RNA Biology

Non-coding RNAs as Structural Regulators of Protein Interactions and Biomolecular Assemblies

Non-coding RNAs are increasingly recognized not only as regulators of gene expression but also as active participants in the organization and modulation of molecular interactions. Through direct interactions with proteins, ligands, and macromolecular assemblies, non-coding RNAs may influence protein conformation, interaction-site accessibility, complex formation, molecular localization, and the assembly or disassembly of biomolecular complexes.

Recent advances in structural biology, RNA–protein interaction profiling, single-molecule approaches, computational modeling, and artificial-intelligence-based structure prediction now provide new opportunities to investigate these effects at the molecular level. These developments raise the possibility that RNA context constitutes an additional layer of molecular regulation beyond protein sequence and static protein structure.

The functional consequences of protein sequence variation have traditionally been interpreted primarily through changes in protein structure, binding affinity, or catalytic activity. However, proteins operate in molecular environments containing diverse RNA species, and growing evidence indicates that RNA–protein interactions can influence protein localization, conformational states, phase behavior, complex formation, and molecular accessibility.

A broader framework may therefore be required in which molecular interaction states are considered in the context of both protein structure and the surrounding RNA environment. Such a perspective may be particularly relevant to cancer-associated mutations, signaling pathways, innate immunity, metabolic enzymes, RNA-binding proteins, and biomolecular condensates.

The rapid development of cryo-EM, cross-linking technologies, RNA interactomics, computational RNA–protein prediction, molecular simulations, and AI-based structural modeling makes this an especially timely area for interdisciplinary investigation.

This Article Collection will bring together experimental, computational, and conceptual studies addressing how non-coding RNAs influence protein interactions and biomolecular assemblies in physiological and pathological contexts. The Collection would welcome original Research Articles, Review Articles, Methods papers, and where appropriate, Commentaries or other perspective-oriented contributions consistent with the editorial policies of RNA Biology.

Topics may include, but are not limited to:

• Structural mechanisms of non-coding RNA–protein interactions
• Non-coding RNAs as modulators of protein–protein interactions
• RNA-dependent changes in protein conformational states and molecular accessibility
• microRNAs, snoRNAs, lncRNAs, circRNAs, and other regulatory RNAs interacting directly with proteins
• RNA regulation of multiprotein complexes and biomolecular assemblies
• RNA-mediated organization of biomolecular condensates and phase-separated systems
• Effects of disease-associated protein mutations on RNA–protein interaction landscapes
• RNA-dependent regulation of signaling, metabolism, immunity, and cancer-related proteins
• Experimental approaches for characterizing RNA-dependent structural regulation
• Computational and AI-based prediction of RNA–protein complexes
• Integration of structural biology, RNA interactomics, and functional experiments
• Therapeutic implications of RNA-mediated regulation of protein interactions

keywords:

• non-coding RNA
• RNA–protein interaction
• structural RNA biology
• protein–protein interaction
• biomolecular assemblies
• molecular accessibility
• RNA-mediated regulation
• computational structural biology

Guest Advisor

Dr. Masanobu Chinami, MD, PhD, is a distinguished medical scientist and visionary researcher in oncology and structural biology. After receiving his MD and PhD from the prestigious Kurume University School of Medicine, he served with distinction as an Associate Professor. His international scholarly pursuits led him to the NMRFAM (University of Wisconsin-Madison) for advanced postdoctoral research, followed by an impactful Research Fellow at Osaka University (X-ray crystallography). Upon concluding a lauded career as Professor at Kyushu Women’s University, Dr. Chinami founded the Bio-Functional Structure Research Institute (BFSRI) and established the Tinami-Cancer Clinic, where he serves as Director. A true pioneer in translational cancer research, his groundbreaking work focuses on miRNA regulation in oncology and the intricate mechanics of protein-protein interactions driving cell cycle control. For more details about Dr. Chinami's work, please visit https://www.bfsri.com/doctor/ or https://orcid.org/0009-0005-9049-9005.

Disclosure Statement: Guest Advisor declares no conflict of interest regarding this work.

All manuscripts submitted to this Article Collection will undergo a full peer-review. Please review the journal scope and author submission instructions prior to submitting a manuscript.

To submit your papers to this Article Collection, please:

1. Check "yes" for the question, "Are you submitting your paper for a specific special issue or article collection?"
2. Select the Article Collection ‘Non-coding RNAs as Structural Regulators of Protein Interactions and Biomolecular Assemblies’ from the drop-down menu under the question, "Special Issue or Article Collection Name."

Please contact Changluan Zhou at changluan.zhou@taylorandfrancis.com with any queries and discount codes regarding this Article Collection.