Automated High-Throughput RNAi Screening in Human Cells Combined with Reporter mRNA Transfection to Identify Novel Regulators of Translation

PLoS ONE

Volumn 7, Issue 9, 2012, Pages

  Casanova, Claudia M ^a,b   Sehr, Peter ^b   Putzker, Kerstin ^b   Hentze, Matthias W ^b   Neumann, Beate ^b   Duncan, Kent E ^c   Thoma, Christian ^a,b  

^a UNIVERSITY OF FREIBURG   (Germany)

^b EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

^c UNIVERSITY MEDICAL CENTER HAMBURG EPPENDORF   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; MITOGEN ACTIVATED PROTEIN KINASE 3; POLO LIKE KINASE 1; SMALL INTERFERING RNA; VASCULOTROPIN;

ARTICLE; AUTOMATION; CONTROLLED STUDY; ENZYME ACTIVITY; ENZYME REGULATION; GENETIC TRANSCRIPTION; GENETIC TRANSFECTION; HIGH THROUGHPUT SCREENING; HUMAN; HUMAN CELL; PROTEIN ANALYSIS; PROTEIN EXPRESSION; PROTEIN FUNCTION; RNA INTERFERENCE; RNA TRANSLATION;

HELA CELLS; HIGH-THROUGHPUT SCREENING ASSAYS; HUMANS; MITOGEN-ACTIVATED PROTEIN KINASE 3; PHOSPHORIC MONOESTER HYDROLASES; PHOSPHOTRANSFERASES; PROTEIN BIOSYNTHESIS; RNA INTERFERENCE; RNA, MESSENGER; TRANSFECTION; VASCULAR ENDOTHELIAL GROWTH FACTOR A;

EID: 84866914741     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0045943     Document Type: Article

References (47)

1. Gebauer F, Hentze MW, (2004) Molecular mechanisms of translational control. Nat Rev Mol Cell Biol 5: 827-835.
2. Silvera D, Formenti SC, Schneider RJ, (2010) Translational control in cancer. Nat Rev Cancer. 10: 254-66.
3. Jackson RJ, Hellen CU, Pestova TV, (2010) The mechanism of eukaryotic translation initiation and principles of its regulation. Nat Rev Mol Cell Biol 11: 113-127.
4. Sonenberg N, Hinnebusch AG, (2009) Regulation of translation initiation in eukaryotes: mechanisms and biological targets. Cell 136: 731-745.
5. Pestova TV, Lomakin IB, Lee JH, Choi SK, Dever TE, et al. (2000) The joining of ribosomal subunits in eukaryotes requires eIF5B. Nature 403: 332-335.
6. Holcik M, Sonenberg N, (2005) Translational control in stress and apoptosis. Nat Rev Mol Cell Biol 6: 318-327.
7. Gilbert WV, Zhou K, Butler TK, Doudna JA, (2007) Cap-independent translation is required for starvation-induced differentiation in yeast. Science 317: 1224-1227.
8. Johannes G, Carter MS, Eisen MB, Brown PO, Sarnow P, (1999) Identification of eukaryotic mRNAs that are translated at reduced cap binding complex eIF4F concentrations using a cDNA microarray. Proc Natl Acad Sci U S A 96: 13118-13123.
9. Holcik M, (2004) Targeting translation for treatment of cancer-a novel role for IRES? Current cancer drug targets 4: 299-311.
10. Stoneley M, Willis AE, (2004) Cellular internal ribosome entry segments: structures, trans-acting factors and regulation of gene expression. Oncogene 23: 3200-3207.
11. Hanahan D, Weinberg RA, (2011) Hallmarks of cancer: the next generation. Cell 144: 646-674.
12. Harris AL, (2002) Hypoxia-a key regulatory factor in tumour growth. Nature reviews 2: 38-47.
13. de Almodovar CR, Lambrechts D, Mazzone M, Peter Carmeliet, (2009) Role and Therapeutic Potential of VEGF in the Nervous System. Physiol Rev 89: 607-648.
14. Mackenzie F, Ruhrberg C, (2012) Diverse roles for VEGF-A in the nervous system. Development 139: 1371-80.
15. Huez I, Creancier L, Audigier S, Gensac MC, Prats AC, et al. (1998) Two independent internal ribosome entry sites are involved in translation initiation of vascular endothelial growth factor mRNA. Mol Cell Biol 18: 6178-6190.
16. Akiri G, Nahari D, Finkelstein Y, Le SY, Elroy-Stein O, et al. (1998) Regulation of vascular endothelial growth factor (VEGF) expression is mediated by internal initiation of translation and alternative initiation of transcription. Oncogene 17: 227-236.
17. Stein I, Itin A, Einat P, Skaliter R, Grossman Z, et al. (1998) Translation of vascular endothelial growth factor mRNA by internal ribosome entry: implications for translation under hypoxia. Mol Cell Biol 18: 3112-3119.
18. Braunstein S, Karpisheva K, Pola C, Goldberg J, Hochman T, et al. (2007) A hypoxia-controlled cap-dependent to cap-independent translation switch in breast cancer. Molecular Cell 28: 501-512.
19. Elbashir SM, Harborth J, Weber K, Tuschl T, (2002) Analysis of gene function in somatic mammalian cells using small interfering RNAs. Methods 26: 199-213.
20. Erfle H, Neumann B, Rogers P, Bulkescher J, Ellenberg J, et al. (2008) Work flow for multiplexing siRNA assays by solid-phase reverse transfection in multiwell plates. J Biomol Screen 13: 575-580.
21. Gilbert WV, (2010) Alternative ways to think about cellular internal ribosome entry. J Biol Chem 285: 29033-29038.
22. Gebauer F, Corona DFV, Preiss T, Becker PB, Hentze MW, (1999) Translational control of dosage compensation in Drosophila by Sex-lethal: cooperative silencing via the 5′ and 3′ UTRs of msl-2 mRNA is independent of the poly(A) tail. EMBOJ 18: 6146-6154.
23. Duncan KE, Strein C, Hentze MW, (2009) The SXL-UNR corepressor complex uses a PABP-mediated mechanism to inhibit ribosome recruitment to msl-2 mRNA. Mol. Cell 36: 571-582.
24. Puri N, Wang X, Varma R, Burnett C, Beauchamp L, et al. (2008) LNA incorporated siRNAs exhibit lower off-target effects compared to 2'-OMethoxy in cell phenotypic assays and microarray analysis. Nucleic acids symposium series 52: 25-26.
25. Sumara I, Gimenez-Abian JF, Gerlich D, Hirota T, Kraft C, et al. (2004) Roles of polo-like kinase 1 in the assembly of functional mitotic spindles. Curr Biol 14: 1712-1722.
26. Bushati N, Cohen SM, (2007) microRNA functions. Annu Rev Cell Dev Biol. 23: 175-205.
27. Fabian MR, Sonenberg N, (2012) The mechanics of miRNA-mediated gene silencing: a look under the hood of miRISC. Nat Struct Mol Biol. 19: 586-93.
28. Pasquinelli AE, (2012) MicroRNAs and their targets: recognition, regulation and an emerging reciprocal relationship. Nat Rev Genet. 13: 271-82.
29. Schwanhäusser B, Busse D, Li N, Dittmar G, Schuchhardt J, et al. (2011) Global quantification of mammalian gene expression control. Nature. 473: 337-42.
30. Stumpf CR, Ruggero D, (2011) The cancerous translation apparatus. Curr Opin Genet Dev. 21: 474-83.
31. Robert F, Pelletier J, (2009) Translation initiation: a critical signalling node in cancer. Expert Opin Ther Targets. 13: 1279-93.
32. Lujambio A, Lowe SW, (2012) The microcosmos of cancer. Nature. 482: 347-55.
33. Hsieh AC, Liu Y, Edlind MP, Ingolia NT, Janes MR, et al. (2012) The translational landscape of mTOR signalling steers cancer initiation and metastasis. Nature. 485: 55-61.
34. Malina A, Cencic R, Pelletier J, (2011) Targeting translation dependence in cancer. Oncotarget. 2: 76-88.
35. Averous J, Proud CG, (2006) When translation meets transformation: the mTOR story. Oncogene. 25: 6423-35.
36. Gingras AC, Raught B, Gygi SP, Niedzwiecka A, Miron M, et al. (2001) Hierarchical phosphorylation of the translation inhibitor 4E-BP1. Genes & development 15: 2852-2864.
37. Ma L, Chen Z, Erdjument-Bromage H, Tempst P, Pandolfi PP, (2005) Phosphorylation and functional inactivation of TSC2 by Erk implications for tuberous sclerosis and cancer pathogenesis. Cell. 121: 179-93.
38. Danckwardt S, Gantzert AS, Macher-Goeppinger S, Probst HC, Gentzel M, et al. (2011) p38 MAPK controls prothrombin expression by regulated RNA 3' end processing. Molecular Cell 41(3): 298-310.
39. Mayr C, Bartel DP, (2009) Widespread shortening of 3'UTRs by alternative cleavage and polyadenylation activates oncogenes in cancer cells. Cell 138: 673-684.
40. Grskovic M, Javaherian A, Strulovici B, Daley GQ, (2011) Induced pluripotent stem cells-opportunities for disease modelling and drug discovery. Nat Rev Drug Discov. 10: 915-29.
41. Ding L, Poser I, Paszkowski-Rogacz M, Buchholz F, (2012) From RNAi screens to molecular function in embryonic stem cells. Stem Cell Rev. 8: 32-42.
42. Hu G, Kim J, Xu Q, Leng Y, Orkin SH, et al. (2009) A genome-wide RNAi screen identifies a new transcriptional module required for self-renewal. Genes Dev. 23: 837-48.
43. Luo J, Emanuele MJ, Li D, Creighton CJ, Schlabach MR, et al. (2009) A genome-wide RNAi screen identifies multiple synthetic lethal interactions with the Ras oncogene. Cell. 137: 835-48.
44. Neumann B, Held M, Liebel U, Erfle H, Rogers P, et al. (2006) High-throughput RNAi screening by time-lapse imaging of live human cells. Nat Methods. 3: 385-90.
45. Iizuka N, Najita L, Franzusoff A, Sarnow P, (1994) Cap-dependent and cap-independent translation by internal initiation of mRNAs in cell extracts prepared from Saccharomyces cerevisiae. Mol Cell Biol 14: 7322-7330.
46. Thoma C, Bergamini G, Galy B, Hundsdoerfer P, Hentze MW, (2004) Enhancement of IRES-mediated translation of the c-myc and BiP mRNAs by the poly(A) tail is independent of intact eIF4G and PABP. Molecular cell 15: 925-935.
47. Pfaffl MW, Horgan GW, Dempfle L, (2002) Relative expression software tool (REST) for group-wise comparison and statistical analysis of relative expression results in real-time PCR. Nucleic acids research 30: e36.