Detecting DNA cytosine methylation using nanopore sequencing

Jared T Simpson; Rachael E Workman; P C Zuzarte; Matei David; L J Dursi; Winston Timp

doi:10.1038/nmeth.4184

Detecting DNA cytosine methylation using nanopore sequencing

Nat Methods. 2017 Apr;14(4):407-410. doi: 10.1038/nmeth.4184. Epub 2017 Feb 20.

Authors

Jared T Simpson^{1

2}, Rachael E Workman³, P C Zuzarte¹, Matei David¹, L J Dursi¹, Winston Timp³

Affiliations

¹ Ontario Institute for Cancer Research, Toronto, Ontario, Canada.
² Department of Computer Science, University of Toronto, Toronto, Ontario, Canada.
³ Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, USA.

PMID: 28218898
DOI: 10.1038/nmeth.4184

Abstract

In nanopore sequencing devices, electrolytic current signals are sensitive to base modifications, such as 5-methylcytosine (5-mC). Here we quantified the strength of this effect for the Oxford Nanopore Technologies MinION sequencer. By using synthetically methylated DNA, we were able to train a hidden Markov model to distinguish 5-mC from unmethylated cytosine. We applied our method to sequence the methylome of human DNA, without requiring special steps for library preparation.

MeSH terms

5-Methylcytosine / analysis*
Cell Line, Tumor
CpG Islands
Cytosine / analysis
Cytosine / metabolism*
DNA Methylation*
Escherichia coli / genetics
Genome, Human*
Humans
Markov Chains
Nanopores

Substances

5-Methylcytosine
Cytosine