RNArecognition

RNA recognition refers to the ability of proteins and other molecules to selectively bind RNA sequences or structures. In cellular biology, RNA recognition underlies the regulation of RNA processing, stability, localization, translation, and degradation. Recognition can be driven by sequence specificity, structural features such as stem-loops or bulges, or a combination of both. The proteins that perform RNA recognition are called RNA-binding proteins (RBPs).

Several protein domains are specialized for RNA recognition. The RNA recognition motif (RRM) is the most common, about 90 amino acids, with conserved surfaces that contact the RNA bases, including the RNP1 and RNP2 motifs. Other widespread domains include the KH domain, which binds RNA via a GxxG loop; zinc finger motifs that coordinate Zn ions; the S1 domain; and double-stranded RNA-binding domains (dsRBD) that recognize A-form RNA duplexes. Some RBPs use multiple domains, providing high affinity and cooperativity.

RNA recognition has key biological roles: pre-mRNA splicing (hnRNPs, splicing factors), polyadenylation and mRNA maturation, mRNA export and localization, translation initiation and regulation, and RNA decay pathways. Misrecognition can contribute to disease, including neurodegenerative disorders and cancer.

Examples and methods: well-known RBPs include hnRNPs like A1, Hu proteins, PABP, and the Pumilio family. In RNA interference and silencing pathways, Argonaute proteins recognize target mRNAs guided by small RNAs. Experimental approaches to study RNA recognition include SELEX for selecting RNAs that bind a protein, CLIP-based methods (HITS-CLIP, iCLIP, eCLIP) to map binding sites in vivo, and structural methods (X-ray crystallography, NMR) to reveal contact patterns. Computational approaches predict RNA-protein interactions from sequence and structure.