Coding and Noncoding RNA: An Expanding RNA World

Abstract

A special section in this week's issue of Science , RNA Silencing and Noncoding RNA ( ), reveals how astonishingly abundant and versatile RNA is. Noncoding RNAs are present in prokaryotes and eukaryotes and include those species that do not function as messenger RNA (mRNA), transfer RNA, or ribosomal RNA. For example, small interfering RNAs are about 25 nucleotides in length and have been implicated in a process called gene silencing. These short, double-stranded RNA (dsRNA) fragments complement the sequence of the silenced gene, and the precise mechanisms of RNA silencing are being rapidly revealed in protozoa, plants, fungi, and animals, as described by Zamore ( ). Growing interest in elucidating the natural roles of RNA silencing has led to the application of RNA interference to evaluate gene function, and a Protocol by Worby et al . ( ) describes how treatment of cultured cells with exogenous dsRNA is now a powerful tool for dissecting cellular signaling pathways. Storz ( ) indicates that mRNA stability and processing can be regulated by small nuclear RNAs and by microRNAs, the latter of which are also about 25 nucleotides long. Fritz et al . ( ) provide a Protocol to assess mRNA stability, an important determinant in the mRNA life cycle. STKE complements the Science special issue with information about mRNA, the coding RNA. Much is still being uncovered about how transcription and mRNA processing are regulated. Spatial restriction is even imposed on certain mRNAs. For example, Manseau ( ) describes the specific localization and possible transport mechanisms of mRNAs encoding the signaling molecules transforming growth factor-alpha and wingless in the developing Drosophila oocyte and embryo. A rationale for differential trafficking of mRNA in neurons is explained by Kosik and Krichevsky ( ), in which a dynamic structure called an RNA granule delivers its cargo of specific mRNAs to regions critical for maintaining plasticity. The presence of multiple splicing sites on pre-mRNA and the process of alternative splicing can yield multiple mRNAs for each gene. Cooper ( ) states that approximately 60% of the human genes are alternatively spliced and provides recent insights in understanding cell-specific splicing in vertebrates in his meeting report from the Sixth Annual Meeting of the RNA Society (2001). Finkbeiner ( ) notes that this splicing may depend not only on factors that recognize exons and their flanking sequences, but possibly on similar interactions that occur in introns. Growth factors, cytokines, and hormones all regulate alternative splicing, but the molecular links connecting specific signaling pathways to this process are still under investigation. In neurons, almost all neurotransmitter receptor and ion channel pre-mRNAs undergo alternative splicing to generate multiple isoforms. This strategy underlies specificity in receptor and channel subunit assembly, protein interactions, subcellular localization, and sensitivities to regulatory molecules. O'Donovan and Darnell ( ) describe a connection made between calcium-calmodulin-dependent protein kinase (CaMK) activity in neurons and the alternative splicing of Slowpoke (Slo)/BK mRNAs that encode calcium and voltage-gated potassium channels. CaMK appears to couple transcription and splicing of Slo/BK pre-mRNA, and the presence of a particular RNA element is needed to confer this responsiveness. Fury et al . ( ) also point out that Slo/BK channel activity is further regulated by phosphorylation of subunit-specific sites, whose presence is determined by alternative splicing. Schmauss and Howe ( ) describe how certain neurotransmitter receptors undergo RNA editing, a process that facilitates single-nucleotide changes of pre-mRNA. Such a modification can increase protein diversity by introducing a frame shift or a stop codon, or by altering a single residue in a functionally important region of the protein. For example, a single residue switch within the pore regions of two types of glutamate receptors, the AMPA and kainate receptors, affects the permeability of these channels to calcium, an important intracellular modulator of synaptic plasticity. Particular mRNA secondary strucutures are recognized by the cellular RNA editing machinery, and it is likely that once mRNA is edited, the secondary structure is resolved so that splicing can ensue. A Protocol by Parekh-Olmeda et al . ( ) describes how a direct change of a single nucleotide can be accomplished through a RNA-DNA hybrid in a process called targeted gene repair. As Ahlquist ( ) points out, viral and cellular RNA-dependent RNA polymerases are functionally similar in that they copy mRNA templates to generate dsRNA. DsRNA is an intermediate in the replication of many viruses and the Reviews by D'Acquisto and Ghosh ( ) and by Williams ( ) indicate that binding of such viral dsRNA to the serine-threonine protein kinase R inhibits viral replication. Moreover, Plasterk ( ) mentions that host cells may protect their genomes from viral invasion and from transposon movement by RNA silencing mechanisms that are triggered by such dsRNA. The RNA world has certainly grown beyond its interface between the genome and the proteome. As Storz puts it, the boundaries of the RNome likely extend beyond what is presently apparent. Featured in This Focus Issue on Coding and Noncoding RNA Related Resources at STKE