Thomas Petes

Overview:

My lab is active in three somewhat related research areas: 1) the mechanism of mitotic recombination, 2) the genetic regulation of genome stability, and 3) genetic instability associated with interstitial telomeric sequences. Almost all of our studies are done using the yeast Saccharomyces cerevisiae.

Mechanism of mitotic recombination

Mitotic recombination, an important mechanism for the repair of DNA damage, is less well characterized than meiotic recombination. One difficulty is that mitotic recombination events are 104-fold less frequent than meiotic recombination events. We developed a greatly improved system for identifying and mapping mitotic crossovers at 1-kb resolution throughout the genome. This system uses DNA microarrays to detect loss of heterozygosity (LOH) resulting from mitotic crossovers. We identified motifs associated with high levels of spontaneous mitotic recombination. In particular, we demonstrated that a “hotspot” for mitotic recombination was generated by a pair of inverted retrotransposons. We also used this system to make the first genome-wide map of UV-induced recombination events. Finally, and most importantly, we demonstrated that most spontaneous mitotic recombination events reflect the repair of two sister-chromatids broken at the same position. This result argues that the DNA lesions that initiate mitotic recombination are a consequence of chromosome breakage in unreplicated DNA, contrary to the common belief that most recombinogenic lesions reflect broken replication forks. We are currently analyzing recombination events that occur in the absence of DNA mismatch repair.

Genetic regulation of genome stability

In wild-type cells, the frequency of genomic alterations of any type (point mutations, deletions, insertions, and chromosome rearrangements) is very low. We are interested in the genes that regulate genome stability. One rationale for this interest is that the cells of most solid tumors have very high levels of chromosome rearrangements (deletions, duplications, and translocations) as well as high levels of aneuploidy. To understand this type of instability, we are examining the chromosome instability associated with various genome-destabilizing conditions in yeast. We are currently concentrating on mutations that affect DNA replication. We have mapped chromosome rearrangements in yeast strains with low levels of DNA polymerase alpha. This mapping indicated that DNA breaks occur in regions of the genome in which replication forks are slowed or stalled. This pattern of recombination events is quite different from that observed in cells with normal replication. In collaboration with Sue Jinks-Robertson’s lab, we have also characterized chromosome alterations in strains with mutations in Topoisomerase I and cells treated with Topoisomerase I inhibitors. Our analysis is currently being extended into strains with mutations affecting Topoisomerase II, and mutations in DNA damage repair checkpoint genes. Our preliminary study shows that loss of Topoisomerase II results in an interesting pattern of chromosome non-disjunction in which chromosomes segregate in a manner similar to the first division of meiosis.

Genetic regulation of genome stability

Although telomeric sequences are usually located at the ends of the chromosome, mammalian chromosomes also have interstitial telomeric repeats (ITSs), and these ITSs are often sites of chromosome rearrangements in tumor cells. In collaboration with Sergei Mirkin’s lab, we developed methods of detecting ITS-induced genome instability in yeast. We are currently examining the effects of mutations in recombination (RAD52, RAD51, MUS81, RAD50, MRE11, LIG4, RAD59), DNA repair (RAD1, MSH2), DNA replication (REV3), and telomere length maintenance (TEL1, RIF1) pathways on the rates and types of ITS-induced events. The goal of this project is to identify the proteins required to initiate DNA lesions at ITSs and the proteins required to catalyze the ITS-associated rearrangements.

Positions:

Minnie Geller Distinguished Professor of Research in Genetics, in the School of Medicine

Molecular Genetics and Microbiology
School of Medicine

Professor of Molecular Genetics and Microbiology

Molecular Genetics and Microbiology
School of Medicine

Member of the Duke Cancer Institute

Duke Cancer Institute
School of Medicine

Education:

Ph.D. 1973

University of Washington

Grants:

Novel methods of generating genetic diversity

Administered By
Molecular Genetics and Microbiology
Awarded By
Army Research Office
Role
Principal Investigator
Start Date
End Date

Genetic regulation of genome stability in yeast

Administered By
Molecular Genetics and Microbiology
Awarded By
National Institutes of Health
Role
Principal Investigator
Start Date
End Date

Genetic regulation of genome stability in yeast

Administered By
Molecular Genetics and Microbiology
Awarded By
National Institutes of Health
Role
Principal Investigator
Start Date
End Date

Generation of genomic duplications and deletions in yeast

Administered By
Molecular Genetics and Microbiology
Awarded By
Army Research Office
Role
Principal Investigator
Start Date
End Date

Genetic regulation of genome stability in yeast

Administered By
Molecular Genetics and Microbiology
Awarded By
National Institutes of Health
Role
Principal Investigator
Start Date
End Date

Publications:

Cytological and genetic consequences for the progeny of a mitotic catastrophe provoked by Topoisomerase II deficiency.

Topoisomerase II (Top2) removes topological linkages between replicated chromosomes. Top2 inhibition leads to mitotic catastrophe (MC) when cells unsuccessfully try to split their genetic material between the two daughter cells. Herein, we have characterized the fate of these daughter cells in the budding yeast. Clonogenic and microcolony experiments, in combination with vital and apoptotic stains, showed that 75% of daughter cells become senescent in the short term; they are unable to divide but remain alive. Decline in cell vitality then occurred, yet slowly, uncoordinatedly when comparing pairs of daughters, and independently of the cell death mediator Mca1/Yca1. Furthermore, we showed that senescence can be modulated by ploidy, suggesting that gross chromosome imbalances during segregation may account for this phenotype. Indeed, we found that diploid long-term survivors of the MC are prone to genomic imbalances such as trisomies, uniparental disomies and terminal loss of heterozygosity (LOH), the latter affecting the longest chromosome arms.
Authors
Ramos-Pérez, C; Dominska, M; Anaissi-Afonso, L; Cazorla-Rivero, S; Quevedo, O; Lorenzo-Castrillejo, I; Petes, TD; Machín, F
MLA Citation
Ramos-Pérez, Cristina, et al. “Cytological and genetic consequences for the progeny of a mitotic catastrophe provoked by Topoisomerase II deficiency..” Aging (Albany Ny), vol. 11, no. 23, Dec. 2019, pp. 11686–721. Pubmed, doi:10.18632/aging.102573.
URI
https://scholars.duke.edu/individual/pub1423615
PMID
31812950
Source
pubmed
Published In
Aging
Volume
11
Published Date
Start Page
11686
End Page
11721
DOI
10.18632/aging.102573

Correction for Degtyareva et al., "Chronic Oxidative DNA Damage Due to DNA Repair Defects Causes Chromosomal Instability in Saccharomyces cerevisiae".

Authors
Degtyareva, NP; Chen, L; Mieczkowski, P; Petes, TD; Doetsch, PW
MLA Citation
Degtyareva, Natalya P., et al. “Correction for Degtyareva et al., "Chronic Oxidative DNA Damage Due to DNA Repair Defects Causes Chromosomal Instability in Saccharomyces cerevisiae"..” Mol Cell Biol, vol. 39, no. 21, Nov. 2019. Pubmed, doi:10.1128/MCB.00407-19.
URI
https://scholars.duke.edu/individual/pub1416714
PMID
31604842
Source
pubmed
Published In
Molecular and Cellular Biology
Volume
39
Published Date
DOI
10.1128/MCB.00407-19

Genetic Control of Genomic Alterations Induced in Yeast by Interstitial Telomeric Sequences.

In many organisms, telomeric sequences can be located internally on the chromosome in addition to their usual positions at the ends of the chromosome. In humans, such interstitial telomeric sequences (ITSs) are nonrandomly associated with translocation breakpoints in tumor cells and with chromosome fragile sites (regions of the chromosome that break in response to perturbed DNA replication). We previously showed that ITSs in yeast generated several different types of instability, including terminal inversions (recombination between the ITS and the "true" chromosome telomere) and point mutations in DNA sequences adjacent to the ITS. In the current study, we examine the genetic control of these events. We show that the terminal inversions occur by the single-strand annealing pathway of DNA repair following the formation of a double-stranded DNA break within the ITS. The point mutations induced by the ITS require the error-prone DNA polymerase ζ. Unlike the terminal inversions, these events are not initiated by a double-stranded DNA break, but likely result from the error-prone repair of a single-stranded DNA gap or recruitment of DNA polymerase ζ in the absence of DNA damage.
Authors
Moore, A; Dominska, M; Greenwell, P; Aksenova, AY; Mirkin, S; Petes, T
MLA Citation
Moore, Anthony, et al. “Genetic Control of Genomic Alterations Induced in Yeast by Interstitial Telomeric Sequences..” Genetics, vol. 209, no. 2, June 2018, pp. 425–38. Pubmed, doi:10.1534/genetics.118.300950.
URI
https://scholars.duke.edu/individual/pub1322596
PMID
29610215
Source
pubmed
Published In
Genetics
Volume
209
Published Date
Start Page
425
End Page
438
DOI
10.1534/genetics.118.300950

Genome-wide high-resolution mapping of chromosome fragile sites in Saccharomyces cerevisiae.

In mammalian cells, perturbations in DNA replication result in chromosome breaks in regions termed "fragile sites." Using DNA microarrays, we mapped recombination events and chromosome rearrangements induced by reduced levels of the replicative DNA polymerase-α in the yeast Saccharomyces cerevisiae. We found that the recombination events were nonrandomly associated with a number of structural/sequence motifs that correlate with paused DNA replication forks, including replication-termination sites (TER sites) and binding sites for the helicase Rrm3p. The pattern of gene-conversion events associated with cross-overs suggests that most of the DNA lesions that initiate recombination between homologs are double-stranded DNA breaks induced during S or G2 of the cell cycle, in contrast to spontaneous recombination events that are initiated by double-stranded DNA breaks formed prior to replication. Low levels of DNA polymerase-α also induced very high rates of aneuploidy, as well as chromosome deletions and duplications. Most of the deletions and duplications had Ty retrotransposons at their breakpoints.
Authors
Song, W; Dominska, M; Greenwell, PW; Petes, TD
MLA Citation
Song, Wei, et al. “Genome-wide high-resolution mapping of chromosome fragile sites in Saccharomyces cerevisiae..” Proc Natl Acad Sci U S A, vol. 111, no. 21, May 2014, pp. E2210–18. Pubmed, doi:10.1073/pnas.1406847111.
URI
https://scholars.duke.edu/individual/pub1030040
PMID
24799712
Source
pubmed
Published In
Proc Natl Acad Sci U S A
Volume
111
Published Date
Start Page
E2210
End Page
E2218
DOI
10.1073/pnas.1406847111

Chromosome aberrations resulting from double-strand DNA breaks at a naturally occurring yeast fragile site composed of inverted ty elements are independent of Mre11p and Sae2p.

Genetic instability at palindromes and spaced inverted repeats (IRs) leads to chromosome rearrangements. Perfect palindromes and IRs with short spacers can extrude as cruciforms or fold into hairpins on the lagging strand during replication. Cruciform resolution produces double-strand breaks (DSBs) with hairpin-capped ends, and Mre11p and Sae2p are required to cleave the hairpin tips to facilitate homologous recombination. Fragile site 2 (FS2) is a naturally occurring IR in Saccharomyces cerevisiae composed of a pair of Ty1 elements separated by approximately 280 bp. Our results suggest that FS2 forms a hairpin, rather than a cruciform, during replication in cells with low levels of DNA polymerase. Cleavage of this hairpin results in a recombinogenic DSB. We show that DSB formation at FS2 does not require Mre11p, Sae2p, Rad1p, Slx4p, Pso2p, Exo1p, Mus81p, Yen1p, or Rad27p. Also, repair of DSBs by homologous recombination is efficient in mre11 and sae2 mutants. Homologous recombination is impaired at FS2 in rad52 mutants and most aberrations reflect either joining of two broken chromosomes in a "half crossover" or telomere capping of the break. In support of hairpin formation precipitating DSBs at FS2, two telomere-capped deletions had a breakpoint near the center of the IR. In summary, Mre11p and Sae2p are not required for DSB formation at FS2 or the subsequent repair of these DSBs.
Authors
Casper, AM; Greenwell, PW; Tang, W; Petes, TD
MLA Citation
Casper, Anne M., et al. “Chromosome aberrations resulting from double-strand DNA breaks at a naturally occurring yeast fragile site composed of inverted ty elements are independent of Mre11p and Sae2p..” Genetics, vol. 183, no. 2, Oct. 2009, pp. 423-26SI. Pubmed, doi:10.1534/genetics.109.106385.
URI
https://scholars.duke.edu/individual/pub793078
PMID
19635935
Source
pubmed
Published In
Genetics
Volume
183
Published Date
Start Page
423
End Page
26SI
DOI
10.1534/genetics.109.106385