Genome3D: A viewer-model framework for integrating and visualizing multi-scale epigenomic information within a three-dimensional genome

New technologies permit the measurement of many types of genomic and epigenomic information at scales ranging from the atomic to nuclear. Much of this new data is structural in nature and challenging to coordinate with existing data formats. There is an increasing need to integrate and visualize disparate data sets in order to reveal structural relationships not apparent when viewing these data formats separately. We have developed the Genome3D software package in order to integrate and display epigenomic data within the context of a three-dimensional physical model of the human genome. To our knowledge, this is the first such tool developed to visualize human genome in three dimensions. Here we describe the major features of Genome3D and discuss our multi-scale data framework using a representative basic physical model. Additionally, utilities to generate demonstration models of common chromosome interaction scenarios derived from High-C or CHIA-PET analysis are under development. These models are compatible with existing annotation data formats and can demonstrate common situations where one or more chromosomes are arranged such that two or more interaction sites appear in close proximity. These models can be used to directly create publication images without resorting to intermediate use of image editing software.