Gene silencing in human embryonic stem cells by RNA interference

Biochemical and Biophysical Research Communications

Volumn 390, Issue 4, 2009, Pages 1106-1110

  Rassouli, Fatemeh Behnam ^a   Matin, Maryam M ^a  

^a FERDOWSI UNIVERSITY OF MASHHAD   (Iran)

Author keywords

Gene silencing; Human embryonic stem cells; RNA interference

Indexed keywords

RNA;

CELL MANIPULATION; CLINICAL RESEARCH; EMBRYONIC STEM CELL; GENE; GENE SILENCING; HUMAN; NONHUMAN; PRIORITY JOURNAL; RNA INTERFERENCE; SHORT SURVEY; TECHNOLOGY;

CELL DIFFERENTIATION; EMBRYONIC STEM CELLS; GENE KNOCKDOWN TECHNIQUES; GENE SILENCING; HUMANS; RNA INTERFERENCE; RNA, SMALL INTERFERING;

EID: 70450231611     PISSN: 0006291X     EISSN: 10902104     Source Type: Journal    
DOI: 10.1016/j.bbrc.2009.10.038     Document Type: Short Survey

References (75)

1. Kawasaki H., and Taira K. Transcriptional gene silencing by short interfering RNAs. Curr. Opin. Mol. Ther. 7 (2005) 125-131
2. Fire A., Xu S., Montgomery M.K., et al. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391 (1998) 806-811
3. Nykanen A., Haley B., and Zamore P.D. ATP requirement and small interfering RNA structure in the RNA interference pathway. Cell 107 (2001) 309-321
4. Zamore P.D., Tuschl T., Sharp P.A., et al. RNAi: double-stranded RNA directs the ATP-dependent cleavage of mRNA at 21 to 23 nucleotide intervals. Cell 101 (2000) 25-33
5. Hannon G.J. RNA interference. Nature 418 (2002) 244-251
6. McManus M.T., and Sharp P.A. Gene silencing in mammals by small interfering RNAs. Nat. Rev. Genet. 3 (2002) 737-747
7. Stark G.R., Kerr I.M., Williams B.R., et al. How cells respond to interferons. Annu. Rev. Biochem. 67 (1998) 227-264
8. Zamore P.D. RNA interference: listening to the sound of silence. Nat. Struct. Biol. 8 (2001) 746-750
9. Paddison P.J., Caudy A.A., Bernstein E., et al. Short hairpin RNAs (shRNAs) induce sequence-specific silencing in mammalian cells. Genes Dev. 16 (2002) 948-958
10. Lagos-Quintana M., Rauhut R., Yalcin A., et al. Identification of tissue-specific microRNAs from mouse. Curr. Biol. 12 (2002) 735-739
11. Sijen T., Fleenor J., Simmer F., et al. On the role of RNA amplification in dsRNA triggered gene silencing. Cell 107 (2001) 465-476
12. Lee J., Nam S., Hwang S.B., et al. Functional genomic approaches using the nematode Caenorhabditis elegans as a model system. J. Biochem. Mol. Biol. 37 (2004) 107-113
13. Dasgupta R., and Perrimon N. Using RNAi to catch Drosophila genes in a web of interactions: insights into cancer research. Oncogene 23 (2004) 8359-8365
14. Sachse C., and Echeverri C.J. Oncology studies using siRNA libraries: the dawn of RNAi-based genomics. Oncogene 23 (2004) 8384-8391
15. Miyagishi M., Hayashi M., and Taira K. Comparison of the suppressive effects of antisense oligonucleotides and siRNAs directed against the same targets in mammalian cells. Antisense Nucleic Acid Drug Dev. 13 (2003) 1-7
16. Kopper O., and Benvenisty N. Manipulation of the human genome in human embryonic stem cells. Stem Cell Rev. 1 (2005) 145-150
17. Dann C.T., and Garbers D.L. Production of knockdown rat by lentiviral transduction of embryos with short hairpin RNA transgene. Methods Mol. Biol. 450 (2008) 193-209
18. Elbashir S.M., Harborth J., Lendeckel W., et al. Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature 411 (2001) 494-498
19. Thomson J.A., Itskovitz-Eldor J., Shapiro S.S., et al. Embryonic stem cell lines derived from human blastocysts. Science 282 (1998) 1145-1147
20. Andrews P.W., Matin M., Bahrami A.R., et al. Embryonic stem (ES) cells and embryonal carcinoma (EC) cells: opposite sides of the same coin. Biochem. Soc. Trans. 33 (2005) 1526-1530
21. Smith A.G. Embryo-derived stem cells: of mice and men. Annu. Rev. Cell Dev. Biol. 17 (2001) 435-462
22. Enver T., Soneji S., Joshi C., et al. Cellular differentiation hierarchies in normal and culture-adapted human embryonic stem cells. Hum. Mol. Genet. 14 (2005) 3129-3140
23. Burdon T., Smith A., and Savatier P. Signalling, cell cycle and pluripotency in embryonic stem cells. Trends Cell Biol. 12 (2002) 432-438
24. Nichols J., Zevnik B., Anastassiadis K., et al. Formation of pluripotent stem cells in the mammalian embryo depends on the POU transcription factor Oct4. Cell 95 (1998) 379-391
25. Avilion A.A., Nicolis S.K., Pevny L.H., et al. Multipotent cell lineages in early mouse development depend on SOX2 function. Genes Dev. 17 (2003) 126-140
26. Hanna L.A., Foreman R.K., Tarasenko I.A., et al. Requirement for Foxd3 in maintaining pluripotent cells of the early mouse embryo. Genes Dev. 16 (2002) 2650-2661
27. Mitsui K., Tokuzawa Y., Itoh H., et al. The homeoprotein Nanog is required for maintenance of pluripotency in mouse epiblast and ESCs. Cell 113 (2003) 631-642
28. Chambers I., Colby D., Robertson M., et al. Functional expression cloning of Nanog, a pluripotency sustaining factor in embryonic stem cells. Cell 113 (2003) 643-655
29. Burdon T., Chambers I., Stracey C., et al. Signaling mechanisms regulating self-renewal and differentiation of pluripotent embryonic stem cells. Cells Tissues Organs 165 (1999) 131-143
30. Sato N., Meijer L., Skaltsounis L., et al. Maintenance of pluripotency in human and mouse embryonic stem cells through activation of Wnt signaling by a pharmacological GSK-3-specific inhibitor. Nat. Med. 10 (2004) 55-63
31. Fox V., Gokhale P.J., Walsh J.R., et al. Cell-cell signaling through NOTCH regulates human embryonic stem cell proliferation. Stem Cells 26 (2008) 715-723
32. Niwa H., Burdon T., Chambers I., et al. Self-renewal of pluripotent embryonic stem cells is mediated via activation of STAT3. Genes Dev. 12 (1998) 2048-2060
33. Ying Q.L., Nichols J., Chambers I., et al. BMP induction of Id proteins suppresses differentiation and sustains embryonic stem cell self-renewal in collaboration with STAT3. Cell 115 (2003) 281-292
34. Rodda D.J., Chew J.L., Lim L.H., et al. Transcriptional regulation of nanog by OCT4 and SOX2. J. Biol. Chem. 280 (2005) 24731-24737
35. Suh M.R., Lee Y., Kim J.Y., et al. Human embryonic stem cells express a unique set of microRNAs. Dev. Biol. 270 (2004) 488-498
36. Babinet C., and Cohen-Tannoudji M. Genome engineering via homologous recombination in mouse embryonic stem (ES) cells: an amazingly versatile tool for the study of mammalian biology. An. Acad. Bras. Cienc. 73 (2001) 365-383
37. Misra R.P., and Duncan S.A. Gene targeting in the mouse: advances in introduction of transgenes into the genome by homologous recombination. Endocrine 19 (2002) 229-238
38. Sullenger B.A., and Gilboa E. Emerging clinical applications of RNA. Nature 418 (2002) 252-258
39. Reynolds A., Leake D., Boese Q., et al. Rational siRNA design for RNA interference. Nat. Biotechnol. 22 (2004) 326-330
40. Naito Y., Yamada T., Ui-Tei K., et al. siDirect: highly effective, target-specific siRNA design software for mammalian RNA interference. Nucleic Acids Res. 32 (2004) W124-W129
41. Donze O., and Picard D. RNA interference in mammalian cells with siRNA synthesized with T7 RNA polymerase. Nucleic Acids Res. 30 (2002) e46
42. Yu J.Y., DeRuiter S.L., and Turner D.L. RNA interference by expression of short interfering RNAs and hairpin RNA by mammalian cells. Proc. Natl. Acad. Sci. USA 99 (2002) 6047-6052
43. Calabrese J.M., and Sharp P.A. Characterization of the short RNAs bound by the P19 suppressor of RNA silencing in mouse embryonic stem cells. RNA 12 (2006) 2092-2102
44. Devree E., and Silver P.A. Retrovirus-delivered siRNA. BMC Biotechnol. 2 (2002) 15-19
45. Paul C.P., Good P.D., Winer I., et al. Effective expression of small interfering RNA in human cells. Nat. Biotechnol. 20 (2002) 505-508
46. Brummelkamp T.R., Bernards R., and Agami R. Stable suppression of tumorigenicity by virus-mediated RNA interference. Cancer Cell 2 (2002) 243-247
47. Vallier L., Rugg-Gunn P., Bouhon I.A., et al. Enhancing and diminsing gene function in human embryonic stem cells. Stem Cells 22 (2004) 2-11
48. Hay D.C., Sutherland L., Clark J., et al. Oct-4 knockdown induces similar patterns of endoderm and trophoblast differentiation markers in human and mouse embryonic stem cells. Stem Cells 22 (2004) 225-235
49. Hyslop L., Stojkovic M., Armstrong L., et al. Downregulation of NANOG induces differentiation of human embryonic stem cells to extraembryonic lineages. Stem Cells 23 (2005) 1035-1043
50. Babaie Y., Herwig R., Greber B., et al. Analysis of Oct4-dependent transcriptional networks regulating self-renewal and pluripotency in human embryonic stem cells. Stem Cells 25 (2007) 500-510
51. Zhao M., Yang H., Jiang X., et al. Lipofectamine RNAiMAX: an efficient siRNA transfection reagent in human embryonic stem cells. Mol. Biotechnol. 40 (2008) 19-26
52. Matin M.M., Walsh J.R., Gokhale P.J., et al. Specific knockdown of Oct4 and beta2-microglobulin expression by RNA interference in human embryonic stem cells and embryonic carcinoma cells. Stem Cells 22 (2004) 659-668
53. Lee Y.J., Nah H.Y., Hong S.H., et al. Spa-1 regulates the maintenance and differentiation of human embryonic stem cells. Int. J. Dev. Biol. 52 (2008) 43-53
54. Gerrard L., Zhao D., Clark A.J., et al. Stably transfected human embryonic stem cell clones express OCT4-specific green fluorescent protein and maintain self-renewal and pluripotency. Stem Cells 23 (2005) 124-133
55. Greber B., Lehrach H., and Adjaye J. Silencing of core transcription factors in human EC cells highlights the importance of autocrine FGF signaling for self-renewal. BMC Dev. Biol. 7 (2007) 46
56. Xiong C., Tang D.Q., Xie C.Q., et al. Genetic engineering of human embryonic stem cells with lentiviral vectors. Stem Cells Dev. 14 (2005) 367-377
57. Zaehres H., Lensch M.W., Daheron L., et al. High-efficiency RNA interference in human embryonic stem cells. Stem Cells 23 (2005) 299-305
58. Flygare J., Kiefer T., Miyake K., et al. Deficiency of ribosomal protein S19 in CD34+ cells generated by siRNA blocks erythroid development and mimics defects seen in Diamond-Blackfan anemia. Blood 105 (2005) 4627-4634
59. Rodriguez R.T., Velkey J.M., Lutzko C., et al. Manipulation of OCT4 levels in human embryonic stem cells results in induction of differential cell types. Exp. Biol. Med. 232 (2007) 1368-1380
60. Elbashir S., Harborth M.J., Weber K., et al. Analysis of gene functions in somatic mammalian cells with small interfering RNAs. Methods 26 (2002) 199-213
61. Draper J.S., Pigott C., Thomson J.A., et al. Surface antigens of human embryonic stem cells: changes upon differentiation in culture. J. Anat. 200 (2002) 249-258
62. Daheron L., Opitz S.L., Zaehres H., et al. LIF/STAT3 signaling fails to maintain self-renewal of human embryonic stem cells. Stem Cells 22 (2004) 770-778
63. Rao M. Conserved and divergent paths that regulate self-renewal in mouse and human embryonic stem cells. Dev. Biol. 275 (2004) 269-286
64. Amit M., Carpenter M.K., Inokuma M.S., et al. Clonally derived human embryonic stem cell lines maintain pluripotency and proliferative potential for prolonged periods of culture. Dev. Biol. 227 (2000) 271-278
65. Mitalipova M.M., Rao R.R., Hoyer D.M., et al. Preserving the genetic integrity of human embryonic stem cells. Nat. Biotechnol. 23 (2005) 19-20
66. Amit M., Shariki C., Margulets V., et al. Feeder layer- and serum-free culture of human embryonic stem cells. Biol. Reprod. 70 (2004) 837-845
67. Brandenberger R., Wei H., Zhang S., et al. Transcriptome characterization elucidates signaling networks that control human ES cell growth and differentiation. Nat. Biotechnol. 22 (2004) 707-716
68. Boyer L.A., Lee T.I., Cole M.F., et al. Core transcriptional regulatory circuitry in human embryonic stem cells. Cell 122 (2005) 947-956
69. Lim L.S., Loh Y.H., Zhang W., et al. Zic3 is required for maintenance of pluripotency in embryonic stem cells. Mol. Biol. Cell 18 (2007) 1348-1358
70. Roy B.C., Kohu K., Matsuura K., et al. Rap-specific GTPase activating protein, is present in the NMDA receptor-PSD-95 complex in the hippocampus. Genes Cells 7 (2002) 607-617
71. Gropp M., and Reubinoff B.E. Lentiviral-RNA-interference system mediating homogenous and monitored level of gene silencing in human embryonic stem cells. Cloning Stem Cells 9 (2007) 339-345
72. Wilda M., Fuchs U., Wossmann W., et al. Killing of leukemic cells with a BCR/ABL fusion gene by RNA interference (RNAi). Oncogene 21 (2002) 5716-5724
73. Heidersbach A., Gaspar-Maia A., McManus M.T., et al. RNA interference in embryonic stem cells and the prospects for future therapies. Gene Ther. 13 (2006) 478-486
74. Grimm D., and Kay M.A. RNAi and gene therapy: a mutual attraction. Hematology 1 (2007) 473-481
75. Tsang S.Y., Moore J.C., Huizen R.V., et al. Ectopic expression of systemic RNA interference defective protein in embryonic stem cells. Biochem. Biophys. Res. Commun. 357 (2007) 480-486