The goal of research conducted in our laboratory is to unravel the mechanisms of DNA repair.  Our lab is focusing on double-strand DNA breaks, which can be very dangerous for our cells.  Abnormal repair of these breaks leads to genetic instability, which is believed to promote cancer in humans.  This is why it is critical to determine the mechanisms that maintain genetic integrity by properly repairing DNA breaks.  Because DNA repair pathways are similar in all organisms, our lab is conducting research using a convenient model - baking yeast.


The laboratory research focuses on two areas:


1)The mechanism and genetic control of one particular pathway of DSB repair which is called Break-Induced Replication (BIR).


BIR is one DSB repair mechanism suggested to play an important role in the repair of collapsed replication forks.  However, this pathway is also dangerous because it can lead to several types of genetic instability, including loss of heterozygosity and formation of non-reciprocal translocations similar to those known to promote cancer.

In our lab we developed a new yeast experimental system that enables us to investigate the genetic control of BIR.  Analysis of a series of mutant candidates demonstrated that deletion of POL32, which encodes a third, non-essential subunit of polymerase delta, significantly reduced the efficiency of BIR and led to formation of a dangerous rearrangement termed half-crossovers (Deem, Genetics, 2008).  We proposed that these half-crossovers resulted from aberrant processing of BIR intermediates, and suggested that the half-crossovers observed in our system are analogous to non-reciprocal translocations (NRTs) described in mammalian tumors; therefore, our system represents a model for investigation of the mechanism of NRT formation. Presently we investigate risk factors that mis-route DSBs into the half-crossover repair pathway.

Recently we analyzed the frequency of mutagenesis associated with BIR and discovered that BIR is extremely mutagenic (Deem, PLoS Biology, 2011). We proposed that BIR could be an important source of spontaneous mutations in eukaryotic cells. Since accumulation of mutations is responsible for both evolutionary development, as well as various disease states, including cancer, we believe that our finding is very important.  Presently we investigate BIR replication fork to uncover the reasons for its high mutagenic potential.


2) Mechanisms that channel repair of double-strand breaks (DSBs) into  gross chromosomal rearrangements (GCRs).


We have demonstrated that inverted DNA repeats located in the vicinity of a DSB channel its repair into inter-molecular single-strand-annealing (SSA), which results in formation of dicentric inverted dimers (VanHulle , Mol. and Cell. Biol.,2007).  These molecules are then processed by the cell such that various GCRs, including non-reciprocal translocations, amplifications, deletions, and duplications result.  Given the very large number of repetitive DNA sequences in the mammalian genome, we proposed that this “SSA-GCR” pathway is likely to contribute to genome instability in higher organisms.  We observed that the SSA-GCR pathway, which is mediated by DNA inverted repeats, is suppressed in the presence of Rad51 protein, but is efficient in its absence.  This allowed us to propose that Rad51p is involved in protecting eukaryotic genomes from GCRs (Downing et al., Mutation Res., 2008).  Presently we investigate mechanisms of two pathways of DSB repair mediated by inverted repeats (inter-and intra-molecular SSA).