The 3D Genome Browser: A web-based browser for visualizing 3D genome organization and long-range chromatin interactions

Yanli Wang, Bo Zhang, Lijun Zhang, Lin An, Jie Xu, Daofeng Li, Mayank N.K. Choudhary, Yun Li, Ming Hu, Ross Hardison, Ting Wang*, Feng Yue

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

Abstract

Recent advent of 3C-based technologies such as Hi-C and ChIA-PET provides us an opportunity to explore chromatin interactions and 3D genome organization in an unprecedented scale and resolution. However, it remains a challenge to visualize chromatin interaction data due to its size and complexity. Here, we introduce the 3D Genome Browser (http://3dgenome.org), which allows users to conveniently explore both publicly available and their own chromatin interaction data. Users can also seamlessly integrate other “omics” data sets, such as ChIP-Seq and RNA-Seq for the same genomic region, to gain a complete view of both regulatory landscape and 3D genome structure for any given gene. Finally, our browser provides multiple methods to link distal cis-regulatory elements with their potential target genes, including virtual 4C, ChIA-PET, Capture Hi-C and cross-cell-type correlation of proximal and distal DNA hypersensitive sites, and therefore represents a valuable resource for the study of gene regulation in mammalian genomes.

Original languageEnglish (US)
JournalUnknown Journal
DOIs
StatePublished - Feb 27 2017
Externally publishedYes

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)
  • Immunology and Microbiology(all)
  • Neuroscience(all)
  • Pharmacology, Toxicology and Pharmaceutics(all)

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