The DOI matches its Crossref record; 38 of the 38 references it cites were found in a registry or an index.
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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“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]
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Conversion of 5-Methylcytosine to 5-Hydroxymethylcytosine in Mammalian DNA by MLL Partner TET1
Tahiliani, M., Koh, K. P., Shen, Y., Pastor, W. A., Bandukwala, H., Brudno, Y., Agarwal, S., Iyer, L. M., Liu, D. R., Aravind, L., et al. (2009) · Science · doi:10.1126/science.1170116 · Cited by 5,836
Real-Time DNA Sequencing from Single Polymerase Molecules
Eid, J., Fehr, A., Gray, J., Luong, K., Lyle, J., Otto, G., Peluso, P., Rank, D., Baybayan, P., Bettman, B., et al. (2009) · Science · doi:10.1126/science.1162986 · Cited by 3,732
Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine
Ito, S., Shen, L., Dai, Q., Wu, S. C., Collins, L. B., Swenberg, J. A., He, C., & Zhang, Y. (2011) · Science · doi:10.1126/science.1210597 · Cited by 3,451
Characterization of individual polynucleotide molecules using a membrane channel
Kasianowicz, J. J., Brandin, E., Branton, D., & Deamer, D. W. (1996) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.93.24.13770 · Cited by 3,350
Bird, A. (2007) · Nature · doi:10.1038/nature05913 · Cited by 3,011
The Nuclear DNA Base 5-Hydroxymethylcytosine Is Present in Purkinje Neurons and the Brain
Kriaucionis, S., & Heintz, N. (2009) · Science · doi:10.1126/science.1169786 · Cited by 2,700
The potential and challenges of nanopore sequencing
Branton, D., Deamer, D. W., Marziali, A., Bayley, H., Benner, S. A., Butler, T. J., Ventra, M. D., Garaj, S., Hibbs, A. H., Huang, X. C., et al. (2008) · Nature Biotechnology · doi:10.1038/nbt.1495 · Cited by 2,534
Principles and challenges of genome-wide DNA methylation analysis
Laird, P. W. (2010) · Nature Reviews Genetics · doi:10.1038/nrg2732 · Cited by 1,611
Das, P. M., & Singal, R. (2004) · Journal of Clinical Oncology · doi:10.1200/jco.2004.07.151 · Cited by 1,469
Direct detection of DNA methylation during single-molecule, real-time sequencing
Flusberg, B. A., Webster, D. R., Lee, J. H., Travers, K. J., Olivares, E. C., Clark, T. A., Korlach, J., & Turner, S. W. (2010) · Nature Methods · doi:10.1038/nmeth.1459 · Cited by 1,460
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Nanopore sequencing and assembly of a human genome with ultra-long reads
Jain, M., Koren, S., Miga, K. H., Quick, J., Rand, A. C., Sasani, T. A., Tyson, J. R., Beggs, A. D., Dilthey, A. T., Fiddes, I. T., et al. (2018) · Nature Biotechnology · doi:10.1038/nbt.4060 · Cited by 1,892
Nanopore sequencing technology, bioinformatics and applications
Wang, Y., Zhao, Y., Bollas, A., Wang, Y., & Au, K. F. (2021) · Nature Biotechnology · doi:10.1038/s41587-021-01108-x · Cited by 1,863
Three decades of nanopore sequencing
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Cancer biomarker detection: recent achievements and challenges
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Detecting DNA cytosine methylation using nanopore sequencing
Simpson, J. T., Workman, R. E., Zuzarte, P. C., David, M., Dursi, L. J., & Timp, W. (2017) · Nature Methods · doi:10.1038/nmeth.4184 · Cited by 1,149
Metadata
- 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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