We show by whole genome sequence analysis that loss of RNase H2 activity increases loss of heterozygosity (LOH) in Saccharomyces cerevisiae diploid strains harboring the pol2-M644G allele encoding a mutant version of DNA polymerase e that increases ribonucleotide incorporation. This led us to analyze the effects of loss of RNase H2 on LOH and on nonallelic homologous recombination (NAHR) in mutant diploid strains with deletions of genes encoding RNase H2 subunits (rnh201D, rnh202D, and rnh203D), topoisomerase 1 (TOP1D), and/or carrying mutant alleles of DNA polymerases e, a, and d. We observed an 7-fold elevation of the LOH rate in RNase H2 mutants encoding wild-type DNA polymerases. Strains carrying the pol2-M644G allele displayed a 7-fold elevation in the LOH rate, and synergistic 23-fold elevation in combination with rnh201D. In comparison, strains carrying the pol2-M644L mutation that decreases ribonucleotide incorporation displayed lower LOH rates. The LOH rate was not elevated in strains carrying the pol1-L868M or pol3-L612M alleles that result in increased incorporation of ribonucleotides during DNA synthesis by polymerases a and d, respectively. A similar trend was observed in an NAHR assay, albeit with smaller phenotypic differentials. The ribonucleotide-mediated increases in the LOH and NAHR rates were strongly dependent on TOP1. These data add to recent reports on the asymmetric mutagenicity of ribonucleotides caused by topoisomerase 1 processing of ribonucleotides incorporated during DNA replication. KEYWORDS LOH; NAHR; genome stability; recombination; ribonucleotides T HE replicative DNA polymerases of Saccharomyces cerevisiae, DNA polymerases a (Pol a), d (Pol d), and e (Pol e), frequently incorporate ribonucleotides into DNA both in vitro and during nuclear DNA replication in vivo (Nick McElhinny et al. 2010a,b;Williams and Kunkel 2014;Williams et al. 2015). These ribonucleotides are efficiently removed when RNase H2 incises the DNA backbone containing a ribonucleotide to initiate ribonucleotide excision repair (RER) (Nick McElhinny et al. 2010a;Sparks et al. 2012). When the RNH201 gene that encodes the catalytic subunit of RNase H2 (Cerritelli and Crouch 2009) is deleted, RER is defective and many unrepaired ribonucleotides remain in the genome. A subset of these unrepaired ribonucleotides can be removed when topoisomerase 1 (TOP1) incises a DNA backbone containing a ribonucleotide . However, TOP1 incision creates nicks with unligatable ends and elicits several RNA-DNA damage phenotypes, including slow growth, activation of the genome integrity checkpoint and altered progression through the cell cycle, sensitivity to the replication inhibitor hydroxyurea (HU), and strongly elevated rates for deletion of 2-5 bp from low-complexity DNA sequences (Nick McElhinny et al. 2010a;Clark et al. 2011;Kim et al. 2011). These effects are elicited primarily by ribonucleotides incorporated by Pol e, but not by ribonucleotides incorporated by Pol a or Pol d (Williams et al. 2015). Loss of RNase H2 is a...

Although human mesenchymal stem cells (hMSCs) are a powerful tool for cell therapy, prolonged culture times result in replicative senescence or acquisition of tumorigenic features. To identify a molecular signature for senescence, we compared the transcriptome of senescent and young hMSCs with normal karyotype (hMSCs/n) and with a constitutional inversion of chromosome 3 (hMSC/inv). Senescent and young cells from both lineages showed differentially expressed genes (DEGs), with higher levels in senescent hMSCs/inv. Among the 30 DEGs in senescent hMSC/inv, 11 are new candidates for biomarkers of cellular senescence. The functional categories most represented in senescent hMSCs were related to cellular development, cell growth/proliferation, cell death, cell signaling/interaction, and cell movement. Mapping of DEGs onto biological networks revealed matrix metalloproteinase-1, thrombospondin 1, and epidermal growth factor acting as topological bottlenecks. In the comparison between senescent hMSCs/n and senescent hMSCs/inv, other functional annotations such as segregation of chromosomes, mitotic spindle formation, and mitosis and proliferation of tumor lines were most represented. We found that many genes categorized into functional annotations related to tumors in both comparisons, with relation to tumors being highest in senescent hMSCs/inv. The data presented here improves our understanding of the molecular mechanisms underlying the onset of cellular senescence as well as tumorigenesis.

Titanium (Ti) is currently the most widely used material for the manufacture of orthopedic and dental implants. Changes in the surface of commercial pure Ti (cp Ti) can determine the functional response of cells, and is therefore a critical factor for the success of the implant. However, the genotoxicity of titanium surfaces has been poorly studied. Thus, the purpose of this study was to evaluate the genotoxic potential of a new titanium surface developed by plasma treatment using argon-ion bombardment and compare it with an untreated titanium surface. Accordingly, comet assay, analysis of chromosomal aberrations (CAs), and Cytokinesis Block Micronucleus (CBMN) assay were carried out, using CHO-K1 (Chinese hamster ovary) cells grown on both titanium surfaces. Our results show that the untreated titanium surface caused a significant increase in % tail moment, in the number of cells with CAs, tetraploidy, micronucleus frequency, and other nuclear alterations when compared with the negative control and with the plasma-treated titanium surface. This difference may be attributed to increased surface roughness and changes in titanium oxide layer thickness.

Cells carrying deletions of genes encoding H-class ribonucleases display elevated rates of chromosome instability. The role of these enzymes is to remove RNA-DNA associations including persistent mRNA-DNA hybrids (R-loops) formed during transcription, and ribonucleotides incorporated into DNA during replication. RNases H1 and H2 can degrade the RNA component of R-loops, but only RNase H2 can initiate accurate ribonucleotide excision repair (RER). In order to examine the specific contributions of these activities to chromosome stability, we measured rates of loss-of-heterozygosity (LOH) in diploid Saccharomyces cerevisiae yeast strains carrying the rnh201-RED separation-of-function allele, encoding a version of RNase H2 that is RER-defective, but partly retains its other activity. The LOH rate in rnh201-RED was intermediate between RNH201 and rnh201Δ. In strains carrying a mutant version of DNA polymerase ε (pol2-M644G) that incorporates more ribonucleotides than normal, the LOH rate in rnh201-RED was as high as the rate measured in rnh201Δ. Topoisomerase 1 cleavage at sites of ribonucleotide incorporation has been recently shown to produce DNA double strand breaks. Accordingly, in both the POL2 and pol2-M644G backgrounds, the LOH elevation in rnh201-RED was suppressed by top1Δ. In contrast, in strains that incorporate fewer ribonucleotides (pol2-M644L) the LOH rate in rnh201-RED was low and independent of topoisomerase 1. These results suggest that both R-loop removal and RER contribute substantially to chromosome stability, and that their relative contributions may be variable across different regions of the genome. In this scenario, a prominent contribution of R-loop removal may be expected at highly transcribed regions, whereas RER may play a greater role at hotspots of ribonucleotide incorporation.