Genome-wide mapping of methylated adenine residues in pathogenic Escherichia coli using single-molecule real-time sequencing
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Single-molecule real-time (SMRT) DNA sequencing allows the systematic detection of chemical modifications such as methylation but has not previously been applied on a genome-wide scale. We used this approach to detect 49,311 putative 6-methyladenine (m6A) residues and 1,407 putative 5-methylcytosine (m5C) residues in the genome of a pathogenic Escherichia coli strain. We obtained strand-specific information for methylation sites and a quantitative assessment of the frequency of methylation at each modified position. We deduced the sequence motifs recognized by the methyltransferase enzymes present in this strain without prior knowledge of their specificity. Furthermore, we found that deletion of a phage-encoded methyltransferase-endonuclease (restriction-modification; RM) system induced global transcriptional changes and led to gene amplification, suggesting that the role of RM systems extends beyond protecting host genomes from foreign DNA.
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Advanced next generation sequencing platforms such as Single Molecule Real-Time sequencing can be employed to reliably detect certain methylation signatures, as done for C. autoethanogenum.
“Advanced next generation sequencing platforms such as Single Molecule Real-Time (SMRT) sequencing can be employed to reliably detect certain methylation signatures (Flusberg et al., 2010; Fang et al., 2012) as it has been done for C. autoethanogenum (Utturkar et al., 2015).”
From Gas Fermentation—A Flexible Platform for Commercial Scale Production of Low-Carbon-Fuels and Chemicals from Waste and Renewable Feedstocks (2016) · cites this paper as Fang et al., 2012
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- Authors
- Fang, G., Munera, D., Friedman, D. I., Mandlik, A., Chao, M. C., Banerjee, O., Feng, Z., Losic, B., Mahajan, M. C., Jabado, O. J., Deikus, G., Clark, T. A., Luong, K., Murray, I. A., Davis, B. M., Keren-Paz, A., Chess, A., Roberts, R. J., Korlach, J., Turner, S. W., Kumar, V., Waldor, M. K., & Schadt, E. E.
- Affiliations
- University of Minnesota (US)
- Brigham and Women's Hospital (US)
- University of Michigan (US)
- Pacific Biosciences (United States) (US)
- Stanford University (US)
- Icahn School of Medicine at Mount Sinai (US)
- New England Biolabs (United States) (US)
- Corresponding author
- Waldor, Matthew K
- Schadt, Eric E
- ORCID
- Venue
- Nature Biotechnology
- Published
- 2012-11-08
- Volume
- 30
- Issue
- 12
- Pages
- 1232-1239
- ISSN
- 0733-222X (ISSN-L)
- 1087-0156
- 1546-1696
- PMC
- PMC3879109
- OpenAlex
- W2025361601
- Cited by
- 360
- References
- 51
- Citations by year
- 2026: 7 · 2025: 21 · 2024: 19 · 2023: 19 · 2022: 24 · 2021: 24 · 2020: 29 · 2019: 30 · 2018: 36 · 2017: 19 · 2016: 25 · 2015: 44 · 2014: 31 · 2013: 25 · 2012: 4
- FWCI
- 13.38
- Type
- journal article
- Language
- en
- Update notices
- erratum (2013-06-10)
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Nature Biotechnology (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Science Foundation (0916439)
- Howard Hughes Medical Institute
- National Institutes of Health
- National Institute of General Medical Sciences (R44GM100560, R44GM105125)
- National Institute of Allergy and Infectious Diseases (R37AI-42347, R37AI042347)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA modifications and cancer
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
- Keywords
- DNA methylation, 6-methyladenine, 5-methylcytosine, Escherichia coli, single-molecule real-time sequencing, restriction-modification systems, gene amplification, gene expression changes, genome-wide methylation mapping
- MeSH terms
- Adenine, Biotechnology, Chromosome Mapping, DNA, Bacterial, Escherichia coli, Gene Amplification, Spiro Compounds, Substrate Specificity, DNA Restriction-Modification Enzymes, Genome, Bacterial, Gene Deletion, Sequence Analysis, DNA, DNA Methylation, 5-Methylcytosine
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