The RNA-induced Silencing Complex: A Versatile Gene-silencing Machine

RNA interference is a powerful mechanism of gene silencing that underlies many aspects of eukaryotic biology. On the molecular level, RNA interference is mediated by a family of ribonucleoprotein complexes called RNA-induced silencing complexes (RISCs), which can be programmed to target virtually any nucleic acid sequence for silencing. The ability of RISC to locate target RNAs has been co-opted by evolution many times to generate a broad spectrum of gene-silencing pathways. Here, we review the fundamental biochemical and biophysical properties of RISC that facilitate gene targeting and describe the various mechanisms of gene silencing known to exploit RISC activity. RNA interference is a powerful mechanism of gene silencing that underlies many aspects of eukaryotic biology. On the molecular level, RNA interference is mediated by a family of ribonucleoprotein complexes called RNA-induced silencing complexes (RISCs), which can be programmed to target virtually any nucleic acid sequence for silencing. The ability of RISC to locate target RNAs has been co-opted by evolution many times to generate a broad spectrum of gene-silencing pathways. Here, we review the fundamental biochemical and biophysical properties of RISC that facilitate gene targeting and describe the various mechanisms of gene silencing known to exploit RISC activity. RISC 2The abbreviations used are: RISCRNA-induced silencing complexdsRNAdouble-stranded RNARNAiRNA interferencesiRNAsmall interfering RNAmiRNAmicroRNApiRNAPIWI-interacting RNAscnRNAsmall scan RNARNPribonucleoproteinP-bodiesprocessing bodies. 2The abbreviations used are: RISCRNA-induced silencing complexdsRNAdouble-stranded RNARNAiRNA interferencesiRNAsmall interfering RNAmiRNAmicroRNApiRNAPIWI-interacting RNAscnRNAsmall scan RNARNPribonucleoproteinP-bodiesprocessing bodies. is a generic term for a family of heterogeneous molecular complexes that can be programmed to target almost any gene for silencing. In general, RISC programming is triggered by the appearance of dsRNA in the cytoplasm of a eukaryotic cell (Fig. 1). The dsRNA is processed into small regulatory RNAs (20–30 nucleotides in length) that assemble into RISC and guide the complex to complementary RNA targets through base-pairing interactions. Once programmed with a small RNA, RISC can silence targeted genes by one of several distinct mechanisms, working at (a) the level of through of the level through the level of the through the of by the mechanisms used to gene by RISC to at RISC a of the family that to the small regulatory in the small regulatory RNA a guide that RISC to target through with RNA The of the is to the small RNA and in a that target can target RNAs gene-silencing to Here, we review small RNAs to target of of and distinct which the mechanism of gene and RNA in many of the used to describe and RISC is The small regulatory RNAs that guide RISC been a of and the of the small RNA the of RISC in which the RNA is a to small regulatory RNAs in the for gene silencing through base-pairing with target RNA of is that molecular for RISC has been and the term RISC has been used to describe several distinct gene-silencing The for target RNA and to be to a small RNA can of which assemble one distinct complex in of RISC a of to and many to complexes and in that in to and the gene and to silence targeted genes through The to of silencing complexes is that the of a small regulatory RNA into the mechanism of RISC and the gene silencing by of the in in and in many and and in The of genes in one in the to in In of gene in and to for one is for the genes in to be and eukaryotic family can be into acid sequence The is we to in the level, in the cytoplasm and in at distinct which and The the for is in and in the silencing of The of and of genes has been into a called biochemical is the by which guide guide RNAs dsRNA in the cytoplasm by a (Fig. 1). of the to guide RNAs in a mechanism in which the target RNA of one is and the guide RNA of guide to gene-silencing guide RNAs by of and of The of eukaryotic is of several been and small guide and can to locate and target RNAs in in a to the small of eukaryotic The of and small in the to be of the a of the and a with for of the guide (Fig. The a which the of the small guide The a which to the of the guide and the with the of a The a and can target RNAs mechanism has been of target of a the in the the to to a to the guide and RNA target of a with guide and of to a to a guide a guide with a target RNA and The of the guide the and and the the and is a of and of the and guide The the of of the guide is in a the and which for the in the In the small RNAs for into the The the into a small the to with the in the which eukaryotic for the the in the guide RNA to target The of the the almost through can to any guide of The the into a in the the of the guide to in the a of for of the guide guide of various of RNA a target RNA, the nucleic in to guide and target in the (Fig. of the guide a with a complementary of the target The of the is that the in the that the of the to with the that the of the guide RNA in RISC with target the of the guide and the in a is a of the the the of the guide for target the the RISC nucleotides for RNA targets the complex the the with which RISC can locate RNA that RISC can and target almost times the small guide and target RNAs can in is by the ability of RISC to with RNAs and a scan for target of of and guide RNA RISC to locate targets the of has been co-opted by evolution many times to generate distinct of RISC that in many (Fig. In general, the of by RISC is of the targeted in be to in any of of gene several RISC in a target gene Once to target RNA, RISC gene by one of several mechanisms, the of and In the targets can be RISC In the RISC can the of which with RNA and RNA and to of and of target is which can the of the and target by The for target a a and a sequence guide and target that targets the in is a of the the of target is and is a many for is a the and acid and the is for a The and a for of the in the target the RNA is into a one and a the the target nucleotides that with and of the guide in and a guide RNA for the In RISC can of target In of is to be the of gene silencing by RISC in is the of by of small regulatory RNAs in and that which processed and into (Fig. 1). the sequence guide and target a of the guide RNA to a target to that targets and in the in of the in the and of genes to be the regulatory of several mechanisms by which can is in which at distinct that by The mechanism of RISC can eukaryotic and which to a complex the target On the by target and RISC the which the complex and the complex to target is in target to called which that of mechanisms of the and used by to be and of targeting the The of is the which with a called and the The complex by RNA in the target the complex which with the The of the complex at the of the complex with The complex with RNA which the targeted into the dsRNA into which can be into a silencing the level of molecular is in and for small of In the to in silencing and of of RISC is in the has a complex distinct in a The is for the a the is and a is of the any that in the in a of of the the In the the of the is into small RNAs called which into The scan the of the complementary to the in a of that target to the cell locate in the and for through The is that through the a mechanism and the ability of RISC to locate target is regulatory can be with a guide RNA of any sequence and can be to many distinct in the be to many of RISC in and the biochemical of of is known the biochemical in RISC the by which with and the to which the molecular of the various of a of RISC be that is at by a of the of to a for and at and a for to and biochemical in a we to the of regulatory RISC 2The abbreviations used are: RISCRNA-induced silencing complexdsRNAdouble-stranded RNARNAiRNA interferencesiRNAsmall interfering RNAmiRNAmicroRNApiRNAPIWI-interacting RNAscnRNAsmall scan RNARNPribonucleoproteinP-bodiesprocessing bodies. 2The abbreviations used are: RISCRNA-induced silencing complexdsRNAdouble-stranded RNARNAiRNA interferencesiRNAsmall interfering RNAmiRNAmicroRNApiRNAPIWI-interacting RNAscnRNAsmall scan RNARNPribonucleoproteinP-bodiesprocessing bodies. is a generic term for a family of heterogeneous molecular complexes that can be programmed to target almost any gene for silencing. In general, RISC programming is triggered by the appearance of dsRNA in the cytoplasm of a eukaryotic cell (Fig. 1). The dsRNA is processed into small regulatory RNAs (20–30 nucleotides in length) that assemble into RISC and guide the complex to complementary RNA targets through base-pairing interactions. Once programmed with a small RNA, RISC can silence targeted genes by one of several distinct mechanisms, working at (a) the level of through of the level through the level of the through the of by RNA-induced silencing complex RNA RNA interference small interfering RNA RNA small scan RNA ribonucleoprotein bodies. RNA-induced silencing complex RNA RNA interference small interfering RNA RNA small scan RNA ribonucleoprotein bodies. the mechanisms used to gene by RISC to at RISC a of the family that to the small regulatory in the small regulatory RNA a guide that RISC to target through with RNA The of the is to the small RNA and in a that target can target RNAs gene-silencing to Here, we review small RNAs to target of of and distinct which the mechanism of gene RISC and RNA in many of the used to describe and RISC is The small regulatory RNAs that guide RISC been a of and the of the small RNA the of RISC in which the RNA is a to small regulatory RNAs in the for gene silencing through base-pairing with target RNA of is that molecular for RISC has been and the term RISC has been used to describe several distinct gene-silencing The for target RNA and to be to a small RNA can of which assemble one distinct complex in of RISC a of to and many to complexes and in that in to and the gene and to silence targeted genes through The to of silencing complexes is that the of a small regulatory RNA into the mechanism of RISC and the gene silencing by of the in many of the used to describe and RISC is The small regulatory RNAs that guide RISC been a of and the of the small RNA the of RISC in which the RNA is a to small regulatory RNAs in the for gene silencing through base-pairing with target RNA of is that molecular for RISC has been and the term RISC has been used to describe several distinct gene-silencing The for target RNA and to be to a small RNA can of which assemble one distinct complex in of RISC a of to and many to complexes and in that in to and the gene and to silence targeted genes through The to of silencing complexes is that the of a small regulatory RNA into the mechanism of RISC and the gene silencing by of the in in and in many and and in The of genes in one in the to in In of gene in and to for one is for the genes in to be and eukaryotic family can be into acid sequence The is we to in the level, in the cytoplasm and in at distinct which and The the for is in and in the silencing of The of and of genes has been into a called biochemical is the by which guide guide RNAs dsRNA in the cytoplasm by a (Fig. 1). of the to guide RNAs in a mechanism in which the target RNA of one is and the guide RNA of guide to gene-silencing guide RNAs by of and in and in many and and in The of genes in one in the to in In of gene in and to for one is for the genes in to be and The eukaryotic family can be into acid sequence The is we to in the level, in the cytoplasm and in at distinct which and The the for is in and in the silencing of The of and of genes has been into a called biochemical is the by which guide guide RNAs dsRNA in the cytoplasm by a (Fig. 1). of the to guide RNAs in a mechanism in which the target RNA of one is and the guide RNA of guide to gene-silencing guide RNAs by of and of The of eukaryotic is of several been and small guide and can to locate and target RNAs in in a to the small of eukaryotic The of and small in the to be of the a of the and a with for of the guide (Fig. The a which the of the small guide The a which to the of the guide and the with the of a The a and can target RNAs mechanism has been of target of a the in the the to to a to the guide and RNA target eukaryotic is of several been and small guide and can to locate and target RNAs in in a to the small of eukaryotic The of and small in the to be of the a of the and a with for of the guide (Fig. The a which the of the small guide The a which to the of the guide and the with the of a The a and can target RNAs mechanism has been of target of a the in the the to to a to the guide and RNA target of the guide is in a the and which for the in the In the small RNAs for into the The the into a small the to with the in the which eukaryotic for the the in the guide RNA to target The of the the almost through can to any guide of The the into a in the the of the guide to in the a of for of the guide guide of various The of the guide is in a the and which for the in the In the small RNAs for into the The the into a small the to with the in the which eukaryotic for the the in the guide RNA to target The of the the almost through can to any guide of The the into a in the the of the guide to in the a of for of the guide guide of various of RNA a target RNA, the nucleic in to guide and target in the (Fig. of the guide a with a complementary of the target The of the is that the in the that the of the to with the that the of the guide RNA in RISC with target the of the guide and the in a is a of the the the of the guide for target the the RISC nucleotides for RNA targets the complex the the with which RISC can locate RNA that RISC can and target almost times the small guide and target RNAs can in is by the ability of RISC to with RNAs and a scan for target a target RNA, the nucleic in to guide and target in the (Fig. of the guide a with a complementary of the target The of the is that the in the that the of the to with the that the of the guide RNA in RISC with target the of the guide and the in a is a of the the the of the guide for target the the RISC nucleotides for RNA targets the complex the the with which RISC can locate RNA that RISC can and target almost times the small guide and target RNAs can in is by the ability of RISC to with RNAs and a scan for target of of and guide RNA RISC to locate targets the of has been co-opted by evolution many times to generate distinct of RISC that in many (Fig. In general, the of by RISC is of the targeted in be to in any of of gene several RISC in a target gene of and of target is which can the of the and target by The for target a a and a sequence guide and target that targets the in is a of the the of target is and is a many for is a the and acid and the is for a The and a for of the in the target the RNA is into a one and a the the target nucleotides that with and of the guide in and a guide RNA for the In RISC can of target In of is to be the of gene silencing by RISC in is the of by of small regulatory RNAs in and that which processed and into (Fig. 1). the sequence guide and target a of the guide RNA to a target to that targets and in the in of the in the and of genes to be the regulatory of several mechanisms by which can is in which at distinct that by The mechanism of RISC can eukaryotic and which to a complex the target On the by target and RISC the which the complex and the complex to target is in target to called which that of mechanisms of the and used by to be and of targeting the The of is the which with a called and the The complex by RNA in the target the complex which with the The of the complex at the of the complex with The complex with RNA which the targeted into the dsRNA into which can be into a silencing the level of molecular is in and for small of In the to in silencing and of of RISC is in the has a complex distinct in a The is for the a the is and a is of the any that in the in a of of the the In the the of the is into small RNAs called which into The scan the of the complementary to the in a of that target to the cell locate in the and for through The is that through the a mechanism and the ability of RISC to locate target The of and guide RNA RISC to locate targets the of has been co-opted by evolution many times to generate distinct of RISC that in many (Fig. In general, the of by RISC is of the targeted in be to in any of of gene several RISC in a target gene of and of target is which can the of the and target by The for target a a and a sequence guide and target that targets the in is a of the the of target is and is a many for is a the and acid and the is for a The and a for of the in the target the RNA is into a one and a the the target nucleotides that with and of the guide in and a guide RNA for the In RISC can of target In of is to be the of gene silencing by RISC in is the of by of small regulatory RNAs in and that which processed and into (Fig. 1). the sequence guide and target a of the guide RNA to a target to that targets and in the in of the in the and of genes to be the regulatory of several mechanisms by which can is in which at distinct that by The mechanism of RISC can eukaryotic and which to a complex the target On the by target and RISC the which the complex and the complex to target is in target to called which that of mechanisms of the and used by to be and of targeting the The of is the which with a called and the The complex by RNA in the target the complex which with the The of the complex at the of the complex with The complex with RNA which the targeted into the dsRNA into which can be into a silencing the level of molecular is in and for small of In the to in silencing and of of RISC is in the has a complex distinct in a The is for the a the is and a is of the any that in the in a of of the the In the the of the is into small RNAs called which into The scan the of the complementary to the in a of that target to the cell locate in the and for through The is that through the a mechanism and the ability of RISC to locate target of and of target is which can the of the and target by The for target a a and a sequence guide and target that targets the in is a of the the of target is and is a many for is a the and acid and the is for a The and a for of the in the target the RNA is into a one and a the the target nucleotides that with and of the guide in and a guide RNA for the In RISC can of target In of is to be the of gene silencing by RISC in is the of by of small regulatory RNAs in and that which processed and into (Fig. 1). the sequence guide and target a of the guide RNA to a target to that targets and in the in of the in the and of genes to be the regulatory of several mechanisms by which can is in which at distinct that by The mechanism of RISC can eukaryotic and which to a complex the target On the by target and RISC the which the complex and the complex to target is in target to called which that of mechanisms of the and used by to be and of targeting the The of is the which with a called and the The complex by RNA in the target the complex which with the The of the complex at the of the complex with The complex with RNA which the targeted into the dsRNA into which can be into a silencing the level of molecular is in and for small of In the to in silencing and of of RISC is in the has a complex distinct in a The is for the a the is and a is of the any that in the in a of of the the In the the of the is into small RNAs called which into The scan the of the complementary to the in a of that target to the cell locate in the and for through The is that through the a mechanism and the ability of RISC to locate target of and of target is which can the of the and target by The for target a a and a sequence guide and target that targets the in is a of the the of target is and is a many for is a the and acid and the is for a The and a for of the in the target the RNA is into a one and a the the target nucleotides that with and of the guide in and a guide RNA for the In RISC can of target In of is to be the The and of target is which can the of the and target by The for target a a and a sequence guide and target that targets the in is a The of the the of target is and is a many for is a the and acid and the is for a The and a for of the in the target the RNA is into a one and a the the target nucleotides that with and of the guide in and a guide RNA for the In RISC can of target In of is to be the of gene silencing by RISC in is the of by of small regulatory RNAs in and that which processed and into (Fig. 1). the sequence guide and target a of the guide RNA to a target to that targets and in the in of the in the and of genes to be the regulatory of several mechanisms by which can is in which at distinct that by The mechanism of RISC can eukaryotic and which to a complex the target On the by target and RISC the which the complex and the complex to target is in target to called which that of mechanisms of the and used by to be The of gene silencing by RISC in is the of by of small regulatory RNAs in and that which processed and into (Fig. 1). the sequence guide and target a of the guide RNA to a target to that targets and in the in of the in the and of genes to be the regulatory of several mechanisms by which can is in which at distinct that by The mechanism of RISC can eukaryotic and which to a complex the target On the by target and RISC the which the complex and the complex to target is in target to called which that of mechanisms of the and used by to be and of targeting the The of is the which with a called and the The complex by RNA in the target the complex which with the The of the complex at the of the complex with The complex with RNA which the targeted into the dsRNA into which can be into a silencing the level of molecular is in and for small of In the to in silencing and of targeting the The of is the which with a called and the The complex by RNA in the target the complex which with the The of the complex at the of the complex with The complex with RNA which the targeted into the dsRNA into which can be into a silencing the level of molecular is in and for small of In the to in silencing and of of RISC is in the has a complex distinct in a The is for the a the is and a is of the any that in the in a of of the the In the the of the is into small RNAs called which into The scan the of the complementary to the in a of that target to the cell locate in the and for through The is that through the a mechanism and the ability of RISC to locate target The of RISC is in the has a complex distinct in a The is for the a the is and a is of the any that in the in a of of the the In the the of the is into small RNAs called which into The scan the of the complementary to the in a of that target to the cell locate in the and for through The is that through the a mechanism and the ability of RISC to locate target is regulatory can be with a guide RNA of any sequence and can be to many distinct in the be to many of RISC in and the biochemical of of is known the biochemical in RISC the by which with and the to which the molecular of the various of a of RISC be that is at by a of the of to a for and at and a for to and biochemical in a we to the of regulatory RISC is regulatory can be with a guide RNA of any sequence and can be to many distinct in the be to many of RISC in and the biochemical of of is known the biochemical in RISC the by which with and the to which the molecular of the various of a of RISC be that is at by a of the of to a for and at and a for to and biochemical in a we to the of regulatory