title: Mapping DNA methylation with high-throughput nanopore sequencing.
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.
authors.affiliation: Department of Biomolecular Engineering and Genomics Institute, University of California, Santa Cruz, Santa Cruz, California, USA.
authors.forename: Arthur C
authors.initials: AC
authors.lastname: Rand
authors.affiliation: Department of Biomolecular Engineering and Genomics Institute, University of California, Santa Cruz, Santa Cruz, California, USA.
authors.forename: Miten
authors.initials: M
authors.lastname: Jain
authors.affiliation: Department of Biomolecular Engineering and Genomics Institute, University of California, Santa Cruz, Santa Cruz, California, USA.
authors.forename: Jordan M
authors.identifier: http://orcid.org/0000-0001-8345-8356
authors.initials: JM
authors.lastname: Eizenga
authors.affiliation: Department of Biomolecular Engineering and Genomics Institute, University of California, Santa Cruz, Santa Cruz, California, USA.
authors.forename: Audrey
authors.initials: A
authors.lastname: Musselman-Brown
authors.affiliation: Department of Biomolecular Engineering and Genomics Institute, University of California, Santa Cruz, Santa Cruz, California, USA.
authors.forename: Hugh E
authors.initials: HE
authors.lastname: Olsen
authors.affiliation: Department of Biomolecular Engineering and Genomics Institute, University of California, Santa Cruz, Santa Cruz, California, USA.
authors.forename: Mark
authors.initials: M
authors.lastname: Akeson
authors.affiliation: Department of Biomolecular Engineering and Genomics Institute, University of California, Santa Cruz, Santa Cruz, California, USA.
authors.forename: Benedict
authors.initials: B
authors.lastname: Paten
mesh_terms: D044503:5-Methylcytosine / Q000032:analysis / Q000378:metabolism*; D019175:DNA Methylation; D004926:Escherichia coli / Q000235:genetics; D016680:Genome, Bacterial; D059014:High-Throughput Nucleotide Sequencing / Q000295:instrumentation / Q000379:methods*; D008390:Markov Chains; D008957:Models, Genetic; D058608:Nanopores
chemical_list: D044503:5-Methylcytosine