Professor Emeritus of Molecular Genetics and Microbiology
Member of the Duke Cancer Institute
DNA repair and surveillance mechanisms are essential for the maintenance of eukaryotic genome integrity. In humans, these mechanisms protect somatic tissue from the accumulation of the genetic changes associated with cancer and ensure that informational content is stably transmitted from one generation to the next. My laboratory uses the yeast Saccharomyces cerevisiae as a model genetic system to understand the pathways/mechanisms that regulate mitotic genome stability. There are two major areas of focus within the lab: (1) defining molecular mechanisms of homologous recombination and (2) understanding mechanisms that contribute to transcription-associated genetic instability.
Mechanisms of homologous recombination
Mitotic recombination is an essential repair process that fills single-strand gaps and repairs double-strand breaks (DSBs). Though most recombination likely occurs between identical sister chromatids and hence is of no genetic consequence, recombination also can involve homologous chromosomes, leading to loss of heterozygosity and expression of recessive markers. In addition, interactions between dispersed repeated sequences can generate a variety of detrimental genome rearrangements including deletions/duplications, inversions and translocations. We have developed novel molecular approaches and tools that allow us to precisely follow the swapping of single strands between duplex DNAs during the repair of defined DSBs. This is accomplished through the use of substrates with engineered single-nucleotide polymorphisms (SNPs) at ~50 bp intervals. Strand exchange generates mismatch-containing “heteroduplex” DNA (hetDNA), the length and position of which can be determined by sequencing recombination products. The position of hetDNA in individual recombinants can be used to infer the underlying molecular mechanism of recombination. Alterations in hetDNA patterns in defined mutant backgrounds provide molecular detail that cannot be obtained using more traditional methods. Our molecular analyses have confirmed, for example, that most mitotic recombination occurs via the synthesis-dependent strand-annealing pathway and have clarified how individual helicases regulate recombination outcome.
The basic framework for mapping hetDNA was developed using a transformation-based assay in which a broken plasmid is repaired using a SNP-containing chromosomal template. More recent work has employed chromosomal substrates, one of which contains a inducible DSB, and has confirmed basic hetDNA patterns observed in the transformation-based assay. To complement analysis of DSB-initiated recombination, substrates are being developed that will allow the molecular features of recombination initiated either spontaneously or by a defined single-strand nick to be ascertained. Finally, computational tools are being developed to sequence recombination events en masse using the high throughput, single-molecule PacBio platform.
Transcription and genome stability
Because the DNA metabolic processes of transcription, replication, recombination and repair are not temporally separated, one process has the potential to influence the occurrence of another. Our work has demonstrated that the stability of DNA is related not only to its primary sequence, but also is influenced by its level of transcription. Reporters fused to the highly inducible pGAL or doxycycline-regulated pTet promoter have been used to study how transcription locally stimulates mutagenesis, a phenomenon referred to as transcription-associated mutagenesis or TAM. We have discovered that there are multiple sources of TAM, including elevated damage accumulation and increased substitution of uracil for thymine in the underlying DNA template. The major source of TAM in an unbiased forward mutation assay, however, is due to activity of Topoisomerase 1 (Top1), the enzyme that removes transcription-associated supercoils. Top1-dependent mutations have a distinctive molecular signature comprised of 2-5 bp deletions that eliminate a single repeat unit of a sequence repeated 2-4 times. Genetic studies suggest that deletions reflect either (1) the mutagenic processing of a trapped Top1 cleavage complex or (2) the sequential action of Top1 when the initial incision occurs at the site of a ribonucleotide monophosphate embedded in DNA. Current work is further exploring the mechanisms of Top1-dependent mutagenesis.
In addition to TAR studies, we are collaborating with Tom Petes to determine how and where persistent base pairing of the RNA transcript with the DNA template (an R-loop) affects recombination on a genome-wide scale. R-loops specifically accumulate in an RNaseH-defective strain, which is unable to degrade the RNA component of R-loops. Using a selective system that genetically detects loss-of heterozygosity (LOH) on a single yeast chromosome, we have found that R-loop persistence elevates recombination ~10 fold. Microarrays that monitor SNP status across the entire yeast genome are being used to detect R-loop associated LOH on a genome-wide scale.
Sue Jinks-Robertson grew up in the panhandle of Florida on the Gulf Coast. From an early age she had an interest in and aptitude for science, and her career path was set when she took her first Genetics course in college. She graduated from Agnes Scott College (a liberal arts women’s college in Decatur, GA) in 1977, and obtained a PhD in Genetics from the University of Wisconsin-Madison in 1983. Her thesis research focused on the regulation of ribosome biosynthesis in E. coli and was done under the tutelage of Masayasu Nomura. As a postdoc at the University of Chicago, Sue moved into the yeast model system under the expert guidance of now-colleague Tom Petes. She returned to Georgia in 1986 and spent the first 20 years of her faculty career in the Biology Department at Emory University. In 2006, she moved to Duke University where she has continued her work on DNA repair and surveillance mechanisms in yeast. Current studies are focused on elucidating molecular mechanisms of homologous recombination and on understanding how transcription destabilizes the underlying DNA template.
Sue was elected as a Fellow of the American Academy of Microbiology in 2010 and of the American Association for the Advancement of Science in 2011. She currently serves as Treasurer of the Genetic Society of America and as an Editor for the journals DNA Repair and PLoS Genetics.
Sloan R, Huang SN, Pommier Y, Jinks-Robertson S.Effects of camptothecin or TOP1 overexpression on genetic stability in Saccharomyces cerevisiae. DNA Repair (Amst). 2017 Nov;59:69-75. doi: 10.1016/j.dnarep.2017.09.004. Epub 2017 Sep 18.
Guo X, Hum YF, Lehner K, Jinks-Robertson S.Regulation of hetDNA Length during Mitotic Double-Strand Break Repair in Yeast. Mol Cell. 2017 Aug 17;67(4):539-549.e4. doi: 10.1016/j.molcel.2017.07.009. Epub 2017 Aug 3. PMID:
Hum YF, Jinks-Robertson S.Mitotic Gene Conversion Tracts Associated with Repair of a Defined Double-Strand Break in Saccharomyces cerevisiae. Genetics. 2017 Sep;207(1):115-128. doi: 10.1534/genetics.117.300057. Epub 2017 Jul 25. PMID:
Kim N, Jinks-Robertson S.The Top1 paradox: Friend and foe of the eukaryotic genome.
DNA Repair (Amst). 2017 Aug;56:33-41. doi: 10.1016/j.dnarep.2017.06.005. Epub 2017 Jun 9. Review.
Cho JE, Jinks-Robertson S.Ribonucleotides and Transcription-Associated Mutagenesis in Yeast.
J Mol Biol. 2017 Oct 27;429(21):3156-3167. doi: 10.1016/j.jmb.2016.08.005. Epub 2016 Aug 7. Review. PMID:
Cho, J.E., Huang, S.N., Burgers, P.M., Shuman, S., Pommier. Y.and Jinks-Robertson S. (2016). Parallel analysis of ribonucleotide-dependent deletions produced by yast Top1 in vitro and in vivo. Nucleic Acids Res. 44, 7714-7721.
Andersen, S.L., Sloan, R., Petes, T.D. and Jinks-Robertson, S. (2015). Genome-destabilizing effects associated with Top1 loss or accumulation of Top1 cleavage complexes in yeast. PLoS Genet. 11, e1005098.
Guo X., Lehner, K., O’Connell, K., Zhang, J., Dave, S.S. and Jinks-Robertson, S. (2015). SMRT sequencing for parallel analysis of multiple targets and accurate SNP phasing. G3 5, 2801-2808.
O’Connell, K., Jinks-Robertson, S. and Petes, T.D. (2015). Elevated genome-wide instability in yeast mutants lacking RNase H activity. Genetics 201, 963-975.
Cho, J.E., Kim, N. and Jinks-Robertson, S. (2015). Topoisomerase 1-dependent deletions initiated by incision at ribonucleotides are biased to the non-transcribed strand of a highly activated reporter. Nucleic Acids Res. 43, 9306-9313.
Lehner, K. and Jinks-Robertson, S. (2014). Shared genetic pathways contribute to the tolerance of endogenous and low-dose exogenous DNA damage in yeast. Genetics 198, 519-530.
Guo, X. and Jinks-Robertson, S. (2013). Roles of exonucleases and translesion synthesis DNA polymerases during mitotic gap repair in yeast. DNA Repair 12, 1024-1030.
Guo, X. and Jinks-Robertson, S. (2013). Removal of N-6-methyladenine by the nucleotide excision repair pathway triggers the repair of mismatches in yeast gap-repair intermediates. DNA Repair 12, 1053-1061.
Kim, N. and Jinks-Robertson, S. (2013). RNA:DNA hybrids initiate quasi-palindrome-associated mutations in highly transcribed yeast DNA. PLoS Genet. 9, e100392.
Boiteux, S. and Jinks-Robertson, S. (2013). DNA repair mechanisms and the bypass of DNA damage. Genetics, 193, 1025-64.
Mitchel, K., Lehner, K. and Jinks-Robertson, S. (2013). Heteroduplex DNA position defines the roles of the Sgs1, Srs2 nad Mph1 helicases in promoting distinct recombination outcomes. PLoS Genet., 9, e1003340
Kozmin, S.G. and Jinks-Robertson, S. (2013). UV-induced mutagenesis in non-dividing yeast cells. Genetics, 193, 803-817.
Cho, J.-E., Kim, N. and Jinks-Robertson, S. (2013). Two distinct mechanisms of Topoisomerase 1-dependent mutatgenesis in yeast. DNA Repair, 1, 205-11.
Kim N, Jinks-Robertson, S. (2012). Transcription as a source of genome instability. Nat. Rev. Genet. 13, 204-214.
Lehner K, Mudrak SV, Minesinger BK, Jinks-Robertson S. (2012). Frameshift mutagenesis: the roles of primer-template misalignment and the nonhomologous end-joining pathway in Saccharomyces cerevisiae. Genetics 190, 501-510.
Kim, N., Mudrak, S.V. and Jinks-Robertson, S. (2011). The dCMP transferase activity of yeast Rev1 is biologically relevant during the bypass of endogenous AP sites in yeast. DNA Repair 10, 1262-1271.
Kim, N. and Jinks-Robertson, S. (2011). Guanine repeat-containing sequences confer transcription-dependent instability in an orientation-specific manner in yeast. DNA Repair 10, 953-960.
Lippert, M.J., Kim, N., Cho, J.E., Larson, R.P., Schoenly, N.E., O’Shea, S.H. and Jinks-Robertson, S. (2011). Role for topoisomerase 1 in transcription-associated mutagenesis in yeast. Proc. Natl. Acad. Sci. USA 108, 698-703.
Kim, N., Huang, S.Y., Williams, J.S., Li, Y.C., Clark, A.B., Cho, J.E., Kunkel, T.A., Pommier, Y., and Jinks-Robertson, S. (2011) Mutagenic processing of ribonucleotides in DNA by yeast topoisomerase I. Science 24, 1561-1564.
Kim, N., and Jinks-Robertson, S. (2010) Abasic sites in the transcribed strand of yeast DNA are removed by transcription-coupled necleotide excision repair. Mol. Cell. Bio. 30, 3206-3215.
Mitchel, K., Zhang, H., Welz-Voegele, C., and Jinks-Robertson, S. (2010) Molecular structures of crossover and noncrossover intermediates during gap repair in yeast: Implications for recombination. Mol. Cell. 38, 211-222.
Mudrak, S.V., Welz-Voegele, C., and Jinks-Robertson, S. (2009) The polymerase eta translesion synthesis DNA polymerase acts independently of the mismatch repair system to limit mutagenesis caused by 7,8-dihydro-8-oxoguanine in yeast. Mol. Cell. Biol. 29, 5316-5326.
Kim, N. and Jinks-Robertson, S. (2009) dUTP incorporation into genomic DNA is linked to transcription in yeast. Nature 459,1150-1153.
Lehner, K. and Jinks-Robertson, S. (2009) The mismatch repair system promotes DNA polymerase zeta-dependent translesion synthesis in yeast.Proc. Natl. Acad. Sci. USA 106, 5749-5754.
Welz-Voegele, C. and Jinks-Robertson, S. (2008) Sequence divergence impedes crossover more than noncrossover events during mitotic gap repair in yeast. Genetics 179, 1251-1262.
Stone, J.E., Ozbirn, R.G., Petes, T.D and Jinks-Robertson, S. (2008). Role of proliferating cell nuclear antigen interactions in the mismatch repair-dependent processing of mitotic and meiotic recombination intermediates in yeast. Genetics 178, 1221-1236.
Abdulovic, A.L., Minesinger, B.K. and Jinks-Robertson, S. (2008). The effect of sequence context on spontaneious Polzeta-dependent mutagenesis in Saccharomyces cerevisiae. Nucleic Acids Res. 36, 2082-2093.
Welz-Voegele, C. and Jinks-Robertson, S. (2008). Sequence divergence impedes crossover more than noncrossover events during mitotic gap repair in yeast. Genetics 179, 1251-1262.
Abdulovic, A.L., Minesinger, B.K. and Jinks-Robertson, S. (2007). Identification of a strand-related bias in the PCNA-mediated bypass of spontaneous lesions by yeast Poleta. DNA Repair (Amst). 6, 1307-1318.
Kow, Y.W., Bao, G., Reeves, J.W., Jinks-Robertson, S. and Crouse, G.F. (2007). Oligonucleotide transformation of yeast reveals mismatch repair complexes to be differentially active on DNA replication strands. Proc. Natl. Acad. Sci. USA 104, 11352-11357.
Abdulovic, A.L., Kim, N. and Jinks-Robertson, S. (2006). Mutagenesis and the three R’s in yeast. DNA Repair 5, 409-421.
Abdulovic, A.L. and Jinks-Robertson, S. (2006). The in vivo characterization of translesion synthesis across UV-induced lesions in Saccharomyces cerevisiae: novel insight into Polζ and Polη dependent frameshift mutagenesis. Genetics 172, 1487-1498.
Sabbioneda, S., Minesinger, B.K., Giannattasio, M., Plevani, P., Muzi-Falconi, M. and Jinks-Robertson, S. (2005). The 9-1-1 checkpoint clamp physically interacts with Polζ and is partially required for spontaneous Polζ-dependent mutagenesis in Sacchaormyces cerevisiae. J. Biol. Chem. 280, 38657-38665.
Minesinger, B.K. and Jinks-Robertson, S. (2005). Roles of RAD6 epistasis group members in spontaneous Polζ-dependent translesion synthesis in Saccharomyces cerevisiae. Genetics 169, 1939-1955.
Lippert, M.J., Freedman, J.A., Barber, M.A. and Jinks-Robertson, S. (2004). Identification of a distinctive mutation spectrum associated with high levels of transcription in yeast. Mol. Cell. Biol. 24, 4801-4809.
Welz-Voegele, C., Stone, J.E., Tran, P.T., Kearney, H.M., Liskay, R.M., Petes, T.D. and Jinks-Robertson, S. (2002). Separation-of-function alleles of the yeast PMS1 mismatch repair gene differentially affect recombination- and replication-related processes. Genetics 162, 1131-1145.
Harfe, B.D. and Jinks-Robertson, S (2000). DNA polymerase ζ introduces multiple mutations when bypassing spontaneous DNA damage in Saccharomyces cerevisiae. Mol. Cell 6, 1491-1499.
Saxe, D., Datta, A. and Jinks-Robertson, S. (2000). Stimulation of mitotic gene conversion and crossover events by high levels of RNA polymerase II transcription in yeast. Mol. Cell. Biol. 20, 5404-5414.
Chen, W. and Jinks-Robertson, S. (1998). Mismatch repair proteins regulate heteroduplex formation during mitotic recombination in yeast. Mol. Cell. Biol. 18, 6525-6537.
Datta, A., Hendrix, M., Lipsitch, M. and Jinks-Robertson, S. (1997). Dual roles for DNA sequence identity and the mismatch repair system in the regulation of mitotic recombination in yeast. Proc. Natl. Acad. Sci. USA 94, 9757-9762.
Greene, C.N. and Jinks-Robertson, S. (1996). Frameshift intermediates in homopolymer runs are removed efficiently by yeast mismatch repair proteins. Mol. Cell. Biol. 17, 2844-2850.
Datta, A. and Jinks-Robertson, S. (1995). Association of increased spontaneous mutation rates with high levels of transcription in yeast. Science 268, 1616-1619.