The long term goal of this grant is to identify genes and structures that promote genome integrity and determine their mechanism of action. In the past 3 funding periods, we focused on Pif1 family DNA helicases, multi-functional helicases with critical roles in maintenance of nuclear and mitochondrial (mt) DNA. Although most studies on replication fork progression study the effects of exogenous damage, even the genomes of undamaged cells present challenges for DNA replication. Protein complexes, highly transcribed genes, DNA secondary structures, and converged replication forks are natural replication barriers that are encountered in every S phase. Pif1 family helicases are the only identified enzymes that promote replisome movement past all of these structures.
Aim I presents genetic approaches to determine the unique &overlapping roles of ScPif1 and Rrm3, the two S. cerevisiae Pif1 family members, and their interactions with other genes. We will develop site specific assays to quantitate the impact of Rrm3 on hard to replicate DNA sequences by modifying the gross chromosomal rearrangement (GCR) assay;e.g., we will insert a tRNA gene that causes strong fork pausing in rrm3 cells into the GCR test interval and determine its impact on GCR rates in WT and mutant strains. We will identify genes that act in concert with/in place of Rrm3 to suppress GCR damage at this and other sites and determine the sequence of events that promote replication at the sites. Mutations in the Pif1 signature motif, a 21 amino acid motif that distinguishes Pif1 helicases from other proteins, as well as heterologous Pif1 helicases, will be tested for ability to suppress GCR events in site-specific GCR strains. We will use synthetic genetic analysis to identify which of the ~5000 non-essential yeast genes cause death or slow growth when absent in pif1-m2 cells. Similar screens will identify single or double mutants that are hyper- sensitive to G4-stabilizing drugs.
Aim II, which complements aim I, describes biochemical approaches to determine the unique and overlapping activities of Pif1 helicases. After years of being unable to purify eukaryotic Pif1 family helicases other than ScPif1, we purified six bacterial Pif1 helicases and showed that, like ScPif1, all robustly unwind G4 DNA. ScPif1 has three uncommon activities (e.g., preferential unwinding of RNA/DNA substrates). We will determine if these activities are conserved within the Pif1 family. Proteins with mutations in the Pif1 signature motif, including a mutation associated with increased risk of human breast cancer, will be tested to determine the molecular role of the motif. Collaborative structural and single molecule experiments are described.
Aim III presents experiments to determine molecular mechanisms of ScPif1 action at both telomeres and mtDNA. We will determine if Rif2 recruits ScPif1 preferentially to long telomeres and if direct interaction betwee ScPif1 &telomerase is required for its ability to evict telomerase from telomeres. We will ask if ScPif1 promotes mtDNA stability by suppressing G4-induced damage by determining if ScPif1 binds G4 motifs in WT mtDNA and if loss and/or rearrangement of mtDNA in pif1 cells initiates at G4 motifs.

Public Health Relevance

All parts of this proposal, which focuses on Pif1 family helicases and their unique functions in replication fork progression and telomerase regulation, are relevant to human health. Pif1 helicases have critical roles in replication of both mitochondrial and telomeric DNA, whose integrity impacts both life span and cancer in humans. We will use yeast as test tubes to determine the effects of breast cancer associated alleles of human PIF1 on replication fork progression and telomere maintenance.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
Project #
Application #
Study Section
Molecular Genetics B Study Section (MGB)
Program Officer
Reddy, Michael K
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
Princeton University
Schools of Arts and Sciences
United States
Zip Code
Tran, Phong Lan Thao; Pohl, Thomas J; Chen, Chi-Fu et al. (2017) PIF1 family DNA helicases suppress R-loop mediated genome instability at tRNA genes. Nat Commun 8:15025
Geronimo, Carly L; Zakian, Virginia A (2016) Getting it done at the ends: Pif1 family DNA helicases and telomeres. DNA Repair (Amst) 44:151-158
Phillips, Jane A; Chan, Angela; Paeschke, Katrin et al. (2015) The pif1 helicase, a negative regulator of telomerase, acts preferentially at long telomeres. PLoS Genet 11:e1005186
Lin, Kah Wai; Zakian, Virginia A (2015) 21st Century Genetics: Mass Spectrometry of Yeast Telomerase. Cold Spring Harb Symp Quant Biol 80:111-6
Stundon, Jennifer L; Zakian, Virginia A (2015) Identification of Saccharomyces cerevisiae Genes Whose Deletion Causes Synthetic Effects in Cells with Reduced Levels of the Nuclear Pif1 DNA Helicase. G3 (Bethesda) 5:2913-8
Willis, Nicholas A; Chandramouly, Gurushankar; Huang, Bin et al. (2014) BRCA1 controls homologous recombination at Tus/Ter-stalled mammalian replication forks. Nature 510:556-9
Zhou, Ruobo; Zhang, Jichuan; Bochman, Matthew L et al. (2014) Periodic DNA patrolling underlies diverse functions of Pif1 on R-loops and G-rich DNA. Elife 3:e02190
McDonald, Karin R; Sabouri, Nasim; Webb, Christopher J et al. (2014) The Pif1 family helicase Pfh1 facilitates telomere replication and has an RPA-dependent role during telomere lengthening. DNA Repair (Amst) 24:80-86
Bochman, Matthew L; Paeschke, Katrin; Chan, Angela et al. (2014) Hrq1, a homolog of the human RecQ4 helicase, acts catalytically and structurally to promote genome integrity. Cell Rep 6:346-56
Sabouri, Nasim; Capra, John A; Zakian, Virginia A (2014) The essential Schizosaccharomyces pombe Pfh1 DNA helicase promotes fork movement past G-quadruplex motifs to prevent DNA damage. BMC Biol 12:101

Showing the most recent 10 out of 49 publications