Decoding the interactions and functions of non-coding RNA with artificial intelligence.

Journal: Nature reviews. Molecular cell biology
Published Date: Jun 19, 2025

Abstract

In addition to encoding proteins, mRNAs have context-specific regulatory roles that contribute to many cellular processes. However, uncovering new mRNA functions is constrained by limitations of traditional biochemical and computational methods. In this Roadmap, we highlight how artificial intelligence can transform our understanding of RNA biology by fostering collaborations between RNA biologists and computational scientists to drive innovation in this fundamental field of research. We discuss how non-coding regions of the mRNA, including introns and 5' and 3' untranslated regions, regulate the metabolism and interactomes of mRNA, and the current challenges in characterizing these regions. We further discuss large language models, which can be used to learn biologically meaningful RNA sequence representations. We also provide a detailed roadmap for integrating large language models with graph neural networks to harness publicly available sequencing and knowledge data. Adopting this roadmap will allow us to predict RNA interactions with diverse molecules and the modelling of context-specific mRNA interactomes.

Authors

  • Vincent Jung
    Idiap Research Institute, Martigny, Switzerland.
  • Cédric Vincent-Cuaz
    Signal Processing Laboratory (LTS4), School of Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
  • Charlotte Tumescheit
    Institute for Implementation Science in Health Care, University of Zurich, Zurich, Switzerland.
  • Lisa Fournier
    Department of Kinesiology and Educational Psychology, Washington State University, Pullman, USA.
  • Marousa Darsinou
    UCL Laboratory for Molecular Cell Biology, University College London, London, UK.
  • Zhi Ming Xu
    Idiap Research Institute, Martigny, Switzerland.
  • Ali Saadat
    Swiss Institute of Bioinformatics, Lausanne, Switzerland.
  • Yiran Wang
    College of Computer Science and Technology, Qingdao University, Qingdao, Shandong Province, China.
  • Petros Tsantoulis
    Department of Oncology, Geneva University Hospital (HUG), Geneva, Switzerland.
  • Olivier Michielin
    Molecular Modeling Group, SIB Swiss Institute of Bioinformatics, University of Lausanne, Quartier UNIL-Sorge, Bâtiment Amphipôle, Lausanne, Switzerland.
  • Jacques Fellay
    Swiss Institute of Bioinformatics, Lausanne, Switzerland.
  • Rickie Patani
    Human Stem Cells and Neurodegeneration Laboratory, The Francis Crick Institute, London, UK.
  • Andres Ramos
  • Pascal Frossard
    LTS4 laboratory, School of Engineering, EPFL, Lausanne, Switzerland.
  • Janna Hastings
    Institute for Implementation Science in Health Care, Faculty of Medicine, University of Zurich, Zürich, Zurich, Switzerland.
  • Antonella Riccio
    UCL Laboratory for Molecular Cell Biology, University College London, London, UK.
  • Lonneke van der Plas
    Idiap Research Institute, Martigny, Switzerland.
  • Raphaëlle Luisier
    Genomics and Health Informatics Group, Idiap Research Institute, Martigny, Switzerland.

Keywords

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