Genetically regulated eRNA expression predicts chromatin contact frequency and reveals genetic mechanisms at GWAS loci.

ABSTRACT: The biological functions of extragenic enhancer RNAs and their impact on disease risk remain relatively underexplored. In this work, we develop in silico models of genetically regulated expression of enhancer RNAs across 49 cell and tissue types, characterizing their degree of genetic control. Leveraging the estimated genetically regulated expression for enhancer RNAs and canonical genes in a large-scale DNA biobank (N > 70,000) and high-resolution Hi-C contact data, we train a deep learning-based model of pairwise three-dimensional chromatin contact frequency for enhancer-enhancer and enhancer-gene pairs in cerebellum and whole blood. Notably, the use of genetically regulated expression of enhancer RNAs provides substantial tissue-specific predictive power, supporting a role for these tra

SUBMITTER: Betti MJ 

PROVIDER: S-EPMC11968980 | biostudies-literature | 2025 Apr

REPOSITORIES: biostudies-literature