title: High resolution mapping of modified DNA nucleobases using excision repair enzymes.
abstract: The incorporation and creation of modified nucleobases in DNA have profound effects on genome function. We describe methods for mapping positions and local content of modified DNA nucleobases in genomic DNA. We combined in vitro nucleobase excision with massively parallel DNA sequencing (Excision-seq) to determine the locations of modified nucleobases in genomic DNA. We applied the Excision-seq method to map uracil in E. coli and budding yeast and discovered significant variation in uracil content, wherein uracil is excluded from the earliest and latest replicating regions of the genome, possibly driven by changes in nucleotide pool composition. We also used Excision-seq to identify sites of pyrimidine dimer formation induced by UV light exposure, where the method could distinguish between sites of cyclobutane and 6-4 photoproduct formation. These UV mapping data enabled analysis of local sequence bias around pyrimidine dimers and suggested a preference for an adenosine downstream from 6-4 photoproducts. The Excision-seq method is broadly applicable for high precision, genome-wide mapping of modified nucleobases with cognate repair enzymes.
authors.affiliation: Department of Biochemistry and Molecular Genetics, Program in Molecular Biology, University of Colorado School of Medicine, Aurora, Colorado 80045, USA.
authors.forename: D Suzi
authors.initials: DS
authors.lastname: Bryan
authors.affiliation: Department of Biochemistry and Molecular Genetics, Program in Molecular Biology, University of Colorado School of Medicine, Aurora, Colorado 80045, USA.
authors.forename: Monica
authors.initials: M
authors.lastname: Ransom
authors.affiliation: Department of Biochemistry and Molecular Genetics, Program in Molecular Biology, University of Colorado School of Medicine, Aurora, Colorado 80045, USA.
authors.forename: Biniam
authors.initials: B
authors.lastname: Adane
authors.affiliation: Department of Biochemistry and Molecular Genetics, Program in Molecular Biology, University of Colorado School of Medicine, Aurora, Colorado 80045, USA.
authors.forename: Kerri
authors.initials: K
authors.lastname: York
authors.affiliation: Department of Biochemistry and Molecular Genetics, Program in Molecular Biology, University of Colorado School of Medicine, Aurora, Colorado 80045, USA jay.hesselberth@ucdenver.edu.
authors.forename: Jay R
authors.initials: JR
authors.lastname: Hesselberth
mesh_terms: D019175:DNA Methylation; D004260:DNA Repair; D045643:DNA Repair Enzymes / Q000737:chemistry* / Q000378:metabolism; D004926:Escherichia coli / Q000235:genetics; D009154:Mutation; D011740:Pyrimidine Dimers / Q000737:chemistry* / Q000235:genetics; D012441:Saccharomyces cerevisiae / Q000235:genetics; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D011740:Pyrimidine Dimers; D045643:DNA Repair Enzymes