damage has an effect on transcription and replication — the processes responsible for gene expression and DNA duplication, respectively — and so attracts transcription and replication researchers. It also interests crystallo- graphers working towards resolving how proteins recognise DNA damage. “There has always been cross fertilisation between the DNA repair people and other more general areas of research,” says Professor Naegeli. He and his colleagues use a combination
of biochemical methods that allow them to observe how repair proteins and enzymes operate on the DNA. “There is a whole queue of new techniques that we can use to work in the cell,” explains Professor Naegeli. “We are able to do actual biochemistry in the cell,” he adds. Some of these approaches involve the use of small-interfering RNA, which allows them to block the expression of specific gene so they can study what happens when a particular factor is missing. Other approaches make use of real-time imaging methods. As Professor Naegeli describes, “You can tag the protein with a fluorescent marker and then you can follow the movement and interactions of that fluorescent protein in the cell nucleus.” One of the key challenges in
determining the mechanisms involved in DNA damage recognition and repair is the complexity of the systems involved. “We kind of understand how the process works when we use a very artificial system where the DNA substrate is very accessible,” he says. “But every human cell has about
two
metres of DNA.” As a result, the DNA is very densely packed and additional so far unknown mechanisms are required to make
the DNA accessible to the
process of DNA repair and the enzymes and proteins involved. Yet the researchers have already
succeeded in identifying a model for DNA damage recognition. “Our own model is different from what you would find in the literature,” says Professor Naegeli. He describes how a group of protein factors, which he calls ‘matchmakers’, recruit the damage recognition sensor onto the DNA. The key damage recognition protein is actually an enzyme that scans the DNA, and it is this scanning enzyme that identifies the damaged site on the DNA. “That is our model,” he concludes. “It differs in the sense that the proteins that we call matchmakers are not directly
www.projectsmagazine.eu.com
responsible for DNA damage recognition — it turns out that these matchmaker proteins are found everywhere on the DNA, not only on damaged sites but also on native DNA.” Professor Naegeli and his colleagues
found that the function of
these matchmaker proteins is to get the scanning enzyme onto the DNA where, together, they set to work on the process of damage recognition. The focus of their research has now
moved onto examining DNA repair takes place in the complex cellular context. “The mechanism we are studying is called nucleotide excision repair.” He explains that there is a well-studied repair mechanism for UV damage that involves cleavage of the DNA on either side of the damage. The damaged segment is then removed and replaced by normal DNA. But as he has pointed out, DNA is very densely packed in the cell. “What we have to understand is how DNA repair is possible in a very condensed environment.”
Project Information AT A GLANCE
Project Title: How the nucleotide excision repair ‘big enzyme machine’ overcomes mammalian chromatin
Project Objective: Genome stability is essential to prevent mutagenesis, premature aging and cancer. A ‘big enzyme’ machine promotes genome stability by excising DNA adducts generated by insults like UV radiation, carcinogens and certain drugs. This repair mechanism has been established in reconstitution studies using naked substrates that are not representative of condensed DNA filaments in living cells. We, therefore, focus on accessory players and regulatory circuits that are required to repair DNA in the compacted cellular landscape.
Project Duration and Timing: 3 years, October 2012 to October 2015
Project Funding: Swiss National Science Foundation, Swiss Cancer Ligue, Velux Foundation
“If we have
knowledge of how cancer cells repair
DNA we can try to optimise how we kill them”
The field abounds with new lines of
enquiry. Having applied their technical capabilities, knowledge and expertise so fruitfully to the question of damage recognition, there is little doubt that the mysteries at the focus of the group’s current research will also be resolved in due course. Work in the field in general has already lead to promising inroads into clinical applications and may even contribute to the fight against cancer. These potential clinical applications alone suffice to command vast interest from academia, industry and the general public alike. But in dealing with the fundamental processes
that maintain life, Professor
Naegeli’s research holds an additional fascination that drives it forward, an example of another fundamental attribute of human life — curiosity.
★
Project Partners: University of Konstanz, Functional Genomics Center Zürich, ETH Zürich, University of Basel
Main Contact:
Hanspeter Naegeli Prof. Dr. Hanspeter Naegeli is Head of the Toxicology Division at the Institute of Veterinary Pharmacology and Toxicology of the University of Zürich. Dr. Naegeli studied Veterinary Medicine in Zürich. After completing his thesis, he moved to the U.S. for a 3-year post-doctoral project in the field of DNA Repair. Dr. Naegeli returned to Zürich in 1993 and has been promoted to the degree of Professor of Toxicology in 2002. His activities are characterized by a strong commitment to basic research and an offensive approach to practical and clinical problems. The main competence of his research group involves innovative techniques of functional genomics and live cell imaging
Contact: Tel: +41 44 635 87 63 Email:
naegelih@vetpharm.uzh.ch Web:
www.vpt.uzh.ch
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