RNAbinding

RNA binding refers to the interaction between RNA molecules and proteins that recognize and bind RNA. RNA-binding proteins (RBPs) comprise a large and diverse class that regulate post-transcriptional gene expression by associating with RNA throughout its life cycle. RBPs can recognize RNA through sequence-specific motifs, structural elements, or chemically modified bases, and they can bind single-stranded RNA, double-stranded RNA, or RNA junctions such as stem–loops and bulges.

Common RNA-binding domains include the RNA recognition motif (RRM), KH domain, S1 motif, dsRNA-binding domain, zinc finger motifs, and RGG boxes. Not all RBPs contain canonical domains; many use intrinsically disordered regions to contact RNA or partner with other proteins in ribonucleoprotein complexes.

Functions cover mRNA splicing, 3' end processing and export, cytoplasmic localization, stability, storage, and control of translation and decay. RBPs also participate in ribosome biogenesis, RNA localization in neurons, mitochondrial RNA regulation, and viral RNA handling.

Binding can be sequence-specific, recognizing elements such as AU-rich elements or polypyrimidine tracts, or structure-specific, targeting stem-loops, hairpins, or G-quadruplexes. Interaction outcomes include recruitment of decay factors, translational regulation, or transport to specific cellular compartments.

Methods used to study RNA–protein interactions include CLIP-seq, RIP-seq, iCLIP and eCLIP for transcriptome-wide mapping, as well as EMSA and SELEX for in vitro binding. Examples of well-known RBPs are hnRNPs, Hu/ELAV proteins, FMRP, TDP-43, and PABP in eukaryotes; Hfq in bacteria.

RBPs are essential for normal development and cellular homeostasis; their dysfunction is associated with diseases such as neurodegeneration and cancer, illustrating the importance of RNA binding in biology.