Tasks and Visual Abstractions for 3D Chromatin Representation

Abstract The spatial organization of chromatin fiber directly influences its function. However, the high visual complexity of chromatin spatial models makes the understanding of the structure extremely challenging. Therefore, genomic researchers still primarily rely on indirect analysis of chromatin through 2D views, missing the advantages that 3D visualization can offer. In this paper, we first analyze the task space of genomic research and identify biological domain tasks that can benefit from dedicated spatial representations. We organize these tasks into four categories: tasks related to structural features, additional meta‐data, structural relationships, and comparative tasks. We analyze these tasks in terms of their complexity, co‐dependence, and potential benefits of 3D‐based solutions. Secondly, we present four newly designed visual representations of chromatin 3D structure, focused on enhancing the understanding of structural features and solving relationships tasks. These include the hierarchical nature of spatial chromatin sub‐units, their visual abstractions, spatial interactions, and a cumulative representation of chromatin dynamic behavior. We also include feedback from four domain researchers and discuss future steps necessary to make spatial representations valid and valuable part of genomic research.