A group of scientists, software developers and artists have taken to using virtual reality (VR) technology to visualise complex interactions between genes and their regulatory elements.
The team, which comprises of members from Oxford University, Universita’ di Napoli and Goldsmiths, University of London, have been using VR to visualise simulations of a composite of data from genome sequencing, data on the interactions of DNA and microscopy data.
When all this data is combined the team are provided with an interactive, 3D image that shows where different regions of the genome sit relative to others, and how they interact with each other.
“Being able to visualise such data is important because the human brain is very good at pattern recognition – we tend to think visually,” said Stephen Taylor, head of the Computational Biology Research Group at Oxford’s MRC Weatherall Institute of Molecular Medicine (WIMM).
“It began at a conference back in 2014 when we saw a demonstration by researchers from Goldsmiths who had used software called CSynth to model proteins in three dimensions. We began working with them, feeding in seemingly incomprehensible information derived from our studies of the human alpha globin gene cluster and we were amazed that what we saw on the screen was an instantly recognisable model.”
The team believe that being able to visualise the interactions between genes and their regulatory elements will allow them to understand the basis of human genetic diseases, and are currently applying their techniques to study genetic diseases such as diabetes, cancer and multiple sclerosis.
“Our ultimate aim in this area is to correct the faulty gene or its regulatory elements and be able to re-introduce the corrected cells into a patient’s bone marrow: to perfect this we have to fully understand how genes and their regulatory elements interact with one another” said Professor Doug Higgs, a principal researcher at the WIMM.
“Having virtual reality tools like this will enable researchers to efficiently combine their data to gain a much broader understanding of how the organisation of the genome affects gene expression, and how mutations and variants affect such interactions.”
There are around 37 trillion cells in the average adult human body, and each cell contains two meters of DNA tightly packed into its nucleus.
While the technology to sequence genomes is well established, it has been shown that the manner in which DNA is folded within each cell affects how genes are expressed.
“There are more than three billion base pairs in the human genome, and a change in just one of these can cause a problem. As a model we’ve been looking at the human alpha globin gene cluster to understand how variants in genes and their regulatory elements may cause human genetic disease,” said Prof Jim Hughes, associate professor of Genome Biology at Oxford University.