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The role of fork stalling and DNA structures in causing chromosome fragility.Kaushal, S., and Freudenreich, C.H. (2019). Genes, chromosomes & cancer 58, 270-283.

Mrc1 and Tof1 prevent fragility and instability at long CAG repeats by their fork stabilizing function. Gellon, L., Kaushal, S., Cebrian, J., Lahiri, M., Mirkin, S.M., and Freudenreich, C.H. (2019). Nucleic acids research 47, 794-805.

Guidelines for DNA recombination and repair studies: Cellular assays of DNA repair pathways. Klein, H.L., Bacinskaja, G., Che, J., Cheblal, A., Elango, R., Epshtein, A., Fitzgerald, D.M., Gomez-Gonzalez, B., Khan, S.R., Kumar, S., et al. (2019). Microb Cell 6, 1-64.

Distinct Mechanisms of Nuclease-Directed DNA-Structure-Induced Genetic Instability in Cancer Genomes. Zhao, J., G. Wang, I. M. Del Mundo, J. A. McKinney, X. Lu, A. Bacolla, S. B. Boulware, C. Zhang, H. Zhang, P. Ren, C. H. Freudenreich and K. M. Vasquez (2018). Cell Rep 22(5): 1200-1210.

R-loops: targets for nuclease cleavage and repeat instability. Freudenreich CH. (2018). Curr Genet. 64(4): 789-794. Jan 11. doi: 10.1007/s00294-018-0806-z. Review. PMID:29327083

The Chromatin Remodeler Isw1 Prevents CAG Repeat Expansions During Transcription in Saccharomyces cerevisiae. Koch MR, House NCM, Cosetta CM, Jong RM, Salomon CG, Joyce CE, Philips EA, Su XA, Freudenreich CH. Genetics (2018) Mar;208(3):963-976. doi: 10.1534/genetics.117.300529. Epub 2018 Jan 5.  PMID:29305386

Methods to Study Repeat Fragility and Instability in Saccharomyces cerevisiae. Polleys EJ, Freudenreich CH. Methods in Molecular Biology (2018) 1672:403-419. doi: 10.1007/978-1-4939-7306-4_28. PMID: 29043639

Su XA, Freudenreich CH. 2017. Cytosine deamination and base excision repair cause R-loop-induced CAG repeat fragility and instability in Saccharomyces cerevisiae. Proc Natl Acad Sci USA [Epub ahead of print].

Role of recombination and replication fork restart in repeat instability. Polleys EJ, House NCM, Freudenreich CH. DNA Repair 2017 Jun 9. pii: S1568-7864(17)30218-5. doi: 10.1016/j.dnarep.2017.06.018. [Epub ahead of print] Review. PMID: 28641941

Differential requirement of Srs2 helicase and Rad51 displacement activities in replication of hairpin-forming CAG/CTG repeats. Nguyen JH, Viterbo D, Anand RP, Verra L, Sloan L, Richard GF, Freudenreich CH. Nucleic Acids Res. 2017 May 5;45(8):4519-4531. doi: 10.1093/nar/gkx088. PMID: 28175398

Relocalization of DNA lesions to the nuclear pore complex. Freudenreich CH and Su, XA. FEMS Yeast Research 16, 2016, fow095; doi: 10.1093/femsyr/fow095. PMID: 27799300

Regulation of recombination at yeast nuclear pores controls repair and triplet repeat stability. Su XA, Dion V, Gasser SM, Freudenreich CH. Genes Dev. 2015 May 15; 29(10):1006-17. doi: 10.1101/gad.256404.114. Epub 2015 May 4. PMID: 25940904

Repeat instability during DNA repair: Insights from model systems. Karen Usdin, Nealia C. M. House, Catherine H. Freudenreich. Critical Reviews in Biochemistry and Molecular Biology (2015). 1–26. Posted online on 22 Jan 2015. doi:10.3109/10409238.2014.999192.

NuA4 initiates dynamic histone H4 acetylation to promote high-fidelity sister chromatid recombination at post-replication gaps. Nealia C.M. House, Jiahui Yang, Stephen Walsh, Jonathan Moy, C.H. Freudenreich (2014). Molecular Cell Sept. 18, 55(6). doi: 10.1016/j.molcel.2014.07.007. PMID: 25132173.

Chromatin modifications and DNA repair: Beyond double-strand breaks. Nealia C.M. House, Melissa R. Koch, Catherine H. Freudenreich. Frontiers in Genetics (Cancer Genetics) (2014). 05 September 2014 | doi: 10.3389/fgene.2014.00296.

RTEL1 Inhibits Trinucleotide Repeat Expansions and Fragility. Aisling Frizzell, Jennifer H.G. Nguyen, Mark I.R. Petalcorin, Katherine D. Turner, Simon J. Boulton, Catherine H. Freudenreich, and Robert S. Lahue. Cell Reports (2014). Volume 6, Issue 5, 13 March 2014, Pages 827–835; doi: 10.1016/j.celrep.2014.01.034. PMID: 24561255.

Ranjith P. Anand, Kartik A. Shah, Hengyao Niu, Patrick Sung, Sergei M. Mirkin and Catherine H. Freudenreich. Overcoming natural replication barriers: Differential helicase requirements. Nucleic Acids Research (2012) Nucleic Acids Res. Feb; 40(3):1091-105, PMID: 21984413. (PDF)

Aisling Frizzell, Jennifer H.G. Nguyen, Mark I.R. Petalcorin, Katherine D. Turner, Simon J. Boulton, Catherine H. Freudenreich, and Robert S. Lahue. RTEL1 Inhibits Trinucleotide Repeat Expansions and Fragility. Cell Reports 2014. Vol. 6, Issue 5, p827–835. Published online: February 20, 2014.

Nicole Cherng, Alexander A. Shishkin, Lucas I. Schlager, Ryan H. Tuck, Laura Sloan, Partha S. Sarkar, Tetsuo Ashizawa, Catherine H. Freudenreich and Sergei M. Mirkin Expansions of the SCA10 pentanucleotide repeat in yeast. (2011) Proceedings of the National Academy of Sciences Feb 15;108(7):2843-8.

Lionel Gellon, David F. Razidlo, Olive Gleeson, Lauren Verra, Danae Schulz, Robert S. Lahue, and Catherine H. Freudenreich New functions of Ctf18-RFC in preserving genome stability outside its role in sister chromatid cohesion. (2011) PloS Genetics Feb 10 7 (2) e1001298. (PDF)

Rangapriya Sundararajan and Catherine.H. Freudenreich. Expanded CAG/CTG Repeat DNA induces a checkpoint response that impacts cell proliferation in S. cerevisiae. (2011) PloS Genetics March 17; 7(3) e1001339. press release (PDF)

Jiahui Yang and Catherine H. Freudenreich. (2010) "The RTT109 histone acetyltransferase facilitates error-free replication to prevent CAG/CTG repeat contractions." DNA Repair 9 (2010) 414-420.

Sundararajan R., Gellon, L., Zunder, R. M., and Freudenreich, C. H. (2010). "Double-Strand Break Repair Pathways Protect against CAG/CTG Repeat Expansions, Contractions and Repeat-mediated Chromosomal Fragility in Saccharomyces cerevisiae." Genetics Jan 2010,184(1):65-77.

Irina Voineagu, Catherine H. Freudenreich, Sergei M. Mirkin (2009) "Checkpoint responses to unusual structures formed by DNA repeats." Molecular Carcinogenesis Volume 48 Issue 4 (p 309-318). (April 2009 Special Issue: Intrinsic Genomic Instability from Naturally Occurring DNA Structures, Edited by Karen Vasquez, Philip Hanawalt).

Alix Kerrest, Ranjith P. Anand, Rangapriya Sundararajan, Rodrigo Bermejo, Giordano Liberi, Bernard Dujon, Catherine H. Freudenreich and Guy-Franck Richard (2009) "SRS2/ and /SGS1/ Prevent Chromosomal Breaks and Stabilize Triplet Repeats by Restraining Recombination." Nature Structural and Molecular Biology 16 (Feb) 159-167.

Zhang H. and Freudenreich, C.H. (2007) An AT-rich sequence in human common fragile site FRA16D causes fork stalling and chromosome breakage in S. cerevisiae. Molecular Cell 27, 367-379.
(profiled in Science/ News Focus "DNAs Molecular Gymnastics", June 9, 2006 312: 1467-68.) press release

C.H. Freudenreich. Chromosome fragility: molecular mechanisms and cellular consequences. Front Biosci. 2007 Sep 1;12:4911-24. Review.

Yang, J. and Freudenreich, C.H. (2007) Haploinsufficiency of yeast FEN1 causes instability of expanded CAG/CTG tracts in a length-dependent manner. Gene Vol. 393, Issues 1-2, May 15, 2007, p.110-115.

Freudenreich, C. H. (2005) Molecular Mechanisms of Chromosome Fragility. ChemTracks-Biochemistry and Molecular Biology, Vol 18, No.3, March 2005 (invited review for special theme issue “Unstable Microsatellites in the Human Genome, Part 2”.)

C.H. Freudenreich and Mayurika Lahiri (2004) "Structure-Forming CAG/CTG repeat sequences are sensitive to breakage in the absence of Mrcl checkpoint function and S-phase checkpoint signaling: Implications for trinucleotide repeat expansion diseases." Cell Cycle Vol. 3 (11) 1370-1374.

Lahiri M., Gustafson T.L., Majors E.R., Freudenreich C.H. (2004) "Expanded CAG repeats activate the DNA damage checkpoint pathway." Mol Cell 15: 287-293.

Liu Y., Zhang H., Veeraraghavan J., Bambara R.A., Freudenreich C.H. (2004) "Saccharomyces cerevisiae Flap Endonuclease 1 Uses Flap Equilibration to Maintain Triplet Repeat Stability." Mol Cell Biol. 24: 4040-4064.

Callahan JL, Andrews KJ, Zakian VA, Freudenreich CH. (2003) "Mutations in yeast replication proteins that increase CAG/CTG expansions also increase repeat fragility." Mol Cell Biol. 21:7849-60.

Lenzmeier BA, Freudenreich CH. (2003) "Trinucleotide repeat instability: a hairpin curve at the crossroads of replication, recombination, and repair." Cytogenet Genome Res. 100(1-4):7-24.

Balakumaran, B. S., Freudenreich, C. H., and Zakian, V. A. (2000) "CGG/CCG repeats exhibit orientation-dependent instability and orientation-independent fragility in Saccharomyces cerevisiae." Human Molecular Genetics 9: 93-100.

Freudenreich, C. H., Kantrow, S. M., and Zakian, V. A. (1998) "Expansion and Length-Dependent Fragility of CTG Repeats in Yeast." Science 279: 853-856.

Freudenreich, C. H., Stavenhagen, J. B. and Zakian, V. A. (1997) "Stability of a CTG/CAG trinucleotide repeat in yeast is dependent on its orientation in the genome." Molecular and Cellular Biology, 17: 2090-2098.

Freudenreich, C. H., Chang, C., and Kreuzer, K. N. (1998) "Mutations of the bacteriophage T4 type II DNA topoisomerase that alter sensitivity to antitumor agent 4'-(9-acridinylamino) methanesulfon-m-anisidide and an antibacterial quinolone. Cancer Research 58: 1260-1267.

Kreuzer, K. N., Freudenreich, C. H., and Pommier, Y. (2001) "Analysis of cleavage complexes using reactive inhibitor derivitives." Methods in Molecular Biology: Protocols in DNA Topology and DNA Topoisomerases, 95:89-99. (Humana Press).

Freudenreich, C. H. and Kreuzer, K. N. (1994) "Localization of an aminoacridine antitumor agent in a type II topoisomerase-DNA complex." Proc. Natl. Acad. Sci. USA, 91: 11007-11011.

Freudenreich, C. H. and Kreuzer, K. N. (1994) "Differentially labeled mutant oligonucleotides for analysis of protein-DNA interactions." BioTechniques, 16:104-108.

Freudenreich, C. H. and Kreuzer, K. N. (1993) "Mutational analysis of a type II topoisomerase cleavage site: distinct requirements for enzyme and inhibitors." EMBO J., 12: 2085-2097.

Longmire, J.L., Gee, G.F., Hardekopf, C.L., and Graham, M.A. (1992) "Establishing Paternity in Whooping Cranes (Grus Americana) by DNA analysis. The Auk 109: 522-529.

Longmire J.L., Kraemer, P.M., Brown, N.C., Hardekopf, C.L. and Deaven, L.L. (1990) "A new multi-locus DNA fingerprinting probe: pV47-2." Nuc. Acids. Res. 18:1658.