bims-mirnam 2026-05-17 papers

Issue of 2026–05–17
three papers selected by
Hana Antonicka, McGill University

Nucleic Acids Res. 2026 May 05. pii: gkag452. [Epub ahead of print]54(9):

Signal or noise? RNA-binding proteins and the challenges of binding site assignments.

Sudeep Sahadevan, Thileepan Sekaran, Matthias W Hentze, Joel I Perez-Perri, Thomas Schwarzl.

A significant body of research has been devoted to pinpointing and cataloguing the binding sites of RNA-binding proteins (RBPs) on target transcripts. The most common techniques involve crosslinking and immunoprecipitation (CLIP) followed by high-throughput sequencing. In this review, we provide a comprehensive summary of the major advancements in CLIP-based techniques and state-of-the-art data analysis methods designed for identifying and analysing the binding sites of RBPs. We also brief on methods used to determine the functional relevance of these binding sites and, in addition, delve into the major hurdles faced in the detection and elucidation of the binding sites of RBPs. Finally, we explore reproducibility concerns in the CLIP field, and conclude by suggesting potential avenues for future improvements.

DOI: https://doi.org/10.1093/nar/gkag452

Biology (Basel). 2026 Apr 26. pii: 680. [Epub ahead of print]15(9):

Emerging Technologies in RNA-Protein Interaction Analysis.

Nishinki T Muthumuni, Jia Guo.

RNA-protein interactions (RPIs), mediated primarily by RNA-binding proteins (RBPs), are central to post-transcriptional gene regulation and govern RNA splicing, transport, localization, translation, and decay. Dysregulation of RBPs and their associated RNA networks contributes to diverse pathologies, including cancer, neurodegenerative disorders, and viral infections. However, profiling RPIs remains a challenge due to their inherent transience, low binding affinity, and shifting spatial dynamics. This review provides a comprehensive and systematic overview of current methodologies for investigating RPIs. We discuss RNA-centric and protein-centric strategies. In addition, imaging-based approaches are evaluated for their capacity to resolve spatial and temporal dynamics of RBP-RNA interactions in situ. We compare these methodologies in terms of resolution, sensitivity, specificity, and biological applicability, emphasizing the importance of integrative strategies for constructing high-resolution, context-dependent RPI maps in physiological and disease settings.

Keywords: CLIP-seq; CRISPR/Cas13; RNA interactome; RNA-binding proteins; RNA–protein interactions; imaging-based approaches; proximity labeling

DOI: https://doi.org/10.3390/biology15090680