Erratum: Engineering and optimization of the miR-106b cluster for ectopic expression of multiplexed anti-HIV RNAs (Gene Therapy (2008) vol. 15 (1536-1549) 10.1038/gt.2008.147);Engineering and optimization of the miR-106b cluster for ectopic expression of multiplexed anti-HIV RNAs

Gene Therapy

Volumn 15, Issue 23, 2008, Pages 1536-1549

  Aagaard, L A ^a   Zhang, J ^a   von Eije, K J ^a,b   Li, H ^a   Saetrom P ^a,c   Amarzguioui, M ^a,d   Rossi, J J ^a  

^a CITY OF HOPE NATIONAL MEDICAL CENTER   (United States)

^b UNIVERSITY OF AMSTERDAM   (Netherlands)

^c NORWEGIAN UNIVERSITY OF SCIENCE AND TECHNOLOGY   (Norway)

^d UNIVERSITY OF OSLO   (Norway)

Author keywords

[No Author keywords available]

Indexed keywords

LENTIVIRUS VECTOR; MICRORNA; MINICHROMOSOME MAINTENANCE PROTEIN 7; REV PROTEIN; RNA POLYMERASE II; SMALL INTERFERING RNA; SMALL NUCLEOLAR RNA; TRANSACTIVATOR PROTEIN;

ARTICLE; CONTROLLED STUDY; DOWN REGULATION; GENE CLUSTER; GENE EXPRESSION; GENE INSERTION; GENE SEQUENCE; GENE TARGETING; GENETIC ENGINEERING; GENETIC TRANSCRIPTION; HUMAN; HUMAN CELL; HUMAN IMMUNODEFICIENCY VIRUS 1; INTRON; PLASMID; PRIORITY JOURNAL; PROCESS OPTIMIZATION; RNA PROCESSING; RNA SEQUENCE; RNA SPLICING; SEQUENCE ANALYSIS; VIRUS TRANSCRIPTION;

HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 56349155978     PISSN: 09697128     EISSN: 14765462     Source Type: Journal    
DOI: 10.1038/gt.2008.163     Document Type: Erratum

References (72)

1. 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: 806-811.
2. 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: 494-498.
3. Hannon GJ, Rossi JJ. Unlocking the potential of the human genome with RNA interference. Nature 2004; 431: 371-378.
4. Dykxhoorn DM, Lieberman J. Silencing viral infection. PLoS Med 2006; 3: E242.
5. Kim DH, Rossi JJ. Strategies for silencing human disease using RNA interference. Nat Rev Genet 2007; 8: 173-184.
6. Brummelkamp TR, Bernards R, Agami R. A system for stable expression of short interfering RNAs in mammalian cells. Science 2002; 296 550-553.
7. 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: 948-958.
8. 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: 1327-1333.
9. Bartel DP, Chen CZ. Micromanagers of gene expression: The potentially widespread influence of metazoan microRNAs. Nat Rev Genet 2004; 5: 396-400.
10. Gitlin L, Karelsky S, Andino R. Short interfering RNA confers intracellular antiviral immunity in human cells. Nature 2002; 418: 430-434.
11. Lee NS, Dohjima T, Bauer G, Li H, Li MJ, Ehsani A et al. Expression of small interfering RNAs targeted against HIV-1 rev transcripts in human cells. Nat Biotechnol 2002; 20: 500-505.
12. Li MJ, Bauer G, Michienzi A, Yee JK, Lee NS, Kim J et al. Inhibition of HIV-1 infection by lentiviral vectors expressing Pol III-promoted anti-HIV RNAs. Mol Ther 2003; 8: 196-206.
13. Rubinson DA, Dillon CP, Kwiatkowski AV, Sievers C, Yang L, Kopinja J et al. A lentivirus-based system to functionally silence genes in primary mammalian cells, stem cells and transgenic mice by RNA interference. Nat Genet 2003; 33: 401-406.
14. Snove Jr O, Rossi JJ. Expressing short hairpin RNAs in vivo. Nat Methods 2006; 3: 689-695.
15. Grimm D, Kay MA. Combinatorial RNAi: A winning strategy for the race against evolving targets? Mol Ther 2007; 15: 878-888.
16. Boden D, Pusch O, Lee F, Tucker L, Ramratnam B. Human immunodeficiency virus type 1 escape from RNA interference. J Virol 2003; 77: 11531-11535.
17. Das AT, Brummelkamp TR, Westerhout EM, Vink M, Madiredjo M, Bernards R et al. Human immunodeficiency virus type 1 escapes from RNA interference-mediated inhibition. J Virol 2004; 78: 2601-2605.
18. Westerhout EM, Ooms M, Vink M, Das AT, Berkhout B. HIV-1 can escape from RNA interference by evolving an alternative structure in its RNA genome. Nucleic Acids Res 2005; 33: 796-804.
19. Wilson JA, Richardson CD. Hepatitis C virus replicons escape RNA interference induced by a short interfering RNA directed against the NS5b coding region. J Virol 2005; 79: 7050-7058.
20. von Eije KJ, ter Brake O, Berkhout B. Human immunodeficiency virus type 1 escape is restricted when conserved genome sequences are targeted by RNA interference. J Virol 2008; 82: 2895-2903.
21. Song E, Lee SK, Dykxhoorn DM, Novina C, Zhang D, Crawford K et al. Sustained small interfering RNA-mediated human immunodeficiency virus type 1 inhibition in primary macrophages. J Virol 2003; 77: 7174-7181.
22. Andersson MG, Haasnoot PC, Xu N, Berenjian S, Berkhout B, Akusjärvi G. Suppression of RNA interference by adenovirus virus-associated RNA. J Virol 2005; 79: 9556-9565.
23. Chang LJ, Liu X, He J. Lentiviral siRNAs targeting multiple highly conserved RNA sequences of human immunodeficiency virus type 1. Gene Therapy 2005; 12: 1133-1144.
24. Henry SD, van der Wegen P, Metselaar HJ, Tilanus HW, Scholte BJ, van der Laan LJ. Simultaneous targeting of HCV replication and viral binding with a single lentiviral vector containing multiple RNA interference expression cassettes. Mol Ther 2006; 14: 485-493.
25. Li M, Rossi JJ. Lentiviral vector delivery of siRNA and shRNA encoding genes into cultured and primary hematopoietic cells. Methods Mol Biol 2005; 309: 261-272.
26. ter Brake O, Konstantinova P, Ceylan M, Berkhout B. Silencing of HIV-1 with RNA interference: A multiple shRNA approach. Mol Ther 2006; 14: 883-892.
27. ter Brake O, 't Hooft K, Liu YP, Centlivre M, von Eije KJ, Berkhout B. Lentiviral vector design for multiple shRNA expression and durable HIV-1 inhibition. Mol Ther 2008; 16: 557-564.
28. Leonard JN, Schaffer DV. Computational design of antiviral RNA interference strategies that resist human immunodeficiency virus escape. J Virol 2005; 79: 1645-1654.
29. An DS, Qin FX, Auyeung VC, Mao SH, Kung SK, Baltimore D et al. Optimization and functional effects of stable short hairpin RNA expression in primary human lymphocytes via lentiviral vectors. Mol Ther 2006; 14: 494-504.
30. Grimm D, Streetz KL, Jopling CL, Storm TA, Pandey K, Davis CR et al Fatality in mice due to oversaturation of cellular microRNA/short hairpin RNA pathways. Nature 2006; 441: 537-541.
31. Bartel DP. MicroRNAs: Genomics, biogenesis, mechanism, and function. Cell 2004; 116: 281-297.
32. Kim VN. MicroRNA biogenesis: Coordinated cropping and dicing. Nat Rev Mol Cell Biol 2005; 6: 376-385.
33. Kim VN. Small RNAs: Classification, biogenesis, and function. Mol Cells 2005; 19: 1-15.
34. Mourelatos Z, Dostie J, Paushkin S, Sharma A, Charroux B, Abel L et al. miRNPs: A novel class of ribonucleoproteins containing numerous microRNAs. Genes Dev 2002; 16: 720-728.
35. Cai X, Hagedorn CH, Cullen BR. Human microRNAs are processed from capped, polyadenylated transcripts that can also function as mRNAs. RNA 2004; 10: 1957-1966.
36. Lee Y, Kim M, Han J, Yeom KH, Lee S, Baek SH et al. MicroRNA genes are transcribed by RNA polymerase II. EMBO J 2004; 23: 4051-4060.
37. Denli AM, Tops BB, Plasterk RH, Ketting RF, Hannon GJ. Processing of primary microRNAs by the Microprocessor complex. Nature 2004; 432: 231-235.
38. Gregory RI, Yan KP, Amuthan G, Chendrimada T, Doratotaj B, Cooch N et al. The microprocessor complex mediates the genesis of microRNAs. Nature 2004; 432: 235-240.
39. Han J, Lee Y, Yeom KH, Kim YK, Jin H, Kim VN. The Drosha-DGCR8 complex in primary microRNA processing. Genes Dev 2004; 18: 3016-3027.
40. Landthaler M, Yalcin A, Tuschl T. The human DiGeorge syndrome critical region gene 8 and its D. melanogaster homolog are required for miRNA biogenesis. Curr Biol 2004; 14: 2162-2167.
41. Lee Y, Ahn C, Han J, Choi H, Kim J, Yim J et al. The nuclear RNase III Drosha initiates microRNA processing. Nature 2003; 425: 415-419.
42. Lund E, Guttinger S, Calado A, Dahlberg JE, Kutay U. Nuclear export of microRNA precursors. Science 2004; 303: 95-98.
43. Yi R, Qin Y, Macara IG, Cullen BR. Exportin-5 mediates the nuclear export of pre-microRNAs and short hairpin RNAs. Genes Dev 2003; 17: 3011-3016.
44. Zeng Y, Cullen BR. Structural requirements for pre-microRNA binding and nuclear export by Exportin 5. Nucleic Acids Res 2004; 32: 4776-4785.
45. Chendrimada TP, Gregory RI, Kumaraswamy E, Norman J, Cooch N, Nishikura K et al. TRBP recruits the Dicer complex to Ago2 for microRNA processing and gene silencing. Nature 2005; 436: 740-744.
46. Gregory RI, Chendrimada TP, Cooch N, Shiekhattar R. Human RISC couples microRNA biogenesis and posttranscriptional gene silencing. Cell 2005; 123: 631-640.
47. Lee Y, Jeon K, Lee JT, Kim S, Kim VN. MicroRNA maturation: Stepwise processing and subcellular localization. EMBO J 2002; 21: 4663-4670.
48. Altuvia Y, Landgraf P, Lithwick G, Elefant N, Pfeffer S, Aravin A et al. Clustering and conservation patterns of human microRNAs. Nucleic Acids Res 2005; 33: 2697-2706.
49. He L, Thomson JM, Hemann MT, Hernando-Monge E, Mu D, Goodson S et al A microRNA polycistron as a potential human oncogene. Nature 2005; 435: 828-833.
50. Tanzer A, Stadler PF. Molecular evolution of a microRNA cluster. J Mol Biol 2004; 339: 327-335.
51. Kim YK, Kim VN. Processing of intronic microRNAs. EMBO J 2007; 26: 775-783.
52. Rodriguez A, Griffiths-Jones S, Ashurst JL, Bradley A. Identification of mammalian microRNA host genes and transcription units. Genome Res 2004; 14: 1902-1910.
53. Chang K, Elledge SJ, Hannon GJ. Lessons from Nature: MicroRNA-based shRNA libraries. Nat Methods 2006; 3: 707-714.
54. Silva JM, Li MZ, Chang K, Ge W, Golding MC, Rickles RJ et al. Second-generation shRNA libraries covering the mouse and human genomes. Nat Genet 2005; 37: 1281-1288.
55. 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: 13212-13217.
56. Dickins RA, Hemann MT, Zilfou JT, Simpson DR, Ibarra I, Hannon GJ et al. Probing tumor phenotypes using stable and regulated synthetic microRNA precursors. Nat Genet 2005; 37: 1289-1295.
57. Zhou H, Xia XG, Xu Z. An RNA polymerase II construct synthesizes short-hairpin RNA with a quantitative indicator and mediates highly efficient RNAi. Nucleic Acids Res 2005; 33: E62.
58. Chung KH, Hart CC, Al-Bassam S, Avery A, Taylor J, Patel PD et al. Polycistronic RNA polymerase II expression vectors for RNA interference based on BIC/miR-155. Nucleic Acids Res 2006; 34: E53.
59. Du G, Yonekubo J, Zeng Y, Osisami M, Frohman MA. Design of expression vectors for RNA interference based on miRNAs and RNA splicing. FEBS J 2006; 273: 5421-5427.
60. Han J, Lee Y, Yeom KH, Nam JW, Heo I, Rhee JK et al. Molecular basis for the recognition of primary microRNAs by the Drosha-DGCR8 complex. Cell 2006; 125: 887-901.
61. Zeng Y, Yi R, Cullen BR. Recognition and cleavage of primary microRNA precursors by the nuclear processing enzyme Drosha. EMBO J 2005; 24: 138-148.
62. Michienzi A, Li S, Zaia JA, Rossi JJ. A nucleolar TAR decoy inhibitor of HIV-1 replication. Proc Natl Acad Sci USA 2002; 99: 14047-14052.
63. Tomari Y, Matranga C, Haley B, Martinez N, Zamore PD. A protein sensor for siRNA asymmetry. Science 2004; 306: 1377-1380.
64. Schwarz DS, Hutvágner G, Du T, Xu Z, Aronin N, Zamore PD. Asymmetry in the assembly of the RNAi enzyme complex. Cell 2003; 115: 199-208.
65. Hirose T, Shu MD, Steitz JA. Splicing-dependent and -independent modes of assembly for intron-encoded box C/D snoRNPs in mammalian cells. Mol Cell 2003; 12: 113-123.
66. Hirose T, Steitz JA. Position within the host intron is critical for efficient processing of box C/D snoRNAs in mammalian cells. Proc Natl Acad Sci USA 2001; 98: 12914-12919.
67. Pumfery A, de la Fuente C, Berro R, Nekhai S, Kashanchi F, Chao SH. Potential use of pharmacological cyclin-dependent kinase inhibitors as anti-HIV therapeutics. Curr Pharm Des 2006; 12: 1949-1961.
68. Aagaard L, Amarzguioui M, Sun G, Santos LC, Ehsani A, Prydz H et al A facile lentiviral vector system for expression of doxycycline-inducible shRNAs: Knockdown of the pre-miRNA processing enzyme Drosha. Mol Ther 2007; 15: 938-945.
69. Helvik SA, Snove Jr O, Saetrom P. Reliable prediction of Drosha processing sites improves microRNA gene prediction. Bioinformatics 2007; 23: 142-149.
70. Khvorova A, Reynolds A, Jayasena SD. Functional siRNAs and miRNAs exhibit strand bias. Cell 2003; 115: 209-216.
71. Li MJ, Kim J, Li S, Zaia J, Yee JK, Anderson J et al. Long-term inhibition of HIV-1 infection in primary hematopoietic cells by lentiviral vector delivery of a triple combination of anti-HIV shRNA, anti-CCR5 ribozyme, and a nucleolar-localizing TAR decoy. Mol Ther 2005; 12: 900-909.
72. Unwalla HJ, Li MJ, Kim JD, Li HT, Ehsani A, Alluin J et al. Negative feedback inhibition of HIV-1 by TAT-inducible expression of siRNA. Nat Biotech 2004; 22: 1573-1578.