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

Jung, Vincent; Vincent-Cuaz, Cédric; Tumescheit, Charlotte; Fournier, Lisa; Darsinou, Marousa; Xu, Zhi Ming; Saadat, Ali; ... Luisier, Raphaëlle; + view all (2025) Decoding the interactions and functions of non-coding RNA with artificial intelligence. Nature Reviews Molecular Cell Biology 10.1038/s41580-025-00857-w. (In press).

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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.

Type: Article
Title: Decoding the interactions and functions of non-coding RNA with artificial intelligence
Location: England
DOI: 10.1038/s41580-025-00857-w
Publisher version: https://doi.org/10.1038/s41580-025-00857-w
Language: English
Additional information: This version is the author accepted manuscript. For information on re-use, please refer to the publisher’s terms and conditions.
UCL classification: UCL
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Brain Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Brain Sciences > UCL Queen Square Institute of Neurology
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Brain Sciences > UCL Queen Square Institute of Neurology > Department of Neuromuscular Diseases
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences > Structural and Molecular Biology
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Lab for Molecular Cell Bio MRC-UCL
URI: https://discovery.ucl.ac.uk/id/eprint/10213569
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