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

Abstract

We present ChromoSkein, a web-based tool for visualizing three-dimensional chromatin models. The spatial organization of chromatin is essential to its function. Experimental methods, namely Hi-C, reveal the spatial conformation but output a 2D matrix representation. Biologists leverage simulation to bring this information back to 3D, assembling a 3D chromatin shape prediction using the 2D matrices as constraints. Our overview of existing chromatin visualization software shows that the available tools limit the utility of 3D through ineffective shading and a lack of advanced interactions. We designed ChromoSkein to encourage analytical work directly with the 3D representation. Our tool features a 3D view that supports understanding the shape of the highly tangled chromatin fiber and the spatial relationships of its parts. Users can explore and filter the 3D model using two interactions. First, they can manage occlusion both by toggling the visibility of semantic parts and by adding cutting planes. Second, they can segment the model through the creation of custom selections. To complement the 3D view, we link the spatial representation with non-spatial genomic data, such as 2D Hi-C maps and 1D genomic signals. We demonstrate the utility of ChromoSkein in two exemplary use cases that examine functional genomic loci in the spatial context of chromosomes and the whole genome.