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The Henry Wellcome Laboratories for Integrative Neuroscience and Endocrinology, Dorothy Hodgkin Building, University of Bristol, Whitson Street, Bristol BS1 3NY, UK
1 The Cyprus Institute of Neurology and Genetics, 6 International Airport Avenue, P.O. Box 3462, 1683 Nicosia, Cyprus
(Requests for offprints should be addressed to J B Uney; Email: james.uney{at}bristol.ac.uk)
| Abstract |
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| Introduction |
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| The cell biology of the RNAi pathway |
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A proposed model for the action of Dicer involves the ATP-dependent translocation of the enzyme along its dsRNA target. The efficiency with which Dicer cleaves a particular dsRNA molecule has also been shown to be directly proportional to the length of the target, since the longer the dsRNA, the greater the amount of siRNA produced and hence the more potent the silencing effect (Bernstein et al. 2001). This size limitation may prevent Dicer binding to small intramolecular base-paired regions of endogenous mRNAs. Human Dicer-mediated cleavage of dsRNA is thought to occur sequentially, beginning at the termini of the dsRNA, and by the excision of small dsRNA fragments of a defined length (Ketting et al. 2001, Zhang et al. 2002).
Following the cleavage of dsRNA into siRNAs by Dicer the second important stage of mRNA degradation occurs. This is mediated by a protein complex with nuclease activity known as RISC which is guided to its target RNA by siRNA (Hammond et al. 2000). This guide role of siRNA was proposed after the observation that dsRNA would only lead to the degradation of an mRNA with a homologous sequence, leaving the rest of the RNA in the cell unaffected. Moreover, it was shown that both siRNA and protein were required to mediate cleavage of the target (Hammond et al. 2000). Following the initial discovery of the existence of a ribonucleoprotein complex as a mediator of RNAi, the components and mechanism of action of RISC began to be elucidated and both inactive and active forms of RISC complex (the active termed RISC*) were found. Nykanen et al.(2001) found that a second ATP-dependent step was involved in the pathway and showed that following unwinding of the siRNA duplex, RISC was converted to RISC*. In a separate seminal study, RISC* was found to be associated only with the antisense strand of the siRNA (Martinez et al. 2002). Hence, although the siRNA needs to be double stranded in order to be efficiently recognised and bound to RISC, the two siRNA strands must unwind before RISC becomes active. Accordingly, it was concluded that either the RISC complex has ATP-dependent helicase activity or a helicase enzyme is associated with RISC. The efficient cleavage of the target mRNA by RISC was also shown to be dependent on the phosphorylation of the 5' siRNA duplex (Nykanen et al. 2001, Martinez et al. 2002).
In non-mammalian cells, there is evidence that an alternative branch of the RNAi pathway that results in the amplification of the original message can account for the efficiency of gene silencing (Sijen et al. 2001) (Fig. 1
). In this case, the unwound siRNA no longer acts as a guide to bring RISC to the target mRNA but merely as a primer for an RNA-dependent RNA polymerase (RdRP), which uses the target mRNA as a template to produce new dsRNA. This can subsequently be recognised and cleaved by Dicer, thus re-entering the RNAi pathway and initiating a new round of silencing. Therefore, not only is the mRNA targeted via the specific oligonuclotide sequence (and hence gene expression silenced) but also new dsRNAs arising from the entire mRNA sequence are created and thus amplify the original RNAi trigger. Several RdRPs participating in RNAi have been identified in fungi, plants and invertebrates (Cogoni & Macino 1999, Dalmay et al. 2000, Mourrain et al. 2000, Smardon et al. 2000, Sijen et al. 2001, Martens et al. 2002). However, evidence to suggest that a similar amplification mechanism is present in mammalian cells has not yet been found.
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miRNAs are short RNA molecules that prevent gene expression by inhibiting translation (Lagos-Quintana et al. 2001, reviewed in Grosshans & Slack 2002). The first two miRNAs to be studied were let-7 and lin-4, which control the expression of genes involved in developmental timing in C. elegans and Drosophila and hence were therefore also named small temporal RNAs (Lee et al. 1993, Olsen & Ambros 1999, Reinhart et al. 2000). miRNAs are initially transcribed as hairpin structures (pre-miRNA) and are then processed to yield mature (single-stranded) miRNA (Grishok et al. 2001, Lagos-Quintana et al. 2001, Lau et al. 2001, Mourelatos et al. 2002). This maturation step was shown to be catalysed by Dicer in a number of organisms (Grishok et al. 2001, Hutvagner et al. 2001, Ketting et al. 2001), although with the aid of co-factors distinct from the RNAi pathway (Grishok et al. 2001, Tabara et al. 2002). The mature miRNA can then bind to the 3'-UTRs of their corresponding mRNAs, although their complementarity to the targets is not perfect as is the case for siRNA (Provost et al. 2002b). A RISC-like complex was also shown to participate in the miRNA pathway (Hutvagner & Zamore 2002). The RNAi machinery and especially RISC is also thought to be involved in mediating hetro-chromatic and transposon silencing (Ketting et al. 1999, Volpe et al. 2002, Schramke & Allshire 2003). Dicer and RISC can therefore be perceived as two central points, where several molecular pathways controlling gene expression converge.
| Developing RNAi for use in mammalian cells |
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RNAi induced by long dsRNA has been used to study gene function in plants, worms and Drosophila. However, when dsRNAs more than 30 bp in length were used to study mammalian gene function it was noted that there was an inhibition of protein translation within the cell due to the activation of the interferon (IFN) system (one of the bodys defences against viral infection) (Provost et al. 2002a). Over 100 cellular genes can be activated by IFNs and some encode enzymes that are dsRNA-binding proteins. This includes protein kinase R (PKR) which phosphorylates and inactivates eukaryotic initiation factor 2
and hence inhibits mRNA translation (Manche et al. 1992). Therefore, to apply RNAi technology to studies using mammalian systems (without inducing an IFN response) the silencing pathway had to be induced without the use of long dsRNA. Since synthetic 2122 bp-long siRNAs could bypass the initial Dicer step, while retaining the ability to mediate gene silencing in Drosophila, they were used in studies using mammalian cells. Numerous studies have now shown that synthetic siRNAs can be used to silence both exogenous and endogenous gene expression in mammalian cells (Fig. 2
). Synthetic siRNAs are now used in most investigations of gene expression and a number of methods of production are used (see below). At present, however, identifying the best target sequence is currently a process of trial and error, and a number of siRNAs must be tested against different sites on a particular mRNA. Nonetheless, it is recommended that the first 75100 nucleotides of any mRNA be avoided as potential target sites, since they may contain protein-binding regulatory sequences (5'-UTR) that could interfere with the action of siRNA (Elbashir et al. 2002). Further studies to date have attempted to provide clues so as to rationalise siRNA design. Intriguingly, it was reported that sequence preference meant that only one strand of the siRNA duplex was incorporated into RISC* (Schwarz et al. 2003). It would therefore be desirable to design the siRNA duplex so that the antisense strand is the one to be preferentially used by RISC. Thus, it has been shown that when siRNA are thermodynamically unstable (A/U rich) or even contain mismatches towards the 5' end of the antisense strand, then that strand is preferentially used by RISC resulting in more efficient silencing (Khvorova et al. 2003, Reynolds et al. 2004, Ui-Tei et al. 2004).
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shRNAs
Synthetic siRNAs do not have long half-lives once transfected into cells and inhibition of the target genes is correspondingly short lived. To increase the length of siRNA expression, eukaryotic polymerase III (PolIII) promoters were used to express siRNA from expression cassettes. The strategy (Fig. 4A
) involved the cloning of a sequence coding for the sense strand of the siRNA of interest, followed by a spacer and then the equivalent to the anti-sense strand, which ended in a series of 5 U residues. The inclusion of the spacer in the sequence mediated the formation of a hairpin structure, which allowed the sense and antisense sequences to form base pairs. The eukaryotic H1 and U6 PolIII promoters were used to drive expression of these shRNAs as they possess characteristics which make them suited to drive the expression of siRNAs: (i) they initiate from position +1 of the transcripts and (ii) the transcripts do not terminate with a poly-A tail but with a series of four to five thymidine residues, which results in a series of 3' U residues (Brummelkamp et al. 2002a). This means that a fully functional shRNA sequence can be transcribed since it will not contain any inhibitory 5' nucleotide sequences and it can be designed to end in a uridine dimer. Indeed, the structure transcribed closely resembles the synthetic double-stranded siRNA, but with the two strands linked by a spacer sequence. This system has now been used to successfully inhibit gene expression in mammalian cells lines, with efficiencies comparable with that of synthetic siRNA. In a slightly different approach, the two siRNA strands were transcribed separately from two U6-based transcription cassettes included in the same or different vectors. The two strands were then shown to anneal within the cell to form an siRNA (see Fig. 4B
) (Lee et al. 2002). Interestingly, it was reported that this method of expressing siRNA results in less potent gene silencing than when a hairpin siRNA (shRNA) is expressed (Miyagishi & Taira 2003).
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In both cases and regardless of the enhancers orientation the silencing of the target gene observed was significantly greater than that mediated by the unmodified U6 promoter. Furthermore, an inducible system for siRNA expression under the control of PolIII promoters has been developed (van de Wetering et al. 2003). In this case, the Tet operator (tet-O) sequence was used to replace a non-essential part of the H1 promoter. The resultant cassette was used to stably transfect cell lines. It was then shown that the expression of siRNA and hence silencing was dependent on the presence of tetracycline (or doxycycline) in the cells culturing medium.
shRNA libraries that can also target every gene for silencing have been constructed recently. This technology involves ligating a large number of diverse shRNA-expressing inserts corresponding to a large number of genes to suitable vectors and then screening the resultant constructs for silencing activity (Berns et al. 2004, Hsieh et al. 2004, Miyagishi et al. 2004). Some research groups have also described the creation of siRNA libraries against specific genes (or genomes) where the shRNA-expressing inserts are derived from enzymatically processing the cDNA of the gene of interest (or a cDNA library respectively). The result is the creation of multiple vectors expressing shRNAs against target sites spanning the length of the gene (or genome) so that the most efficient ones can subsequently be selected (Luo et al. 2004, Sen et al. 2004, Shirane et al. 2004).
| Virally-mediated delivery of shRNAs |
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| Cell-type dependence on the efficiency and specificity of siRNA after transient or vector-based delivery |
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T3 cells caused extensive toxic effects and death within a 24-h period. This was true even at the lowest siRNA concentration used (1 nM) and the effect was not due to the transfection reagent as toxic effects were almost absent in cells treated with the reagent only. Equally differing results were obtained when the anti-luciferase shRNA (note that this was the same sequence as the siRNA apart from the inclusion of the 9 bp spacer sequence) under the control of the U6 promoter was delivered using an adenoviral vector. Figure 5
T3 by the active anti-luciferase shRNA and the shRNA scrambled control. Since adenoviral vectors can transduce all of these cell types with approximately equal efficiency, the difference in the results is unlikely to be due to shRNA expression levels. Instead, critical factors in determining the effectiveness of the shRNA may possibly be the concentration of Dicer enzyme (which may cleave the shRNA) and the IFN response (IFR) elicited by the adenoviral shRNA construct. If there was a significant IFR (where activation of the PKR pathway leads to indiscriminate down-regulation of gene expression) then PC-3 cells would appear especially prone to this non-specific effect, as similar concentrations of siRNA in other cell types have been shown in the past to mediate only specific silencing (e.g. Elbashir et al. 2001). The cellular level of Dicer and the IFR could also presumably influence the effectiveness of siRNA following transfection into the different cell types. However, in this case the differential efficiency of transfection and toxicity of the lipid-based reagents may also play major roles in determining the intracellular concentration of the siRNA and thereby its effectiveness.
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| Conclusion |
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| Acknowledgements |
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Received 5 May 2004
Accepted 14 July 2004
Made available online as an Accepted Preprint 26 July 2004
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