Tracking replication enzymology in vivo by genome-wide mapping of ribonucleotide incorporation

Nat Struct Mol Biol. 2015 Mar;22(3):185-91. doi: 10.1038/nsmb.2957. Epub 2015 Jan 26.


Ribonucleotides are frequently incorporated into DNA during replication in eukaryotes. Here we map genome-wide distribution of these ribonucleotides as markers of replication enzymology in budding yeast, using a new 5' DNA end-mapping method, hydrolytic end sequencing (HydEn-seq). HydEn-seq of DNA from ribonucleotide excision repair-deficient strains reveals replicase- and strand-specific patterns of ribonucleotides in the nuclear genome. These patterns support the roles of DNA polymerases α and δ in lagging-strand replication and of DNA polymerase ɛ in leading-strand replication. They identify replication origins, termination zones and variations in ribonucleotide incorporation frequency across the genome that exceed three orders of magnitude. HydEn-seq also reveals strand-specific 5' DNA ends at mitochondrial replication origins, thus suggesting unidirectional replication of a circular genome. Given the conservation of enzymes that incorporate and process ribonucleotides in DNA, HydEn-seq can be used to track replication enzymology in other organisms.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, N.I.H., Intramural

MeSH terms

  • Chromosome Mapping*
  • DNA Replication / physiology*
  • DNA, Mitochondrial / chemistry
  • DNA-Directed DNA Polymerase / metabolism
  • DNA-Directed DNA Polymerase / physiology
  • Fungal Proteins / metabolism
  • Fungal Proteins / physiology
  • High-Throughput Nucleotide Sequencing
  • Replication Origin
  • Ribonucleotides / chemistry
  • Ribonucleotides / physiology*
  • Saccharomyces cerevisiae / genetics
  • Sequence Analysis


  • DNA, Mitochondrial
  • Fungal Proteins
  • Ribonucleotides
  • DNA-Directed DNA Polymerase

Associated data

  • GEO/GSE62181