The genomes of all organisms are subject to change including alterations in chromosome number, chromosome structure (translocations, deletions, duplications), or single-base-pair mutations (point mutations). Although the frequency of these changes is very low in wild-type cells, certain mutations (mutators) greatly elevate the rate of instability. Most solid tumors have very high rates of chromosome rearrangements. In this proposal, DNA microarrays and high-throughput DNA sequencing will be used to perform a genome-wide analysis of recombination events in strains of the yeast Saccharomyces cerevisae that are genetically unstable as a model for understanding cancers with high levels of chromosome rearrangements. In addition, the mapping of recombination events in yeast strains lacking topoisomerases will be relevant to understanding the possible consequences of the chemotherapeutic use of topoisomerase inhibitors. One rationale for this analysis is that regions that have high levels of mitotic recombination also have high levels of double-stranded DNA breaks (DSBs), and that mapping the positions of the recombination events maps the positions of these DSBs. Mitotic recombination events in diploid strains in which the two homologous chromosomes are not identical result in loss of heterozygosity (LOH). Diploid strains heterozygous for about 55,000 single-nucleotide-polymorphisms (SNPs) were constructed and will be analyzed using microarrays that can detect whether strains are heterozygous or homozygous for these polymorphisms (SNP arrays) to map LOH events. These events will be mapped throughout the genome in strains known to have very high levels of genetic instability including: 1) strains with low levels of alpha DNA polymerase, 2) tel1 mec1 sml1 strains (lacking homologues of the human ATM and ATR genes), and 3) strains with mutations in the topoisomerases Top1p and/or Top2p. These studies will define regions of the genome that are prone to DSB formation under these three different types of genome-destabilizing conditions. As a proof of principle, we mapped more than 200 LOH events in strains with 10-fold reduced levels of alpha DNA polymerase and showed that these events are non-randomly associated with DNA sequence motifs known to slow DNA replication forks. To complement this approach, microarrays will be used to map the locations of gamma-H2AX in strains with low alpha DNA polymerase or mutations in topoisomerase genes. Since gamma-H2AX is recruited to sites of DNA damage, the regions frequently associated with LOH are likely to co-localize with regions that have high levels of gamma-H2AX. High-throughput DNA sequencing of isolates of the same three types of strains described above will also be done to detect genetic alterations (single-base-pair changes and small insertions/deletions) that cannot be detected by SNP microarrays. Finally, we plan to map LOH events in mammalian cells that are exposed to topoisomerase inhibitors.

Public Health Relevance

Genetic instability, resulting in high levels of chromosome rearrangements, is found in the cells of most solid tumors. We will use DNA microarrays and high-throughput DNA sequencing to perform a genome-wide analysis of strains of the yeast Saccharomyces cerevisae that have very high levels of chromosome rearrangements. Our mapping of yeast chromosome regions that are prone to rearrangements will help us understand the genetic instability associated with cancer.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM052319-18
Application #
8638011
Study Section
Molecular Genetics B Study Section (MGB)
Program Officer
Janes, Daniel E
Project Start
1995-05-01
Project End
2016-03-31
Budget Start
2014-04-01
Budget End
2015-03-31
Support Year
18
Fiscal Year
2014
Total Cost
$434,708
Indirect Cost
$143,839
Name
Duke University
Department
Genetics
Type
Schools of Medicine
DUNS #
044387793
City
Durham
State
NC
Country
United States
Zip Code
27705
Zhang, Ke; Wu, Xue-Chang; Zheng, Dao-Qiong et al. (2017) Effects of Temperature on the Meiotic Recombination Landscape of the Yeast Saccharomyces cerevisiae. MBio 8:
Zhao, Ying; Dominska, Margaret; Petrova, Aleksandra et al. (2017) Properties of Mitotic and Meiotic Recombination in the Tandemly-Repeated CUP1 Gene Cluster in the Yeast Saccharomyces cerevisiae. Genetics 206:785-800
Yin, Yi; Dominska, Margaret; Yim, Eunice et al. (2017) High-resolution mapping of heteroduplex DNA formed during UV-induced and spontaneous mitotic recombination events in yeast. Elife 6:
Omer, Sumita; Lavi, Bar; Mieczkowski, Piotr A et al. (2017) Whole Genome Sequence Analysis of Mutations Accumulated in rad27? Yeast Strains with Defects in the Processing of Okazaki Fragments Indicates Template-Switching Events. G3 (Bethesda) 7:3775-3787
Zheng, Dao-Qiong; Zhang, Ke; Wu, Xue-Chang et al. (2016) Global analysis of genomic instability caused by DNA replication stress in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A 113:E8114-E8121
Andersen, Sabrina L; Zhang, Aimee; Dominska, Margaret et al. (2016) High-Resolution Mapping of Homologous Recombination Events in rad3 Hyper-Recombination Mutants in Yeast. PLoS Genet 12:e1005938
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O'Connell, Karen; Jinks-Robertson, Sue; Petes, Thomas D (2015) Elevated Genome-Wide Instability in Yeast Mutants Lacking RNase H Activity. Genetics 201:963-75
Chan, Kin; Roberts, Steven A; Klimczak, Leszek J et al. (2015) An APOBEC3A hypermutation signature is distinguishable from the signature of background mutagenesis by APOBEC3B in human cancers. Nat Genet 47:1067-72
Yin, Yi; Petes, Thomas D (2015) Recombination between homologous chromosomes induced by unrepaired UV-generated DNA damage requires Mus81p and is suppressed by Mms2p. PLoS Genet 11:e1005026

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