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Mapping Mammalian 3D Genome Interactions with Micro-C-XL
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3DIV: A 3D-genome Interaction Viewer and database.

Dongchan Yang1, Insu Jang2, Jinhyuk Choi2

  • 1Department of Bio and Brain engineering, KAIST, Daejeon 34141, Korea.

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|November 7, 2017
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Summary

3DIV is a new database that simplifies the analysis of three-dimensional (3D) chromatin structure using Hi-C data. It offers processed interaction data and visualization tools to aid gene regulation research.

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Three-dimensional (3D) chromatin structure is crucial for understanding gene regulation.
  • High-throughput chromatin conformation capture (Hi-C) enables genome-wide 3D structure analysis.
  • Hi-C data processing complexity and large file sizes limit its widespread application.

Purpose of the Study:

  • To develop a comprehensive database and viewer for human 3D genome interactions.
  • To overcome limitations in Hi-C data accessibility and analysis.
  • To facilitate the interpretation of chromatin interactions in gene regulation.

Main Methods:

  • Collected and uniformly processed all publicly available human Hi-C data.
  • Integrated genomic and epigenomic annotations with chromatin interaction data.
  • Developed a dynamic browsing and visualization tool for interaction data.

Main Results:

  • Constructed 3DIV, a database containing 66 billion uniformly processed Hi-C read pairs from 80 human cell/tissue types.
  • Provided normalized chromatin interaction frequencies against distance-dependent background signals.
  • Enabled dynamic visualization of long-range chromatin interactions.

Conclusions:

  • 3DIV is the first database to consolidate and uniformly process extensive human Hi-C data.
  • The database and visualization tools significantly advance the interpretation of 3D chromatin structure and gene regulation.
  • 3DIV enhances the accessibility and utility of Hi-C data for researchers.