3D genome browser and real time chromatin modeller to visualise models of chromatin capture data.
Frederic Fol Leymarie, William Latham, Stephen Todd, Peter Todd Goldsmiths, University of London.
Stephen Taylor, Jim Hughes, Veronica Buckle Weatherall Institute, University of Oxford
Part of chr16 from white and red blood cells, modelled using CSynth:
CSynth is a physics based interactive visualisation platform for visualizing the 3D structure of the biological molecules.
It is primarily designed to provide an engaging way to explore and understand the complex structure of the genome in 3D by
integrating data from next generation sequencing (Hi-C) and modelling. For example, it allows the user to see a traditional
Hi-C heat map overlaid with dynamically generated or precomputed 3D structures.
CSynth has now been published: Bioinformatics. 2020 Aug 31;btaa75
Recently scientists have begun to look at different groups of cells using so called ‘capture’ or ‘C’ techniques to look at where regions of the genome interact with each other. After some processing this produces a 2D interaction map which infers which part of the genome interacts with another part of the genome forming Topologically Active Domains or TADs.
However, these maps are not very intuitive to understand because we know the structure is in 3D. Steve Taylor (Computational Biology Research Group, MRC WIMM) and Frederic Fol Leymarie (Department of Computing, Goldsmiths University) began discussions after Steve saw Frederic presenting FoldSynth at BioVis and with Jim Hughes (Genome Biology, MRC WIMM), Stephen Todd (London Geometry) and Peter Todd (London Geometry) and William Latham (Department of Computing, Goldsmiths University) developed a prototype viewer called CSynth based on the 3D molecule viewer FoldSynth. They are seeking funding from various sources to continue develop this into a complete software package that also will allow import of public data, cutting edge 3D super resolution microscopy and detailed polymer models of the genome to get a much better understanding of how the genome is folded in cell and understand the complex mechanisms involved.
Even though the current prototype model of CSynth at this stage is not a ‘full’ modelling package (it uses simplified rules to model the DNA and currently does include any of the scaffolding proteins) it is allowing scientists to think about and pose questions more intuitively how and why genes, promoters and enhancers in different regions of the genome interact.
CSynth is now available to try out yourself at CSynth.org. Video walk-throughs are available in the Help section. Your own data may be uploaded to CSynth, but be sure to try out the examples first. If you have a connected HTC Vive headset, Virtual Reality allows a completely new way to look at the data in 3D!