Functional Mechanism of RNA Interference Technology: A Review

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1 VEGETOS Vol. 24 (1) : (2011) Functional Mechanism of RNA Interference Technology: A Review D. Singh*, A. Kumar, and S. Kumar 1 Molecular Biology Laboratory S V P University of Agricultural and Technology, Meerut, U.P , India 1 International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi The RNA interference (RNAi) mechanism suppresses the expression of homologous genes when catalytically triggered by dsrna. The ever-growing list of potential applications of RNAi has contributed to the rapid growth of this technique and to the understanding of its biology. The RNAi technology has not only provided us with a powerful molecular tool to study the functions of genes and manipulation of their expression but also has realised expectations about its applications in the areas of medicines and crop improvement. Keywords: RNAi, dsrna, gene, crop improvement INTRODUCTION Long double-stranded RNAs (dsrnas; typically >200 nt) can be used to silence the expression of target genes in a variety of organisms and cell types (e.g., worms, fruit flies, and plants). Upon introduction, the long dsrnas enter a cellular pathway that is commonly referred to as the RNA interference (RNAi) pathway. First, the dsrnas get processed into nucleotide (nt) small interfering RNAs (sirnas) by an RNase III-like enzyme called Dicer (initiation step). Then, the sirnas assemble into known as RNA-induced silencing complexes (RISCs) or endoribonuclease-containing complexes unwinding in the process. The sirna strands subsequently guide the RISCs to complementary RNA molecules, where they cleave and destroy the cognate RNA (effecter step). Cleavage of cognate RNA takes place near the middle of the region bound by the sirna strand. The discovery of double stranded DNA, ascribing the structure and functional relationship to the genome has been a major challenge before scientists. Applicability of various gene-targeting techniques has been the major limiting factors for the human pursuit to decipher the phenotype associated with the genetic factors. The two major levels amenable to gene silencing are the pre- and post-transcriptional states. While the former involves silencing of genes at DNA level including changes in promoter and enhancer efficiencies, alterations in the methylation status and deletion or alterations in a part or the whole gene itself. The *Corresponding author devisingh11@gmail.com post-transcriptional gene silencing involves breakdown of the mrna itself by various techniques like Ribozymes, antisense RNA, DNAzymes and RNA interference (RNAi). Among all these techniques RNA interference has emerged as most potent tool to effect targeted gene silencing and is being used to determine the function of genes which are expressed in a constitutive or cell-fate dependent manner. It is also a potential tool for therapeutic interventions involving elimination of pathogenic gene expression. This review focuses on the recent advances in RNAi biology and its application in medicines and agriculture. In the late nineties, Jorgensen (1990) made attempts to manipulate plant genetically by introducing additional copies of the gene chalcone synthase under a strong promoter responsible for pigmentation to over-express the protein to get higher pigmentation levels, intensified deeper purple colors in petunia in In this experiment, purple original color was disappeared and unexpectedly variegated white flowers were obtained. The phenomenon was called cosupression of expression of both homologous endogenous gene and transgenic copy of the gene. Though the mechanistic aspect of this phenomenon remained unknown at that time, later on post-transcriptional gene silencing was most accepted proposal (Ambros et al., 2003; Bass, 2002 and Bernstein et al., 2001). This phenomenon of suppression of endogeous gene by transformation with homologous sequences was 136

2 D. Singh et al. also observed in the fungi Neurospora crassa where it was called as quelling (Bernstein et al. 2001, Billy et al. 2001). When Guo and Kempheus (1995) tried to knock down par-1 gene expression in C. elegans by antisense RNA, they found similar loss of expression in their sense RNA controls also (Brummelkamp et al. 2002). The reason for this finding remained unknown at that time. In 1998, Andrew Fire, Craig C. Mello and colleagues for the first time showed potent and specific genetic interference by double-stranded RNA (a mixture of both sense and antisense RNA) in the nematode Ceanorhabdites elegans. The interference was evident in both the injected animals and their progeny and was more potent than the antisense strategy. Also, dsrna segments corresponding to various intron and promoter sequences did not produce detectable interference. The ability of dsrna to work at a distance from the site of injection, and particularly to move into both germline and muscle cells was suggestive of the fact that there was an effective RNA transport mechanism in C. elegans. The mechanism involved was named as RNAi or RNA interference by Fire and colleagues (Cogoni and Macino 2000, Cullen 2002, Denli and Hannon 2003). RNAi regulates expression of protein coding genes and mediates resistance to both exogenous parasitic and exogenous pathogenic nucleic acid. Later Lisa Timmons and Andrew Fire showed that feeding C. elegans on genetically engineered bacteria expressing dsrna for unc-22 and fem-1 genes was enough to cause the specific silencing of unc-22 and fem-1 genes individually in the nematode in a reversible manner (Dykxhoorn 2003, Elbashir et al. 2001). Either soaking or injecting the nematode with dsrna or by feeding them on genetically engineered bacteria expressing dsrna has developed high throughput screens. Functional genomic analysis of C. elegans chromosomes I and III have been done by groups led by Fraser and Gonczy respectively, using the RNA interference strategy (Elbashir et al. 2001, Elbashir et al. 2002). The RNAi tool has also been used in Drosophila to mediate specific gene silencing in the flies, embryo extracts as well as cultured cells. dsrnamediated gene silencing was used to demonstrate that frizzled and frizzled 2 act in the wingless pathway. Zamore and colleagues used Drosophila melanogaster embryo extracts to show the cleavage of long dsrna into short interfering dsrna species (sirna) of ~22 nucleotides (Elbashir et al. 2002). Later Elbashir and colleagues showed that introduction of chemically synthesized 21- and 22-nt dsrna with 3 overhangs can mediate efficient target RNA cleavage in Drosophila embryo lysates (Fire et al. 1998). The RNAibased functional genomics approach was also successfully applied in Drosophila S2 and cl-8 cultured cells. The power of the tool in Drosophila became really evident when Hedgehog pathway components were identified by a group led by P. A. Beachy (Fraser et al.,2000; Grishok et al. 2001, Guo and Kempheus 1995, Hamada, 2002). Exposing mammalian cells to more than 30 base pair long dsrna was known to cause a global nonspecific protein synthesis inhibition. This nonspecific pathway was caused by two enzymes, the first one being the RNA-dependent protein kinase (PKR), which phosphorylates the translation initiation factor eif-2a to shut down all protein synthesis. The second one is 2, 5 oligoadenylate synthetase (2, 5 -AS). This enzyme (2, 5 -AS) synthesizes a molecule that activates RNaseL, which in turn degrades all mrnas nonspecifically. Both of these enzymes are activated by long dsrnas-induced interferon response in mammalian cells. These nonspecific pathways represent the response of the mammalian cell to stress or viral infection (Hammond et al. 2001). Tuschl and colleagues for the first time showed that sirnas could be directly used to mediate RNAi in cultured mammalian cells (Hammond et al. 2000). But the RNAi response was only transient. So Hannon and coworkers went further step ahead and used RNA Pol III promoter (like U6 or H1)-dependent short hairpin RNAs (shrnas) which were modeled on mirnas, to induce stable suppression of target genes in mammalian cells (Hannon 2002, Hutvagner et al. 2001). Since then various approaches have been successfully tried to effect successful gene silencing in mammalian cells (Jorgensen et al. 1996, Kawasaki and Taira 2003). Mechanism of action of RNAi The active molecules which effect the RNA interference-mediated gene silencing are sirnas (small interfering RNAs). So the first step in the RNAi process is the cleavage of (dsrnas; typically >200- nucleotide) long dsrna into 21- to 25-nucleotide long pieces of sirnas (Elbashir et al. 2001, Fire et al. 1998, Lipardi et al. 2001). This process occurs in the cytoplasm and is catalyzed by the enzyme Dicer (Lum 2003, Martinez et al. 2003). These sirnas are incorporated into the silencing complexes called RNAinduced silencing complex (RISC). The sirna duplex is then unwound and the RISC complex is remodeled in an active conformation. Afterward the mrna to be degraded is recognized. The sirna strands subsequently guide the RISCs to complementary RNA molecules, where they cleave and destroy the cognate RNA (effecter step). Cleavage of the homologous mrna takes place near the middle of the region bound by the sirna strand. The directionality of dsrna processing and the target RNA cleavage sites were defined by T. Tuschl and colleagues. According to them the target mrna is cleaved in the centre of the region recognized by the sequence complimentary 137

3 Functional Mechanism of RNAi Technology guide sirna, nt from the 5 end of sirna (14). The last step in the RNAi process is the amplification of the sirna molecules itself. It has now been well characterized that a next generation of sirnas is generated from the priming of the RNA dependent RNA polymerase (RdRp) on the target mrna by existing sirnas. These secondary sirnas are able to induce a secondary RNA interference, which is also known as transitive RNAi. Transitive RNAi is known to cause a systemic RNAi in plants and C. elegans. However, RdRp is probably absent in Drosophila and mammals and hence transitive and systemic RNAi is absent in both (Napoli et al. 1990). RNAi has also been linked to chromatin remodeling (Napoli et al. 1990). In plants, dsrna works at two levels TGS (transcriptional gene silencing) and PTGS (post-transcriptional gene silencing). Though both are related silencing pathways, only TGS is heritable and causes methylation of endogenous sequences. Many proteins like Polycomb in C. elegans and Drosophila (Hutvagner et al. 2001), and Piwi in Drosophila (Nykanen et al. 2000), are known to mediate silencing at both, transcriptional and pot-transcriptional levels. In S. pombe, Volpe and colleagues have shown that RNAi proteins, Dicer, Agronaute and RdRp, are required for centromeric silencing (Paddison 2002). This indicates a direct link between RNAi and maintenance of genome stability. Enzymes involved in RNAi Technology Dicer This enzyme was first characterized by Bernstein et al. in Drosophila (Pal-Bhadra et al. 2000). This enzyme belongs to the RNase III-class and is involved in the production of sirnas from long dsrnas in an ATP-dependent manner. However cleavage by Human Dicer is ATP independent (Parrish 2000). It is a large (~220 kda) multidomain protein acting as an antiparallel dimer. Its domains include a putative N-terminal DExH/DEAH RNA helicase/atpase domain, a PAZ domain (evolutionarily conserved domain, involed in developmental control and found in Piwi/Argonaute/Zwille proteins in Drosophila and Arabidopsis), two neighbouring RNase III-like domains and a double stranded RNA-binding domain. dsrna binding domain and RNaseIII domains are involved in dsrna binding and cleavage however the function of other domains are not yet known. DICER has been found in S. pombe, A. thaliana (CAF or CARPEL FACTORY), C. elegans (DCR-1), Drosophila (DCR-1 and DCR- 2), mouse and humans. The biological role of Dicer is not confined to RNAi only. It is also responsible for the formation of micrornas in various organisms (Romano and Macino 1992). A role of Dicer in early development is also consistent from the finding that EC cells and embryonic stem cells have much higher levels of Dicer (Schwarz et al. 2002). RNA-induced silencing complex It is an RNA-protein complex that degrades mrnas through the generation of a sequence-specific nuclease; the sequence specificity is determined by the 22-nucleotide sirnas. Zamore and colleagues found a precursor complex of ~250 KDa in Drosophila embryo extracts, which upon the addition of ATP gets converted into an activated complex of 100 KDa (Smardon et al. 2000). However, Hannon and colleagues identified a complex of 500 KDa from Drosophila S2 cells. The first component of the RISC complex to be identified was sirna which directs the complex to the target mrna molecule. As of now four RISC protein-components have been identified in Drosophila and mammalian RISC complexes, each. These components are not fully overlapping, showing perhaps the evolutionarily nonconserved or developmental stage specific nature of the RISC complex (Napoli et al. 1990). Agronaute-2 which is a homologue of C. elegans RDE-1, was the first RISC protein-component to be identified (Sui et al. 2002). Argonaute proteins constitute an evolutionarily conserved family of proteins and have been implicated in RNAi, developmental regulation, determination of stem cell character, and tumorigenesis. These are highly basic proteins of ~100 KDa containing PAZ and PIWI domains (Szweykowska-Kulińska et al. 2003). The PAZ domain is supposedly involved in protein-protein interactions, while the role of PIWI is still uncertain. RNA helicases These proteins are responsible for unwinding of dsrna. But since Dicer has its own N-terminal helicase domain, these proteins are supposedly involved somewhere downsteam of the RISC assembly. Two main RNA helicase families have been characterized for their involvement in RNAi (Szweykowska- Kulińska et al. 2003). The first one comprises of SDE3 from A. thaliana and homologous proteins from mouse, human and Drosophila. The other one contains a conserved cysteine-rich motif and multiple C- terminal SQ doublets and comprises of Upf1p from yeast and its homologue SMG-2 in C. elegans. Since RNAi has not been characterized in S. cerevisiae, the function of Upf1p is slightly unclear. Another C. elegans protein, MUT 6 is a DEAH-box helicase family member and is supposedly involved in suppression of transposons. Germin3 has been identified as an RNA helicase residing in a complex with Human EIF2C2/ hago2 (Tabara et al. 1999). RNA-dependent RNA polymerase (RdRp) This is the key enzyme responsible for the am- 138

4 D. Singh et al. plification of the small amount of trigger RNAi. It catalyses the sirna primed polymerase chain reaction and converts mrna into dsrnas that are degraded to generate new sirnas (Timmons and Fire, 1998). Although RdRp-like activity has clearly been demonstrated in Drosophila embryo extract by Lipardi et al. (2001), the enzyme homologue has not been discovered in the Drosophila or human genome. Small interference RNAs (sirnas) These are 21- to 23- nucleotide RNA duplexes with characteristic 2- to 3- nucleotide overhangs at 3 termini. They are normally generated by RNaseIII (Dicer) processing of long double-stranded RNAs (Elbashir et al. 2001). To enter into the RISC complex, they should be phosphorylated at their 5 termini. This can be achieved by endogenous kinases (Smardon et al. 2000).The hydroxyl groups at the 3 termini are required for the sirna-primed amplification step by RdRps. However, Zamore and coworkers have shown that non-priming modifications of 3 hydroxyl group had no adverse effect on RNAi mediated silencing phenomenon. According to them sirnas function as guide RNAs for the silencing and not as primers in the Drosophila and human RNAi pathways (Timmons et al. 2001). On the contrary, Hamada and colleagues have shown in cultured mammalian cells that though chemical modifications at the 3 end of sense strand did not harm the RNAi activity, same modifications at the 3 end of antisense strand abolished the RNAi effect (Volpe et al. 2002). This finding supports the hypotheses that the two strands have different functions in RNAi and that the 3 hydroxyl of the antisense strand may actually prime the amplification step. However, endogenously encoded sirnas have not been observed in mammals. Ambros and coworkers (Yang et al. 2000) have found endogenous sirna from more than 500 different genes to be present in normal C. elegans, this indicates the possibility that sirna might be a global property of various genomes (Zamore et al. 2000). Micro RNAs (mirnas) These are short nt RNA species with few mismatched nucleotides, and are generated by Dicermediated processing of endogenous noncoding ~70 nt stem-loop precursors. Due to the presence of mismatches, mirnas translationally repress the target mrnas, instead of directing its destruction. However Hutvagner and Zamore have shown that let-7 mirna naturally enters the RNAi pathway in human cell extracts and cleaves the target mrna (Zamore et al. 2000). This suggests that only the degree of complementarity between a mirna and its RNA target determines its function. lin-4 and let-7 were among the first mirnas found in C. elegans. Till date more than 200 different mirnas have been found in plants and animals and some of them are evolutionarily conserved, while others have more developmental or speciesspecific roles. Recently bantam mirna from Drosophila was found to regulate cell proliferation and cell death. Another Drosophila mirna gene mir-14, has been shown to be involved in cell death and fat metabolism (Zeng and Cullen 2002). Sometimes a different terminology is used by some authors. According to them, the mirnas with well characterized functions (like lin-4 and let-7) are called small temporal RNAs (strnas) and other similar small RNAs of uncharacterized functions are called mirnas (Zhang et al. 2002). Tiny noncoding RNAs This is a relatively new class of small RNAs, first discovered in C. elegans by Ambros and colleagues (Zhang 2002). They found 33 new members of this class in C. elegans by cdna sequencing and comparative genetics. They are very similar to the previously described mirnas in terms of there size, single stranded nature and lack of precise complementarity to any worm mrna. But they are different in the sense that they are not processed from short hairpin structures and are not phylogenetically conserved. Like mirna they are also transcribed from noncoding genomic sequence but their role in development has not yet been shown. Though the direct link of mirna to RNAi has not yet been shown but due to their sensitivity to Dicer and some sequence overlaps with longer ESTs, Ambros and colleagues have proposed that at least some of them might be generated from noncoding transcripts in the course of RNAi. Thus the recent advances in RNAi technology have made its use for reverse genetics and therapeutic interventions. However, mechanistic complexities of the process still need to be unraveled for further details. 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