The RNA recognition motif and messenger RNA

Messenger RNA in metazoans is regulated during and after transcription and during translation. In the nucleus as pre-mRNA, it is capped, spliced, and polyadenylated, then transported into the cytoplasm where it becomes a template for the ribosome. Proteins are responsible for much of the regulatory mechanisms involving pre-mRNA, and many of those proteins contain an RNA Recognition Motif (RRM) for binding RNA. Despite the common structure and conserved sequences of an RRM, this small globular domain is used for both specific and nonspecific binding to RNA. The RNA targets of an RRM range from a single nucleotide to eight nucleotides displayed in a hairpin loop; there is competition between RRMs for RNA-binding sites; there is exchange between proteins and interactions between RRMs. The story of how the RRM regulates mRNA is still being written. There are too many RRMs and too many RNAs to simply review how this protein domain in fl uences the structure and activity of RNAs. To begin to convey the variety and versatility of interactions between RRMs and RNA, my approach here is to select one class of RNAs and describe when and how protein RRMs become associated with it. That class is messenger RNA (mRNA), beginning with a pre-mRNA transcript, progressing to a translated mRNA, and ending with mRNA decay. This is also an impossible task, because from the time an mRNA is transcribed in the nucleus until the time it is enzymatically degraded in the cytoplasm, it will encounter protein RRMs at every moment of its existence. With that apologia in mind, this is a description of those interactions.