ENCODE4 catalog maps 92 million enhancer-gene interactions
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The ENCODE4 consortium published an encyclopedia of over 92 million enhancer–gene regulatory interactions in Nature on July 15. The resource integrates data from thousands of cell types and conditions to map how distant DNA elements control gene expression. The catalog is expected to accelerate studies of gene regulation and human genetics.
The ENCODE4 Resource
The ENCODE4 project, a continuation of the Encyclopedia of DNA Elements, has produced a comprehensive map of enhancer–gene regulatory interactions. The catalog includes 92,089,616 interactions across 1,366 cell types and 1,024 biosamples, as reported in Nature. Each interaction is supported by multiple lines of evidence, including chromatin conformation, eQTL, and CRISPR perturbation data.
Data Integration and Access
The encyclopedia integrates data from the ENCODE4 consortium's assays, such as Hi-C, ChIP-seq, and single-cell RNA-seq. Researchers can access the interactions via the ENCODE portal, which provides a searchable database and visualization tools. The resource covers 1,024 biosamples, including primary cells, tissues, and cell lines from human and mouse.
Implications for Genetics
The map links over 92 million enhancer–gene pairs, many of which are associated with disease-associated variants from GWAS studies. For example, the catalog identifies regulatory interactions for 87% of known GWAS loci, providing a mechanistic basis for non-coding variants. This resource is expected to aid in interpreting genetic variants linked to cancer, developmental disorders, and other diseases.
What's Next
The ENCODE4 consortium plans to update the encyclopedia annually with new data and cell types. It remains unclear how the resource will be integrated with other regulatory databases, such as FANTOM and Roadmap Epigenomics, to create a unified view of gene regulation.
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ENCODE4 catalog maps 92 million enhancer-gene interactions
