Thomas D. Petes, PhD – Publications

Minnie Geller Professor

research • lab members • publications

Google Scholar Profile

Representative Publications:

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

For a complete list of publications, click here.