PAIRNet: Predicting PIWI cleavage specificity via position-aware RNA interaction modeling

PIWI proteins maintain genome integrity by piRNA-guided cleavage of complementary RNA targets. While Cleave-N'-Seq (CNS-seq) has advanced our understanding of PIWI targeting logic through quantitative mapping of cleavage rates and pairing rules, its labor-intensive workflows hinder systematic exploration of sequence determinants. Here, we present PAIRNet, a deep learning framework that predicts PIWI-mediated RNA cleavage rates by explicitly modeling guide-target interactions. Recognizing that interaction geometry, not just sequence, dictates cleavage efficiency, PAIRNet integrates biochemical insights with computational innovation: it encodes pairing states, mismatch types, insertions, and deletions alongside learnable positional embeddings to quantify spatial dependencies; employs a hybrid CNN-Transformer architecture prioritizing duplex dynamics over static sequence features to resolve both local catalytic motifs (e.g., contiguous base-pairing at g10-g11) and distal structural perturbations; and incorporates interpretability modules (saliency maps, counterfactual analysis) to link interaction patterns to biochemical insights and uncover position-specific cleavage rules. Validated across four PIWI-guide datasets, PAIRNet consistently ranks among the top two performers in all experimental conditions, achieving the most pronounced relative improvements in PCC, 34.7% for MILI and 14.6% for MIWI, over second-ranking methods. Critically, PAIRNet recapitulates key biological principles-stringent complementarity at catalytic residues (g10-g11) and tolerance for 3' mismatches-aligning with structural studies of PIWI dynamics. By bridging biochemical precision with computational scalability, PAIRNet establishes a roadmap for designing high-specificity piRNA silencing tools while accelerating mechanistic studies of RNA-guided genome defense.