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

Joaquin Reyna1,2, Kyra Fetter1,3, Romeo Ignacio1,4

  • 1Centers for Cancer Immunotherapy and Autoimmunity, La Jolla Institute for Immunology, La Jolla, CA 92037 USA.

Biorxiv : the Preprint Server for Biology
|May 15, 2024
PubMed
Summary

Loop Catalog is a new database that provides over 4.19 million chromatin loops from HiChIP and Hi-C experiments. This resource aids in interpreting genetic variants and understanding genome regulation.

Keywords:
GWASHiChIPSNP-to-gene linkingchromatin loopsdatabase

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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.