Mismatch Repair Balances Leading and Lagging Strand DNA Replication Fidelity

Abstract

The two DNA strands of the nuclear genome are replicated asymmetrically using three DNA polymerases, α, δ, and ε. Current evidence suggests that DNA polymerase ε (Pol ε) is the primary leading strand replicase, whereas Pols α and δ primarily perform lagging strand replication. The fact that these polymerases differ in fidelity and error specificity is interesting in light of the fact that the stability of the nuclear genome depends in part on the ability of mismatch repair (MMR) to correct different mismatches generated in different contexts during replication. Here we provide the first comparison, to our knowledge, of the efficiency of MMR of leading and lagging strand replication errors. We first use the strand-biased ribonucleotide incorporation propensity of a Pol ε mutator variant to confirm that Pol ε is the primary leading strand replicase in Saccharomyces cerevisiae. We then use polymerase-specific error signatures to show that MMR efficiency in vivo strongly depends on the polymerase, the mismatch composition, and the location of the mismatch. An extreme case of variation by location is a T-T mismatch that is refractory to MMR. This mismatch is flanked by an AT-rich triplet repeat sequence that, when interrupted, restores MMR to >95% efficiency. Thus this natural DNA sequence suppresses MMR, placing a nearby base pair at high risk of mutation due to leading strand replication infidelity. We find that, overall, MMR most efficiently corrects the most potentially deleterious errors (indels) and then the most common substitution mismatches. In combination with earlier studies, the results suggest that significant differences exist in the generation and repair of Pol α, δ, and ε replication errors, but in a generally complementary manner that results in high-fidelity replication of both DNA strands of the yeast nuclear genome.

Human mismatch repair system balances mutation rates between strands by removing more mismatches from the lagging strand

“…This is in agreement with the biochemical property of the MMR to preferentially eliminate mismatched nucleotides on the DNA strand containing the nick (Pluciennik et al 2010). As the lagging strand is replicated in Okazaki fragments, their ends could represent a signal of the nascent strand for the MMR, facilitating its recruitment to this strand (Lujan et al 2012). Our observations are strongly concordant with experiments in yeasts (Lujan et al 2014), indicating that basic principles of MMR are conserved between yeasts and humans.…”

Exonuclease mutations in DNA polymerase epsilon reveal replication strand specific mutation patterns and human origins of replication

“…The S459F POLE variant shows high error rates for two additional errors, T!G and G!C transversions, which may indicate a more complex effect on the exonucleolytic mechanism for this mutant. Transversion errors are the most poorly corrected group of errors by mismatch repair (Schaaper and Dunn 1991;Lujan et al 2012), suggesting that a POLE mutant-mediated increase in the C•dT mispairing-induced C!A errors could more easily saturate or circumvent the already less efficient mismatch repair correction. C!T transitions can arise in the lacZ forward mutation assay due to dA misinsertion opposite an undamaged C or opposite the uracil formed as a product of cytosine deamination.…”

Sister chromatid telomere fusions, but not NHEJ-mediated inter-chromosomal telomere fusions, occur independently of DNA ligases 3 and 4

“…5C,D) might reflect the distinct DNA polymerases that replicate leading-versus lagging-strand DNA. Leading-strand DNA synthesis is coordinately mediated by DNA polymerases delta and epsilon, resulting in minimal error incorporation (Nick McElhinny et al 2008;Lujan et al 2012;Johnson et al 2015), whereas lagging-strand replication occurs by ligation of Okazaki fragments synthesized by DNA polymerases alpha and delta with reduced proof-reading capacity Reijns et al 2015). We hypothesized that the shorter chromatid partner of each 17p intra-chromosomal fusion might result predominantly from lagging-strand DNA synthesis and thus display a higher frequency of nonconstitutive nucleotide changes (Supplemental Fig.…”