Juicebox.js Provides a Cloud-Based Visualization System for Hi-C Data

Abstract

Contact mapping experiments such as Hi-C explore how genomes fold in 3D. Here, we introduce Juicebox.js, a cloud-based web application for exploring the resulting datasets. Like the original Juicebox application, Juicebox.js allows users to zoom in and out of such datasets using an interface similar to Google Earth. Juicebox.js also has many features designed to facilitate data reproducibility and sharing. Furthermore, Juicebox.js encodes the exact state of the browser in a shareable URL. Creating a public browser for a new Hi-C dataset does not require coding and can be accomplished in under a minute. The web app also makes it possible to create interactive figures online that can complement or replace ordinary journal figures. When combined with Juicer, this makes the entire process of data analysis transparent, insofar as every step from raw reads to published figure is publicly available as open source code.

Keywords: 3D genomics; Hi-C; contact domains; contact map; enhancers; genome architecture; loop extrusion; loops; nuclear architecture; visualization.

Figure 1. Juicebox.js Makes It Easy to Share Interactive Visualizations of Contact Mapping Data Derived from Hi-C and Other Experiments

Hi-C maps from new experiments can be easily added and juxtaposed with tracks from ENCODE and other sources. It is possible to zoom in and out in real time using either a mouse or touch-screen gestures. Display parameters such as the color scale and the normalization can be adjusted interactively. The complete state of the browser can always be encoded as a sharable URL. No programming is necessary to share and explore new datasets. Left: A loop resolution Hi-C map showing all contacts within an 700 kb genomic interval, generated using HCT-116 human colorectal carcinoma cells. Loops, which form here due to physical tethering between two CTCF- and cohesin-bound loci, manifest as bright peaks away from the diagonal. Contact domains, genomic intervals that exhibit enhanced contact frequency within themselves, manifest as bright squares along the diagonal. When the two anchors of a loop demarcate a contact domain, the resulting feature is called a “loop domain.” Right: The same region in HCT-116 cells after the RAD21 subunit of the cohesin complex has been degraded using an auxin-inducible degron system. The loop domains all disappear completely, demonstrating that they are dependent on cohesin. An interactive version of this figure is available at https://aidenlab.org/figures/Robinson-Cell-Systems-2017/figure1.html (see also Table S1).