions. This study indicates that CpGs with different stabilities are involved in different functions and traits, and thus, they are potential indicators that can be applied for clinical epigenetic studies to outline underlying mechanisms.

Sections du résumé

BACKGROUND
One of the fundamental assumptions of DNA methylation in clinical epigenetics is that DNA methylation status can change over time with or without interplay with environmental and clinical conditions. However, little is known about how DNA methylation status changes over time under ordinary environmental and clinical conditions. In this study, we revisited the high frequency longitudinal DNA methylation data of two Japanese males (24 time-points within three months) and characterized the longitudinal dynamics.
RESULTS
The results showed that the majority of CpGs on Illumina HumanMethylation450 BeadChip probe set were longitudinally stable over the time period of three months. Focusing on dynamic and stable CpGs extracted from datasets, dynamic CpGs were more likely to be reported as epigenome-wide association study (EWAS) markers of various traits, especially those of immune- and inflammatory-related traits; meanwhile, the stable CpGs were enriched in metabolism-related genes and were less likely to be EWAS markers, indicating that the stable CpGs are stable both in the short-term within individuals and under various environmental and clinical conditions.
CONCLUSIONS
This study indicates that CpGs with different stabilities are involved in different functions and traits, and thus, they are potential indicators that can be applied for clinical epigenetic studies to outline underlying mechanisms.

Identifiants

DOI: 10.1186/s13148-021-01202-6 PMID: 34903243 PMC: PMC8670275
pubmed: 34903243
doi: 10.1186/s13148-021-01202-6
pii: 10.1186/s13148-021-01202-6
pmc: PMC8670275
doi:

Types de publication

Journal Article Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Pagination

219

Informations de copyright

© 2021. The Author(s).

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Auteurs

Shohei Komaki (S)

Division of Biomedical Information Analysis, Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University, 1-1-1, Idaidori, Yahaba, Iwate, 028-3694, Japan.

Hideki Ohmomo (H)

Division of Biomedical Information Analysis, Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University, 1-1-1, Idaidori, Yahaba, Iwate, 028-3694, Japan.

Tsuyoshi Hachiya (T)

Division of Biomedical Information Analysis, Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University, 1-1-1, Idaidori, Yahaba, Iwate, 028-3694, Japan.

Yoichi Sutoh (Y)

Division of Biomedical Information Analysis, Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University, 1-1-1, Idaidori, Yahaba, Iwate, 028-3694, Japan.

Kanako Ono (K)

Division of Biomedical Information Analysis, Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University, 1-1-1, Idaidori, Yahaba, Iwate, 028-3694, Japan.

Ryohei Furukawa (R)

Division of Biomedical Information Analysis, Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University, 1-1-1, Idaidori, Yahaba, Iwate, 028-3694, Japan.
Department of Biology, Research and Education Center for Natural Sciences, Keio University, 4-1-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa, 223-8521, Japan.

So Umekage (S)

Division of Biomedical Information Analysis, Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University, 1-1-1, Idaidori, Yahaba, Iwate, 028-3694, Japan.

Yayoi Otsuka-Yamasaki (Y)

Division of Biomedical Information Analysis, Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University, 1-1-1, Idaidori, Yahaba, Iwate, 028-3694, Japan.

Kozo Tanno (K)

Division of Clinical Research and Epidemiology, Iwate Tohoku Medical Megabank Organization, Iwate Medical University, Iwate, Japan.
Department of Hygiene and Preventive Medicine, Iwate Medical University, 1-1-1 Idaidori, Yahaba, Shiwa, Iwate, 028-3694, Japan.

Makoto Sasaki (M)

Iwate Tohoku Medical Megabank Organization, Iwate Medical University, Iwate, Japan.
Division of Ultrahigh Field MRI, Institute for Biomedical Sciences, Iwate Medical University, 1-1-1 Idaidori, Yahaba, Shiwa, Iwate, 028-3694, Japan.

Atsushi Shimizu (A)

Division of Biomedical Information Analysis, Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University, 1-1-1, Idaidori, Yahaba, Iwate, 028-3694, Japan. ashimizu@iwate-med.ac.jp.
Division of Biomedical Information Analysis, Institute for Biomedical Sciences, Iwate Medical University, 1-1-1 Idaidori, Yahaba, Shiwa, Iwate, 028-3694, Japan. ashimizu@iwate-med.ac.jp.
ORCID: 0000-0001-8307-2461

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Classifications MeSH

questionsmedicales.fr › Phénomènes génétiques › Méthylation de l'ADN › Longitudinal DNA methylation dynamics as a...
questionsmedicales.fr › Disciplines des sciences naturelles › Disciplines des sciences biologiques › Biologie › Génétique › Génomique › Épigénomique › Longitudinal DNA methylation dynamics as a...
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