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We present ChromoSkein, a web-based tool for visualizing three-dimensionalchromatin models. The spatial organization of chromatin is essential to itsfunction. Experimental methods, namely Hi-C, reveal the spatial conformationbut output a 2D matrix representation. Biologists leverage simulation to bringthis information back to 3D, assembling a 3D chromatin shape prediction usingthe 2D matrices as constraints. Our overview of existing chromatinvisualization software shows that the available tools limit the utility of 3Dthrough ineffective shading and a lack of advanced interactions. We designedChromoSkein to encourage analytical work directly with the 3D representation.Our tool features a 3D view that supports understanding the shape of the highlytangled chromatin fiber and the spatial relationships of its parts. Users canexplore and filter the 3D model using two interactions. First, they can manageocclusion both by toggling the visibility of semantic parts and by addingcutting planes. Second, they can segment the model through the creation ofcustom selections. To complement the 3D view, we link the spatialrepresentation with non-spatial genomic data, such as 2D Hi-C maps and 1Dgenomic signals. We demonstrate the utility of ChromoSkein in two exemplary usecases that examine functional genomic loci in the spatial context ofchromosomes and the whole genome.

ChromoSkein: Untangling Three-Dimensional Chromatin Fiber With a Web-Based Visualization Framework