Volumetric Visualization of the Genome

Keywords

Genome, volume, DNA, 3D Hi-C, volumetric, abstraction.

Abstract

Within the nucleus of a cell, the genetic material (DNA) is condensed, supercoiled, and wrapped around proteins called histones, so to form chromatin. Unlike its traditional visualization, the organization of chromatin is 3D and can be measured with whole-genome sequencing technologies such as Hi-C sequencing, the results of which are often graphically represented as flat 2D heat-maps or a 1D curve that looks like a hairball. Here we discuss a novel approach to represent these and other genomic data by transforming the visualization of the genome from a 1D curve embedded in 3D into a structured 3D volume. This abstraction prioritizes 3D spatial proximity of chromatin and enables advanced techniques like clipping, thresholding, and contouring. Our method allows for multi-variable encoding, thereby enhancing our ability to interpret multivariate relationships, offering a more complete and effective representation of genomic structures, chromosome organization, and data relationships.