Dissecting MicroRNA-Mediated Gene Regulation and Function in T-Cell Development

Methods in Enzymology

Volumn 427, Issue , 2007, Pages 171-189

  Mao, Tin Ky ^a   Chen, Chang Zheng ^a  

^a STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA;

ANIMAL CELL; ANIMAL EXPERIMENT; ANIMAL MODEL; ANIMAL TISSUE; CELL DIFFERENTIATION; CONTROLLED STUDY; GENE EXPRESSION REGULATION; GENE FUNCTION; GENE IDENTIFICATION; GENE OVEREXPRESSION; GENE TARGETING; HUMAN; IN VITRO STUDY; MOLECULAR CLONING; MOLECULAR MECHANICS; MOUSE; NONHUMAN; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; REGULATORY RNA SEQUENCE; REPRESSOR GENE; REVIEW; RNA ANALYSIS; RNA DEGRADATION; T LYMPHOCYTE ACTIVATION; VALIDATION PROCESS; ARTICLE; CYTOLOGY; GENETICS; PHYSIOLOGY; RETROVIRUS; T LYMPHOCYTE;

ANIMALIA;

CLONING, MOLECULAR; GENE EXPRESSION REGULATION; MICRORNAS; POLYMERASE CHAIN REACTION; RETROVIRIDAE; T-LYMPHOCYTES;

EID: 42949153447     PISSN: 00766879     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0076-6879(07)27010-7     Document Type: Review

References (38)

1. Altuvia Y., Landgraf P., Lithwick G., Elefant N., Pfeffer S., Aravin A., Brownstein M.J., Tuschl T., and Margalit H. Clustering and conservation patterns of human microRNAs. Nucleic Acids Res. 33 (2005) 2697-2706
2. Bagga S., Bracht J., Hunter S., Massirer K., Holtz J., Eachus R., and Pasquinelli A.E. Regulation by let-7 and lin-4 miRNAs results in target mRNA degradation. Cell 122 (2005) 553-563
3. Balciunaite G., Ceredig R., Fehling H.J., Zuniga-Pflucker J.C., and Rolink A.G. The role of Notch and IL-7 signaling in early thymocyte proliferation and differentiation. Eur. J. Immunol. 35 (2005) 1292-1300
4. Bartel D.P. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116 (2004) 281-297
5. Bartel D.P., and Chen C.Z. Micromanagers of gene expression: the potentially widespread influence of metazoan microRNAs. Nat. Rev. Genet. 5 (2004) 396-400
6. Berezikov E., Guryev V., van de Belt J., Wienholds E., Plasterk R.H., and Cuppen E. Phylogenetic shadowing and computational identification of human microRNA genes. Cell 120 (2005) 21-24
7. Brennecke J., Hipfner D.R., Stark A., Russell R.B., and Cohen S.M. bantam encodes a developmentally regulated microRNA that controls cell proliferation and regulates the proapoptotic gene hid in Drosophila. Cell 113 (2003) 25-36
8. Brennecke J., Stark A., Russell R.B., and Cohen S.M. Principles of microRNA-target recognition. PLoS Biol. 3 (2005) e85
9. Chen C., Ridzon D.A., Broomer A.J., Zhou Z., Lee D.H., Nguyen J.T., Barbisin M., Xu N.L., Mahuvakar V.R., Andersen M.R., et al. Real-time quantification of microRNAs by stem-loop RT-PCR. Nucleic Acids Res. 33 (2005) e179
10. Chen C.Z., Li L., Lodish H.F., and Bartel D.P. MicroRNAs modulate hematopoietic lineage differentiation. Science 303 (2004) 83-86
11. Cullen B.R. RNAi the natural way. Nat. Genet. 37 (2005) 1163-1165
12. de Pooter R., and Zuniga-Pflucker J.C. T-cell potential and development in vitro: the OP9-DL1 approach. Curr. Opin. Immunol. 19 (2007) 163-168
13. 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
14. Elbashir S.M., Leneckel W., and Tuschl T. RNA interference is mediated by 21-and 22-nucleotide RNAs. Genes Dev. 15 (2001) 188-200
15. Esau C., Kang X., Peralta E., Hanson E., Marcusson E.G., Ravichandran L.V., Sun Y., Koo S., Perera R.J., Jain R., et al. MicroRNA-143 regulates adipocyte differentiation. J. Biol. Chem. 279 (2004) 52361-52365
16. Fazi F., Rosa A., Fatica A., Gelmetti V., De Marchis M.L., Nervi C., and Bozzoni I. A minicircuitry comprised of microRNA-223 and transcription factors NFI-A and C/EBPalpha regulates human granulopoiesis. Cell 123 (2005) 819-831
17. Fire A., Xu S., Montgomery M.K., Kostas S.A., Driver S.E., and Mello C.C. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391 (1998) 806-811
18. Hare K.J., Jenkinson E.J., and Anderson G. In vitro models of T cell development. Semin. Immunol. 11 (1999) 3-12
19. Hernandez-Hoyos G., and Alberola-Ila J. Analysis of T-cell development by using short interfering RNA to knock down protein expression. Methods Enzymol. 392 (2005) 199-217
20. Kiriakidou M., Nelson P.T., Kouranov A., Fitziev P., Bouyioukos C., Mourelatos Z., and Hatzigeorgiou A. A combined computational-experimental approach predicts human microRNA targets. Genes Dev. 18 (2004) 1165-1178
21. Krek A., Grun D., Poy M.N., Wolf R., Rosenberg L., Epstein E.J., MacMenamin P., da Piedade I., Gunsalus K.C., Stoffel M., et al. Combinatorial microRNA target predictions. Nat. Genet. 37 (2005) 495-500
22. Lee R.C., Feinbaum R.L., and Ambros V. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75 (1993) 843-854
23. 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
24. 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
25. Lewis B.P., Shih I.H., Jones-Rhoades M.W., Bartel D.P., and Burge C.B. Prediction of mammalian microRNA targets. Cell 115 (2003) 787-798
26. Li Q.-J., Chau J., Ebert P.J., Sylvester G., Min H., Liu G., Braich R., Manoharan M., Soutschek J., Skare P., Klein L.O., Davis M.M., et al. miR-181a is an intrinsic modulator of T cell sensitivity and selection. Cell 129 (2007) 147 61
27. Lim L.P., Lau N.C., Garrett-Engele P., Grimson A., Schelter J.M., Castle J., Bartel D.P., Linsley P.S., and Johnson J.M. Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature 433 (2005) 769-773
28. Min H., and Chen C.Z. Methods for analyzing microRNA expression and function during hematopoietic lineage differentiation. Methods Mol. Biol. 342 (2006) 209-227
29. Miranda K.C., Huynh T., Tay Y., Ang Y.S., Tam W.L., Thomson A.M., Lim B., and Rigoutsos I. A pattern-based method for the identification of MicroRNA binding sites and their corresponding heteroduplexes. Cell 126 (2006) 1203-1217
30. Poy M.N., Eliasson L., Krutzfeldt J., Kuwajima S., Ma X., Macdonald P.E., Pfeffer S., Tuschl T., Rajewsky N., Rorsman P., et al. A pancreatic islet-specific microRNA regulates insulin secretion. Nature 432 (2004) 226-230
31. Rajewsky N. microRNA target predictions in animals. Nat. Genet. 38 Suppl. (2006) S8-S13
32. Schmitt T.M., and Zuniga-Pflucker J.C. Induction of T cell development from hematopoietic progenitor cells by delta-like-1 in vitro. Immunity 17 (2002) 749-756
33. 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., et al. Second-generation shRNA libraries covering the mouse and human genomes. Nat. Genet. 37 (2005) 1281-1288
34. Wienholds E., and Plasterk R.H. MicroRNA function in animal development. FEBS Lett. 579 (2005) 5911
35. Wightman B., Ha I., and Ruvkun G. Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans. Cell 75 (1993) 855-862
36. Xu P., Vernooy S.Y., Guo M., and Hay B.A. The Drosophila microRNA Mir-14 suppresses cell death and is required for normal fat metabolism. Curr. Biol. 13 (2003) 790-795
37. Zhao Y., Samal E., and Srivastava D. Serum response factor regulates a muscle-specific microRNA that targets Hand2 during cardiogenesis. Nature 436 (2005) 214-220
38. Zuniga-Pflucker J.C. T-cell development made simple. Nat. Rev. Immunol. 4 (2004) 67-72