Gene silencing by small regulatory RNAs in mammalian cells

Cell Cycle

Volumn 6, Issue 4, 2007, Pages 444-449

  Scherr, Michaela ^a   Eder, Matthias ^a  

^a HANNOVER MEDICAL SCHOOL   (Germany)

Author keywords

Gene silencing; Gene transfer; miRNA; RNAi; shRNA

Indexed keywords

MESSENGER RNA; MICRORNA; SHORT HAIRPIN RNA; SMALL INTERFERING RNA;

GENE EXPRESSION; GENE IDENTIFICATION; GENE SILENCING; GENE TARGETING; HUMAN; MAMMAL CELL; NONHUMAN; REVIEW; RNA INTERFERENCE;

MAMMALIA;

EID: 33847793202     PISSN: 15384101     EISSN: 15514005     Source Type: Journal    
DOI: 10.4161/cc.6.4.3807     Document Type: Review

References (70)

1. van Blokland K, van der Geest N, Mol J, Kooter J. Transgene-mediated suppression of chalcone synthase expression in Petunia hybrida results from an increase in RNA turnover. Plant J. 1994; 6:861-77.
2. Dougherty WG, Parks TD. Transgenes and suppression: telling us something new? Curr. Opin. Cell Biol. 1995; 7: 399-405.
3. Metzlaff M, O'Dell M, Cluster PD, Flavell RB. RNA-mediated RNA degradation and chalcone synthase A silencing in petunia. Cell 1997; 88:845-54.
4. Fire A, Xu S, Montgomery MK, Kostas SA, Driver SE, Mello CC. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 1998; 391:806-11.
5. Montgomery MK, Xu S, Fire A. RNA as a target of double-stranded RNA-mediated genetic interference in Caenorhabditis elegans. Proc Natl Acad Sci USA 1998; 95:15502-7.
6. Rocheleau CE, Downs WD, Lin R, Wittmann C, Bei Y, Cha YH, Ali M, Priess JR, Mello CC. Wnt signaling and an APC-related gene specify endoderm in early C. elegans embryos. Cell 1997;90:707-16.
7. Kennerdell JR, Carthew RW. Use of dsRNA-mediated genetic interference to demonstrate that frizzled and frizzled 2 act in the wingless pathway. Cell 1998; 95:1017-26.
8. Waterhouse PM, Graham MW, Wang MB. Virus resistance and gene silencing in plants can be induced by simultaneous expression of sense and antisense RNA. Proc Natl Acad Sci U S A 1998; 95:13959-64.
9. Montgomery MK, Fire A. Double-stranded RNA as a mediator in sequence-specific genetic silencing and co-suppression. Trends Genet 1998; 14:255-58.
10. Cogoni C, Macino G. Gene silencing in Neurospora crassa requires a protein homologous to RNA-dependent RNA polymerase. Nature 1999; 399:166-69.
11. Jensen S, Gassama MP, Heidmann T. Cosuppression of I transposon activity in Drosophila by I-containing sense and antisense transgenes. Genetics 1999; 153:1767-74.
12. Hamilton AJ, Baulcombe DC. A species of small antisense RNA in posttranscriptional gene silencing in plants. Science 1999; 286:950-52.
13. Sharp PA, Zamore PD. Molecular biology. RNA interference. Science 2000; 287:2431-33.
14. Zamore PD, Tuschl T, Sharp PA, Bartel DP. RNAi: double-stranded RNA directs the ATP-dependent cleavage of mRNA at 21 to 23 nucleotide intervals. Cell 2000; 101:25-33.
15. Hammond SM, Bernstein E, Beach D, Hannon, GJ. An RNA-directed nuclease mediates post-transcriptional gene silencing in Drosophila cells. Nature 2002; 404:293-96.
16. Bernstein E, Caudy AA, Hammond SM, Hannon, GJ. Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature 2001; 409:363-66.
17. Hannon, GJ. RNA interference. Nature 2002; 418:244-51.
18. Sontheimer EJ. Assembly and function of RNA silencing complexes. Nat Rev Mol Cell Biol 2005; 6:127-38.
19. Tomari Y, Zamore PD. Perspective: machines for RNAi.Genes Dev 2005; 19:517-29.
20. Valencia-Sanchez MA, Liu J, Hannon GJ, Parker R. Control of translation and mRNA degradation by miRNAs and siRNAs. Genes Dev 2006; 20:515-24.
21. Elbashir SM, Harborth J, Lendeckel W, Yalcin A, Weber K, Tuschl T. Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature 2001; 411:494-98.
22. Caplen NJ, Parrish S, Imani F, Fire A, Morgan RA. Specific inhibition of gene expression by small double-stranded RNAs in invertebrate and vertebrate systems. Proc Natl Acad Sci USA 2001; 98:9742-47.
23. Paddison PJ, Hannon GJ. RNA interference: the new somatic cell genetics? Cancer Cell 2002; 2:17-23.
24. Hemann MT, Fridmann JS, Zilfou JT, Hernando E, Paddison PJ, Cordon-Cardo C, Hannon GJ, Lowe SW. An epi-allelic series of p53 hypomorphs created by stable RNAi produces distinct tumor phenotypes in vivo. Nat Genet 2003; 33:396-400.
25. Paddison PJ, Caudy AA, Bernstein E, Hannon GJ, Conklin DS. Short hairpin RNAs (shRNAs) induce sequence-specific silencing in mammalian cells. Genes Dev 2002; 16:948-58.
26. Brummelkamp TR, Bernards R, Agami R. A system for stable expression of short interfering RNAs in mammalian cells.Science 2002; 296:550-53.
27. Bartel DP. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 2004; 116:281-97.
28. He L, Hannon GJ MicroRNAs: small RNAs with a big role in gene regulation. Nat Rev Genet. 2004; 5:522-31.
29. Lee Y, Ahn C, Han J, Choi H, Kim J, Yim J, Lee J, Provost P, Radmark O, Kim S, Kim VN. The nuclear RNase III Drosha initiates microRNA processing. Nature 2003; 425:415-19.
30. Schwarz DS, Hutvagner G, Du T, Xu Z, Aronin N, Zamore PD. Asymmetry in the assembly of the RNAi enzyme complex. Cell 2003;115199-208.
31. Khvorova A, Reynolds A, Jayasensa SD. Functional siRNAs and miRNAs exhibit strand bias. Cell 2003; 115:209-16.
32. Wu L, Fan J, Belasco JG. MicroRNAs direct rapid deadenylation of mRNA. Proc Natl Acad Sci USA 2006;103:4034-39.
33. Lewis BP, Burge CP, Bartel DP. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 2005; 120:15-20.
34. Wang B, Love TM, Call ME, Doench JG, Novina CD. Recapitulation of short RNA-directed translational gene silencing in vitro. Mol Cell 2006; 22:553-60.
35. Cullen BR. Transcription and processing of human microRNA precursors. Mol Cell 2004; 16:861-65.
36. Zeng Y, Wagner EJ, Cullen BR. Both natural and designed micro RNAs can inhibit the expression of cognate mRNAs when expressed in human cells. Mol Cell 2002; 9:1327-33.
37. Stegmeier F, Hu G, Rickles RJ, Hannon GJ, Elledge SJ. A lentiviral microRNA-based system for single-copy polymerase II-regulated RNA interference in mammalian cells. Proc Natl Acad Sci USA 2005; 102:13212-17.
38. Chung KH, Hart CC, Al-Bassam S, Avery A, Taylor J, Patel PD, Vojtek AB, Turner DL. Polycistronic RNA polymerase II expression vectors for RNA interference based on BIC/miR-155. Nuc Acids Res 2006; 34:e53.
39. Wiznerowicz M, Trono. Tuning silence: conditional systems for RNA interference. Nat Methods 2006; 3:682-88.
40. Rubinson DA, Dillon CP, Kwiatkowski AV, Sievers C, Yang L, Kopinja J, Zhang M, Mc Manus MT, Gertler FP, Scott ML, Van Parijs L A lentivirus-based system to functionally silence genes in primary mammalian cells, stem cells and transgenic mice by RNA interference. Nat Genet 2003; 33:401-6.
41. Tiscornia G, Singer O, Ikawa M, Verma IM. A general method for gene knockdown in mice by using lentiviral vectors expressing small interfering RNA. Proc Natl Acad Sci USA 2003; 100:1844-48.
42. Scherr M, Battmer K, Ganser A, Eder M. Modulation of gene expression by lentiviral-mediated delivery of small interfering RNA. Cell Cycle 2003; 2:251-57.
43. Cullen BR. Induction of stable RNA interference in mammalian cells. Gene Ther 2006; 13:503-8.
44. Sui G, Soohoo C, Affar el B, Gay F, Shi Y, Forrester WC, Shi Y. DNA vector-based RNAi technology to suppress gene expression in mammalian cells. Proc Natl Acad Sci USA 2002; 99:5515-20.
45. Paul CP, Good PD, Winer I, Engelke DR. Effective expression of small interfering RNA in human cells. Nat Biotechnol 2002; 20:505-8.
46. Shen C, Buck AK, Liu X, Winkler M, Reske SN. Gene silencing by adenovirus-delivered siRNA. FEBS Lett. 2003; 539:111-14.
47. Pfeifer A, Ikawa M, Dayn Y, Verma IM. Transgenesis by lentiviral vectors: lack of gene silencing in mammalian embryonic stem cells and preimplantation embryos. Proc Natl Acad Sci USA 2002; 99:2140-45.
48. Schomber T, Kalberer CP, Wodnar-Filipowicz A, Skoda RC. Gene silencing by lentivirus-mediated delivery of siRNA in human CD34+ cells. Blood 2004; 103:4511-13.
49. Scherr M, Battmer K, Dallmann I, Ganser A, Eder M. Inhibition of GM-CSF receptor function by stable RNA interference in a NOD/SCID mouse hematopoietic stem cell transplantation model. Oligonucleotides 2003; 13:353-63.
50. Scherr M, Battmer K, Schultheis B, Ganser A, Eder M. Stable RNA interference (RNAi) as an option for anti-bcr-abl therapy. Gene Ther 2005; 12:12-21.
51. Scherr M, Chaturvedi A, Battmer K, Schultheis B, Ganser A, Eder M. Enhanced sensitivity to inhibition of SHP2, STAT5, and Gab2 expression in chronic myeloid leukemia (CML). Blood 2006; 107:3279-87.
52. van de Wetering M, Oving I, Muncan V, Pon Fong MT, Brantjes H, van Leenen D, Holstege FC, Brummelkamp TR, Agami R, Clevers H. Specific inhibition of gene expression using a stably integrated, inducible small-interfering-RNA vector. EMBO Rep 2003; 4:609-15.
53. Matsukura S, Jones PA, Takai D. Establishment of conditional vectors for hairpin siRNA knockdowns. 2003 Nuc Acids Res 2003; 31: e77.
54. Gupta S, Schoer RA, Egan JE, Hannon GJ, Mittal V. Inducible, reversible, and stable RNA interference in mammalian cells Proc Natl Acad Sci USA 2004; 101:1927-32.
55. Wiznerowicz M, Trono D. Conditional suppression of cellular genes: lentivirus vector-mediated drug-inducible RNA interference. J Virol 2003; 77:8957-61.
56. Zheng L, Liu J, Batalov S, Zhou D, Orth A, Ding S, Schultz PG. An approach to genomewide screens of expressed small interfering RNAs in mammalian cells. Proc Natl Acad Sci USA 2004;101:135-40.
57. Shirane D, Sugao K, Namiki S, Tanabe M, Iino M, Hirose K. Enzymatic production of RNAi libraries from cDNAs. Nat Genetics 2004; 36:190-96
58. Sen G, Wehrman TS, Myers JW, Blau HM. Restriction enzyme-generated siRNA (REGS) vectors and libraries. Nat Genet 2004; 36:183-89.
59. Buchholz F, Kittler R, Slabicki M, Theis M. Enzymatically prepared RNAi libraries. Nat Methods 2006; 3:696-700.
60. 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. A large-scale RNAi screen in human cells identifies new components of the p53 pathway. Nature 2004; 428:431-37.
61. Kolfschoten IG, van Leeuwen B, Berns K, Mullenders J, Beijersbergen RL, Bernards R, Voorhoeve PM, Agami R. A genetic screen identifies PITX1 as a suppressor of RAS activity and tumorigenicity. Cell 2005; 121:849-58.
62. Westbrook TF, Martin ES, Martin ES, Schlabach MR, Leng Y, Liang AC, Feng B, Zhao JJ, Roberts TM, Mandel G, Hannon GJ, Depinho RA, Chin L, Elledge SJ. A genetic screen for candidate tumor suppressors identifies REST. Cell 2005; 121:837-48.
63. Ngo Vu N, Davis RE, Lamy L, Yu X, Zhao H, Lenz G, Lam LT, Dave S, Yang L, Powell J, Staudt LM. A loss-of-function RNA interference screen for molecular targets in cancer. Nature 2006 ; 441:106-10.
64. Siolas D, Lerner C, Burchard J, Ge W, Linsley PS, Paddison PJ, Hannon GJ, Cleary MA. Synthetic shRNAs as potent RNAi triggers. Nat Biotechnol 2005; 23:227-31.
65. Kim DH, Behlke MA, Rose SD, Chang MS, Choi S, Rossi JJ. Synthetic dsRNA Dicer substrates enhance RNAi potency and efficacy. Nat Biotechnol 2005; 23:222-26.
66. 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, Kulkami A, Cavet G, Sachidanandam R, McCombie WR, Cleary MA, Elledge SJ, Hannon GJ. Second-generation shRNA libraries covering the mouse and human genomes. Nat Genetic 2005; 37:1281-88.
67. Cullen BR. Enhancing and confirming the specificity of RNAi experiments. Nat Methods 2006; 3:677-81.
68. Thomson JM, Newman M, Parker JS, Morin-Kensicki EM, Wright T, Hammond SM. Extensive post-transcriptional regulation of microRNAs and its implications for cancer. Genes Dev 2006; 20:2202-07.
69. Yi R, Doehle BP, Qin Y, Macara IG, Cullen BR.Overexpression of exportin 5 enhances RNA interference mediated by short hairpin RNAs and microRNAs. RNA 2005; 11:220-26.
70. Chen J, Yu WM, Daino H, Broxmeyer HE, Druker BJ, Qu CK. SHP-2 phosphatase is required for hematopoietic cell transformation by Bcr-Abl. Blood 2006 Sep 26 [Epub ahead of print].