Mapping DNA methylation with high-throughput nanopore sequencing
Open accessPublished version of a preprint
Abstract
DNA chemical modifications regulate genomic function. We present a framework for mapping cytosine and adenosine methylation with the Oxford Nanopore Technologies MinION using this nanopore sequencer's ionic current signal. We map three cytosine variants and two adenine variants. The results show that our model is sensitive enough to detect changes in genomic DNA methylation levels as a function of growth phase in Escherichia coli.
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Usage of nanopore sequencing reduces sample preparation processes and increases detection speed.
“The usage of this technology reduces sample preparation processes and increases the detection speed (300).”
From Epigenetic Modifications in Stress Response Genes Associated With Childhood Trauma (2019) · cites this paper as [300]
The Abstract says the authors’ methylation-detection method requires no additional sample preparation for MinION experiments using genomic DNA. Online Methods (MinION sequencing) says the R9 protocol has increased sequencing speed relative to R7.3, but does not establish that using nanopore sequencing increases detection speed generally. (LLM, conf=0.85)
Experimental — accuracy not yet measuredNanopore sequencing framework is able to distinguish five types of methylation variants with high-throughput.
“For example, the nanopore sequencing framework, able to distinguish five types of methylation variants with high-throughput (300).”
From Epigenetic Modifications in Stress Response Genes Associated With Childhood Trauma (2019) · cites this paper as [300]
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- Authors
- Rand, A. C., Jain, M., Eizenga, J. M., Musselman-Brown, A., Olsen, H. E., Akeson, M., & Paten, B.
- Affiliations
- University of California, Santa Cruz (US)
- Corresponding author
- Paten, Benedict
- Venue
- Nature Methods
- Published
- 2017-02-20
- Volume
- 14
- Issue
- 4
- Pages
- 411-413
- ISSN
- 1548-7091 (ISSN-L)
- 1548-7105
- PMC
- PMC5704956
- OpenAlex
- W2590641123
- Cited by
- 507
- References
- 36
- Citations by year
- 2026: 41 · 2025: 47 · 2024: 50 · 2023: 43 · 2022: 57 · 2021: 76 · 2020: 52 · 2019: 58 · 2018: 53 · 2017: 26 · 2016: 4
- FWCI
- 21.00
- Type
- journal article
- Language
- en
- Open access
- green
- doi.org
- Licence
- cc-by-nd
- www.springer.com/tdm (tdm)
- Locations
- Nature Methods (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nd)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- Funders
- National Human Genome Research Institute (R01HG007827, R01HG006321, U41HG007234, U54HG007990)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
- Physical Sciences › Engineering › Biomedical Engineering › Nanopore and Nanochannel Transport Studies
- Keywords
- DNA methylation, nanopore sequencing, Oxford Nanopore MinION, hidden Markov models, hierarchical Dirichlet process, Escherichia coli, growth phase, chemical modification of DNA
- MeSH terms
- Escherichia coli, Markov Chains, Models, Genetic, Genome, Bacterial, DNA Methylation, 5-Methylcytosine, Nanopores, High-Throughput Nucleotide Sequencing
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