Protocols for Expression and Functional Analysis of Viral MicroRNAs

Methods in Enzymology

Volumn 427, Issue , 2007, Pages 229-243

  Gottwein, Eva ^a   Cullen, Bryan R ^a  

^a DUKE UNIVERSITY MEDICAL CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

KAPOSI SARCOMA ASSOCIATED HERPESVIRUS VECTOR MIRNA K1; LENTIVIRUS VECTOR; LENTIVIRUS VECTOR PNL SIN CMV BLR; MICRORNA; UNCLASSIFIED DRUG; VIRUS RNA; VIRUS VECTOR;

ANIMAL CELL; CELL TYPE; DISEASE DURATION; EXPRESSION VECTOR; GENE CASSETTE; GENE EXPRESSION REGULATION; GENE REPLICATION; HERPES VIRUS; HUMAN; HUMAN CELL; INFECTION; NONHUMAN; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEIN FUNCTION; REVIEW; RNA ANALYSIS; TRANSCRIPTION REGULATION; VALIDATION STUDY; VIRAL GENE DELIVERY SYSTEM; VIRUS CELL INTERACTION; ARTICLE; CELL LINE; GENE VECTOR; GENETICS; PHYSIOLOGY;

ANIMALIA; DNA VIRUSES;

CELL LINE; GENETIC VECTORS; HUMANS; MICRORNAS; RNA, VIRAL;

EID: 37249073643     PISSN: 00766879     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0076-6879(07)27013-2     Document Type: Review

References (54)

1. Amarzguioui M., Rossi J.J., and Kim D. Approaches for chemically synthesized siRNA and vector-mediated RNAi. FEBS Lett. 579 (2005) 5974-5981
2. Bartel D.P. MicroRNAs: Genomics, biogenesis, mechanism, and function. Cell 116 (2004) 281-297
3. Bernstein E., Caudy A.A., Hammond S.M., and Hannon G.J. Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature 409 (2001) 363-366
4. Brummelkamp T.R., Bernards R., and Agami R. A system for stable expression of short interfering RNAs in mammalian cells. Science 296 (2002) 550-553
5. Burnside J., Bernberg E., Anderson A., Lu C., Meyers B.C., Green P.J., Jain N., Isaacs G., and Morgan R.W. Marek's disease virus encodes MicroRNAs that map to meq and the latency-associated transcript. J. Virol. 80 (2006) 8778-8786
6. Cai X., Hagedorn C.H., and Cullen B.R. Human microRNAs are processed from capped, polyadenylated transcripts that can also function as mRNAs. RNA 10 (2004) 1957-1966
7. Cai X., Lu S., Zhang Z., Gonzalez C.M., Damania B., and Cullen B.R. Kaposi's sarcoma-associated herpesvirus expresses an array of viral microRNAs in latently infected cells. Proc. Natl. Acad. Sci. USA 102 (2005) 5570-5575
8. Cai X., Schafer A., Lu S., Bilello J.P., Desrosiers R.C., Edwards R., Raab-Traub N., and Cullen B.R. Epstein-Barr virus microRNAs are evolutionarily conserved and differentially expressed. PLoS Pathog. 2 (2006) e23
9. Chang K., Elledge S.J., and Hannon G.J. Lessons from nature: MicroRNA-based shRNA libraries. Nat. Methods 3 (2006) 707-714
10. Chen C.Z., Li L., Lodish H.F., and Bartel D.P. MicroRNAs modulate hematopoietic lineage differentiation. Science 303 (2004) 83-86
11. Cui C., Griffiths A., Li G., Silva L.M., Kramer M.F., Gaasterland T., Wang X.J., and Coen D.M. Prediction and identification of herpes simplex virus 1-encoded microRNAs. J. Virol. 80 (2006) 5499-5508
12. Cullen B.R. Transcription and processing of human microRNA precursors. Mol. Cell 16 (2004) 861-865
13. Cullen B.R. Enhancing and confirming the specificity of RNAi experiments. Nat. Methods 3 (2006) 677-681
14. Cullen B.R. Induction of stable RNA interference in mammalian cells. Gene Ther. 13 (2006) 503-508
15. Cullen B.R. Viruses and microRNAs. Nat. Genet. 38 Suppl. (2006) S25-S30
16. Denli A.M., Tops B.B., Plasterk R.H., Ketting R.F., and Hannon G.J. Processing of primary microRNAs by the Microprocessor complex. Nature 432 (2004) 231-235
17. Dickins R.A., Hemann M.T., Zilfou J.T., Simpson D.R., Ibarra I., Hannon G.J., and Lowe S.W. Probing tumor phenotypes using stable and regulated synthetic microRNA precursors. Nat. Genet. 37 (2005) 1289-1295
18. Doench J.G., Petersen C.P., and Sharp P.A. siRNAs can function as miRNAs. Genes Dev. 17 (2003) 438-442
19. Dunn W., Trang P., Zhong Q., Yang E., van Belle C., and Liu F. Human cytomegalovirus expresses novel microRNAs during productive viral infection. Cell Microbiol. 7 (2005) 1684-1695
20. Elbashir S.M., Harborth J., Lendeckel W., Yalcin A., Weber K., and Tuschl T. Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature 411 (2001) 494-498
21. Gottwein E., Cai X., and Cullen B.R. A novel assay for viral microRNA function identifies a single nucleotide polymorphism that affects Drosha processing. J. Virol. 80 (2006) 5321-5326
22. Gregory R.I., Yan K.P., Amuthan G., Chendrimada T., Doratotaj B., Cooch N., and Shiekhattar R. The Microprocessor complex mediates the genesis of microRNAs. Nature 432 (2004) 235-240
23. Grey F., Antoniewicz A., Allen E., Saugstad J., McShea A., Carrington J.C., and Nelson J. Identification and characterization of human cytomegalovirus-encoded microRNAs. J. Virol. 79 (2005) 12095-12099
24. Grishok A., Pasquinelli A.E., Conte D., Li N., Parrish S., Ha I., Baillie D.L., Fire A., Ruvkun G., and Mello C.C. Genes and mechanisms related to RNA interference regulate expression of the small temporal RNAs that control C. elegans developmental timing. Cell 106 (2001) 23-34
25. Grundhoff A., Sullivan C.S., and Ganem D. A combined computational and microarray-based approach identifies novel microRNAs encoded by human gamma-herpesviruses. RNA 12 (2006) 733-750
26. Gupta A., Gartner J.J., Sethupathy P., Hatzigeorgiou A.G., and Fraser N.W. Anti-apoptotic function of a microRNA encoded by the HSV-1 latency-associated transcript. Nature 442 (2006) 82-85
27. Hutvagner G., and Zamore P.D. A microRNA in a multiple-turnover RNAi enzyme complex. Science 297 (2002) 2056-2060
28. Hutvagner G., McLachlan J., Pasquinelli A.E., Balint E., Tuschl T., and Zamore P.D. A cellular function for the RNA-interference enzyme Dicer in the maturation of the let-7 small temporal RNA. Science 293 (2001) 834-838
29. Ketting R.F., Fischer S.E., Bernstein E., Sijen T., Hannon G.J., and Plasterk R.H. Dicer functions in RNA interference and in synthesis of small RNA involved in developmental timing in C. elegans. Genes Dev. 15 (2001) 2654-2659
30. Khvorova A., Reynolds A., and Jayasena S.D. Functional siRNAs and miRNAs exhibit strand bias. Cell 115 (2003) 209-216
31. Kim V.N., and Nam J.W. Genomics of microRNA. Trends Genet. 22 (2006) 165-173
32. Knight S.W., and Bass B.L. A role for the RNase III enzyme DCR-1 in RNA interference and germ line development in Caenorhabditis elegans. Science 293 (2001) 2269-2271
33. Krek A., Grun D., Poy M.N., Wolf R., Rosenberg L., Epstein E.J., MacMenamin P., da Piedade I., Gunsalus K.C., Stoffel M., and Rajewsky N. Combinatorial microRNA target predictions. Nat. Genet. 37 (2005) 495-500
34. Lee M.T., Coburn G.A., McClure M.O., and Cullen B.R. Inhibition of human immunodeficiency virus type 1 replication in primary macrophages by using Tat- or CCR5-specific small interfering RNAs expressed from a lentivirus vector. J. Virol. 77 (2003) 11964-11972
35. Lee Y., Ahn C., Han J., Choi H., Kim J., Yim J., Lee J., Provost P., Radmark O., Kim S., and Kim V.N. The nuclear RNase III Drosha initiates microRNA processing. Nature 425 (2003) 415-419
36. Lee Y., Kim M., Han J., Yeom K.H., Lee S., Baek S.H., and Kim V.N. MicroRNA genes are transcribed by RNA polymerase II. EMBO J. 23 (2004) 4051-4060
37. Lewis B.P., Burge C.B., and Bartel D.P. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120 (2005) 15-20
38. Lund E., Guttinger S., Calado A., Dahlberg J.E., and Kutay U. Nuclear export of microRNA precursors. Science 303 (2004) 95-98
39. Olsen P.H., and Ambros V. The lin-4 regulatory RNA controls developmental timing in Caenorhabditis elegans by blocking lin-14 protein synthesis after the initiation of translation. Dev. Biol. 216 (1999) 671-680
40. Paddison P.J., Caudy A.A., Bernstein E., Hannon G.J., and Conklin D.S. Short hairpin RNAs (shRNAs) induce sequence-specific silencing in mammalian cells. Genes Dev. 16 (2002) 948-958
41. Pfeffer S., Zavolan M., Grasser F.A., Chien M., Russo J.J., Ju J., John B., Enright A.J., Marks D., Sander C., and Tuschl T. Identification of virus-encoded microRNAs. Science 304 (2004) 734-736
42. Pfeffer S., Sewer A., Lagos-Quintana M., Sheridan R., Sander C., Grasser F.A., van Dyk L.F., Ho C.K., Shuman S., Chien M., Russo J.J., Ju J., et al. Identification of microRNAs of the herpesvirus family. Nat. Methods 2 (2005) 269-276
43. Rodriguez A., Griffiths-Jones S., Ashurst J.L., and Bradley A. Identification of mammalian microRNA host genes and transcription units. Genome Res. 14 (2004) 1902-1910
44. Samols M.A., Hu J., Skalsky R.L., and Renne R. Cloning and identification of a microRNA cluster within the latency-associated region of Kaposi's sarcoma-associated herpesvirus. J. Virol. 79 (2005) 9301-9305
45. Sano M., Kato Y., and Taira K. Sequence-specific interference by small RNAs derived from adenovirus VAI RNA. FEBS Lett. 580 (2006) 1553-1564
46. Schwarz D.S., Hutvagner G., Du T., Xu Z., Aronin N., and Zamore P.D. Asymmetry in the assembly of the RNAi enzyme complex. Cell 115 (2003) 199-208
47. Silva J.M., Li M.Z., Chang K., Ge W., Golding M.C., Rickles R.J., Siolas D., Hu G., Paddison P.J., Schlabach M.R., Sheth N., Bradshaw J., et al. Second-generation shRNA libraries covering the mouse and human genomes. Nat. Genet. 37 (2005) 1281-1288
48. Stegmeier F., Hu G., Rickles R.J., Hannon G.J., and Elledge S.J. A lentiviral microRNA-based system for single-copy polymerase II-regulated RNA interference in mammalian cells. Proc. Natl. Acad. Sci. USA 102 (2005) 13212-13217
49. Sullivan C.S., Grundhoff A.T., Tevethia S., Pipas J.M., and Ganem D. SV40-encoded microRNAs regulate viral gene expression and reduce susceptibility to cytotoxic T cells. Nature 435 (2005) 682-686
50. Yekta S., Shih I.H., and Bartel D.P. MicroRNA-directed cleavage of HOXB8 mRNA. Science 304 (2004) 594-596
51. Yi R., Qin Y., Macara I.G., and Cullen B.R. Exportin-5 mediates the nuclear export of pre-microRNAs and short hairpin RNAs. Genes Dev. 17 (2003) 3011-3016
52. Zeng Y., Cai X., and Cullen B.R. Use of RNA polymerase II to transcribe artificial microRNAs. Methods Enzymol. 392 (2005) 371-380
53. Zeng Y., Wagner E.J., and Cullen B.R. Both natural and designed microRNAs can inhibit the expression of cognate mRNAs when expressed in human cells. Mol. Cell 9 (2002) 1327-1333
54. Zeng Y., Yi R., and Cullen B.R. MicroRNAs and small interfering RNAs can inhibit mRNA expression by similar mechanisms. Proc. Natl. Acad. Sci. USA 100 (2003) 9779-9784