LEAP: Long sequence enhancer activity analysis and prediction framework

Enhancer activity is central to the regulation of gene expression. Despite extensive computational research on enhancers, there is still a lack of understanding of the relationship between DNA sequences and enhancer activity, overlooking the importance of sequence scale, which poses particular challenges for predicting enhancer activity. This study aims to develop an interpretable framework for predicting enhancer activity by: (a) using longer-scale information and explore the relationship between scale and task sensitivity; and (b) designing multi-angle experiments to analyze key motifs and conduct cross-cell validation.

This research have constructed LEAP (Learn Enhancer Activity and Predict), an interpretable framework based on the Performer model. It directly captures longer-scale information on enhancers from DNA sequences for predicting enhancer activity and exploring enhancer grammar. Compared to previous models with shorter inputs, this architecture first integrates gene information within a 1001bp range of enhancers to achieve accurate activity prediction and conducts exploration at multiple scales. Experiments show that LEAP outperforms the currently published state-of-the-art(SOTA)methods, achieving the highest PCC and the lowest MSE, the mean values reached 0.794 and 0.406 across all datasets, respectively. Contribution score visualization delineates the heterogeneous functional importance across critical motifs.

Our study underscores that LEAP provides a new perspective for predicting and analyzing enhancer activity.it explores the impact of DNA sequences of different bp lengths on enhancer activity prediction, analyzing motifs that have a key influence on the prediction task from multiple perspectives, providing insights into the internal grammar of enhancers, thereby better understanding the significance of long-sequence enhancers.