EukaUTR: a foundation model for functional modelling and design of eukaryotic 3' UTRs
Journal:
bioRxiv
Published Date:
Sep 8, 2026
Abstract
Eukaryotic mRNA 3' UTRs encode regulatory signals that shape post-transcriptional regulation, RNA fate and gene expression. However, a foundation model that spans broad eukaryotic 3' UTR sequence space while unifying prediction, interpretation and design within a single framework is still lacking. Here we present EukaUTR, a 3' UTR-specific foundation model trained on a large-scale eukaryotic 3' UTR sequence corpus spanning diverse evolutionary lineages. Across 13 prediction tasks of post-transcriptional regulation, RNA fate and expression output, EukaUTR showed strong transferability, achieving relative improvements of up to 27.45% over the strongest baselines. Extending these capabilities to sequence design, EukaUTR generated novel 3' UTRs that captured natural sequence patterns and regulatory features and EukaUTR-Guide extracted stability signals from small sets of 3' UTRs to guide editing toward enhanced predicted stability. Together, EukaUTR establishes a sequence-to-function-to-design framework that connects broad eukaryotic representation learning with transferable functional prediction and mRNA design.
