Journal Article

Illuminating the silence: understanding the structure and function of small RNAs

Rana, Tariq M.

2007

Overview

Key Points RNA interference (RNAi) is an ancient and evolutionarily conserved gene-silencing mechanism that is triggered by double-stranded (ds)RNA. dsRNA, which is produced endogenously or introduced exogenously, is processed into small (∼21–23-nucleotide (nt)) duplexes, and the antisense strands are loaded onto RNA-induced silencing complexes (RISCs). Dictated by complementarity to its target mRNA, the antisense strand guides RISC to hybridize with the target and induces gene silencing by initiating either target cleavage or assembly into RNA–protein complexes that are destined for translation suppression and localization to cytoplasmic RNA-processing foci. These two gene-silencing pathways are discussed in terms of kinetic models and the structural basis of the underlying mechanisms. The major determinant of small RNAs that functions as specific triggers of gene silencing is the A-form helical geometry of RNA. The A-form helix and high-resolution structural studies provide a context for discussing the importance of phosphate groups at the 5′ end of the guide strand. Small RNAs can bind to mRNAs with partial complementarity and induce silencing of unintended mRNA transcripts, known as off-target effects. Drawing on the structure and function of small RNAs and kinetic models for RNAi, this review presents plausible mechanisms for off-target effects and discusses how chemical modifications can reduce unintended gene silencing. Gene silencing has been modulated and the in vivo half-life of triggers has been enhanced by effective chemical modification of RNA triggers. The review develops and discusses guidelines for the chemical modification of RNA triggers. Clarifying the structure and function of the triggers of the RNAi machinery and developing RNA-delivery technologies will increase the applicability of RNAi to biology and medicine. This, in turn, will enhance our understanding of the various cellular pathways that are controlled by small RNAs. To clarify the mechanisms by which RNA molecules silence genes, the structural and functional characteristics of various RNA triggers, such as small interfering RNAs and microRNAs, must be determined. This knowledge will also help us to optimize the efficiency of RNA interference. RNA interference (RNAi) is triggered by double-stranded RNA helices that have been introduced exogenously into cells as small interfering (si)RNAs or that have been produced endogenously from small non-coding RNAs known as microRNAs (miRNAs). RNAi has become a standard experimental tool and its therapeutic potential is being aggressively harnessed. Understanding the structure and function of small RNAs, such as siRNAs and miRNAs, that trigger RNAi has shed light on the RNAi machinery. In particular, it has highlighted the assembly and function of the RNA-induced silencing complex (RISC), and has provided guidelines to efficiently silence genes for biological research and therapeutic applications of RNAi.

• Publisher: Nature Publishing Group UK,Nature Publishing Group
• Subject: Animals / Apoptosis / Biochemistry / Biological research / Biomedical and Life Sciences / Caenorhabditis elegans / Cancer Research / Cell Biology / Cell proliferation / Developmental Biology / Enzymes / Genes / Humans / Kinases / Life Sciences / MicroRNAs / MicroRNAs - chemistry / MicroRNAs - metabolism / Proteins / review-article / RNA Caps - metabolism / RNA Interference / RNA, Small Interfering - chemistry / RNA, Small Interfering - metabolism / RNA-Induced Silencing Complex - metabolism / Stem Cells / Structure-Activity Relationship