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High-Throughput Functional MicroRNA Profiling Using Recombinant AAV-Based MicroRNA Sensor Arrays

  • Wenhong Tian
  • Xiaoyan Dong
  • Xiaobing Wu
  • Zhijian Wu
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1039)

Abstract

There is a lack of methods for high-throughput functional microRNA (miRNA) profiling. In this chapter, we describe a recombinant adeno-associated virus-based miRNA sensor array (miRNA Asensor array), which is able to profile functional miRNAs in cultured cells. The preparation of an miRNA Asensor array and its usage are discussed.

Key words

miRNA miRNA activity high-throughput miRNA Asensor array 

Notes

Acknowledgment

This work was supported by a grant from the National High Technology Research and Development Program of China (No. 2012AA020810).

References

  1. 1.
    Miska EA, Alvarez-Saavedra E, Townsend M, Yoshii A, Sestan N, Rakic P et al (2004) Microarray analysis of microRNA expression in the developing mammalian brain. Genome Biol 5:R68PubMedCrossRefGoogle Scholar
  2. 2.
    Katada T, Ishiquro H, Kuwabara Y, Kimura M, Mitui A, Mori Y et al (2009) microRNA expression profile in undifferentiated gastric cancer. Int J Oncol 34:537–542PubMedGoogle Scholar
  3. 3.
    Creighton CJ, Reid JG, Gunaratne PH (2009) Expression profiling of microRNAs by deep sequencing. Brief Bioinform 10:490–497PubMedCrossRefGoogle Scholar
  4. 4.
    Chen B, Zhang B, Luo H, Yuan J, Skogerbø G, Chen R (2012) Distinct microRNA subcellular size and expression patterns in human cancer cells. Int J Cell Biol 2012, article ID 672462Google Scholar
  5. 5.
    Garcia DM, Baek D, Shin C, Bell GW, Grimson A, Bartel DP (2011) Weak seed-pairing stability and high target-site abundance decrease the proficiency of Lsy-6 and other microRNAs. Nat Struct Mol Biol 18:1139–1146PubMedCrossRefGoogle Scholar
  6. 6.
    Fabian MR, Sonenberg N, Filipowicz W (2010) Regulation of mRNA translation and stability by microRNAs. Annu Rev Biochem 79:351–379PubMedCrossRefGoogle Scholar
  7. 7.
    John B, Enright AJ, Aravin A, Tuschl T, Sander C, Marks DS (2004) Human microRNA targets. PLoS Biol 2:e363PubMedCrossRefGoogle Scholar
  8. 8.
    Kan Z, Rouchka EC, Gish WR, States DJ (2001) Gene structure prediction and alternative splicing analysis using genomically aligned ESTs. Genome Res 11:889–900PubMedCrossRefGoogle Scholar
  9. 9.
    Mayr C, Bartel DP (2009) Widespread shortening of 3′UTRs by alternative cleavage and polyadenylation activates oncogenes in cancer cells. Cell 138:673–684PubMedCrossRefGoogle Scholar
  10. 10.
    Mansfield JH, Harfe BD, Nissen R, Obenauer J, Srineel J, Chaudhuri A et al (2004) MicroRNA responsive ‘sensor’ transgenes uncover Hox-like and other developmentally regulated patterns of vertebrate microRNA expression. Nat Genet 36:1079–1083PubMedCrossRefGoogle Scholar
  11. 11.
    Skalsky RL, Samols MA, Plaisance KB, Boss IW, Riva A, Lopez MC et al (2007) Kaposi’s sarcoma-associated herpesvirus encodes an ortholog of miR-155. J Virol 81:12836–12845PubMedCrossRefGoogle Scholar
  12. 12.
    Cunningham C, Davison A (1993) A cosmid-based system for constructing mutants of herpes simplex virus type 1. Virology 197:116–124PubMedCrossRefGoogle Scholar
  13. 13.
    Samulski RJ, Chang LS, Shenk T (1989) Helper-free stocks of recombinant adeno-associated viruses: normal integration does not require viral gene expression. J Virol 63:3822–3828PubMedGoogle Scholar
  14. 14.
    Dong X, Tian W, Wang G, Dong Z, Shen W, Zheng G et al (2010) Establishment of an AAV reverse infection-based array. PLoS One 5:e13479PubMedCrossRefGoogle Scholar
  15. 15.
    Tian W, Dong X, Liu X, Wang G, Dong Z, Shen W et al (2012) High-throughput functional microRNAs profiling by recombinant AAV-based microRNA sensor arrays. PLoS One 7:e29551PubMedCrossRefGoogle Scholar
  16. 16.
    Wu ZJ, Wu XB, Hou YD (1999) Construction of a recombinant herpes simplex virus which can provide packaging function for recombinant adeno-associated virus. Chin Sci Bull 44:715–719CrossRefGoogle Scholar
  17. 17.
    Blaho JA, Morton ER, Yedowitz JC (2005) Herpes simplex virus: propagation, quantification, and storage. Curr Protoc Microbiol,  Chapter 14, Unit 14E.1
  18. 18.
    Wu X, Dong X, Wu Z, Cao H, Niu D, Qu J et al (2001) A novel method for purification of recombinant adeno-associated virus vectors on a large scale. Chin Sci Bull 46:485–489CrossRefGoogle Scholar
  19. 19.
    Haberman RA, Kroner-Lux G, McCown TJ, Samulski RJ (1999) Production of recombinant adeno-associated viral vectors and use in in vitro and in vivo administration. Curr Protoc Neurosci (Suppl 9), Unit 4.17Google Scholar

Copyright information

© Springer Science+Business Media, New York 2013

Authors and Affiliations

  • Wenhong Tian
    • 1
  • Xiaoyan Dong
    • 2
  • Xiaobing Wu
    • 2
  • Zhijian Wu
    • 3
  1. 1.College of Life ScienceJilin UniversityChangchunChina
  2. 2.Beijing FivePlus Molecular Medicine InstituteBeijingChina
  3. 3.Unit on Ocular Gene TherapyNational Eye Institute, NIHBethesdaUSA

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