HiC-3DViewer: a new tool to visualize Hi-C data in 3D space
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Although significant progress has been made to map chromatin structure at unprecedented resolution and scales, we are short of tools that enable the intuitive visualization and navigation along the three-dimensional (3D) structure of chromatins. The available tools people have so far are generally script-based or present basic features that do not easily enable the integration of genomic data along with 3D chromatin structure, hence, many scientists find themselves in the obligation to hack tools designed for other purposes such as tools for protein structure study.
We present HiC-3DViewer, a new browser-based interactive tool designed to provide an intuitive environment for investigators to facilitate the 3D exploratory analysis of Hi-C data along with many useful annotation functionalities. Among the key features of HiC-3DViewer relevant to chromatin conformation studies, the most important one is the 1D-to-2D-to-3D mapping, to highlight genomic regions of interest interactively. This feature enables investigators to explore their data at different levels/angels. Additionally, investigators can superpose different genomic signals (such as ChIP-Seq, SNP) on the top of the 3D structure.
As a proof of principle we applied HiC-3DViewer to investigate the quality of Hi-C data and to show the spatial binding of GATA1 and GATA2 along the genome.
KeywordsHi-C 3D genome visualization chromatin structure prediction
This work is supported by State Key Research Development Program of China (No. 2016YFC1200303), and the National Natural Science Foundation of China (Nos. 31361163004 and 31671383). We thank Yanjian Li (Tsinghua University) for sharing his Hi-C data. MQZ was partially supported by UTD funds.
- 1.Lieberman-Aiden, E., van Berkum, N. L., Williams, L., Imakaev, M., Ragoczy, T., Telling, A., Amit, I., Lajoie, B. R., Sabo, P. J., Dorschner, M. O., et al. (2009) Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science, 326, 289–293CrossRefPubMedPubMedCentralGoogle Scholar
- 8.Thongjuea, S., Stadhouders, R., Grosveld, F. G., Soler, E. and Lenhard, B. (2013) r3Cseq: an R/Bioconductor package for the discovery of long-range genomic interactions from chromosome conformation capture and next-generation sequencing data. Nucleic Acids Res., 41, e132CrossRefPubMedPubMedCentralGoogle Scholar
- 10.Schrödinger, LLC (2010) The PyMOL Molecular Graphics System, Versio1 1.3r1. Available: http://www.pymol.orgGoogle Scholar
- 16.Grinberg, M. (2014) Flask Web Development. Sebastopol: O’Reilly MediaGoogle Scholar
- 19.Rao, S. S., Huntley, M. H., Durand, N. C., Stamenova, E. K., Bochkov, I. D., Robinson, J. T., Sanborn, A. L., Machol, I., Omer, A. D., Lander, E. S., et al. (2014) A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell, 159, 1665–1680CrossRefPubMedPubMedCentralGoogle Scholar
- 21.Ay, F., Bunnik, E. M., Varoquaux, N., Bol, S. M., Prudhomme, J., Vert, J. P., Noble, W. S. and Le Roch, K. G. (2014) Three-dimensional modeling of the P. falciparum genome during the erythrocytic cycle reveals a strong connection between genome architecture and gene expression. Genome Res., 24, 974–988CrossRefPubMedPubMedCentralGoogle Scholar