title: Genome-wide mapping of methylated adenine residues in pathogenic Escherichia coli using single-molecule real-time sequencing.
abstract: 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.
authors.affiliation: Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota, USA.
authors.forename: Gang
authors.initials: G
authors.lastname: Fang
authors.forename: Diana
authors.initials: D
authors.lastname: Munera
authors.forename: David I
authors.initials: DI
authors.lastname: Friedman
authors.forename: Anjali
authors.initials: A
authors.lastname: Mandlik
authors.forename: Michael C
authors.initials: MC
authors.lastname: Chao
authors.forename: Onureena
authors.initials: O
authors.lastname: Banerjee
authors.forename: Zhixing
authors.initials: Z
authors.lastname: Feng
authors.forename: Bojan
authors.initials: B
authors.lastname: Losic
authors.forename: Milind C
authors.initials: MC
authors.lastname: Mahajan
authors.forename: Omar J
authors.initials: OJ
authors.lastname: Jabado
authors.forename: Gintaras
authors.initials: G
authors.lastname: Deikus
authors.forename: Tyson A
authors.initials: TA
authors.lastname: Clark
authors.forename: Khai
authors.initials: K
authors.lastname: Luong
authors.forename: Iain A
authors.initials: IA
authors.lastname: Murray
authors.forename: Brigid M
authors.initials: BM
authors.lastname: Davis
authors.forename: Alona
authors.initials: A
authors.lastname: Keren-Paz
authors.forename: Andrew
authors.initials: A
authors.lastname: Chess
authors.forename: Richard J
authors.initials: RJ
authors.lastname: Roberts
authors.forename: Jonas
authors.initials: J
authors.lastname: Korlach
authors.forename: Steve W
authors.initials: SW
authors.lastname: Turner
authors.forename: Vipin
authors.initials: V
authors.lastname: Kumar
authors.forename: Matthew K
authors.initials: MK
authors.lastname: Waldor
authors.forename: Eric E
authors.initials: EE
authors.lastname: Schadt
mesh_terms: D044503:5-Methylcytosine / Q000378:metabolism; D000225:Adenine / Q000031:analogs & derivatives / Q000378:metabolism; D001709:Biotechnology; D002874:Chromosome Mapping; D019175:DNA Methylation / Q000235:genetics; D015280:DNA Restriction-Modification Enzymes / Q000172:deficiency / Q000235:genetics / Q000378:metabolism; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D004926:Escherichia coli / Q000235:genetics* / Q000378:metabolism / Q000472:pathogenicity; D005784:Gene Amplification; D017353:Gene Deletion; D016680:Genome, Bacterial; D017422:Sequence Analysis, DNA / Q000379:methods; D013141:Spiro Compounds; D013379:Substrate Specificity
chemical_list: D044503:5-Methylcytosine; D000225:Adenine; D015280:DNA Restriction-Modification Enzymes; D004269:DNA, Bacterial; D013141:Spiro Compounds; C529377:BAS 100; C000730567:6-methyladenine