title: Methods for Genome-Wide Methylome Profiling of Campylobacter jejuni.
abstract: Methylation has a profound role in the regulation of numerous biological processes in bacteria including virulence. The study of methylation in bacteria has greatly advanced thanks to next-generation sequencing technologies. These technologies have expedited the process of uncovering unique features of many bacterial methylomes such as characterizing previously uncharacterized methyltransferases, cataloging genome-wide DNA methylations in bacteria, identifying the frequency of methylation at particular genomic loci, and revealing regulatory roles of methylation in the biology of various bacterial species. For instance, methylation has been cited as a potential source for the pathogenicity differences observed in C. jejuni strains with syntenic genomes as seen in recent publications. Here, we describe the methodology for the use of Pacific Biosciences' single molecule real-time (SMRT) sequencing for detecting methylation patterns in C. jejuni and bioinformatics tools to profile its methylome.
authors.affiliation: Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA.
authors.forename: Kathy T
authors.initials: KT
authors.lastname: Mou
authors.affiliation: Pacific Biosciences, Menlo Park, CA, USA.
authors.forename: Tyson A
authors.initials: TA
authors.lastname: Clark
authors.affiliation: Genome Informatics Facility, Office of Biotechnology, Iowa State University, Ames, IA, USA.
authors.forename: Usha K
authors.initials: UK
authors.lastname: Muppirala
authors.affiliation: Genome Informatics Facility, Office of Biotechnology, Iowa State University, Ames, IA, USA.
authors.forename: Andrew J
authors.initials: AJ
authors.lastname: Severin
authors.affiliation: Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, Ames, IA, 50011, USA. pplummer@iastate.edu.|Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, 2426 Lloyd Vet Med Ctr., Ames, IA, 50011, USA. pplummer@iastate.edu.
authors.forename: Paul J
authors.initials: PJ
authors.lastname: Plummer
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D016123:Campylobacter jejuni / Q000235:genetics / Q000378:metabolism* / Q000472:pathogenicity; D019295:Computational Biology / Q000379:methods*; D019175:DNA Methylation; D004269:DNA, Bacterial / Q000235:genetics / Q000378:metabolism*; D044127:Epigenesis, Genetic; D015870:Gene Expression; D020869:Gene Expression Profiling; D016680:Genome, Bacterial; D055106:Genome-Wide Association Study; D008780:Methyltransferases / Q000235:genetics / Q000378:metabolism; D017422:Sequence Analysis, DNA / Q000379:methods*; D014774:Virulence
chemical_list: D001426:Bacterial Proteins; D004269:DNA, Bacterial; D008780:Methyltransferases
keywords: Campylobacter jejuni; Methylation; Methylome; Motif; NGS; PacBio; Pacific Biosciences; REBASE; Restriction modification; SMRT sequencing