Clamping down on DNA damage

Posted: 23rd April 2020

It was the end of a long 16-hour experiment and PhD student Winnie Tan didn’t have a good feeling. She was preparing to use the new electron microscope at Melbourne University and her precious sample, the culmination of 3 years of work, looked ‘clumpy’.

Electron microscopy allows very small structures in the cell to be seen. Normally proteins themselves are too small to be ‘seen’, but Winnie knew that her proteins fitted together to make a much larger structure and was hoping they would be within the resolution of the technique.

However, to work properly, the sample that is being examined must contain proteins that are ordered and uniform. Winnie’s sample preparation was already more complicated than most: the protein she was interested in needed to be present at a certain concentration, along with the correct ratios of DNA and nine other partner proteins. Given that it had taken so long to prepare her sample, Winnie decided to run it anyway.

Looking at the results, she knew immediately that what she was seeing was possibly the answer to a 20-year-old mystery. It had been long known that a protein called FANCD2, the subject of Winnie’s PhD, was a key part of the vast and intertangled protein network that the cell uses to repair DNA damage, but its exact role was unclear.

Winnie was interested in the role of FANCD2 because people missing an ‘active’ version of the protein have the disease Fanconi Anaemia. This means that their cells are not able to repair damage to their DNA. The disease leads to affected children losing the ability to produce blood cells. On average, in order to survive, a child with Fanconi Anaemia has to undergo a bone marrow transplant by the time they are 8 years old.

Winnie’s experiment allowed her to see, for the first time, how FANCD2 interacted with its protein partners in the cell.

Looking at the results from the analysis of her sample, Winnie could see string-like structures, a bit like little worms, where it seemed the protein clusters were lined up along the strands of DNA. Further experiments showed that the FANCD2 protein and its partners clamped onto the DNA only if they had first been modified by a protein called ubiquitin. This allowed them to coat the DNA, protecting it from further damage and helping to activate the DNA repair process.

Winnie’s results point to potential treatments for Fanconi Anaemia. The researchers will now look at finding ways to mimic the modifications that are required to make FANCD2 and its partners work properly, and look for other ways to protect DNA when the protein partners are absent.

The results form the basis of Winnie’s PhD thesis, which was passed in February. The newly minted doctor intends to remain in the lab for a period in order to bring her findings closer to a treatment for people with Fanconi Anaemia.

Image: Associate Profesor Andrew Deans (supervisor) and Winnie Tan, at her final PhD presentation. Winnie is now Dr Winnie Tan.

For more information please see: Genome stability