Journal Article

Interplay between RNA‐protein interactions and RNA structures in gene regulation

Änkö, Minna‐Liisa, Scaravilli, Mauro, Rapakko, Jenni

2026

Overview

Cellular RNAs are not linear single‐stranded stretches of nucleic acids as depicted in textbook cartoons but fold into secondary and tertiary structures through intra‐ and intermolecular base‐pairing. They also interact with proteins to form ribonucleoproteins (RNPs), the functional units of RNA in cells. Recent methodological developments utilising high‐throughput sequencing have enabled the detailed mapping of cellular RNA‐protein interactions and RNA structures. While methods for the direct determination of cellular RNP structures are still lacking, the integration of high‐throughput approaches and advancements with in vitro techniques such as cryogenic electron microscopy have provided insights into the functional significance of RNP structures. In this review, we will summarise the key methods used to probe cellular RNA‐protein interactions and RNA structures and then provide examples of how these approaches have led to an enhanced understanding of RNP structures in gene regulation and how this has also opened new avenues for drug development. Methodological advances in mapping transcriptome‐wide RNA‐protein interactions and RNA structures have started to uncover the potential of RNP conformations in gene regulation. Competing RNA–RNA, RNA‐protein and protein–protein interactions shape the compaction and function of RNPs throughout their lifetime and may provide novel therapeutic targets in various pathological conditions.

• Publisher: John Wiley & Sons, Inc,Wiley
• Subject: Adenosine / Animals / Apolipoproteins / Binding sites / Chemical bonds / CLIP / Drug development / Editing / Electron microscopy / Enzymes / Gene Expression Regulation - genetics / Gene regulation / genes / Humans / Labeling / Localization / Mass spectrometry / MicroRNAs / NMR / Nuclear magnetic resonance / Nucleic Acid Conformation / Peptide mapping / Protein Binding / Protein interaction / Review / Ribonucleic acid / ribonucleoprotein (RNP) / Ribonucleoproteins / Ribonucleoproteins - chemistry / Ribonucleoproteins - genetics / Ribonucleoproteins - metabolism / RNA / RNA - chemistry / RNA - genetics / RNA - metabolism / RNA probes / RNA structure / RNA-Binding Proteins - chemistry / RNA-Binding Proteins - genetics / RNA-Binding Proteins - metabolism / RNA-protein interactions / RNA‐binding protein / RNA‐protein interaction / Scientific imaging / SHAPE