Skip to main content

RNA Interference in Mammalian Cell Systems

  • Chapter
RNA Interference

Part of the book series: Current Topics in Microbiology and Immunology ((CT MICROBIOLOGY,volume 320))

Abstract

The use of RNA interference (RNAi) to evoke gene silencing in mammalian cells has almost become routine laboratory practice. Through refinement of double-stranded RNA (dsRNA) triggers of RNAi and creation of genome-scale libraries, the first genome-wide loss of function screens have been carried out in mammals. This review discusses some of the key features of RNAi in mammalian systems.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Subscribe and save

Springer+ Basic
$34.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or eBook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 169.00
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 219.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 219.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

Similar content being viewed by others

References

  • Abraham N, Stojdl DF, Duncan PI, Methot N, Ishii T, Dube M, Vanderhyden BC, Atkins HL, Gray DA, McBurney MW, Koromilas AE, Brown EG, Sonenberg N, Bell JC (1999) Characterization of transgenic mice with targeted disruption of the catalytic domain of the double-stranded RNA-dependent protein kinase, PKR. J Biol Chem 274:5953–5962.

    Article  PubMed  CAS  Google Scholar 

  • Ashrafi K, Chang FY, Watts JL, Fraser AG, Kamath RS, Ahringer J, Ruvkun G (2003) Genome-wide RNAi analysis of Caenorhabditis elegans fat regulatory genes. Nature 421:268–272.

    Article  PubMed  CAS  Google Scholar 

  • Aza-Blanc P, Cooper CL, Wagner K, Batalov S, Deveraux QL, Cooke MP (2003) Identification of modulators of TRAIL-induced apoptosis via RNAi-based phenotypic screening. Mol Cell 12:627–637.

    Article  PubMed  CAS  Google Scholar 

  • Baeg GH, Zhou R, Perrimon N (2005) Genome-wide RNAi analysis of JAK/STAT signaling components in Drosophila. Genes Dev 19:1861–1870.

    Article  PubMed  Google Scholar 

  • Baglioni C, Nilsen TW (1983) Mechanisms of antiviral action of interferon. Interferon 5:23–42.

    PubMed  CAS  Google Scholar 

  • Bard F, Casano L, Mallabiabarrena A, Wallace E, Saito K, Kitayama H, Guizzunti G, Hu Y, Wendler F, Dasgupta R, Perrimon N, Malhotra V (2006) Functional genomics reveals genes involved in protein secretion and Golgi organization. Nature 439:604–607.

    Article  PubMed  CAS  Google Scholar 

  • Barton GM, Medzhitov R (2002) Retroviral delivery of small interfering RNA into primary cells. Proc Natl Acad Sci U S A 99:14943–14945.

    Article  PubMed  CAS  Google Scholar 

  • Bartz SR, Zhang Z, Burchard J, Imakura M, Martin M, Palmieri A, Needham R, Guo J, Gordon M, Chung N, Warrener P, Jackson AL, Carleton M, Oatley M, Locco L, Santini F, Smith T, Kunapuli P, Ferrer M, Strulovici B, Friend SH, Linsley PS (2006) Small interfering RNA screens reveal enhanced cisplatin cytotoxicity in tumor cells having both BRCA network and TP53 disruptions. Mol Cell Biol 26:9377–9386.

    Article  PubMed  CAS  Google Scholar 

  • Berns K, Hijmans EM, Mullenders J, Brummelkamp TR, Velds A, Heimerikx M, Kerkhoven RM, Madiredjo M, Nijkamp W, Weigelt B, Agami R, Ge W, Cavet G, Linsley PS, Beijersbergen RL, Bernards R (2004) A large-scale RNAi screen in human cells identifies new components of the p53 pathway. Nature 428:431–437.

    Article  PubMed  CAS  Google Scholar 

  • Bernstein E, Caudy AA, Hammond SM, Hannon GJ (2001a) Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature 409:363–366.

    Article  PubMed  CAS  Google Scholar 

  • Bernstein E, Denli AM, Hannon GJ (2001b) The rest is silence. Rna 7:1509–1521.

    PubMed  CAS  Google Scholar 

  • Billy E, Brondani V, Zhang H, Muller U, Filipowicz W (2001) Specific interference with gene expression induced by long, double-stranded RNA in mouse embryonal teratocarcinoma cell lines. Proc Natl Acad Sci U S A 98:14428–14433.

    Article  PubMed  CAS  Google Scholar 

  • Birmingham A, Anderson EM, Reynolds A, Ilsley-Tyree D, Leake D, Fedorov Y, Baskerville S, Maksimova E, Robinson K, Karpilow J, Marshall WS, Khvorova A (2006) 3s UTR seed matches, but not overall identity, are associated with RNAi off-targets. Nat Methods 3:199–204.

    Article  PubMed  CAS  Google Scholar 

  • Birrell GW, Giaever G, Chu AM, Davis RW, Brown JM (2001) A genome-wide screen in Saccharomyces cerevisiae for genes affecting UV radiation sensitivity. Proc Natl Acad Sci U S A 98:12608–12613.

    Article  PubMed  CAS  Google Scholar 

  • Bitko V, Musiyenko A, Shulyayeva O, Barik S (2005) Inhibition of respiratory viruses by nasally administered siRNA. Nat Med 11:50–55.

    Article  PubMed  Google Scholar 

  • Bohnsack MT, Czaplinski K, Gorlich D (2004) Exportin 5 is a RanGTP-dependent dsRNA-binding protein that mediates nuclear export of pre-miRNAs. RNA 10:185–191.

    Article  PubMed  CAS  Google Scholar 

  • Boutros M, Kiger AA, Armknecht S, Kerr K, Hild M, Koch B, Haas SA, Paro R, et al (2004) Genome-wide RNAi analysis of growth and viability in Drosophila cells. Nat Med 303:832–835.

    CAS  Google Scholar 

  • Brummelkamp TR, Bernards R, Agami R (2002a) A system for stable expression of short interfering RNAs in mammalian cells. Science 296:550–553.

    Article  PubMed  CAS  Google Scholar 

  • Brummelkamp TR, Bernards R, Agami R (2002b) Stable suppression of tumorigenicity by virus-mediated RNA interference. Cancer Cell 2:243–247.

    Article  PubMed  CAS  Google Scholar 

  • Caplen NJ, Parrish S, Imani F, Fire A, Morgan RA (2001) Specific inhibition of gene expression by small double-stranded RNAs in invertebrate and vertebrate systems. Proc Natl Acad Sci U S A 98:9742–9747.

    Article  PubMed  CAS  Google Scholar 

  • Carmell MA, Hannon GJ (2004) RNase III enzymes and the initiation of gene silencing. Nat Struct Mol Biol 11:214–218.

    Article  PubMed  CAS  Google Scholar 

  • Carmell MA, Xuan Z, Zhang MQ, Hannon GJ (2002) The Argonaute family: tentacles that reach into RNAi, developmental control, stem cell maintenance, and tumorigenesis. Genes Dev 16:2733–2742.

    Article  PubMed  CAS  Google Scholar 

  • Carmell MA, Zhang L, Conklin DS, Hannon GJ, Rosenquist TA (2003) Germline transmission of RNAi in mice. Nat Struct Biol 10:91–92.

    Article  PubMed  CAS  Google Scholar 

  • Check E (2005) A crucial test. Nat Med 11:243–244.

    Article  PubMed  CAS  Google Scholar 

  • DasGupta R, Kaykas A, Moon RT, Perrimon N (2005) Functional genomic analysis of the Wnt-wingless signaling pathway. Science 308:826–833.

    Article  PubMed  CAS  Google Scholar 

  • Dector MA, Romero P, Lopez S, Arias CF (2002) Rotavirus gene silencing by small interfering RNAs. EMBO J 3:1175–1180.

    Article  CAS  Google Scholar 

  • Denli AM, Tops BB, Plasterk RH, Ketting RF, Hannon GJ (2004) Processing of primary microRNAs by the Microprocessor complex. Nature 432:231–235.

    Article  PubMed  CAS  Google Scholar 

  • Devroe E, Silver PA (2002) Retrovirus-delivered siRNA. BMC Biotechnol 2:15.

    Article  PubMed  Google Scholar 

  • Dickins RA, Hemann MT, Zilfou JT, Simpson DR, Ibarra I, Hannon GJ, Lowe SW (2005) Probing tumor phenotypes using stable and regulated synthetic microRNA precursors. Nat Genet 37:1289–1295.

    PubMed  CAS  Google Scholar 

  • Doench JG, Petersen CP, Sharp PA (2003) siRNAs can function as miRNAs. Genes Dev 17:438–442.

    Article  PubMed  CAS  Google Scholar 

  • Doms RW, Trono D (2000) The plasma membrane as a combat zone in the HIV battlefield. Genes Dev 14:2677–2688.

    Article  PubMed  CAS  Google Scholar 

  • Dykxhoorn DM, Lieberman J (2006) Silencing viral infection. PLoS Med 3:e242.

    Article  PubMed  CAS  Google Scholar 

  • Edgar R, Wood W (1966) Morphogenesis of bacteriophage T4 in extracts of mutant-infected cells. Proc Natl Acad Sci U S A 55:498–505.

    Article  PubMed  CAS  Google Scholar 

  • Elbashir SM, Harborth J, Lendeckel W, Yalcin A, Weber K, Tuschl T (2001) Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature 411:494–498.

    Article  PubMed  CAS  Google Scholar 

  • Filippov V, Solovyev V, Filippova M, Gill SS (2000) A novel type of RNase III family proteins in eukaryotes. Gene 245:213–221.

    Article  PubMed  CAS  Google Scholar 

  • Fire A, Xu S, Montgomery MK, Kostas SA, Driver SE, Mello CC (1998) Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391:806–811.

    Article  PubMed  CAS  Google Scholar 

  • Fortin KR, Nicholson RH, Nicholson AW (2002) Mouse ribonuclease III. cDNA structure, expression analysis, and chromosomal location. BMC Genomics 3:26.

    Article  PubMed  Google Scholar 

  • Fraser AG, Kamath RS, Zipperlen P, Martinez-Campos M, Sohrmann M, Ahringer J (2000) Functional genomic analysis of C. elegans chromosome I by systematic RNA interference. Nature 408:325–330.

    Article  PubMed  CAS  Google Scholar 

  • Friedman A, Perrimon N (2006) A functional RNAi screen for regulators of receptor tyrosine kinase and ERK signalling. Nature 444:230–234.

    Article  PubMed  CAS  Google Scholar 

  • Ge Q, McManus MT, Nguyen T, Shen CH, Sharp PA, Eisen HN, Chen J (2003) RNA interference of influenza virus production by directly targeting mRNA for degradation and indirectly inhibiting all viral RNA transcription. Proc Natl Acad Sci U S A 100:2718–2723.

    Article  PubMed  CAS  Google Scholar 

  • Giaever G, Chu AM, Ni L, Connelly C, Riles L, Veronneau S, Dow S, Lucau-Danila A, Anderson K, Andre B, Arkin AP, Astromoff A, El-Bakkoury M, Bangham R, Benito R, Brachat S, Campanaro S, Curtiss M, Davis K, Deutschbauer A, Entian KD, Flaherty P, Foury F, Garfinkel DJ, Gerstein M, Gotte D, Guldener U, Hegemann JH, Hempel S, Herman Z, Jaramillo DF, Kelly DE, Kelly SL, Kotter P, LaBonte D, Lamb DC, Lan N, Liang H, Liao H, Liu L, Luo C, Lussier M, Mao R, Menard P, Ooi SL, Revuelta JL, Roberts CJ, Rose M, Ross-Macdonald P, Scherens B, Schimmack G, Shafer B, Shoemaker DD, Sookhai-Mahadeo S, Storms RK, Strathern JN, Valle G, Voet M, Volckaert G, Wang CY, Ward TR, Wilhelmy J, Winzeler EA, Yang Y, Yen G, Youngman E, Yu K, Bussey H, Boeke JD, Snyder M, Philippsen P, Davis RW, Johnston M (2002) Functional profiling of the Saccharomyces cerevisiae genome. Nature 418:387–391.

    Article  PubMed  CAS  Google Scholar 

  • Gil J, Esteban M (2000) Induction of apoptosis by the dsRNA-dependent protein kinase (PKR): mechanism of action. Apoptosis 5:107–114.

    Article  PubMed  CAS  Google Scholar 

  • Gönczy P, Echeverri C, Oegema K, Coulson A, Jones SJ, Copley RR, Duperon J, Oegema J, Brehm M, Cassin E, Hannak E, Kirkham M, Pichler S, Flohrs K, Goessen A, Leidel S, Alleaume AM, Martin C, Ozlu N, Bork P, Hyman AA (2000) Functional genomic analysis of cell division in C. elegans using RNAi of genes on chromosome III. Nature 408:331–336.

    Article  PubMed  Google Scholar 

  • Gregory RI, Yan KP, Amuthan G, Chendrimada T, Doratotaj B, Cooch N, Shiekhattar R (2004) The Microprocessor complex mediates the genesis of microRNAs. Nature 432:235–240.

    Article  PubMed  CAS  Google Scholar 

  • Grishok A, Pasquinelli AE, Conte D, Li N, Parrish S, Ha I, Baillie DL, Fire A, Ruvkun G, Mello CC (2001) Genes and mechanisms related to RNA interference regulate expression of the small temporal RNAs that control C. elegans developmental timing. Cell 106:23–34.

    Article  PubMed  CAS  Google Scholar 

  • Ha I, Wightman B, Ruvkun G (1996) A bulged lin-4/lin-14 RNA duplex is sufficient for Caenorhabditis elegans lin-14 temporal gradient formation. Genes Dev 10:3041–3050.

    Article  PubMed  CAS  Google Scholar 

  • Haley B, Zamore PD (2004) Kinetic analysis of the RNAi enzyme complex. Nat Struct Mol Biol 11:599–606.

    Article  PubMed  CAS  Google Scholar 

  • Hall IM, Shankaranarayana GD, Noma K, Ayoub N, Cohen A, Grewal SI (2002) Establishment and maintenance of a heterochromatin domain. Science 297:2232–2237.

    Article  PubMed  CAS  Google Scholar 

  • Hammond SM, Bernstein E, Beach D, Hannon GJ (2000) An RNA-directed nuclease mediates post-transcriptional gene silencing in Drosophila cells. Nature 404:293–296.

    Article  PubMed  CAS  Google Scholar 

  • Han J, Lee Y, Yeom KH, Kim YK, Jin H, Kim VN (2004) The Drosha-DGCR8 complex in primary microRNA processing. Genes Dev 18:3016–3027.

    Article  PubMed  CAS  Google Scholar 

  • Han J, Lee Y, Yeom KH, Nam JW, Heo I, Rhee JK, Sohn SY, Cho Y, Zhang BT, Kim VN (2006) Molecular basis for the recognition of primary microRNAs by the Drosha-DGCR8 complex. Cell 125:887–901.

    Article  PubMed  CAS  Google Scholar 

  • Hannon GJ (2002) RNA interference. Nature 418:244–251.

    Article  PubMed  CAS  Google Scholar 

  • Hartwell LH, Weinert TA (1989) Checkpoints: controls that ensure the order of cell cycle events. Science 246:629–634.

    Article  PubMed  CAS  Google Scholar 

  • Hartwell LH, Culotti J, Pringle JR, Reid BJ (1974) Genetic control of the cell division cycle in yeast. Science 183:46–51.

    Article  PubMed  CAS  Google Scholar 

  • Hemann MT, Fridman JS, Zilfou JT, Hernando E, Paddison PJ, Cordon-Cardo C, Hannon GJ, Lowe SW (2003) An epi-allelic series of p53 hypomorphs created by stable RNAi produces distinct tumor phenotypes in vivo. Nat Genet 33:396–400.

    Article  PubMed  CAS  Google Scholar 

  • Hutvagner G, McLachlan J, Pasquinelli AE, Balint E, Tuschl T, Zamore PD (2001) A cellular function for the RNA-interference enzyme Dicer in the maturation of the let-7 small temporal RNA. Science 293:834–838.

    Article  PubMed  CAS  Google Scholar 

  • Irvine DV, Zaratiegui M, Tolia NH, Goto DB, Chitwood DH, Vaughn MW, Joshua-Tor L, Martienssen RA (2006) Argonaute slicing is required for heterochromatic silencing and spreading. Proc Natl Acad Sci U S A 313:1134–1137.

    CAS  Google Scholar 

  • Jackson AL, Bartz SR, Schelter J, Kobayashi SV, Burchard J, Mao M, Li B, Cavet G, Linsley PS (2003) Expression profiling reveals off-target gene regulation by RNAi. Nat Biotechnol 21:635–637.

    Article  PubMed  CAS  Google Scholar 

  • Jacque JM, Triques K, Stevenson M (2002) Modulation of HIV-1 replication by RNA interference. Nature 418:435–438.

    Article  PubMed  CAS  Google Scholar 

  • Jia Q, Sun R (2003) Inhibition of gammaherpesvirus replication by RNA interference. J Virol 77:3301–3306.

    Article  PubMed  CAS  Google Scholar 

  • Kapadia SB, Brideau-Andersen A, Chisari FV (2003) Interference of hepatitis C virus RNA replication by short interfering RNAs. Proc Natl Acad Sci U S A 100:2014–2018.

    Article  PubMed  CAS  Google Scholar 

  • Ketting RF, Fischer SE, Bernstein E, Sijen T, Hannon GJ, Plasterk RH (2001) Dicer functions in RNA interference and in synthesis of small RNA involved in developmental timing in C. elegans. Genes Dev 15:2654–2659.

    Article  PubMed  CAS  Google Scholar 

  • Kittler R, Putz G, Pelletier L, Poser I, Heninger AK, Drechsel D, Fischer S, Konstantinova I, Habermann B, Grabner H, Yaspo ML, Himmelbauer H, Korn B, Neugebauer K, Pisabarro MT, Buchholz F (2004) An endoribonuclease-prepared siRNA screen in human cells identifies genes essential for cell division. Nature 432:1036–1040.

    Article  PubMed  CAS  Google Scholar 

  • Knight SW, Bass BL (2001) A role for the RNase III enzyme DCR-1 in RNA interference and germ line development in Caenorhabditis elegans. Science 293:2269–2271.

    Article  PubMed  CAS  Google Scholar 

  • Kurihara Y, Watanabe Y (2004) Arabidopsis micro-RNA biogenesis through Dicer-like 1 protein functions. Proc Natl Acad Sci U S A 101:12753–12758.

    Article  PubMed  CAS  Google Scholar 

  • Lagos-Quintana M, Rauhut R, Lendeckel W, Tuschl T (2001) Identification of novel genes coding for small expressed RNAs. Science 294:853–858.

    Article  PubMed  CAS  Google Scholar 

  • Lamontagne B, Ghazal G, Lebars I, Yoshizawa S, Fourmy D, Elela SA (2003) Sequence dependence of substrate recognition and cleavage by yeast RNase III. J Mol Biol 327:985–1000.

    Article  PubMed  CAS  Google Scholar 

  • Landthaler M, Yalcin A, Tuschl T (2004) The human DiGeorge syndrome critical region gene 8 and its D. melanogaster homolog are required for miRNA biogenesis. Curr Biol 14:2162–2167.

    Article  PubMed  CAS  Google Scholar 

  • Lau NC, Lim LP, Weinstein EG, Bartel DP (2001) An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science 294:858–862.

    Article  PubMed  CAS  Google Scholar 

  • Lee NS, Dohjima T, Bauer G, Li H, Li MJ, Ehsani A, Salvaterra P, Rossi J (2002) Expression of small interfering RNAs targeted against HIV-1 rev transcripts in human cells. Nat Biotechnol 20:500–505.

    PubMed  CAS  Google Scholar 

  • Lee RC, Ambros V (2001) An extensive class of small RNAs in Caenorhabditis elegans. Science 294:862–864.

    Article  PubMed  CAS  Google Scholar 

  • Lee RC, Feinbaum RL, Ambros V (1993) The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75:843–854.

    Article  PubMed  CAS  Google Scholar 

  • Lee SS, Lee RY, Fraser AG, Kamath RS, Ahringer J, Ruvkun G (2003a) A systematic RNAi screen identifies a critical role for mitochondria in C. elegans longevity. Nat Genet 33:40–48.

    Article  PubMed  CAS  Google Scholar 

  • Lee Y, Ahn C, Han J, Choi H, Kim J, Yim J, Lee J, Provost P, Radmark O, Kim S, Kim VN (2003b) The nuclear RNase III Drosha initiates microRNA processing. Nature 425:41.

    Google Scholar 

  • Lum L, Yao S, Mozer B, Rovescalli A, Von Kessler D, Nirenberg M, Beachy PA (2003) Identification of Hedgehog pathway components by RNAi in Drosophila cultured cells. Science 299:2039–2045.

    Article  PubMed  CAS  Google Scholar 

  • Lund E, Guttinger S, Calado A, Dahlberg JE, Kutay U (2004) Nuclear export of microRNA precursors. Science 303:95–98.

    Article  PubMed  CAS  Google Scholar 

  • MacKeigan JP, Murphy LO, Blenis J (2005) Sensitized RNAi screen of human kinases and phosphatases identifies new regulators of apoptosis and chemoresistance. Nat Cell Biol 7:591–600.

    Article  PubMed  CAS  Google Scholar 

  • MacRae IJ, Zhou K, Li F, Repic A, Brooks AN, Cande WZ, Adams PD, Doudna JA (2006) Structural basis for double-stranded RNA processing by Dicer. Science 311:195–198.

    Article  PubMed  CAS  Google Scholar 

  • McCaffrey AP, Meuse L, Pham TT, Conklin DS, Hannon GJ, Kay MA (2002) RNA interference in adult mice. Nature 418:38–39.

    Article  PubMed  CAS  Google Scholar 

  • McFarland TJ, Zhang Y, Appukuttan B, Stout JT (2004) Gene therapy for proliferative ocular diseases. Expert Opin Biol Ther 4:1053–1058.

    Article  PubMed  CAS  Google Scholar 

  • McManus MT, Haines BB, Dillon CP, Whitehurst CE, van Parijs L, Chen J, Sharp PA (2002) Small interfering RNA-mediated gene silencing in T lymphocytes. J Immunol 169:5754–5760.

    PubMed  CAS  Google Scholar 

  • Miyagishi M, Taira K (2002) U6 promoter driven siRNAs with four uridine 3M overhangs efficiently suppress targeted gene expression in mammalian cells. Nat Biotechnol 20:497–500.

    Article  PubMed  CAS  Google Scholar 

  • Mourelatos Z, Dostie J, Paushkin S, Sharma A, Charroux B, Abel L, Rappsilber J, Mann M, Dreyfuss G (2002) miRNPs: a novel class of ribonucleoproteins containing numerous microRNAs. Genes Dev 16:720–728.

    Article  PubMed  CAS  Google Scholar 

  • Novina CD, Murray MF, Dykxhoorn DM, Beresford PJ, Riess J, Lee SK, Collman RG, Lieberman J, Shankar P, Sharp PA (2002) siRNA-directed inhibition of HIV-1 infection. Nat Med 8:681–686.

    PubMed  CAS  Google Scholar 

  • Nybakken K, Vokes SA, Lin TY, McMahon AP, Perrimon N (2005) A genome-wide RNA interference screen in Drosophila melanogaster cells for new components of the Hh signaling pathway. Nat Genet 37:1323–1332.

    Article  PubMed  CAS  Google Scholar 

  • Nykanen A, Haley B, Zamore PD (2001) ATP requirements and small interfering RNA structure in the RNA interference pathway. Cell 107:309–321.

    Article  PubMed  CAS  Google Scholar 

  • Paddison PJ, Hannon GJ (2002) RNA interference: the new somatic cell genetics? Cancer Cell 2:17–23.

    Article  PubMed  CAS  Google Scholar 

  • Paddison PJ, Caudy AA, Hannon GJ (2002a) Stable suppression of gene expression in mammalian cells by RNAi. Proc Natl Acad Sci U S A 99:1443–1448.

    Article  PubMed  CAS  Google Scholar 

  • Paddison PJ, Caudy AA, Bernstein E, Hannon GJ, Conklin DS (2002b) Short hairpin RNAs (shRNAs) induce sequence-specific silencing in mammalian cells. Genes Dev 16:948–958.

    Article  PubMed  CAS  Google Scholar 

  • Paddison PJ, Silva JM, Conklin DS, Schlabach M, Li M, Aruleba S, Balija V, O’Shaughnessy A, Gnoj L, Scobie K, Chang K, Westbrook T, Cleary M, Sachidanandam R, McCombie WR, Elledge SJ, Hannon GJ (2004) A resource for large-scale RNA-interference-based screens in mammals. Nature 428:427–431.

    Article  PubMed  CAS  Google Scholar 

  • Pai SI, Lin YY, Macaes B, Meneshian A, Hung CF, Wu TC (2006) Prospects of RNA interference therapy for cancer. Gene Ther 13:464–477.

    Article  PubMed  CAS  Google Scholar 

  • Pasquinelli AE, Reinhart BJ, Slack F, Martindale MQ, Kuroda MI, Maller B, Hayward DC, Ball EE, Degnan B, Muller P, Spring J, Srinivasan A, Fishman M, Finnerty J, Corbo J, Levine M, Leahy P, Davidson E, Ruvkun G (2000) Conservation of the sequence and temporal expression of let-7 heterochronic regulatory RNA. Nature 2000 408:86–89.

    Article  PubMed  CAS  Google Scholar 

  • Paul CP, Good PD, Winer I, Engelke DR (2002) Effective expression of small interfering RNA in human cells. Nat Biotechnol 20:505–508.

    Article  PubMed  CAS  Google Scholar 

  • Pothof J, van Haaften G, Thijssen K, Kamath RS, Fraser AG, Ahringer J, Plasterk RH, Tijsterman M (2003) Identification of genes that protect the C. elegans genome against mutations by genome-wide RNAi. Genes Dev 17:443–448.

    Article  PubMed  CAS  Google Scholar 

  • Qin XF, An DS, Chen IS, Baltimore D (2003) Inhibiting HIV-1 infection in human T cells by lentiviral-mediated delivery of small interfering RNA against CCR5. Proc Natl Acad Sci U S A 100:183–188.

    Article  PubMed  CAS  Google Scholar 

  • Randall G, Grakoui A, Rice CM (2003) Clearance of replicating hepatitis C virus replicon RNAs in cell culture by small interfering RNAs. Proc Natl Acad Sci U S A 100:235–240.

    Article  PubMed  CAS  Google Scholar 

  • Raoul C, Barker SD, Aebischer P (2006) Viral-based modeling and correction of neurodegenerative diseases by RNA interference. Gene Ther 13:487–495.

    Article  PubMed  CAS  Google Scholar 

  • Reinhart BJ, Slack FJ, Basson M, Pasquinelli AE, Bettinger JC, Rougvie AE, Horvitz HR, Ruvkun G (2000) The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature 403:901–906.

    Article  PubMed  CAS  Google Scholar 

  • Rossi JJ (2006) RNAi as a treatment for HIV-1 infection. Biotechniques 40:s25–s29.

    Article  CAS  Google Scholar 

  • Rubinson DA, Dillon CP, Kwiatkowski AV, Sievers C, Yang L, Kopinja J, Zhang M, McManus MT, Gertler FB, Scott ML, Van Parijs L (2003) A lentivirus-based system to functionally silence genes in primary mammalian cells, stem cells and transgenic mice by RNA interference. Nat Genet 33:401–406.

    Article  PubMed  CAS  Google Scholar 

  • Schwarz DS, Hutvagner G, Haley B, Zamore PD (2002) Evidence that siRNAs function as guides, not primers, in the Drosophila and human RNAi pathways. Mol Cell 10:537–548.

    Article  PubMed  CAS  Google Scholar 

  • Shin KJ, Wall EA, Zavzavadjian JR, Santat LA, Liu J, Hwang JI, Rebres R, Roach T, Seaman W, Simon MI, Fraser ID (2006) A single lentiviral vector platform for microRNA-based conditional RNA interference and coordinated transgene expression. Proc Natl Acad Sci U S A 103:13759–13764.

    Article  PubMed  CAS  Google Scholar 

  • Sijen T, Fleenor J, Simmer F, Thijssen KL, Parrish S, Timmons L, Plasterk RH, Fire A (2001) On the role of RNA amplification in dsRNA-triggered gene silencing. Cell 107:465–476.

    Article  PubMed  CAS  Google Scholar 

  • Silva JM, Li MZ, Chang K, Ge W, Golding MC, Rickles RJ, Siolas D, Hu G, Paddison PJ, Schlabach MR, Sheth N, Bradshaw J, Burchard J, Kulkarni A, Cavet G, Sachidanandam R, McCombie WR, Cleary MA, Elledge SJ, Hannon GJ (2005) Second-generation shRNA libraries covering the mouse and human genomes. Nat Genet 37:1281–1288.

    PubMed  CAS  Google Scholar 

  • Siolas D, Lerner C, Burchard J, Ge W, Linsley PS, Paddison PJ, Hannon GJ, Cleary MA (2005) Synthetic shRNAs as potent RNAi triggers. Nat Biotechnol 23:227–231.

    Article  PubMed  CAS  Google Scholar 

  • Slack FJ, Basson M, Liu Z, Ambros V, Horvitz HR, Ruvkun G (2000) The lin-41 RBCC gene acts in the C. elegans heterochronic pathway between the let-7 regulatory RNA and the LIN-29 transcription factor. Mol Cell 5:659–669.

    Article  PubMed  CAS  Google Scholar 

  • Song E, Lee SK, Wang J, Ince N, Ouyang N, Min J, Chen J, Shankar P, Lieberman J (2003a) RNA interference targeting Fas protects mice from fulminant hepatitis. Nat Med 9:347–351.

    Article  PubMed  CAS  Google Scholar 

  • Song JJ, Liu J, Tolia NH, Schneiderman J, Smith SK, Martienssen RA, Hannon GJ, Joshua-Tor L (2003b) The crystal structure of the Argonaute2 PAZ domain reveals an RNA binding motif in RNAi effector complexes. Nat Struct Biol 10:1026–1032.

    Article  PubMed  CAS  Google Scholar 

  • Song JJ, Smith SK, Hannon GJ, Joshua-Tor L (2004) Crystal structure of Argonaute and its implications for RISC slicer activity. Science 305:1434–1437.

    Article  PubMed  CAS  Google Scholar 

  • Stegmeier F, Hu G, Rickles RJ, Hannon GJ, Elledge SJ (2005) A lentiviral microRNA-based system for single-copy polymerase II-regulated RNA interference in mammalian cells. Proc Natl Acad Sci U S A 102:13212–13217.

    Article  PubMed  CAS  Google Scholar 

  • Stein P, Svoboda P, Anger M, Schultz RM (2003) RNAi: mammalian oocytes do it without RNA-dependent RNA polymerase. RNA 9:187–192.

    Article  PubMed  CAS  Google Scholar 

  • Sui G, Soohoo C, Affar el B, Gay F, Shi Y, Forrester WC, Shi Y (2002) A DNA vector-based RNAi technology to suppress gene expression in mammalian cells. Proc Natl Acad Sci U S A 99:5515–5520.

    Article  PubMed  CAS  Google Scholar 

  • Svoboda P, Stein P, Hayashi H, Schultz RM (2000) Selective reduction of dormant maternal mRNAs in mouse oocytes by RNA interference. Development 127:4147–4156.

    PubMed  CAS  Google Scholar 

  • Tiscornia G, Singer O, Ikawa M, Verma IM (2003) A general method for gene knockdown in mice by using lentiviral vectors expressing small interfering RNA. Proc Natl Acad Sci U S A 100:1844–1848.

    Article  PubMed  CAS  Google Scholar 

  • Tolia NH, Joshua-Tor L (2007) Slicer and the argonautes. Nat Chem Biol 3:36–43.

    Article  PubMed  CAS  Google Scholar 

  • Tuschl T, Zamore PD, Lehmann R, Bartel DP, Sharp PA (1999) Targeted mRNA degradation by double-stranded RNA in vitro. Genes Dev 13:3191–3197.

    Article  PubMed  CAS  Google Scholar 

  • Valencia-Sanchez MA, Liu J, Hannon GJ, Parker R (2006) Control of translation and mRNA degradation by miRNAs and siRNAs. Genes Dev 20:515–524.

    Article  PubMed  CAS  Google Scholar 

  • Volpe TA, Kidner C, Hall IM, Teng G, Grewal SI, Martienssen RA (2002) Regulation of heterochromatic silencing and histone H3 lysine-9 methylation by RNAi. Science 297:1833–1837.

    Article  PubMed  CAS  Google Scholar 

  • Westbrook TF, Martin ES, Schlabach MR, Leng Y, Liang AC, Feng B, Zhao JJ, Roberts TM, Mandel G, Hannon GJ, Depinho RA, Chin L, Elledge SJ (2005) A genetic screen for candidate tumor suppressors identifies REST. Cell 121:837–848.

    Article  PubMed  CAS  Google Scholar 

  • Wianny F, Zernicka-Goetz M (2000) Specific interference with gene function by double-stranded RNA in early mouse development. Nat Cell Biol 2:70–75.

    Article  PubMed  CAS  Google Scholar 

  • Wightman B, Ha I, Ruvkun G (1993) Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans. Cell 75:855–862.

    Article  PubMed  CAS  Google Scholar 

  • Williams BR (1997) Role of the double-stranded RNA-activated protein kinase (PKR) in cell regulation. Biochem Soc Trans 25:509–513.

    PubMed  CAS  Google Scholar 

  • Winzeler EA, Shoemaker DD, Astromoff A, Liang H, Anderson K, Andre B, Bangham R, Benito R, Boeke JD, Bussey H, Chu AM, Connelly C, Davis K, Dietrich F, Dow SW, El Bakkoury M, Foury F, Friend SH, Gentalen E, Giaever G, Hegemann JH, Jones T, Laub M, Liao H, Liebundguth N, Lockhart DJ, Lucau-Danila A, Lussier M, M’Rabet N, Menard P, Mittmann M, Pai C, Rebischung C, Revuelta JL, Riles L, Roberts CJ, Ross-MacDonald P, Scherens B, Snyder M, Sookhai-Mahadeo S, Storms RK, Veronneau S, Voet M, Volckaert G, Ward TR, Wysocki R, Yen GS, Yu K, Zimmermann K, Philippsen P, Johnston M, Davis RW (1999) Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science 285:901.

    Article  PubMed  CAS  Google Scholar 

  • Wu H, Xu H, Miraglia LJ, Crooke ST (2000) Human RNase III is a 160-kDa protein involved in preribosomal RNA processing. J Biol Chem 275:36957–36965.

    Article  PubMed  CAS  Google Scholar 

  • Yang S, Tutton S, Pierce E, Yoon K (2001) Specific double-stranded RNA interference in undifferentiated mouse embryonic stem cells. Mol Cell Biol 21:7807–7816.

    Article  PubMed  CAS  Google Scholar 

  • Yi R, Qin Y, Macara IG, Cullen BR (2003) Exportin-5 mediates the nuclear export of pre-microRNAs and short hairpin RNAs. Genes Dev 17:3011–3016.

    Article  PubMed  CAS  Google Scholar 

  • Yu JY, DeRuiter SL, Turner DL (2002) RNA interference by expression of short-interfering RNAs and hairpin RNAs in mammalian cells. Proc Natl Acad Sci U S A 99:6047–6052.

    Article  PubMed  CAS  Google Scholar 

  • Zamore PD, Haley B (2005) Ribo-gnome: the big world of small RNAs. Science 309:1519–1524.

    Article  PubMed  CAS  Google Scholar 

  • Zamore PD, Tuschl T, Sharp PA, Bartel DP (2000) RNAi: double-stranded RNA directs the ATP-dependent cleavage of mRNA at 21 to 23 nucleotide intervals. Cell 101:25–33.

    Article  PubMed  CAS  Google Scholar 

  • Zeng Y, Wagner EJ, Cullen BR (2002) Both natural and designed micro RNAs can inhibit the expression of cognate mRNAs when expressed in human cells. Mol Cell 9:1327–1333.

    Article  PubMed  CAS  Google Scholar 

  • Zilberman D, Cao X, Jacobsen SE (2003) Argonaute4 control of locus-specific siRNA accumulation and DNA and histone methylation. Science 299:716–719

    Article  PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2008 Springer-Verlag Berlin Heidelberg

About this chapter

Cite this chapter

Paddison, P.J. (2008). RNA Interference in Mammalian Cell Systems. In: Paddison, P.J., Vogt, P.K. (eds) RNA Interference. Current Topics in Microbiology and Immunology, vol 320. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-75157-1_1

Download citation

Publish with us

Policies and ethics