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PMID: 28218897 Published · ppublish English Journal Article

Mapping DNA methylation with high-throughput nanopore sequencing.

Nature methods ·Vol. 14 ·No. 4 ·2017-04-00 ·Pages 411-413

Rand AC, Jain M, Eizenga JM, Musselman-Brown A, Olsen HE, Akeson M, Paten B

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.

MeSH Terms
5-Methylcytosine/analysis,metabolism DNA Methylation Escherichia coli/genetics Genome, Bacterial High-Throughput Nucleotide Sequencing/instrumentation,methods Markov Chains Models, Genetic Nanopores
Chemicals
5-Methylcytosine
Authors & Affiliations
7 authors, click to expand affiliations / ORCID
Rand Arthur C
Department of Biomolecular Engineering and Genomics Institute, University of California, Santa Cruz, Santa Cruz, California, USA.
Jain Miten
Department of Biomolecular Engineering and Genomics Institute, University of California, Santa Cruz, Santa Cruz, California, USA.
Eizenga Jordan M ORCID
Department of Biomolecular Engineering and Genomics Institute, University of California, Santa Cruz, Santa Cruz, California, USA.
Musselman-Brown Audrey
Department of Biomolecular Engineering and Genomics Institute, University of California, Santa Cruz, Santa Cruz, California, USA.
Olsen Hugh E
Department of Biomolecular Engineering and Genomics Institute, University of California, Santa Cruz, Santa Cruz, California, USA.
Akeson Mark
Department of Biomolecular Engineering and Genomics Institute, University of California, Santa Cruz, Santa Cruz, California, USA.
Paten Benedict
Department of Biomolecular Engineering and Genomics Institute, University of California, Santa Cruz, Santa Cruz, California, USA.
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Article Info
Journal
Nature methods
Abbr.
Nat Methods
ISSN
1548-7105
DOI
10.1038/nmeth.4189
Published
2017-04-00
Epub
2017-00-20
Pages
411-413
Language
English
Region
United States
NLM ID
101215604
PMCID
PMC5704956
Subset
IM
Grants
NHGRI NIH HHS · R01 HG006321 · United States
NHGRI NIH HHS · R01 HG007827 · United States
NHGRI NIH HHS · U41 HG007234 · United States
NHGRI NIH HHS · U54 HG007990 · United States
Corrections
CommentIn
PMID: 28293030
CommentIn
PMID: 28362434
External Links
PubMed source DOI: 10.1038/nmeth.4189 PMC Full Text View journal details
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