TFBindFormer:A Cross-Attention Transformer for Transcription Factor--DNA Binding Prediction

Abstract

Transcription factors (TFs) are central regulators of gene expression, and their selective recognition of genomic DNA underlies various biological processes. Experimental profiling of TF-DNA interactions using chromatin immunoprecipitation followed by sequencing (ChIP-seq) provides high-resolution maps of in vivo TF-DNA binding but remains costly, labor-intensive, and inherently low-throughput, limiting their scalability across different transcription factors, cell types, and regulatory conditions. Computational modeling therefore plays an essential role in inferring TF-DNA interactions at genome scale. However, most existing computational models rely solely on DNA sequence and chromatin features to predict TF-DNA binding, neglecting TF-specific protein information. This omission limits their ability to capture protein-dependent binding specificity. Here, we present TFBindFormer, a hybrid cross-attention transformer that explicitly integrates genomic DNA features with TF-specific representations derived from protein sequences and structures. By modeling protein-conditioned, position-specific TF-DNA interactions, TFBindFormer enables direct learning of molecular determinants underlying DNA recognition. Evaluated across hundreds of cell-type-specific TFs and hundreds of millions of genome-wide DNA bins, TFBindFormer consistently outperforms DNA-only baselines, achieving substantial gains in both area under precision-recall curve (AUPRC) and area under receiver operating characteristic curve (AUROC). Together, these results demonstrate that integrating TF and DNA features via cross-attention enables TFBindFormer to serve as an effective and scalable framework for large-scale TF-DNA binding prediction.