About

Thomas Douglas Petes is the Minnie Geller Distinguished Professor of Research in Genetics at Duke University School of Medicine, where he also serves as Professor of Molecular Genetics and Microbiology and Professor of Cell Biology. He is a member of the Duke Cancer Institute. His research lab focuses on three related areas: the mechanism of mitotic recombination, the genetic regulation of genome stability, and genetic instability associated with interstitial telomeric sequences, primarily using the yeast Saccharomyces cerevisiae as a model organism. Petes' work on mitotic recombination has led to the development of a system for identifying and mapping mitotic crossovers at high resolution across the genome, revealing important insights such as the identification of recombination hotspots generated by inverted retrotransposons and the genome-wide mapping of UV-induced recombination events. His research demonstrated that most spontaneous mitotic recombination events result from the repair of two sister chromatids broken at the same position, challenging previous assumptions about the origins of recombinogenic lesions. In the area of genome stability, Petes investigates genes that regulate the frequency of genomic alterations, which is critical for understanding the high levels of chromosome rearrangements and aneuploidy observed in solid tumors. His studies include mapping chromosome rearrangements in yeast strains with low DNA polymerase alpha levels and characterizing chromosome alterations associated with mutations in topoisomerase enzymes and DNA damage repair checkpoint genes. Additionally, Petes explores the instability caused by interstitial telomeric sequences, which are often sites of chromosome rearrangements in tumor cells. Collaborating with other researchers, he examines the effects of mutations in recombination, DNA repair, replication, and telomere maintenance pathways on the rates and types of genome instability induced by these sequences. The goal of this work is to identify the proteins involved in initiating DNA lesions at interstitial telomeric sequences and those catalyzing the associated chromosomal rearrangements.

Research topics

• Genetics
• Biology
• Molecular biology
• Computational biology

Selected publications

• Loss of Pol32, a subunit of DNA polymerases δ and ζ, leads to different patterns of genome stability than direct impairment of these individual polymerases

  mBio · 2026-04-17

  articleOpen access

  ABSTRACT Pol32 is a subunit shared by DNA polymerases δ and ζ, yet its role in maintaining genome integrity remains incompletely defined. Here, we employed whole-genome sequencing of mutation-accumulation lines to systematically characterize the genome-wide effects of a POL32 deletion in diploid Saccharomyces cerevisiae . Loss of Pol32 led to substantially (>5-fold) elevated rates of loss of heterozygosity (LOH), chromosome rearrangements, and aneuploidy, but resulted in substantially less genome instability than observed in strains with low levels of DNA polymerase δ. In particular, there was only a small (<2-fold) effect of the pol32 mutation on mutation rates. Notably, a prominent hotspot for chromosome rearrangements located near the end of chromosome VII was observed in pol32 strains. Although deletion of REV3 (encoding the catalytic subunit of Pol ζ) had no significant effect on genome integrity in a wild-type background, pol32 rev3 double mutants had reduced rates of most types of chromosome alterations compared to the pol32 single mutant, implicating Pol ζ in driving the genome instability induced by the Pol32 deficiency. Together, these findings provide new insights into how a shared structural subunit of several DNA polymerases contributes to the regulation of genome stability. IMPORTANCE Pol32 is a subunit of DNA polymerases δ (an essential replicative enzyme) and ζ (an error-prone DNA polymerase required for DNA repair). We show that yeast strains that lack this protein have elevated rates of mitotic recombination, large deletions/duplications, translocations, and other types of genomic alterations. The high level of genomic alterations in pol32 mutants is substantially suppressed in strains that lack DNA polymerase ζ, suggesting that this error-prone polymerase may stimulate DNA breaks in conditions of DNA replication stress. Our studies are likely to have wide relevance since sequence variants of POLD3 (the human homolog of Pol32) are associated with certain types of human tumors.

  PublisherDOI

• The fidelity of DNA replication, particularly on GC-rich templates, is reduced by defects of the Fe–S cluster in DNA polymerase δ

  UNC Libraries · 2025-11-06

  articleOpen access

  Iron-sulfur clusters (4Fe-4S) exist in many enzymes concerned with DNA replication and repair. The contribution of these clusters to enzymatic activity is not fully understood. We identified the MET18 (MMS19) gene of Saccharomyces cerevisiae as a strong mutator on GC-rich genes. Met18p is required for the efficient insertion of iron-sulfur clusters into various proteins. met18 mutants have an elevated rate of deletions between short flanking repeats, consistent with increased DNA polymerase slippage. This phenotype is very similar to that observed in mutants of POL3 (encoding the catalytic subunit of Pol δ) that weaken binding of the iron-sulfur cluster. Comparable mutants of POL2 (Pol ϵ) do not elevate deletions. Further support for the conclusion that met18 strains result in impaired DNA synthesis by Pol δ are the observations that Pol δ isolated from met18 strains has less bound iron and is less processive in vitro than the wild-type holoenzyme.

  PublisherDOI

• Mitotic recombination events and single-base mutations induced by ultraviolet light in G1-arrested yeast cells

  Proceedings of the National Academy of Sciences · 2025-10-15 · 4 citations

  articleOpen accessSenior authorCorresponding

  Ultraviolet light (UV) is a potent inducer of both single-base mutations and mitotic recombination. Although these genomic alterations are often attributed to the action of error-prone DNA polymerases on UV-induced DNA lesions during replicative DNA synthesis, UV damage can also result in mutagenic and recombinogenic DNA damage in nondividing cells. We examined the effects of UV on cells of the yeast Saccharomyces cerevisiae arrested in G 1 of the cell cycle. By mating an irradiated haploid with an unirradiated haploid, we found that recombination was initiated only on the irradiated chromosome. This result indicates that trans effects of UV on recombination (for example, induction of recombinogenic proteins stimulating DNA breaks on the unirradiated homolog) are small or negligible. In addition, we show that most of the UV-induced mutations produced in G 1 -irradiated cells result in mutations at identical positions in both strands of the duplex. As observed for recombination events, mutations are almost exclusively on the irradiated chromosome, indicating the near absence of a trans effect on mutations.

  PublisherOA PDFDOI

• A tale of two serines: the effects of histone H2A mutations S122A and S129A on chromosome nondisjunction in <i>Saccharomyces cerevisiae</i>

  Genetics · 2024-11-18 · 1 citations

  articleOpen accessSenior authorCorresponding

  Near the C-terminus of histone H2A in the yeast Saccharomyces cerevisiae, there are 2 serines (S122 and S129) that are targets of phosphorylation. The phosphorylation of serine 129 in response to DNA damage is dependent on the Tel1 and Mec1 kinases. In Schizosaccharomyces pombe and S. cerevisiae, the phosphorylation of serine 122 is dependent on the Bub1 kinase, and S. pombe strains with an alanine mutation of this serine have elevated levels of lagging chromosomes in mitosis. Strains that lack both Tel1 and Mec1 in S. cerevisiae have very elevated rates of nondisjunction. To clarify the functional importance of phosphorylation of serines 122 and 129 in H2A, we measured chromosome loss rates in single-mutant strains and double-mutant combinations. We also examined the interaction of mutations of BUB1, TEL1, and MEC1 in combination with mutations of serines 122 and 129 in H2A. We conclude that the phosphorylation state of S129 has no effect on chromosome disjunction whereas mutations that inactivate Bub1 or a S122A mutation in the histone H2A greatly elevate the rate of chromosome nondisjunction. Based on this analysis, we suggest that Bub1 exerts its primary effect on chromosome disjunction by phosphorylating S122 of histone H2A. However, Tel1, Mec1, and Bub1 are also functionally redundant in a second pathway affecting chromosome disjunction that is at least partially independent of phosphorylation of S122 of H2A.

  PublisherOA PDFDOI

• Dicentric chromosomes are resolved through breakage and repair at their centromeres

  Chromosoma · 2024-01-02 · 7 citations

  articleOpen access

  Chromosomes with two centromeres provide a unique opportunity to study chromosome breakage and DNA repair using completely endogenous cellular machinery. Using a conditional transcriptional promoter to control the second centromere, we are able to activate the dicentric chromosome and follow the appearance of DNA repair products. We find that the rate of appearance of DNA repair products resulting from homology-based mechanisms exceeds the expected rate based on their limited centromere homology (340 bp) and distance from one another (up to 46.3 kb). In order to identify whether DNA breaks originate in the centromere, we introduced 12 single-nucleotide polymorphisms (SNPs) into one of the centromeres. Analysis of the distribution of SNPs in the recombinant centromeres reveals that recombination was initiated with about equal frequency within the conserved centromere DNA elements CDEII and CDEIII of the two centromeres. The conversion tracts range from about 50 bp to the full length of the homology between the two centromeres (340 bp). Breakage and repair events within and between the centromeres can account for the efficiency and distribution of DNA repair products. We propose that in addition to providing a site for kinetochore assembly, the centromere may be a point of stress relief in the face of genomic perturbations.

  PublisherOA PDFDOI

• Splitting the yeast centromere by recombination

  Nucleic Acids Research · 2023-11-22 · 7 citations

  articleOpen accessSenior author

  Although fusions between the centromeres of different human chromosomes have been observed cytologically in cancer cells, since the centromeres are long arrays of satellite sequences, the details of these fusions have been difficult to investigate. We developed methods of detecting recombination within the centromeres of the yeast Saccharomyces cerevisiae (intercentromere recombination). These events occur at similar rates (about 10-8/cell division) between two active or two inactive centromeres. We mapped the breakpoints of most of the recombination events to a region of 43 base pairs of uninterrupted homology between the two centromeres. By whole-genome DNA sequencing, we showed that most (>90%) of the events occur by non-reciprocal recombination (gene conversion/break-induced replication). We also found that intercentromere recombination can involve non-homologous chromosome, generating whole-arm translocations. In addition, intercentromere recombination is associated with very frequent chromosome missegregation. These observations support the conclusion that intercentromere recombination generally has negative genetic consequences.

  PublisherOA PDFDOI

• Shuffling the yeast genome using CRISPR/Cas9-generated DSBs that target the transposable Ty1 elements

  PLoS Genetics · 2023-01-26 · 22 citations

  articleOpen accessSenior authorCorresponding

  Although homologous recombination between transposable elements can drive genomic evolution in yeast by facilitating chromosomal rearrangements, the details of the underlying mechanisms are not fully clarified. In the genome of the yeast Saccharomyces cerevisiae, the most common class of transposon is the retrotransposon Ty1. Here, we explored how Cas9-induced double-strand breaks (DSBs) directed to Ty1 elements produce genomic alterations in this yeast species. Following Cas9 induction, we observed a significant elevation of chromosome rearrangements such as deletions, duplications and translocations. In addition, we found elevated rates of mitotic recombination, resulting in loss of heterozygosity. Using Southern analysis coupled with short- and long-read DNA sequencing, we revealed important features of recombination induced in retrotransposons. Almost all of the chromosomal rearrangements reflect the repair of DSBs at Ty1 elements by non-allelic homologous recombination; clustered Ty elements were hotspots for chromosome rearrangements. In contrast, a large proportion (about three-fourths) of the allelic mitotic recombination events have breakpoints in unique sequences. Our analysis suggests that some of the latter events reflect extensive processing of the broken ends produced in the Ty element that extend into unique sequences resulting in break-induced replication. Finally, we found that haploid and diploid strain have different preferences for the pathways used to repair double-stranded DNA breaks. Our findings demonstrate the importance of DNA lesions in retrotransposons in driving genome evolution.

  PublisherOA PDFDOI

• Ribodysgenesis: sudden genome instability in the yeast <i>Saccharomyces cerevisiae</i> arising from RNase H2 cleavage at genomic-embedded ribonucleotides

  Nucleic Acids Research · 2022-06-24 · 4 citations

  articleOpen access

  Ribonucleotides can be incorporated into DNA during replication by the replicative DNA polymerases. These aberrant DNA subunits are efficiently recognized and removed by Ribonucleotide Excision Repair, which is initiated by the heterotrimeric enzyme RNase H2. While RNase H2 is essential in higher eukaryotes, the yeast Saccharomyces cerevisiae can survive without RNase H2 enzyme, although the genome undergoes mutation, recombination and other genome instability events at an increased rate. Although RNase H2 can be considered as a protector of the genome from the deleterious events that can ensue from recognition and removal of embedded ribonucleotides, under conditions of high ribonucleotide incorporation and retention in the genome in a RNase H2-negative strain, sudden introduction of active RNase H2 causes massive DNA breaks and genome instability in a condition which we term 'ribodysgenesis'. The DNA breaks and genome instability arise solely from RNase H2 cleavage directed to the ribonucleotide-containing genome. Survivors of ribodysgenesis have massive loss of heterozygosity events stemming from recombinogenic lesions on the ribonucleotide-containing DNA, with increases of over 1000X from wild-type. DNA breaks are produced over one to two divisions and subsequently cells adapt to RNase H2 and ribonucleotides in the genome and grow with normal levels of genome instability.

  PublisherOA PDFDOI

• Global genomic instability caused by reduced expression of DNA polymerase ε in yeast

  Proceedings of the National Academy of Sciences · 2022-03-15 · 18 citations

  articleOpen access

  SignificanceAlthough most studies of the genetic regulation of genome stability involve an analysis of mutations within the coding sequences of genes required for DNA replication or DNA repair, recent studies in yeast show that reduced levels of wild-type enzymes can also produce a mutator phenotype. By whole-genome sequencing and other methods, we find that reduced levels of the wild-type DNA polymerase ε in yeast greatly increase the rates of mitotic recombination, aneuploidy, and single-base mutations. The observed pattern of genome instability is different from those observed in yeast strains with reduced levels of the other replicative DNA polymerases, Pol α and Pol δ. These observations are relevant to our understanding of cancer and other diseases associated with genetic instability.

  PublisherOA PDFDOI

• Mitotic recombination in yeast: what we know and what we don’t know

  Current Opinion in Genetics & Development · 2021 · 27 citations

  Senior authorCorresponding
  • Biology
  • Genetics
  • Computational biology

  Saccharomyces cerevisiae is at the forefront of defining the major recombination mechanisms/models that repair targeted double-strand breaks during mitosis. Each of these models predicts specific molecular intermediates as well as genetic outcomes. Recent use of single-nucleotide polymorphisms to track the exchange of sequences in recombination products has provided an unprecedented level of detail about the corresponding intermediates and the extents to which different mechanisms are utilized. This approach also has revealed complexities that are not predicted by canonical models, suggesting that modifications to these models are needed. Current data are consistent with the initiation of most inter-homolog spontaneous mitotic recombination events by a double-strand break. In addition, the sister chromatid is preferred over the homolog as a repair template.

  PublisherDOI

Recent grants

• NIH Grant R01GM052319

  NIH · $6.0M · 2016

• NIH Grant RC1ES018091

  NIH · $993k · 2011

• NIH Grant R01GM034646

  NIH · $246k · 1989

• NIH Grant R01GM024110

  NIH · $9.9M · 2016

• Genetic regulation of genome stability in yeast

  NIH · $7.0M · 2016–2026

Frequent coauthors

• Margaret Dominska

  Duke University

  135 shared

• Patricia W. Greenwell

  Duke University Hospital

  101 shared

• Yi Yin

  62 shared

• Piotr A. Mieczkowski

  University of North Carolina at Chapel Hill

  43 shared

• Robert J. Kokoska

  Research Triangle Park Foundation

  32 shared

• Wei Song

  Duke University Hospital

  31 shared

• Eunice Yim

  Duke University Hospital

  28 shared

• Sue Jinks-Robertson

  Duke Medical Center

  28 shared

Labs

• Petes LabPI

Awards & honors

• Minnie Geller Distinguished Professor of Research in Genetic…