3D structure of DNA may explain how cephalopods evolved complex brains
Octopuses, squid and cuttlefish, collectively known as coleoid cephalopods, have evolved exceptionally large and elaborately structured nervous systems capable of complex behaviours such as problem-solving and rapid camouflage. A new study by scientists at The University of Vienna suggests that the origins of this complexity may lie not just in the genes themselves, but in how the genome is organised in 3D. The researchers found that ancient, extensive reorganisation of the genome altered how DNA is arranged inside the cell. These shifts brought previously distant regions of DNA into contact, changing the way genes are regulated. Understanding this process could change how we think about how new traits emerge during evolution. The findings are currently published in the renowned journal Nature Communications.
image: Californian two-spot octopus ( Octopus bimaculoides ). Embryo at the final stage before hatching. The species is named after the two prominent blue eyespots that can help deter predators. view more Credit: Natalie Grace Schulz Octopuses, squid and cuttlefish, collectively known as coleoid cephalopods, have evolved exceptionally large and elaborately structured nervous systems capable of complex behaviours such as problem-solving and rapid camouflage.
A new study by scientists at The University of Vienna suggests that the origins of this complexity may lie not just in the genes themselves, but in how the genome is organised in 3D. The researchers found that ancient, extensive reorganisation of the genome altered how DNA is arranged inside the cell.
These shifts brought previously distant regions of DNA into contact, changing the way genes are regulated. Understanding this process could change how we think about how new traits emerge during evolution. The findings are currently published in the renowned journal Nature Communications.
The team studied the 3D structure of the genome across octopus, squid and cuttlefish, combining data on DNA structure with gene activity. "The genome isn't just a sequence of genes. It's folded into a complex three-dimensional structure," said lead author Dr Thea Rogers.
"Understanding how that structure evolves is becoming increasingly important for understanding how new forms of biological complexity arise." "Regulatory entanglement" as a consequence of genome reorganisation In cephalopods, a large-scale burst of genome reorganisation, which occurred hundreds of millions of years ago, dramatically reshuffled the genome and brought previously distant regions of chromosomes into close proximity.
The researchers found that when regions of DNA are brought into contact, they can begin to interact and influence each other's activity. Over time, these interactions can become embedded, forming increasingly interconnected regulatory networks. "Regulatory entanglement" balances innovation and stability in genome evolution This process, described by the researchers as "regulatory entanglement", may allow genomes to generate new patterns of gene expression while maintaining essential functions.
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Not all aspects of genome structure appear to respond to genome reorganisation in the same way. The researchers found that large structural units of the genome, known as chromatin domains, remained largely stable over evolutionary time. In contrast, finer-scale connections known as chromatin loops were far more dynamic.
These loops bring distant regions of DNA into contact. They varied widely across species, tissues and developmental stages, and were often found near genes involved in key cephalopod traits, including those linked to the nervous system. This suggests that these more flexible regions may be particularly affected by large-scale changes in DNA organisation.
3D structure of DNA shapes evolutionary processes actively Together, these findings challenge the idea that genome architecture is a passive consequence of evolution. Instead, they suggest that the 3D organisation of DNA actively shapes how evolution unfolds. In cephalopods, this may have played a key role in the emergence of their unusually complex nervous systems.
Summary Scientists at the University of Vienna reconstructed the 3D organisation of the genome in octopus, squid and cuttlefish to investigate how genome architecture evolved following an ancient burst of genome reorganisation. The study found that this large-scale reorganisation brought previously distant regions of DNA into contact, creating new networks of regulatory interactions that became embedded over evolutionary time.
The researchers describe this process as "regulatory entanglement", whereby new DNA interactions become increasingly interconnected, allowing genomes to generate novel patterns of gene regulation while maintaining essential biological functions. The researchers found that not all aspects of the 3D genome respond to genome reorganisation in the same way.
Large chromatin domains remained remarkably stable, whereas finer-scale chromatin loops were far more dynamic. The findings challenge the view of genome architecture as a passive consequence of evolution and instead suggest that the 3D organisation of DNA can actively influence evolutionary change.
About the University of Vienna: For over 650 years the University of Vienna has stood for education, research and innovation. Today, it is ranked among the top 100 and thus the top four per cent of all universities worldwide and is globally connected. With degree programmes covering 188 disciplines, and approximately 11,000 employees, we are one of the largest academic institutions in Europe.
Here, people from a broad spectrum of disciplines come together to carry out research at the highest level and develop solutions for current and future challenges. Its students and graduates develop reflected and sustainable solutions to complex challenges using innovative spirit and curiosity.
Journal Nature Communications Article Title Genome reorganisation and expansion shape 3D genome architecture and define a distinct regulatory landscape in coleoid cephalopods Article Publication Date 9-Oct-2026 Disclaimer: AAAS and EurekAlert! are not responsible for the accuracy of news releases posted to EurekAlert! by contributing institutions or for the use of any information through the EurekAlert system.
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