Loop Catalog: a comprehensive HiChIP database of human and mouse samples.

Area of Science:

• Genomics
• Epigenetics
• Bioinformatics

Background:

• Chromatin looping plays a crucial role in gene regulation.
• High-throughput chromosome conformation capture (Hi-C) and HiChIP techniques offer high-resolution insights into 3D genome organization.
• A centralized resource is needed to manage and analyze the growing volume of HiChIP data.

Purpose of the Study:

• To develop a comprehensive, web-based database of chromatin loops called Loop Catalog.
• To facilitate the interpretation of genetic variants and regulatory elements using HiChIP and Hi-C data.
• To provide integrated analysis tools for exploring chromatin structure and function.

Main Methods:

• Aggregated and curated loop calls from over 1000 human and mouse HiChIP samples across 152 studies.
• Included 44 high-resolution Hi-C datasets for comparative analysis.
• Developed integrated modules for SNP-to-gene linking, motif analysis, and network generation.

Main Results:

• The Loop Catalog database contains over 4.19 million unique chromatin loops.
• Demonstrated utility in interpreting Genome-Wide Association Study (GWAS) and expression Quantitative Trait Loci (eQTL) variants.
• Enabled identification of enriched sequence motifs and motif pairs, and generation of regulatory networks.

Conclusions:

• Loop Catalog serves as a valuable, accessible resource for the genomics and epigenetics research community.
• Facilitates the study of 3D genome architecture and its role in gene regulation and disease.
• Empowers researchers with tools for variant interpretation and regulatory network construction.