Professor of Molecular Genetics and Microbiology
Professor of Cell Biology
Member of the Duke Cancer Institute
Box 3054 DUMC
Durham, N.C. 27710
Phone: (919) 684-4986
Fax: (919) 684-6033
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.
Strand, M., Prolla, T. A., Liskay, R. M. and Petes, T. D. (1993). Destabilization of tracts of simple repetitive DNA in yeast by mutations affecting DNA mismatch repair. Nature 365:274-276.
Fan, Q.-Q., Xu, F. and Petes, T. D. (1995). Meiosis-specific double-strand DNA breaks at the HIS4 recombination hotspot in the yeast Saccharomyces cerevisiae. Mol. Cell. Biol. 15:1679-1688.
Greenwell, P. W., Kronmal, S. L., Porter, S. E., Gassenhuber, J., Obermaier, B., and Petes, T. D. (1995).TEL1, a gene involved in controlling telomere length in S. cerevisiae, is homologous to the human ataxia telangiectasia gene. Cell 82:823-829.
Kirkpatrick, D. and Petes, T. D. (1997). Repair of DNA loops involves DNA mismatch and nucleotide excision repair proteins. Nature 387:929-931.
Moore, H., Greenwell, P. W., Liu, C.-P., Arnheim, N., and Petes, T. D. (1999). Triplet repeats form secondary structures that escape DNA repair in yeast. Proc. Nat. Acad. Sci., U. S. A. 96:1504-1509.
Gerton, J. L., DeRisi, J., Shroff, R., Lichten, M., Brown, P. O., and Petes, T. D. (2000). Global mapping of meiotic recombination hotspots and coldspots in the yeast Saccharomyces cerevisiae. Proc. Nat. Acad. Sci., U. S. A. 97:11383-11390.
Petes, T. D. (2001). Meiotic recombination hot spots and cold spots. Nature Reviews: Genetics 2:360-369.
Craven, R. J., Greenwell, P. W., Dominska, M., and Petes, T. D. (2002). Regulation of genome stability byTEL1 and MEC1, yeast homologues of the mammalian ATM and ATR genes. Genetics 161:493-507.
Mieczkowski, P. A., Mieczkowska, J. O., Dominska, M., and Petes, T. D. (2003). Genetic regulation of telomere-telomere fusions in the yeast Saccharomyces cerevisiae. Proc. Nat. Acad. Sci., U. S. A. 100:10854-10859.
Ben-Aroya, S., Mieczkowski, P. A., Petes, T. D., and Kupiec, M. (2004). The compact chromatin structure of a Ty repeated sequence suppresses recombination hotspot activity in Saccharomyces cerevisiae. Mol. Cell 15:47-63.
Lemoine, F. J., Degtyareva, N. P., Lobachev, K., and Petes, T. D. (2005). Chromosomal translocations in yeast induced by low levels of DNA polymerase: a model for chromosome fragile sites. Cell 120:587-598.
Mieczkowski, P. A., Dominska, M., Buck, M. A., Gerton, J. L., Lieb, J. D., and Petes, T. D. (2006). A global analysis of the relationship between the binding of the Bas1p transcription factor and meiosis-specific double-strand DNA breaks in Saccharomyces cerevisiae. Mol. Cell. Biol. 26:1014-1027.
Narayanan, V., Mieczkowski, P. A., Kim, H.-M., Petes, T. D., and Lobachev, K. S. (2006). The pattern of gene amplification is determined by the chromosomal location of hairpin-capped breaks. Cell 125:1283-1296.
Stone, J. E., Ozbirn, R. G., Petes, T. D., and Jinks-Robertson, S. (2008). Role of PCNA interactions in the mismatch repair-dependent processing of mitotic and meiotic recombination intermediates in yeast. Genetics 178:1221-1236.
Vernon, M., Lobachev, K., and Petes, T. D. (2008). High rates of “unselected” aneuploidy and chromosome rearrangements in tel1 mec1 haploid yeast strains. Genetics 179:237-247.
Argueso, J. L., Westmoreland, J., Mieczkowski, P. A., Gawel, M., Petes, T. D., and Resnick, M. A. (2008). Double-strand breaks associated with repetitive DNA can reshape the genome. Proc. Nat. Acad. Sci., U. S. A.105:11845-11850.
Casper, A. M., Mieczkowski P. A., Gawel, M., and Petes, T. D. (2008). Low levels of DNA polymerase alpha induce mitotic and meiotic instability in the ribosomal DNA gene cluster of Saccharomyces cerevisiae. PLoS Genetics 4: e1000105.
Lemoine, F. J., Degtyareva, N. P., Kokoska, R. J., and Petes, T. D. (2008). Reduced levels of DNA polymerase delta induce chromosome fragile site instability in yeast. Mol. Cell. Biol. 28:5359-5368.
Kim, H.-M., Narayanan, V., Mieczkowski, P. A., Petes, T. D., Krasilnikova, M. M., Mirkin, S. M., and Lobachev, K. S. (2008). Chromosome fragility at GAA tracts in yeast depends on repeat orientation and requires mismatch repair. EMBO J. 27:2896-2906.
Lee, P. S., Greenwell, P. W., Dominska, M., Gawel, M., Hamilton, M., and Petes, T. D. (2009). A fine-structure map of spontaneous mitotic crossovers in the yeast Saccharomyces cerevisiae. PLoS Genetics 5:e1000419.
Argueso, J. L., Carazzolle, M. F., Mieczkowski, P. A., Duarte, F. M., Netto, O. V. C., Missawa, S. K., Galzerani, F., Costa, G. G. L., Vidal, R. O., Noronha, M. F., Dominska, M., Andrietta, M. G. S., Andrietta, S. R., Cunha, A. F., Gomes, L. H., Tavares, F. C. A., Alcare, A. R., Dietrich, F. S., McCusker, J. H., Petes, T. D., and Pereira, G. A. G. (2009). Genome structure of a Saccharomyces cerevisiae strain widely used in bioethanol production. Genome Research 19:2258-2270.
Lee, P. S., and Petes, T. D. (2010). Mitotic gene conversion events induced in G1-synchronized yeast cells by gamma rays are similar to spontaneous conversion events. Proc. Nat. Acad. Sci., U. S. A. 107:7383-7388.
McCulley, J., and Petes, T. D. (2010). Chromosome rearrangements and aneuploidy in yeast strains lacking both Tel1p and Mec1p reflect deficiencies in two different mechanisms. Proc. Nat. Acad. Sci., U. S. A. 107:11465-11470.
St. Charles, J., Hamilton, M. L., and Petes, T. D. (2010).Meiotic chromosome segregation in triploid strains of Saccharomyces cerevisiae. Genetics 186:537-550.
Tang, W., Dominska, M., Greenwell, P. W., Harvanek, J., Lobachev, K. S., Kim, H.-M., Narayanan, V., Mirkin, S. M., and Petes, T. D. (2011). Friedreich¹s Ataxia (GAA)/(TTC) Repeats Strongly Stimulate Mitotic Crossovers in Saccharomyces cerevisiae. PLoS Genet. 7: e1001270.
St. Charles, J., Hazkani-Covo, E., Yin, Y., Andersen, S. L., Dietrich, F.S., Greenwell, P. W., Malc, E., Mieczkowski, P., and Petes, T. D. (2012). High-resolution genome-wide analysis of irradiated (UV and gamma rays) diploid yeast cells reveals a high frequency of genomic loss of heterozygosity (LOH) events. Genetics .190:1267-1284.
Song, W., and Petes, T. D. (2012). Haploidization in Saccharomyces cerevisae induced by a deficiency in homologous recombination. Genetics. 191:279-284.
Andersen, S. L., and Petes, T. D. (2012). Reciprocal uniparental disomy in yeast. Proc. Nat. Acad. Sci., U. S. A. 109:9947-9952.
Andersen, S.L. and Petes, T.D. (2012). Reciprocal uniparental disomy in yeast. Proc Natl Acad Sci U S A. 109:9947-9952.[Epub 2012 Jun 4].
St. Charles, J. and Petes, T. D. (2013). High-resolution mapping of spontaneous mitotic recombination hotspots on the 1.1 mb arm of yeast chromosome IV. PLos Genet. 9:e10034334. [Epub 2013 Apr 4].
Song, W., Gawel, M., Dominska, M., Greenwell, P.W., Hazkani-Covo, E., Bloom, K., and Petes,
T.D. ( 2013) Nonrandom distribution of interhomolog recombination events induced by breakage of a dicentric chromosome in Saccharomyces cerevisiae. Genetics. 194:69-80. [Epub 2013 Feb 14].
Zhang, H., Zeidler, A.F., Song, W., Puccia, C.M., Malc, E., Greenwell, P.W., Mieczkowski, P.A., Petes, T.D., and Argueso, J.L. (2013). Gene copy-number variation in haploid and diploid strains of the yeast
Saccharomyces cerevisiae. Genetics. 193:785-801. [Epub 2013 Jan 10].
Tang, W., Dominska, M., Gawel, M., Greenwell, P.W., and Petes, T.D. (2013). Genomic deletions and point mutations induced in Saccharomyces cerevisiae by the trinucleotide repeats (GAA·TTC) associated with Friedreich’s ataxia. DNA Repair (Amst). 12:10-7. [Epub 2012 Nov 20].
Zhao, Y., Strope, P.K., Kozmin, S.G., McCusker, J.H., Deitrich, F.S., Kokoska, R.J., and Petes, T.D. (2014). Structures of naturally-evolved CUP1 Tandem arrays in yeast indicate that these arrays are generated by unequal non-homologous recombination. G3 [Epub 2014 Sept 17].
Zhang K, Xue-Chang W, Zheng D-Q, Petes TD Effects of temperature on the meiotic recombination landscape of the yeast Saccharomyces cerevisiae. mBio 2017, in press.
McGinty RJ, Rubinstein RG, Neil AJ, Dominska M, Kiktev D, Petes TD, Mirkin SM.Nanopore sequencing of complex genomic rearrangements in yeast reveals mechanisms of repeat-mediated double-strand break repair. Genome Res. 2017 Nov 7. doi: 10.1101/gr.228148.117. [Epub ahead of print] PMID: 29113982 Free Article
Yin Y, Dominska M, Yim E, Petes TD.High-resolution mapping of heteroduplex DNA formed during UV-induced and spontaneous mitotic recombination events in yeast. Elife. 2017 Jul 17;6. pii: e28069. doi: 10.7554/eLife.28069. PMID: 28714850 Free PMC Article
Zhao Y, Dominska M, Petrova A, Bagshaw H, Kokoska RJ, Petes TD.Properties of Mitotic and Meiotic Recombination in the Tandemly-Repeated CUP1 Gene Cluster in the Yeast Saccharomyces cerevisiae. Genetics. 2017 Jun;206(2):785-800. doi: 10.1534/genetics.117.201285. Epub 2017 Apr 4. PMID: 28381587 Free PMC Article
Zheng DQ, Zhang K, Wu XC, Mieczkowski PA, Petes TD. Global analysis of genomic instability caused by DNA replication stress in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A. 2016 Dec 13;113(50):E8114-E8121. Epub 2016 Nov 28. PMID: 27911848 Free PMC Article
Andersen SL, Zhang A, Dominska M, Moriel-Carretero M, Herrera-Moyano E, Aguilera A, Petes TD.High-Resolution Mapping of Homologous Recombination Events in rad3 Hyper-Recombination Mutants in Yeast. PLoS Genet. 2016 Mar 11;12(3):e1005938. doi: 10.1371/journal.pgen.1005938. eCollection 2016 Mar. PMID: 26968037 Free PMC Article
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