Research Highlights

My team's research focuses on dissecting the molecular mechanisms of DNA repair, in particular, homologous recombination (HR), a fundamental, evolutionarily conserved pathway used to maintain genome stability, which also generates genetic variation during gametogenesis. We base much of our work within the unicellular eukaryote, Saccharomyces cerevisiae, in which many of the fundamental molecular pathways that regulate chromosome biology are evolutionarily conserved with those preset in humans. Our work has importance to cancer, mutation, genetic rearrangement, fertility, evolution, and breeding.

Regulation of meiotic DSB repair                                                           PhD/Postdoc; Mol Cell 2002

Understanding how each meiotic cell accurately and concertedly repairs ~200 concurrent DNA breaks (DSBs) is a fascinating area of biological research. During my PhD, under supervision from Prof Alastair Goldman at the University of Sheffield, I developed a meiosis-specific DSB reporter assay that is sensitive to perturbations in the DSB repair mechanism. By using this system, I discovered that the mode of DSB repair is influenced by the total number of DSBs in the cell, implicating the presence of a sensory-feedback-regulatory loop—a concept ­that is central to our later work on ATM/ATR (below). 

Mechanism of Spo11-removal                       Postdoc/PI; Nature 2005, Nature 2006, Mol Cell 2009

Meiotic recombination is initiated by DSBs created by Spo11, a topoisomerase-like enzyme that becomes covalently attached to the broken DNA ends. Understanding how Spo11 is removed is of general interest because similar lesions form when topoisomerases are poisoned by chemotherapy. During my postdoc at Memorial Sloan-Kettering Cancer Centre with Prof Scott Keeney and Dr Jing Pan, we demonstrated that Spo11 is released attached to a bimodal distribution of oligonucleotides in both yeast and mammals, which we proposed derive from asymmetric DSB processing. These findings defined a new DNA repair pathway, led to a follow-up coauthor paper in Molecular Cell with colleagues from the GDSC (Edgar Hartsuiker and Tony Carr), and led international groups to investigate similar reactions in other organisms. Importantly, in collaboration with Scott Keeney (MSKCC) and with Dr Valerie Garcia (GDSC), we have used the assay to probe further aspects of recombination and DSB repair (see below). I subsequently wrote a general review of the meiotic recombination mechanism.

Genome-wide analysis of meiotic recombination initiation                           Postdoc/PI; Cell 2011

Meiotic DSBs are distributed across the genome in a non-random manner. Because each DSB gives rise to a recombination event, the fluidity of the DSB distribution underlies the rate and distribution of genetic change within sexually reproducing organisms. A better understanding of this topic is of general scientific interest. During my postdoc, I realised that the DNA sequences attached to Spo11 could serve as molecular barcodes of the genomic positions where recombination initiates—an idea that through work by Jing Pan, Mariko Sasaki, Scott Keeney and others generated a DSB map of unprecedented spatial resolution. Similar methods to map recombination in plants and mammals are underway, highlighting the impact that my seminal 2005 paper has made. 

Bidirectional resection of DSBs                                                               Nature 2011, Mol Cell 2014

Spo11 removal requires Mre11, an evolutionarily-conserved bifunctional nuclease with known endonuclease function, but no clear role for its exonuclease activity. We generated an Mre11 exonuclease hypomorph and found synergistic defects in DSB repair when another nuclease, Exo1 was also absent. Our molecular assays indicate that DSB processing begins at interstitial nicks (created by Mre11 endo), with resection proceeding bidirectionally both away from, and back towards the DSB end (by Exo1 and Mre11 respectively), something that had not been shown before. Our observations help explain the Spo11-oligo molecule distribution detected earlier, and solve a long-standing conundrum about the role of the Mre11 exonuclease. Via a second collaboration at the GDSC (with Atsushi Shibata and Penny Jeggo), we reported that a similar repair mechanism functions at DSBs in mammalian cells.

DSB regulation by ATM/ATR                                                                 Open Biol 2013; Nature 2015

ATM and ATR are evolutionarily conserved signalling kinases that respond to DNA damage. Whilst a PhD student in my lab, Steve Gray determined that activation of Mec1 (the yeast ATR orthologue) is necessary to promote meiotic DSB formation by transiently delaying cell cycle progression—an unforeseen function that becomes essential when Spo11-DSB catalysis is compromised. By contrast, in work recently published in Nature, we demonstrate that Tel1 (the ATM orthologue) is necessary to suppress clustering of adjacent Spo11-DSBs within chromatin loops. The concept that DSBs might cluster in individual cells is unprecedented, and will have a major impact on the way researchers consider and model rates and distributions of recombination occurring during gametogenesis. These observations were discussed by our team in two review articles: Homeostatic regulation of meiotic DSB formation by ATM/ATR, and Meiotic DSB patterning: A multifaceted process.

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