Tineke: “At our lab, we research transcription regulation at a single-cell and single-molecule level. We try to understand how genes switch on at the right time in the right cell. And we try to grasp how the cell regulates transcription by dissecting the underlying mechanisms. For that, we use living single cells. In the end, within single cells, all molecular processes involved with transcription are dynamic random events. That’s why there’s nothing like studying single cells. They never behave like the average.”

Jurgen: “It’s important to know how the cell copes with the DNA damage that disrupts transcription. At our lab, we study what happens with transcription in the event of DNA damage, how transcription-coupled DNA repair works, and which proteins are involved. We still don’t know what happens to RNA polymerase when it stumbles upon damage in a DNA strand. Is the damage being repaired? Does it make the polymerase fall off the RNA? Is transcription being restarted and if yes, how?”

Jurgen Marteijn

Tineke: “All those questions just didn’t sit right with the both of us. In our lab, we had just implemented a tool with which we could study transcription at single genes in single cells. At one of the Oncode Meetings, Jurgen and I talked about that. Just like transcription, DNA damage happens at random too. That makes the process hard to study using genome-wide techniques. We both ended up seeing how we could use my tool to study RNA polymerase.”

Jurgen: “My lab was looking at all the genes of a single cell at the same time, so we needed something like Tineke’s tool. We gave the idea lots of thought by thinking it through mechanistically. You can see DNA damage as a car breaking down on the highway, and a gene as a single highway. If you want to check for a damaged car at the side of the road, you won’t find it that quickly if you check all highways at the same time. It’s much quicker to check the specific highway on which the damaged car is present. We ended up doing the same thing in a single cell, visualizing a single RNA molecule in a single gene, and checking both ends of a newly synthesized RNA molecule. That way, we can check if it takes longer than expected to transcribe the gene upon DNA damage. Thanks to this mechanistic view, we can infer what happens. Our cooperation enables us to check that in a single cell, on a single gene. That strikes out a lot of variation.” 

Tineke: “We just knew we had to study the transcription dynamics at a single loci in the genome, just as I do in my lab. But thinking mechanistically doesn’t necessarily take you to the right place. After we had our first talks, it took us more than a year to put our theory into practice. We didn’t know if we would succeed. Being part of Oncode Institute was crucial. Oncode’s base funding allowed us to freely research our new plans. We wouldn’t have been able to cover that risk with a grant.”

Tineke Lenstra

Jurgen: “The base funding allowed us to jump-start our cooperation. It allowed us to demonstrate our proof of concept and proved we can work together. On top of that, all the data we managed to gather from our pilot raised the odds of receiving an actual grant. We applied for the NWO ENW-M2 collaborative grant, which we thought was most suitable for our project. And we got it.”

Tineke: “When we were in the process of writing the grant proposal, Jurgen and I did a lot of brainstorming. And because we got such a head start, we were able to take our brainstorming talks a step further quickly. We got around questions like what to do with the knowledge, and what types of experiments we would have to conduct. It was an exciting time, and we learned a lot too. We quickly learned how to fill each other’s knowledge gaps.”

Jurgen: “We found out that our labs had much more synergy than we assumed beforehand. We’re both in cancer research and transcription, but still, our fields of work lie apart.”

Tineke: “I agree. At the average conference, I don’t think we would have met. The Oncode meetings facilitated our collaboration.”

Jurgen Marteijn

Jurgen: “At the moment, we’re in a fun phase. People from our labs are getting to know each other, we’re setting up cooperation, and both groups are just getting started with a PhD student. There are two of them, dedicated to the project.”

Tineke: “Throughout the project, we’ll keep in close contact. We’ll have to share software and conduct experiments in each other’s labs. Both of our PhD students will have to commute between the NKI and the Erasmus MC. It requires some serious intertwining of our labs to optimally profit from all the expertise of both of our labs.”

Jurgen: “It’s a fact of life that every cell gets to cope with approximately 50,000 events of damage per day. You can imagine there’s also damage being done in lots of genes that can disrupt transcription. My hope for this project is that it will give us a deeper understanding of the effects of DNA damage on RNA polymerases, and what happens when the repair machinery of the cell encounters damage. That mechanistic knowledge might in turn help us understand what happens in the body of a cancer patient receiving chemotherapy. Neurotoxicity, for instance, might in part be a result of DNA damage-induced transcription stress.”

Tineke: “This research could also bring more insight into the factors that lead to sensitivity for cancer drugs. If we understand more about the process of DNA damage on a molecular level, we might eventually be able to use that knowledge for better treatments of cancer patients.”