Sue Jinks-Robertson

Overview:

My research focuses on the regulation of genetic stability and primarily uses budding yeast (Saccharomyces cerevisiae) as a model genetic system.  The two primary research goals in the budding yeast system are (1) defining molecular structures and mechanisms of mitotic recombination intermediates and (2) understanding how and why transcription destabilizes the underlying DNA template.  We also have initiated studies of mutagenesis in the pathogenic fungus Cryptococcus neoformans.  We have found that a shift to the human body temperature mobilizes transposable elements, and suggest that this promotes rapid adaptation to the harsh host environment.  

Positions:

James B. Duke Distinguished Professor of Molecular Genetics and Microbiology

Molecular Genetics and Microbiology
School of Medicine

Professor of Molecular Genetics and Microbiology

Molecular Genetics and Microbiology
School of Medicine

Vice-Chair in the Department 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. 1983

University of Wisconsin - Madison

Grants:

Temperature-dependent transposon mobilization in Cryptococcus neoformans

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

Regulation of mitotic genome stability in yeast.

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

What Happens at a Double Strand Break: Investigating the Role of DNA End Structure in Homologous Recombination

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

Investigating the origin of spontaneous mitotic homologous recombination in Saccharomyces cerevisiae

Administered By
Molecular Genetics and Microbiology
Awarded By
American Heart Association
Role
Principal Investigator
Start Date
End Date

Mitotic recombination mechanisms in yeast

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

Publications:

Mitotic recombination in yeast: what we know and what we don't know.

Saccharomyces cerevisiae is at the forefront of defining the major recombination mechanisms/models that repair targeted double-strand breaks during mitosis. Each of these models predicts specific molecular intermediates as well as genetic outcomes. Recent use of single-nucleotide polymorphisms to track the exchange of sequences in recombination products has provided an unprecedented level of detail about the corresponding intermediates and the extents to which different mechanisms are utilized. This approach also has revealed complexities that are not predicted by canonical models, suggesting that modifications to these models are needed. Current data are consistent with the initiation of most inter-homolog spontaneous mitotic recombination events by a double-strand break. In addition, the sister chromatid is preferred over the homolog as a repair template.
MLA Citation
Jinks-Robertson, Sue, and Thomas D. Petes. “Mitotic recombination in yeast: what we know and what we don't know.Current Opinion in Genetics & Development, vol. 71, July 2021, pp. 78–85. Epmc, doi:10.1016/j.gde.2021.07.002.
URI
https://scholars.duke.edu/individual/pub1489698
PMID
34311384
Source
epmc
Published In
Current Opinion in Genetics & Development
Volume
71
Published Date
Start Page
78
End Page
85
DOI
10.1016/j.gde.2021.07.002

Mutagenic repair of a ZFN-induced double-strand break in yeast: Effects of cleavage site sequence and spacer size.

Double-strand breaks are repaired by error-free homologous recombination or by relatively error-prone pathways that directly join broken ends. Both types of repair have been extensively studied in Saccharomyces cerevisiae using enzymes HO or I-SceI, which create breaks with 4-nt 3' overhangs. In the current study, a galactose-regulated zinc-finger nuclease (ZFN) designed to cleave the Drosophila rosy locus was used to generate breaks with 4-nt 5' overhangs at out-of-frame cleavage sites inserted into the yeast LYS2 gene. Mutagenic repair was examined following selection of prototrophs on lysine-deficient medium containing galactose or surviving colonies on galactose-containing rich medium. Following cleavage of the original rosy spacer (ACGAAT), most Lys<sup>+</sup> colonies contained 1- or 4-bp insertions at the cleavage site while most survivors had either a 2-bp insertion or a large deletion. Small insertions reflected nonhomologous end joining (NHEJ) and large deletions were the product of microhomology-mediated end joining (MMEJ). Changing the original ACGAAT spacer to either AGCAAT, ACGCGT or CTATTA altered the molecular features of NHEJ events as well as their frequency relative to MMEJ. Altering the optimal 6-bp spacer size between the zinc-finger protein binding sites to 5 bp or 7 bp eliminated the effect of continuous ZFN expression on survival, but Lys<sup>+</sup> prototrophs were still generated. Analysis of Lys<sup>+</sup> revertants after cleavage of the 5-bp spacer indicated that both the position and spacing of ZFN-generated nicks were variable. Results provide insight into effects of overhang sequence on mutagenic outcomes and demonstrate ZFN cleavage of 5- or 7-bp spacers in vivo.
Authors
MLA Citation
Shaltz, Samantha, and Sue Jinks-Robertson. “Mutagenic repair of a ZFN-induced double-strand break in yeast: Effects of cleavage site sequence and spacer size.Dna Repair, vol. 108, Sept. 2021, p. 103228. Epmc, doi:10.1016/j.dnarep.2021.103228.
URI
https://scholars.duke.edu/individual/pub1497143
PMID
34601383
Source
epmc
Published In
Dna Repair
Volume
108
Published Date
Start Page
103228
DOI
10.1016/j.dnarep.2021.103228

High-Throughput Analysis of Heteroduplex DNA in Mitotic Recombination Products.

Mitotic double-strand breaks (DSBs) are repaired by recombination with a homologous donor duplex. This process involves the exchange of single DNA strands between the broken molecule and the repair template, giving rise to regions of heteroduplex DNA (hetDNA). The creation of a defined DSB coupled with the use of a sequence-diverged repair template allows the fine-structure mapping of hetDNA through the sequencing of recombination products. A high-throughput method is described that capitalizes on the single-molecule real-time (SMRT) sequencing technology developed by PacBio. This method allows simultaneous analysis of the hetDNA contained within hundreds of recombination products.
Authors
Gamble, D; Hum, YF; Jinks-Robertson, S
MLA Citation
Gamble, Dionna, et al. High-Throughput Analysis of Heteroduplex DNA in Mitotic Recombination Products. Vol. 2153, 2021, pp. 503–19. Pubmed, doi:10.1007/978-1-0716-0644-5_34.
URI
https://scholars.duke.edu/individual/pub1460170
PMID
32840801
Source
pubmed
Volume
2153
Published Date
Start Page
503
End Page
519
DOI
10.1007/978-1-0716-0644-5_34

Trapped topoisomerase II initiates formation of de novo duplications via the nonhomologous end-joining pathway in yeast.

Topoisomerase II (Top2) is an essential enzyme that resolves catenanes between sister chromatids as well as supercoils associated with the over- or under-winding of duplex DNA. Top2 alters DNA topology by making a double-strand break (DSB) in DNA and passing an intact duplex through the break. Each component monomer of the Top2 homodimer nicks one of the DNA strands and forms a covalent phosphotyrosyl bond with the 5' end. Stabilization of this intermediate by chemotherapeutic drugs such as etoposide leads to persistent and potentially toxic DSBs. We describe the isolation of a yeast top2 mutant (top2-F1025Y,R1128G) the product of which generates a stabilized cleavage intermediate in vitro. In yeast cells, overexpression of the top2-F1025Y,R1128G allele is associated with a mutation signature that is characterized by de novo duplications of DNA sequence that depend on the nonhomologous end-joining pathway of DSB repair. Top2-associated duplications are promoted by the clean removal of the enzyme from DNA ends and are suppressed when the protein is removed as part of an oligonucleotide. TOP2 cells treated with etoposide exhibit the same mutation signature, as do cells that overexpress the wild-type protein. These results have implications for genome evolution and are relevant to the clinical use of chemotherapeutic drugs that target Top2.
Authors
Stantial, N; Rogojina, A; Gilbertson, M; Sun, Y; Miles, H; Shaltz, S; Berger, J; Nitiss, KC; Jinks-Robertson, S; Nitiss, JL
MLA Citation
Stantial, Nicole, et al. “Trapped topoisomerase II initiates formation of de novo duplications via the nonhomologous end-joining pathway in yeast.Proc Natl Acad Sci U S A, vol. 117, no. 43, Oct. 2020, pp. 26876–84. Pubmed, doi:10.1073/pnas.2008721117.
URI
https://scholars.duke.edu/individual/pub1462541
PMID
33046655
Source
pubmed
Published In
Proc Natl Acad Sci U S A
Volume
117
Published Date
Start Page
26876
End Page
26884
DOI
10.1073/pnas.2008721117

Recombinational Repair of Nuclease-Generated Mitotic Double-Strand Breaks with Different End Structures in Yeast.

Mitotic recombination is the predominant mechanism for repairing double-strand breaks in Saccharomyces cerevisiae Current recombination models are largely based on studies utilizing the enzyme I-SceI or HO to create a site-specific break, each of which generates broken ends with 3' overhangs. In this study sequence-diverged ectopic substrates were used to assess whether the frequent Pol δ-mediated removal of a mismatch 8 nucleotides from a 3' end affects recombination outcomes and whether the presence of a 3' vs. 5' overhang at the break site alters outcomes. Recombination outcomes monitored were the distributions of recombination products into crossovers vs. noncrossovers, and the position/length of transferred sequence (heteroduplex DNA) in noncrossover products. A terminal mismatch that was 22 nucleotides from the 3' end was rarely removed and the greater distance from the end did not affect recombination outcomes. To determine whether the recombinational repair of breaks with 3' vs. 5' overhangs differs, we compared the well-studied 3' overhang created by I-SceI to a 5' overhang created by a ZFN (Zinc Finger Nuclease). Initiation with the ZFN yielded more recombinants, consistent with more efficient cleavage and potentially faster repair rate relative to I-SceI. While there were proportionally more COs among ZFN- than I-SceI-initiated events, NCOs in the two systems were indistinguishable in terms of the extent of strand transfer. These data demonstrate that the method of DSB induction and the resulting differences in end polarity have little effect on mitotic recombination outcomes despite potential differences in repair rate.
Authors
Gamble, D; Shaltz, S; Jinks-Robertson, S
MLA Citation
Gamble, Dionna, et al. “Recombinational Repair of Nuclease-Generated Mitotic Double-Strand Breaks with Different End Structures in Yeast.G3 (Bethesda), vol. 10, no. 10, Oct. 2020, pp. 3821–29. Pubmed, doi:10.1534/g3.120.401603.
URI
https://scholars.duke.edu/individual/pub1463388
PMID
32826304
Source
pubmed
Published In
G3 (Bethesda, Md.)
Volume
10
Published Date
Start Page
3821
End Page
3829
DOI
10.1534/g3.120.401603

Research Areas:

DNA Repair
Gene Conversion
Genetic recombination
Insertional mutagenesis
Mutagenesis
Recombinational DNA Repair
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