title: Ribose-seq: global mapping of ribonucleotides embedded in genomic DNA.
abstract: Abundant ribonucleotide incorporation in DNA during replication and repair has profound consequences for genome stability, but the global distribution of ribonucleotide incorporation is unknown. We developed ribose-seq, a method for capturing unique products generated by alkaline cleavage of DNA at embedded ribonucleotides. High-throughput sequencing of these fragments in DNA from the yeast Saccharomyces cerevisiae revealed widespread ribonucleotide distribution, with a strong preference for cytidine and guanosine, and identified hotspots of ribonucleotide incorporation in nuclear and mitochondrial DNA. Ribonucleotides were primarily incorporated on the newly synthesized leading strand of nuclear DNA and were present upstream of (G+C)-rich tracts in the mitochondrial genome. Ribose-seq is a powerful tool for the systematic profiling of ribonucleotide incorporation in genomic DNA.
authors.affiliation: School of Biology, Georgia Institute of Technology, Atlanta, Georgia, USA.
authors.forename: Kyung Duk
authors.initials: KD
authors.lastname: Koh
authors.affiliation: School of Biology, Georgia Institute of Technology, Atlanta, Georgia, USA.
authors.forename: Sathya
authors.initials: S
authors.lastname: Balachander
authors.affiliation: Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical School, Aurora, Colorado, USA.
authors.forename: Jay R
authors.initials: JR
authors.lastname: Hesselberth
authors.affiliation: School of Biology, Georgia Institute of Technology, Atlanta, Georgia, USA.
authors.forename: Francesca
authors.initials: F
authors.lastname: Storici
mesh_terms: D004261:DNA Replication; D004271:DNA, Fungal / Q000235:genetics; D004272:DNA, Mitochondrial / Q000235:genetics; D020862:GC Rich Sequence; D005821:Genetic Techniques; D016681:Genome, Fungal; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D012265:Ribonucleotides / Q000032:analysis* / Q000235:genetics; D012441:Saccharomyces cerevisiae / Q000235:genetics*; D051981:Uracil-DNA Glycosidase / Q000235:genetics / Q000378:metabolism
chemical_list: D004271:DNA, Fungal; D004272:DNA, Mitochondrial; D012265:Ribonucleotides; D051981:Uracil-DNA Glycosidase