Article Science

Investigating accidents on the DNA highway

A long-haul truck clocks up the miles as it journeys across the land, dealing with the ebb and flow of commuters around it. A motorway fills with traffic, then slowly empties. The police secure the scene of an accident and redirect oncoming vehicles out of the way.

01 August 2023

Similar scenes are playing out every day within each cell in our bodies. The smooth flow of traffic along DNA leads to successful replication - while accidents can cause genome instability. 

This is a process Conrad Nieduszynski and his group at the Earlham Institute have been studying in detail.

“This is fundamental science in every sense,” says Dr Nieduzynski. “The ability to reliably and repeatedly replicate genetic material is the basis of all life on this planet. Yet it’s a process we still don’t fully understand.”

His group is researching how errors in DNA replication cause genomic and phenotypic variation, contributing to disease. 

This research has major implications for human health, particularly among older people. A single error has the potential to be catastrophic at any age but it’s more often the accumulation of mistakes over a lifetime that leads to disease. 

It is also relevant to researchers who are designing new genes and organisms.

Dr Conrad Nieduszynski leads the DNA Replication Group at the Earlham Institute
Conrad Research Lab

Vehicles of change

Dr Nieduszynski compares the different actors on the DNA to traffic on our highways and byways.

The long-haul truck, for example, symbolises a DNA polymerase replicating the entire genome – a process which happens when the cell divides. 

All DNA in the cell must be copied perfectly from end to end, a process which can take several hours. During the course of this mammoth undertaking, every base of the cell’s DNA must be accessed. 

Other cellular traffic ebbs and flows; some regions of the DNA will be quiet and some will be busy. Within genes, transcription happens continuously. There can be many RNA polymerases queued to transcribe the same short section of DNA. 

These busy roads have their own one-way systems, stop and go signals, and even the occasional dangerous roadblock.

It’s not a perfect metaphor but thinking about highway traffic helps bring to life the complex world of DNA replication. In both cases, avoiding accidents depends on the complex interaction of multiple moving parts.

And, also in both cases, if something does go wrong, an emergency response can help avoid a catastrophic consequence for the system as a whole. 

This is fundamental research in every sense. The ability to reliably and repeatedly replicate genetic material is the basis of all life on this planet. Yet it’s a process we still don’t fully understand.

Replication, DNA and disease

“The challenge of studying errors during DNA replication is that, almost all the time, it works fine,” explains Dr Nieduszynski. 

“Mistakes are rare, but biologically very important. Essentially, we are looking for ‘needle in a haystack’ events.”

Mistakes during DNA replication are the major source of genome instability that underlies disease and fuels evolution and novel phenotypes. When replication is compromised, the DNA is more prone to mutations and breaks. These can mean chromosome rearrangements, associated with diseases and disorders. 

A working hypothesis is that certain regions may be more difficult to copy. So the question is ‘why would this be?’ 

In some cases, RNA polymerases could form heavy ‘traffic’. In others, tightly bound proteins form ‘roadblocks’. It could even be possible that, in some regions, the classic DNA double helical structure doesn’t form and alternative structures cause problems.

Members of the Nieduszynski Group in a team seminar
Sathish Thiyagarajan
EI researcher Angela Man

Pictured left to right: members of the Nieduszynski Group, including Anna Rogers, Sathish Thiyagarajan and Angela Man.

In all these regions, DNA replication is believed to be more prone to errors. Dr Nieduszynski’s group are working to identify and characterise them.

“There are some interesting implications,” explains Dr Nieduszynski. “The hope is that eventually we’ll be able to predict where there might be problems in DNA replication – where a mutation might occur. 

“For example, there’s a frequent mutation in a yeast which causes antifungal resistance – it’s a mutation occurring in one very specific area, which may be difficult to replicate. 

“In the future, it might be possible to predict how likely it is for an organism to acquire resistance to treatment.”

Accumulation of DNA replication errors during an organism's lifetime is called somatic variation. Within the Nieduszynski group, Dr Angela Man is looking at errors during DNA replication of highly repetitive DNA sequences and how they may contribute to this variation. 

This work, part of the Earlham Institute’s Cellular Genomics research programme, aims to understand the source and impact of this genomic variation.

Researchers in the DNA Replication lab at the Earlham Institute

Budding yeast and molecular police

Projects within the group are focused on different aspects of DNA replication. Dr Anna Rogers and Dr Sathish Thiyagarajan are working on finding replication pause sites in budding yeast, as well as the causes and rescue mechanisms. 

“This project takes a broad view of the genome overall,” says Dr Nieduszynski. “Where do we observe problems? What is the ‘traffic flow’ like?”

And Dr Isabel Diez Santos is working on the role of senataxins.

The function of this protein is not well understood, but it is thought to be involved in resolving conflicts between replication and transcription, playing an important role in preventing damage to DNA and maintaining stability of the genome. 

“We don’t yet understand whether it resolves the conflicts before they happen, or whether it clears up the mess left afterwards, or both,” acknowledges Dr Nieduszynski.

“To return to the traffic metaphor, senataxin is like the police dealing with a traffic accident. 

In the absence of the police we see more accidents - but is that because they haven’t forestalled collisions or they haven’t cleared the road after an accident?”

The group’s research has already driven fundamental discoveries about how genomes replicate in bacteria, archaea, and eukaryotes - measuring replication both in populations of cells and on single molecules. 

This has been possible thanks to the group developing the first single molecule sequencing method for the study of genome replication. Their work has discovered mechanisms that ensure stable chromosome inheritance and show how synthetic chromosomes can be designed to ensure stable replication.

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Amy Lyall

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