Cloning and Detecting Signature MicroRNAs from Mammalian Cells

Methods in Enzymology

Volumn 427, Issue , 2007, Pages 123-138

  Sun, Guihua ^a   Li, Haitang ^a   Rossi, John J ^a  

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

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; MICRORNA; POLYADENYLATED RNA; SMALL INTERFERING RNA; POLYADENYLIC ACID;

3' UNTRANSLATED REGION; BASE PAIRING; BIOINFORMATICS; CELL DIFFERENTIATION; CELL PROLIFERATION; CELL SPECIFICITY; COMPUTER PREDICTION; DISEASE COURSE; DNA FINGERPRINTING; EMBRYO DEVELOPMENT; GENE AMPLIFICATION; GENE EXPRESSION REGULATION; GENE SILENCING; GENE TARGETING; GENETIC CONSERVATION; HUMAN; IN VIVO STUDY; MAMMAL CELL; MOLECULAR CLONING; NONHUMAN; NUCLEOTIDE SEQUENCE; PATHOGENESIS; POLYADENYLATION; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; REVERSE TRANSCRIPTION; REVIEW; RNA ANALYSIS; RNA MICROARRAY; TISSUE SPECIFICITY; ANIMAL; ARTICLE; GENETIC TRANSCRIPTION; GENETICS; METABOLISM; NORTHERN BLOTTING; POLYACRYLAMIDE GEL ELECTROPHORESIS;

MAMMALIA;

ANIMALS; BASE SEQUENCE; BLOTTING, NORTHERN; CLONING, MOLECULAR; DNA, COMPLEMENTARY; ELECTROPHORESIS, POLYACRYLAMIDE GEL; MICRORNAS; POLY A; POLYMERASE CHAIN REACTION; TRANSCRIPTION, GENETIC;

EID: 39449094132     PISSN: 00766879     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0076-6879(07)27007-7     Document Type: Review

References (42)

1. Ambros V., and Lee R.C. "Identification of microRNAs and other tiny noncoding RNAs by cDNA cloning.". Methods Mol. Biol. 265 (2004) 131-158
2. Aravin A., Gaidatzis D., Pfeffer S., Lagos-Quintana M., Landgraf P., Iovino N., Morris P., Brownstein M.J., Kuramochi-Miyagawa S., Nakano T., Chien M., Russo J.J., et al. "A novel class of small RNAs bind to MILI protein in mouse testes.". Nature 442 7099 (2006) 203-207
3. Barad O., Meiri E., Avniel A., Aharonov R., Barzilai A., Bentwich I., Einav U., Gilad S., Hurban P., Karov Y., Lobenhofer E.K., Sharon E., et al. "MicroRNA expression detected by oligonucleotide microarrays: System establishment and expression profiling in human tissues.". Genome Res. 14 12 (2004) 2486-2494
4. Bartel D.P. "MicroRNAs: Genomics, biogenesis, mechanism, and function.". Cell 116 2 (2004) 281-297
5. Berezikov E., van Tetering G., Verheul M., van de Belt J., van Laake L., Vos J., Verloop R., van de Wetering M., Guryev V., Takada S., van Zonneveld A.J., Mano H., et al. "Many novel mammalian microRNA candidates identified by extensive cloning and RAKE analysis.". Genome Res. 16 10 (2006) 1289-1298
6. Bhattacharyya S.N., Habermacher R., Martine U., Closs E.T., and Filipowicz W. "Relief of microRNA-mediated translational repression in human cells subjected to stress.". Cell 125 6 (2006) 1111-1124
7. 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 12 (2004) 1957-1966
8. Castoldi M., Schmidt S., Benes V., Noerholm M., Kulozik A.E., Hentze M.W., and Muckenthaler M.U. "A sensitive array for microRNA expression profiling (miChip) based on locked nucleic acids (LNA).". RNA 12 5 (2006) 913-920
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., Lao K.Q., Livak K.J., et al. "Real-time quantification of microRNAs by stem-loop RT-PCR.". Nucleic Acids Res. 33 20 (2005) e179
10. Chendrimada T.P., Gregory R.I., Kumaraswamy E., Norman J., Cooch N., Nishikura K., and Shiekhattar R. "TRBP recruits the Dicer complex to Ago2 for microRNA processing and gene silencing.". Nature 436 7051 (2005) 740-744
11. Chu C.Y., and Rana T.M. "Translation Repression in Human Cells by MicroRNA-Induced Gene Silencing Requires RCK/p54.". PLoS Biol. 4 7 (2006) e210
12. Doi N., Zenno S., Ueda R., Ohki-Hamazaki H., Ui-Tei K., and Saigo K. "Short-interfering-RNA-mediated gene silencing in mammalian cells requires Dicer and eIF2C translation initiation factors.". Curr. Biol. 13 1 (2003) 41-46
13. Fu H., Tie Y., Xu C., Zhang Z., Zhu J., Shi Y., Jiang H., Sun Z., and Zheng X. "Identification of human fetal liver miRNAs by a novel method.". FEBS Lett. 579 17 (2005) 3849-3854
14. Girard A., Sachidanandam R., Hannon G.J., and Carmell M.A. "A germline-specific class of small RNAs binds mammalian Piwi proteins.". Nature 442 7099 (2006) 199-202
15. Haase A.D., Jaskiewicz L., Zhang H., Laine S., Sack R., Gatignol A., and Filipowicz W. "TRBP, a regulator of cellular PKR and HIV-1 virus expression, interacts with Dicer and functions in RNA silencing.". EMBO Rep. 6 10 (2005) 961-967
16. Han J., Lee Y., Yeom K.H., Kim Y.K., Jin H., and Kim V.N. "The Drosha-DGCR8 complex in primary microRNA processing.". Genes Dev. 18 24 (2004) 3016-3027
17. Hofacker I.L. "Vienna RNA secondary structure server.". Nucleic Acids Res. 31 13 (2003) 3429-3431
18. Humphreys D.T., Westman B.J., Martin D.J., and Preiss T. "MicroRNAs control translation initiation by inhibiting eukaryotic initiation factor 4E/cap and poly(A) tail function.". Proc. Natl. Acad. Sci. USA 102 47 (2005) 16961-16966
19. Lagos-Quintana M., Rauhut R., Yalcin A., Meyer J., Lendeckel W., and Tuschl T. "Identification of tissue-specific microRNAs from mouse.". Curr. Biol. 12 9 (2002) 735-739
20. Lau N.C., Lim L.P., Weinstein E.G., and Bartel D.P. "An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans.". Science 294 5543 (2001) 858-862
21. Lau N.C., Seto A.G., Kim J., Kuramochi-Miyagawa S., Nakano T., Bartel D.P., and Kingston R.E. "Characterization of the piRNA complex from rat testes.". Science 313 5785 (2006) 363-367
22. Lee R.C., and Ambros V. "An extensive class of small RNAs in Caenorhabditis elegans.". Science 294 5543 (2001) 862-864
23. 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 5 (1993) 843-854
24. 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 6956 (2003) 415-419
25. Lee Y., Jeon K., Lee J.T., Kim S., and Kim V.N. "MicroRNA maturation: Stepwise processing and subcellular localization.". EMBO J. 21 17 (2002) 4663-4670
26. 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 1 (2005) 15-20
27. Li M.J., and Rossi J.J. "Lentiviral vector delivery of recombinant small interfering RNA expression cassettes.". Methods Enzymol 392 (2005) 218-226
28. Liang R.Q., Li W., Li Y., Tan C.Y., Li J.X., Jin Y.X., and Ruan K.C. "An oligonucleotide microarray for microRNA expression analysis based on labeling RNA with quantum dot and nanogold probe". Nucleic Acids Res. 33 (2005) e17
29. Liu C.G., Calin G.A., Meloon B., Gamliel N., Sevignani C., Ferracin M., Dumitru C.D., Shimizu M., Zupo S., Dono M., Alder H., Bullrich F., et al. "An oligonucleotide microchip for genome-wide microRNA profiling in human and mouse tissues.". Proc. Natl. Acad. Sci. USA 101 26 (2004) 9740-9744
30. Liu J., Rivas F.V., Wohlschlegel J., Yates III J.R., Parker R., and Hannon G.J. "A role for the P-body component GW182 in microRNA function.". Nat. Cell. Biol. 7 12 (2005) 1261-1266
31. Liu J., Valencia-Sanchez M.A., Hannon G.A., and Parker R. "MicroRNA-dependent localization of targeted mRNAs to mammalian P-bodies.". Nat. Cell. Biol. 7 7 (2005) 719-723
32. Nelson P.T., Baldwin D.A., Kloosterman W.P., Kauppinen S., Plasterk R.H., and Mourelatos Z. "RAKE and LNA-ISH reveal microRNA expression and localization in archival human brain.". RNA 12 2 (2006) 187-191
33. Nelson P.T., Baldwin D.A., Scearce L.M., Oberholtzer J.C., Tobias J.W., and Mourolatos Z. "Microarray-based, high-throughput gene expression profiling of microRNAs.". Nat. Methods 1 2 (2004) 155-161
34. Pillai R.S., Bhattacharyya S.N., Artus C.G., Zoller T., Cougot N., Basyuk E., Bertrand E., and Filipowicz W. "Inhibition of translational initiation by Let-7 MicroRNA in human cells.". Science 309 5740 (2005) 1573-1576
35. Rehwinkel J., Behm-Ansmant I., Gatfield D., and Izaurralde E. "A crucial role for GW182 and the DCP1:DCP2 decapping complex in miRNA-mediated gene silencing.". RNA 11 11 (2005) 1640-1647
36. Takada S., Berezikov E., Yamashita Y., Lagos-Quintana M., Kloosterman W.P., Enomoto M., Hatanaka H., Fujiwara S., Watanabe H., Soda M., Choi Y.L., Plasterk R.H., et al. "Mouse microRNA profiles determined with a new and sensitive cloning method.". Nucleic Acids Res. 34 17 (2006) e115
37. Thomson J.M., Parker J., Perou C.M., and Hammond S.M. "A custom microarray platform for analysis of microRNA gene expression.". Nat. Methods 1 1 (2004) 47-53
38. Valoczi A., Hornyik C., Varga N., Burgyan J., Kauppinen S., and Havelda Z. "Sensitive and specific detection of microRNAs by Northern blot analysis using LNA-modified oligonucleotide probes.". Nucleic Acids Res. 32 22 (2004) e175
39. 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 5 (1993) 855-862
40. Yeung M.L., Bennasser Y., Myers T.G., Jiang G., Benkirane M., and Jeang K.T. "Changes in microRNA expression profiles in HIV-1-transfected human cells.". Retrovirology 2 (2005) 81
41. 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 24 (2003) 3011-3016
42. Zuker M. "Mfold web server for nucleic acid folding and hybridization prediction.". Nucleic Acids Res. 31 13 (2003) 3406-3415