Enzymatic preparation of an artificial microRNA library

Biochemical and Biophysical Research Communications

Volumn 390, Issue 3, 2009, Pages 791-796

  Xue, Liang ^a   Yuan, Qing ^b   Yang, Ying ^a   Wu, Jiarui ^a,c  

^a INSTITUTE OF BIOCHEMISTRY AND CELL BIOLOGY   (China)

^b SHANGHAI JIAO TONG UNIVERSITY SCHOOL OF MEDICINE   (China)

^c UNIVERSITY OF SCIENCE AND TECHNOLOGY OF CHINA   (China)

Author keywords

AmiRNA library; Enzymatic method; Gene silencing; MicroRNA

Indexed keywords

MICRORNA; PROTEIN P53; RNA INDUCED SILENCING COMPLEX; SMALL INTERFERING RNA; TRANSCRIPTOME; TUBULIN;

5' UNTRANSLATED REGION; ANIMAL CELL; ARTICLE; CONTROLLED STUDY; COST EFFECTIVENESS ANALYSIS; FEASIBILITY STUDY; GENE CONTROL; GENE LIBRARY; GENE SILENCING; GENE TARGETING; MOLECULAR PROBE; MOUSE; NONHUMAN; OPEN READING FRAME; PRIORITY JOURNAL; RNA INTERFERENCE; THERMOSTABILITY;

ANIMALS; BASE SEQUENCE; ENZYMES; GENE LIBRARY; GENE TARGETING; MICE; MICRORNAS; NUCLEIC ACID CONFORMATION; RNA INTERFERENCE; TUMOR SUPPRESSOR PROTEIN P53;

EID: 70450240810     PISSN: 0006291X     EISSN: 10902104     Source Type: Journal    
DOI: 10.1016/j.bbrc.2009.10.051     Document Type: Article

References (35)

1. 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 751 (1993) 843-854
2. Reinhart B.J., Slack F.J., Basson M., Pasquinelli A.E., Bet-tinger J.C., Rougvie A.E., Horvitz H.R., and Ruvkun G. The 21 nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature 403 (2000) 901-906
3. 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 (2001) 858-862
4. Lagos-Quintana M., Rauhut R., Lendeckel W., and Tuschl T. Identification of novel genes coding for small expressed RNAs. Science 294 (2001) 853-858
5. 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
6. 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
7. Bernstein E., Kim S.Y., Carmell M.A., Murchison E.P., Alcorn H., Li M.Z., Mills A.A., Elledge S.J., Anderson K.V., and Hannon G.J. Dicer is essential for mouse development. Nat. Genet. 35 (2003) 215-217
8. Chen J.F., Mandel E.M., Thomson J.M., Wu Q., Callis T.E., Hammond S.M., Conlon F.L., and Wang D.Z. The role of microRNA-1 and microRNA-133 in skeletal muscle proliferation and differentiation. Nat. Genet. 38 (2006) 228-233
9. Yong S.L., and Anindya D. MicroRNAs in cancer. Ann. Rev. Path. 4 (2009) 199-227
10. Van Rooij E., Sutherland L.B., Liu N., Williams A.H., McAnally J., Gerard R.D., Richardson J.A., and Olson E.N. A signature pattern of stress-responsive microRNAs that can evoke cardiac hypertrophy and heart failure. Proc. Natl. Acad. Sci. USA 103 (2006) 18255-18260
11. Cogswell J.P., Ward J., Taylor I.A., Waters M., Shi Y., Cannon B., Kelnar K., Kemppainen J., Brown D., Chen C., et al. Identification of miRNA changes in Alzheimer's disease brain and CSF yields putative biomarkers and insights into disease pathways. J. Alzheimers Dis. 14 (2008) 27-41
12. Valencia-Sanchez M.A., Liu J., Hannon G.J., and Parker R. Control of translation and mRNA degradation by miRNAs and siRNAs. Genes Dev. 20 (2006) 515-524
13. Kim D.H., Saetrom P., Snove O., and Rossi J.J. MicroRNA-directed transcriptional gene silencing in mammalian cells. Proc. Natl. Acad. Sci. USA 105 (2008) 16230-16235
14. Vasudevan S., Tong Y., and Steitz J.A. Switching from repression to activation: microRNAs can up-regulate translation. Science 318 (2007) 1931-1934
15. Vasudevan S., and Steitz J.A. AU-rich-element-mediated upregulation of translation by FXR1 and Argonaute 2. Cell 128 (2007) 1105-1118
16. Orom U.A., Nielsen F.C., and Lund A.H. MicroRNA-10a binds the 5′ UTR of ribosomal protein mRNAs and enhances their translation. Mol. Cell. 30 (2008) 460-471
17. Lee I., Ajay S.S., Yook J.I., Kim H.S., Hong S.H., Kim N.H., Dhanasekaran S.M., Chinnaiyan A.M., and Athey B.D. New class of microRNA targets containing simultaneous 5′-UTR and 3′-UTR interaction sites. Genome Res. 19 (2009) 1175-1183
18. Tay Y., Zhang J., Thomson A.M., Lim B., and Rigoutsos I. MicroRNAs to Nanog, Oct4 and Sox2 coding regions modulate embryonic stem cell differentiation. Nature 455 (2008) 1124-1128
19. Forman J.J., Legesse-Miller A., and Coller H.A. A search for conserved sequences in coding regions reveals that the let-7 microRNA targets Dicer within its coding sequence. Proc. Natl. Acad. Sci. USA 105 (2008) 14879-14884
20. Zeng Y., Wagner E.J., and Cullen B.R. Both natural and designed micro RNAs can inhibit the expression of cognate mRNAs when expressed in human cells. Mol. Cell. 6 (2002) 1327-1333
21. Chung K.H., Hart C.C., Al-Bassam S., Avery A., Taylor J., Patel P.D., Vojtek A.B., and Turner D.L. Polycistronic RNA polymerase II expression vectors for RNA interference based on BIC/miR-155. Nucleic Acids Res. 34 (2006) e53
22. 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
23. Shirane D., Sugao K., Namiki S., Tanabe M., Iino M., and Hirose K. Enzymatic production of RNAi libraries from cDNAs. Nat. Genet. 36 (2004) 190-196
24. Sen G., Wehrman T.S., Myers J.W., and Blau H.M. Restriction enzyme-generated siRNA (REGS) vectors and libraries. Nat. Genet. 36 (2004) 183-189
25. Luo B., Heard A.D., and Lodish H.F. Small interfering RNA production by enzymatic engineering of DNA (SPEED). Proc. Natl. Acad. Sci. USA 101 (2004) 5494-5499
26. Buchholz F., Kittler R., Slabicki M., and Theis M. Enzymatically prepared RNAi libraries. Nat. Met. 3 (2006) 696-700
27. Khvorova A., Reynolds A., and Jayasena S.D. Functional siRNAs and miRNAs exhibit strand bias. Cell 115 (2003) 209-216
28. Schwarz D.S., Hutvágner 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
29. Nilsson M., Malmgren H., Samiotaki M., Kwiatkowski M., Chowdhary B.P., and Landegren U. Padlock probes: circularizing oligonucleotides for localized DNA detection. Science 265 (1994) 2085-2088
30. Banér J., Nilsson M., Mendel-Hartvig M., and Landegren U. Signal amplification of padlock probes by rolling circle replication. Nucleic Acids Res. 26 (1998) 5073-5078
31. Shi R., and Chiang V.L. Facile means for quantifying microRNA expression by real-time PCR. Biotechniques 39 (2005) 519-525
32. Sambrook J., Fritsch E.F., and Maniatis T. Molecular Cloning: A Laboratory Manual. second ed. (1989), CSHL Press pp. 267
33. 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
34. Zeng Y., and Cullen B.R. Sequence requirements for microRNA processing and function in human cells. RNA 9 (2003) 112-123
35. Zeng Y., Yi R., and Cullen B.R. Recognition and cleavage of primary microRNA precursors by the nuclear processing enzyme Drosha. EMBO J. 24 (2005) 138-148