3D chromosome rendering from Hi-C data using virtual reality

Yixin Zhu; Siddarth Selvaraj; Philip Weber; Jennifer Fang; Jürgen P. Schulze; Bing Ren

doi:10.1117/12.2083470

8 February 2015 3D chromosome rendering from Hi-C data using virtual reality

Yixin Zhu, Siddarth Selvaraj, Philip Weber, Jennifer Fang, Jürgen P. Schulze, Bing Ren

Proceedings Volume 9397, Visualization and Data Analysis 2015; 93970Q (2015) https://doi.org/10.1117/12.2083470
Event: SPIE/IS&T Electronic Imaging, 2015, San Francisco, California, United States

Abstract

Most genome browsers display DNA linearly, using single-dimensional depictions that are useful to examine certain epigenetic mechanisms such as DNA methylation. However, these representations are insufficient to visualize intrachromosomal interactions and relationships between distal genome features. Relationships between DNA regions may be difficult to decipher or missed entirely if those regions are distant in one dimension but could be spatially proximal when mapped to three-dimensional space. For example, the visualization of enhancers folding over genes is only fully expressed in three-dimensional space. Thus, to accurately understand DNA behavior during gene expression, a means to model chromosomes is essential. Using coordinates generated from Hi-C interaction frequency data, we have created interactive 3D models of whole chromosome structures and its respective domains. We have also rendered information on genomic features such as genes, CTCF binding sites, and enhancers. The goal of this article is to present the procedure, findings, and conclusions of our models and renderings.

Citation Download Citation

Yixin Zhu, Siddarth Selvaraj, Philip Weber, Jennifer Fang, Jürgen P. Schulze, and Bing Ren "3D chromosome rendering from Hi-C data using virtual reality", Proc. SPIE 9397, Visualization and Data Analysis 2015, 93970Q (8 February 2015); https://doi.org/10.1117/12.2083470

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