Detection and mapping of 5-methylcytosine and 5-hydroxymethylcytosine with nanopore MspA
Open accessAbstract
Significance: Cells attach a methyl group (—CH 3 ) to certain cytosines in DNA to control gene expression. These methylation patterns change over time and can be related to cell differentiation and diseases such as cancer. Existing methylation detection techniques are not ideal for clinical use. We pulled single-stranded DNA molecules through the biological pore MspA and found that ion currents passing through the pore reveal the methylation sites with high confidence. Hydroxymethylation, which differs from methylation by only one oxygen atom, also produces distinct signals. This technique can be developed into a research tool and may ultimately lead to clinical tests.
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Nanopore sequencing is able to detect 5-hmC, which is not adequately covered by traditional array/bisulfite sequencing methods.
“In addition, nanopore sequencing is able to detect 5-hmC (301), which is not adequately covered by traditional array/bisulfite sequencing methods.”
From Epigenetic Modifications in Stress Response Genes Associated With Childhood Trauma (2019) · cites this paper as [301]
The Discussion reports distinct nanopore current signatures for 5-hmC, supporting its detection. The paper also says conventional bisulfite sequencing cannot distinguish 5-hmC from 5-mC, though oxidative bisulfite sequencing can do so with substantial sample loss. It does not assess traditional array methods, so that part of the comparison is unsupported. (LLM, conf=0.86)
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- Authors
- Laszlo, A. H., Derrington, I. M., Brinkerhoff, H., Langford, K. W., Nova, I. C., Samson, J. M., Bartlett, J. J., Pavlenok, M., & Gundlach, J. H.
- Affiliations
- University of Washington (US)
- University of Alabama at Birmingham (US)
- Venue
- Proceedings of the National Academy of Sciences
- Publisher
- National Academy of Sciences
- Published
- 2013-10-28
- Volume
- 110
- Issue
- 47
- Pages
- 18904-18909
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- PMC
- PMC3839702
- OpenAlex
- W2073105380
- Cited by
- 321
- References
- 38
- Citations by year
- 2026: 17 · 2025: 21 · 2024: 32 · 2023: 19 · 2022: 26 · 2021: 38 · 2020: 15 · 2019: 21 · 2018: 21 · 2017: 27 · 2016: 30 · 2015: 33 · 2014: 19 · 2013: 2
- FWCI
- 15.46
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Proceedings of the National Academy of Sciences (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Institutes of Health
- National Human Genome Research Institute (R01HG006321, R01HG005115)
- Topics
- Physical Sciences › Engineering › Biomedical Engineering › Nanopore and Nanochannel Transport Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Nucleic Acid Chemistry
- Keywords
- 5-methylcytosine, 5-hydroxymethylcytosine, DNA methylation, DNA hydroxymethylation, nanopore sequencing, single-molecule detection, epigenetic modifications, ionic currents, phi29 DNA polymerase, DNA strand passage
- MeSH terms
- Bayes Theorem, Cytosine, Models, Molecular, Molecular Structure, Porins, DNA Methylation, 5-Methylcytosine, Epigenomics, Nanopores
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