EPIPDLF: a pretrained deep learning framework for predicting enhancer-promoter interactions

Abstract

Motivation: Enhancers and promoters, as regulatory DNA elements, play pivotal roles in gene expression, homeostasis, and disease development across various biological processes. With advancing research, it has been uncovered that distal enhancers may engage with nearby promoters to modulate the expression of target genes. This discovery holds significant implications for deepening our comprehension of various biological mechanisms. In recent years, numerous high-throughput wet-lab techniques have been created to detect possible interactions between enhancers and promoters. However, these experimental methods are often time-intensive and costly. Results: To tackle this issue, we have created an innovative deep learning approach, EPIPDLF, which utilizes advanced deep learning techniques to predict EPIs based solely on genomic sequences in an interpretable manner. Comparative evaluations across six benchmark datasets demonstrate that EPIPDLF consistently exhibits superior performance in EPI prediction. Additionally, by incorporating interpretable analysis mechanisms, our model enables the elucidation of learned features, aiding in the identification and biological analysis of important sequences.