RNA Interference: Biology, Mechanism, and Applications

Abstract

Double-stranded RNA-mediated interference (RNAi) is a simple and rapid method of silencing gene expression in a range of organisms. The silencing of a gene is a consequence of degradation of RNA into short RNAs that activate ribonucleases to target homologous mRNA. The resulting phenotypes either are identical to those of genetic null mutants or resemble an allelic series of mutants. Specific gene silencing has been shown to be related to two ancient processes, cosuppression in plants and quelling in fungi, and has also been associated with regulatory processes such as transposon silencing, antiviral defense mechanisms, gene regulation, and chromosomal modification. Extensive genetic and biochemical analysis revealed a two-step mechanism of RNAi-induced gene silencing. The first step involves degradation of dsRNA into small interfering RNAs (siRNAs), 21 to 25 nucleotides long, by an RNase III-like activity. In the second step, the siRNAs join an RNase complex, RISC (RNA-induced silencing complex), which acts on the cognate mRNA and degrades it. Several key components such as Dicer, RNA-dependent RNA polymerase, helicases, and dsRNA endonucleases have been identified in different organisms for their roles in RNAi. Some of these components also control the development of many organisms by processing many noncoding RNAs, called micro-RNAs. The biogenesis and function of micro-RNAs resemble RNAi activities to a large extent. Recent studies indicate that in the context of RNAi, the genome also undergoes alterations in the form of DNA methylation, heterochromatin formation, and programmed DNA elimination. As a result of these changes, the silencing effect of gene functions is exercised as tightly as possible. Because of its exquisite specificity and efficiency, RNAi is being considered as an important tool not only for functional genomics, but also for gene-specific therapeutic activities that target the mRNAs of disease-related genes

The mutual responses of higher plants to environment: Physiological and microbiological aspects

“…Physiological and microbiological responses of higher plants to environment have been studied extensively over the world, especially by targeting model plants and crop plants [1][2][3][4][5][6][7][8][9][10][11][12][13][14][15][16][17][18][19]. Abiotic stresses in environment are linked with all the living process of higher plants and greatly influence plant productivity developmental cues and environmental stimuli, most of which are the important factors affecting eco-environment such as low temperature, drought, salinity and UV-B radiation, which often occur in terrestrial ecosystem.…”

Reconstituted influenza virus envelopes as an efficient carrier system for cellular delivery of small-interfering RNAs

“…RNA interference is a mechanism by which short stretches of double-stranded RNA (dsRNA), the socalled small-interfering RNAs (siRNAs), downregulate gene expression in a highly sequence-specific manner (for recent reviews see Dykxhoorn et al, 1 Agrawal et al, 2 Novina and Sharp, 3 Meister and Tusch 4 ). siRNAs have a length of 19-21 bp and are usually processed from longer strands of dsRNA.…”

Efficient RNAi-based gene family knockdown via set cover optimization

“…The basic mechanism of RNAi is considered to be a multistep process [1,2,5]: (1) gene-specific double-stranded RNAs (dsRNAs) are introduced into a cell; (2) the long dsRNAs are cleaved into short 17-25 nucleotide siRNA segments via the RNAse III-family enzyme DICER; (3) each siRNA subsequently assembles with additional protein components, forming RNA-induced silencing complex (RISC); (4) each siRNA directs the RISC to bind to a complementary mRNA transcript by base pairing interactions between the siRNA antisense strand and the mRNA; and (5) the siRNA/RISC complex, bound to the target mRNA, guides an RNA-dependent RNA polymerase (RdRP) enzyme to cleave and degrade the target mRNA, resulting in suppression of the expression of the targeted gene.…”

“…RNA interference (RNAi) is a recently discovered posttranscriptional gene silencing (PTGS) mechanism that seems to play both regulatory and immunological roles in the eukaryotic genetic system [1][2][3][4][5]. RNAi has aroused a great deal of excitement in both therapeutic and genomic experimental communities because of its potentials for treatment of a wide spectrum of diseases such as HIV [6,7]; spinocerebellar ataxia type 1 (SCA1) and Huntington's diseases [8]; and certain classes of cancers [2,9,10] as well as its demonstrated use in functional genomic studies via controlled gene knockdown [11][12][13].…”

“…The complete RNAi process is an involved, multi-stage biochemical process. A number of surveys describe it in detail (e.g., [2,5]). The key aspect of RNAi that is relevant to us, and that makes it so therapeutically promising, is that it can be used to selectively knock down the expression of individual genes in a highly target-specific fashion.…”