Figure 4.

The positive consequences of ribonucleotide incorporation into DNA. (A) RNase H2 nicking at unrepaired nascent strand ribonucleotides acts as a strand-discrimination signal for MMR. (B) During NHEJ of DNA DSBs, ribonucleotides are frequently incorporated by Pol μ or TdT to promote efficient ligation by DNA Ligase 4. These incorporated ribonucleotides can later be removed during RER. (C) In S. pombe, a di-nucleotide imprint in the lagging strand is required for initiation of the mating-type switch. During replication of the mating-type locus, the imprint is suggested to consist of two consecutive ribonucleotides that are preserved after Okazaki fragment maturation. Imprint formation and preservation requires the concerted effort of several factors. The incoming fork is paused by the unknown factor X. The unknown DNA-binding factor Y is thought to protect the imprint from processing. RTS1 is a replication terminator that blocks the incoming fork from opposite direction. The imprint stalls Pol ε during leading strand synthesis in the next round of replication to promote recombination and allow a mating type switch. (D) RNase H2 nicking at ribonucleotides incorporated by Pol ε on the leading strands results in rotational freedom of the newly synthesized DNA strand and may provide relief of torsional stress.