Post-replicative nick translation occurs on the lagging strand during prolonged depletion of DNA ligase I in Saccharomyces cerevisiae

Natasha C. Koussa, Duncan J. Smith

Research output: Contribution to journalArticlepeer-review


During lagging-strand synthesis, strand-displacement synthesis by DNA polymerase delta (Pol ∂), coupled to nucleolytic cleavage of DNA flap structures, produces a nick-translation reaction that replaces the DNA at the 5' end of the preceding Okazaki fragment. Previous work following depletion of DNA ligase I in Saccharomyces cerevisae suggests that DNA-bound proteins, principally nucleosomes and the transcription factors Abf1/Rap1/Reb1, pose a barrier to Pol ∂ synthesis and thereby limit the extent of nick translation in vivo. However, the extended ligase depletion required for these experiments could lead to ongoing, non-physiological nick translation. Here, we investigate nick translation by analyzing Okazaki fragments purified after transient nuclear depletion of DNA ligase I in synchronized or asynchronous Saccharomyces cerevisiae cultures. We observe that, even with a short ligase depletion, Okazaki fragment termini are enriched around nucleosomes and Abf1/Reb1/Rap1-binding sites. However, protracted ligase depletion leads to a global change in the location of these termini, moving them toward nucleosome dyads from a more upstream location and further enriching termini at Abf1/Reb1/Rap1-binding sites. In addition, we observe an under-representation of DNA derived from DNA polymerase alpha-the polymerase that initiates Okazaki fragment synthesis-around the sites of Okazaki termini obtained from very brief ligase depletion. Our data suggest that, while nucleosomes and transcription factors do limit strand-displacement synthesis by Pol ∂ in vivo, post-replicative nick translation can occur at unligated Okazaki fragment termini such that previous analyses represent an overestimate of the extent of nick translation occurring during normal lagging-strand synthesis.

Original languageEnglish (US)
Article numberjkab205
JournalG3: Genes, Genomes, Genetics
Issue number8
StatePublished - Aug 2021


  • DNA ligase I
  • DNA polymerase delta
  • DNA replication
  • Lagging-strand synthesis

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics
  • Genetics(clinical)


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