4DGenome: a comprehensive database of chromatin interactions

Area of Science:

• Genomics
• Bioinformatics
• Molecular Biology

Background:

• The 3D genome structure is crucial for gene expression regulation.
• Advancements in chromatin interaction mapping technologies have accelerated data generation.
• Research in this field is rapidly expanding.

Purpose of the Study:

• To introduce the 4DGenome database, a curated repository of chromatin interaction data.
• To provide a comprehensive resource for studying genome spatial organization and function.

Main Methods:

• Literature curation of chromatin interaction data from low- and high-throughput assays (3C, 4C-Seq, 5C, Hi-C, ChIA-PET, Capture-C).
• Inclusion of computationally predicted interactions using a validated method.
• Standardized data format and confidence scoring for records.

Main Results:

• The 4DGenome database contains approximately 8 million records.
• Data spans 102 cell/tissue types across five organisms.
• Includes both experimentally detected and computationally predicted interactions.

Conclusions:

• 4DGenome offers a valuable, queryable resource for investigating genome 3D structure-function relationships.
• The standardized format and web interface facilitate data accessibility and exchange.
• The database supports diverse genomic analyses through integration with visualization tools like the UCSC genome browser.