Ribonucleotides are signals for mismatch repair of leading-strand replication errors

Abstract

To maintain genome stability, mismatch repair of nuclear DNA replication errors must be directed to the nascent strand, likely by DNA ends and PCNA. Here we show that the efficiency of mismatch repair in Saccharomyces cerevisiae is reduced by inactivating RNase H2, which nicks DNA containing ribonucleotides incorporated during replication. In strains encoding mutator polymerases, this reduction is preferential for repair of mismatches made by leading-strand DNA polymerase ε as compared to lagging-strand DNA polymerase δ. The results suggest that RNase-H2-dependent processing of ribonucleotides transiently present in DNA after replication may direct mismatch repair to the continuously replicated nascent leading strand.

Figure 1. Ribonucleotide incorporation by Pols ε and δ

(A) Stable incorporation of ribonucleotides into DNA was measured in vitro as described (Nick McElhinny et al., 2010c). The average percentages of alkali-sensitive product for two experiments ± the range are displayed. (B) The orientation of the URA3 reporter with respect to coding sequence is shown. The nascent leading strand synthesized by Pol ε is in blue and the nascent lagging strand synthesized by Pol δ is in green. (C) Strand-specific probing for alkali-sensitive sites in genomic DNA. DNA was subjected to alkaline hydrolysis, alkaline-agarose electrophoresis and analysis by Southern blotting using radiolabeled probes specific for nascent leading (Probe B) or nascent lagging (Probe A) strand DNA. DNA marker sizes are indicated on the left. Higher mobility (smaller) fragments reveal the presence of unrepaired ribonucleotides due to lack of RNase H2 activity. (D) Fraction of hydrolysis fragments present in the high mobility peak (see Figure S1 and Experimental Procedures). Error bars represent 95% C.I.

Figure 2. The effect of RNH201 deletion on mutation rates and correction factors

Error bars represent 95% C.I. (A) URA3 mutation rates are shown for pol2-M644G strains with MSH6 deleted (msh6Δ; blue bars) or wild type mismatch repair (WT MMR; red bars). Correction factors (correction efficiency; purple bars), are ratios of mutation rates (msh6Δ : MSH6). Rates and correction factors are shown for transitions (left) and indels (right). RNase H2 status (RNH201 = “+”; rnh201Δ = “−”) and URA3 orientation are indicated below the charts. Ratios of correction factors (RNH201 : rnh201Δ) and the corresponding p-values (indicating confidence that correction factors differ) are shown at bottom, beginning with ratios derived from correction factors shown (“msh6Δ/wt MMR”; Table 1) and continuing for strains with different MMR deficiencies (see Tables S1–S2). ^aNo measurements were made in an msh2Δ rnh201Δ strain (see Table S2). (B) As per the bottom of panel A, but for the pol3-L612M mutator background (δ-LM; see Table S3). (C) As per panel B, but for the wild type polymerase background (wt pols; see Table S4). (D) Fold increases in single-base indel and 2–5 bp tandem repeat deletion rates - due to RNH201 deletion - are shown for three Pol ε variants: M644L Pol ε (blue bars; see Table S7), wild type Pol ε (red bars), and M644G Pol ε (green bars).

Figure 3. Conservation in the polymerase active site of Pols ε and δ

Organisms are grouped by clade with organism counts to the right of each sequence. ^aPutative Polymerase ε from Nosema ceranae [SLYTDII]. ^bPolymerases δ from Trichoplax ahaerens [SLYP(TII,SII,SIM,SVM)] and Loxodonta africana [SMYPSIV].