CSynth: A Dynamic Modelling and Visualisation Tool for 3D Chromatin Structure

Abstract

The 3D structure of chromatin in the nucleus is important for gene expression and regulation. Chromosomal conformation capture techniques, such as Hi-C, generate large amounts of data showing interaction points on the genome but these are hard to interpret using standard tools. We have developed CSynth, a high performance 3D genome browser and real time chromatin restraint-based modeller to visualise dynamic and interactive models of chromatin capture data. CSynth does its calculations in the GPU hence is much faster than existing modelling software to infer and visualise the chromatin structure which also allow real-time interaction with the modelling parameters. It also allows straightforward comparison of interaction data and the results of third party 3D modelling outputs. In addition we include an option to view and manipulate these complicated structures using Virtual Reality (VR) allowing scientists to immerse themselves in the models for further understanding. This VR component has also proven to be a valuable teaching and public engagement tool. CSynth is web based and available to use at http://csynth.org .

Super-Resolution Microscopy of Chromatin

“…( c ) Microscopic images showing FRET data of single chromatin arrays, scale bar: 5 µm. ( d ) Structural data from super-resolution microscopy can be combined with sequencing information (bottom) [91] to yield with higher confidence a model of the underlying structure. (a–c) © 2018 under the Creative Commons license [92] by Kilic et al [83].…”

“…(a–c) © 2018 under the Creative Commons license [92] by Kilic et al [83]. (d) Created with CSynth [91].…”

3DGV: Immersive Exploration of 3D Genome Structures using Virtual Reality

“…But the browsing experience is limited by the representation of 3D objects as 2D projections on a screen and the manipulation of the data through keyboards and mice. Immersive technologies present an opportunity to address this challenge (9,10). In this paper, we introduce the Virtual Reality 3D Genome Viewer (3DGV) -a virtual reality (VR) version of our previous 3D genome browser (6).…”