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Cited by 450Epigenetics and DNA MethylationGenetic Syndromes and ImprintingGenomics and Chromatin Dynamics

DNA methylation: An epigenetic mark of cellular memory

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Kim, Mirang, Costello, Joseph·2017·Experimental & Molecular Medicine
DOI 10.1038/emm.2017.10PMC PMC6130213
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Abstract

DNA methylation is a stable epigenetic mark that can be inherited through multiple cell divisions. During development and cell differentiation, DNA methylation is dynamic, but some DNA methylation patterns may be retained as a form of epigenetic memory. DNA methylation profiles can be useful for the lineage classification and quality control of stem cells such as embryonic stem cells, induced pluripotent cells and mesenchymal stem cells. During cancer initiation and progression, genome-wide and gene-specific DNA methylation changes occur as a consequence of mutated or deregulated chromatin regulators. Early aberrant DNA methylation states occurring during transformation appear to be retained during tumor evolution. Similarly, DNA methylation differences among different regions of a tumor reflect the history of cancer cells and their response to the tumor microenvironment. Therefore, DNA methylation can be a useful molecular marker for cancer diagnosis and drug treatment. Profiling changes to DNA modification in cells over time may help scientists create personalised cancer treatments. Gene expression can be controlled by the addition of methyl groups to DNA without any change in DNA sequence. This process is vital to healthy cell development, but scientists now know that abnormal DNA methylation plays a role in the progression of diseases like cancer. Joseph Costello at the University of California and Mirang Kim at the Korea Research Institute of Bioscience and Biotechnology reviewed understanding of DNA methylation and showed how cells retain some DNA methylation patterns as a form of memory. This means that the origins of faulty methylation states can be traced in individual tumor cells. Tracking these methylation patterns may help researchers unravel the history of individual tumors, and could inform personalised therapies.

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  • 70% of the promoters of total protein-coding genes are associated with CpG islands, and most of these sequences are demethylated.

    “On the other hand, 70% of the promoters of the total protein-coding genes are associated with CpG islands, and most of these sequences are demethylated [54].”

    From Revisiting Epigenetics Fundamentals and Its Biomedical Implications (2024) · cites this paper as [54]

    The DNA methylation section says approximately 70% of annotated gene promoters are associated with CpG islands and that these islands are largely resistant to DNA methylation. It does not specify protein-coding genes as the denominator for the 70% figure. (LLM, conf=0.83)

    Experimental — accuracy not yet measured

  • In the human genome, between 60% and 80% of the total CpG dinucleotide content (29 million sites) is methylated.

    “Interestingly, in the human genome, between 60% and 80% of the total CpG dinucleotide content (29 million sites) is methylated, and these sites are associated with repetitive sequences, transposable elements, and tissue-specific gene promoters.”

    From Revisiting Epigenetics Fundamentals and Its Biomedical Implications (2024) · cites this paper as [54]

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Authors
Kim, M., & Costello, J.
Affiliations
  • Korea Research Institute of Bioscience and Biotechnology (KR)
  • University of California, San Francisco (US)
Corresponding author
Costello, Joseph
ORCID
Venue
Experimental & Molecular Medicine
Publisher
Springer Science and Business Media LLC
Published
2017-04-28
Volume
49
Issue
4
Pages
e322-e322
ISSN
  • 1226-3613 (ISSN-L)
  • 2092-6413
DOI
10.1038/emm.2017.10
PMC
PMC6130213
OpenAlex
W2609789137
Cited by
450
References
139
Citations by year
2026: 44 · 2025: 62 · 2024: 71 · 2023: 63 · 2022: 49 · 2021: 58 · 2020: 50 · 2019: 33 · 2018: 14 · 2017: 6
FWCI
2.64
Type
journal article
Language
en
Open access
Licence
Locations
  • Experimental & Molecular Medicine (publishedVersion, cc-by-nc-nd)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by-nc-nd)
  • PubMed Central (publishedVersion, cc-by-nc-nd)
  • PubMed (publishedVersion)
  • eScholarship (California Digital Library) (submittedVersion, cc-by-nc-nd)
  • eScholarship (California Digital Library) (submittedVersion)
Funders
  • National Research Foundation
  • Korea Research Institute of Bioscience and Biotechnology
  • National Research Foundation of Korea
  • National Institutes of Health
  • National Cancer Institute (R01CA169316, P50CA097257)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Syndromes and Imprinting
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
Keywords
DNA methylation, epigenetic memory, embryonic stem cells, induced pluripotent stem cells, mesenchymal stem cells, cancer epigenetics, tumor heterogeneity, tumor microenvironment, cancer diagnosis, precision oncology, chromatin regulators, cell differentiation
MeSH terms
Animals, Humans, Stem Cells, DNA Methylation, Epigenesis, Genetic, Cellular Reprogramming

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