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Longitudinal DNA methylation dynamics as a practical indicator in clinical epigenetics

Authors
  • Komaki, Shohei1
  • Ohmomo, Hideki1
  • Hachiya, Tsuyoshi1
  • Sutoh, Yoichi1
  • Ono, Kanako1
  • Furukawa, Ryohei1, 2
  • Umekage, So1
  • Otsuka-Yamasaki, Yayoi1
  • Tanno, Kozo3, 4
  • Sasaki, Makoto3, 4
  • Shimizu, Atsushi1, 4
  • 1 Iwate Medical University, 1-1-1, Idaidori, Yahaba, Iwate, 028-3694, Japan , Yahaba (Japan)
  • 2 Keio University, 4-1-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa, 223-8521, Japan , Yokohama (Japan)
  • 3 Iwate Medical University, Iwate, Japan , Iwate (Japan)
  • 4 Iwate Medical University, 1-1-1 Idaidori, Yahaba, Shiwa, Iwate, 028-3694, Japan , Yahaba, Shiwa (Japan)
Type
Published Article
Journal
Clinical Epigenetics
Publisher
Springer-Verlag
Publication Date
Dec 13, 2021
Volume
13
Issue
1
Identifiers
DOI: 10.1186/s13148-021-01202-6
Source
Springer Nature
Keywords
Disciplines
  • Epigenetic Biomarkers
License
Green

Abstract

BackgroundOne 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.ResultsThe 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.ConclusionsThis 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.

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