Ribose-seq: global mapping of ribonucleotides embedded in genomic DNA

Nat Methods. 2015 Mar;12(3):251-7, 3 p following 257. doi: 10.1038/nmeth.3259. Epub 2015 Jan 26.


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.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • DNA Replication
  • DNA, Fungal / genetics
  • DNA, Mitochondrial / genetics
  • GC Rich Sequence
  • Genetic Techniques*
  • Genome, Fungal
  • High-Throughput Nucleotide Sequencing / methods
  • Ribonucleotides / analysis*
  • Ribonucleotides / genetics
  • Saccharomyces cerevisiae / genetics*
  • Uracil-DNA Glycosidase / genetics
  • Uracil-DNA Glycosidase / metabolism


  • DNA, Fungal
  • DNA, Mitochondrial
  • Ribonucleotides
  • Uracil-DNA Glycosidase

Associated data

  • GEO/GSE61464