Every cell in our body contains two metres of DNA that hold our genetic code. Although the DNA is the same in every cell, different genes are active and inactive in different types of cells (e.g. heart cells versus brain cells), giving them their specific characteristics. Recently, scientists have discovered that one of the ways that cells control which genes are switched on, and which are not, is by rearranging the way the DNA is folded up inside the nucleus. However we still understand very little about how and why cells do this, and how it may contribute to certain diseases such as cancer, or to the way our cells change as we get older.
The study of how cells package their DNA is called ‘3D/4D genomics’: 3D because it is about the three dimensional shape of the DNA, 4D because we have to add the dimension of time - the way the DNA is folded in a cell can change from day to day. One of the big problems in this area is that it is a ‘multiscale’ type of science. To understand it properly yone needs to look both at the behaviour of whole cells, and of individual molecules in the cell (which are a million times smaller).
This is a young science, expanding rapidly. All the time new groups discover new ways to study it at the large, medium, or small scale. Enormous amounts of very complicated data are being generated and now we urgently need a good way to help scientists bring this all together and allow them to make sense of it by seeing how it fits together into the ‘big picture’. Computer simulations are a powerful tool to help us do this. They allow us to turn complicated experimental data into pictures of how DNA is packed and folded, from the molecular scale all the way up to the cellular scale. But until now the ways in which these visualisations are done has not been standardized, or adapted to all the new sorts of data that are becoming available, or made simple for non-specialists to use.
The MuG Virtual Research Environment is now a reality available to the scientific community: a sort of specialised web browser - where scientists can:
*Upload, share, find and check all types of 3D/4D genomics data generated by experimentalists anywhere in the world
*Perform data analysis and integration tasks, some of which need a lot of computer power
*Perform computer simulations that turn this data into visualisations of how the DNA is packed into a cell, and how this can change
*See how all this relates to how cells change their behaviour, and so affects growth, development, disease and ageing
This has only been possible through a tight collaboration of a unique multidisciplinary team of experts in experimental 3D/4D genomics, in molecular studies of DNA, and in computer and data science.
