Advertisement

Genome-Wide Profiling of Uncapped mRNA

  • Yuling Jiao
  • José Luis Riechmann
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 876)

Abstract

Gene transcripts are under extensive posttranscriptional regulation, including the regulation of their stability. A major route for mRNA degradation produces uncapped mRNAs, which can be generated by decapping enzymes, endonucleases, and small RNAs. Profiling uncapped mRNA molecules is important for the understanding of the transcriptome, whose composition is determined by a balance between mRNA synthesis and degradation. In this chapter, we describe a method to profile these uncapped mRNAs at the genome scale.

Key words

mRNA Uncapping RNA degradation Transcriptome 

Notes

Acknowledgments

The authors would like to thank Dr. E.M. Meyerowitz for his encouragement and advice. This work was supported by the US National Science Foundation 2010 Project Grant 0520193, by the National Natural Science Foundation of China Grant 31171159, and by the Millard and Muriel Jacobs Genetics and Genomics Laboratory at the California Institute of Technology.

References

  1. 1.
    Gutierrez RA, MacIntosh GC, Green PJ (1999) Current perspectives on mRNA stability in plants: multiple levels and mechanisms of control. Trends Plant Sci 4:429–438PubMedCrossRefGoogle Scholar
  2. 2.
    Parker R, Song H (2004) The enzymes and control of eukaryotic mRNA turnover. Nat Struct Mol Biol 11:121–127PubMedCrossRefGoogle Scholar
  3. 3.
    Mitchell P, Tollervey D (2000) mRNA stability in eukaryotes. Curr Opin Genet Dev 10:193–198PubMedCrossRefGoogle Scholar
  4. 4.
    Liu X, Gorovsky MA (1993) Mapping the 5′ and 3′ ends of tetrahymena thermophila mRNAs using RNA ligase mediated amplification of cDNA ends (RLM-RACE). Nucleic Acids Res 21:4954–4960PubMedCrossRefGoogle Scholar
  5. 5.
    Llave C, Xie Z, Kasschau KD, Carrington JC (2002) Cleavage of scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA. Science 297:2053–2056PubMedCrossRefGoogle Scholar
  6. 6.
    Addo-Quaye C, Eshoo TW, Bartel DP, Axtell MJ (2008) Endogenous siRNA and miRNA targets identified by sequencing of the Arabidopsis degradome. Curr Biol 18:758–762PubMedCrossRefGoogle Scholar
  7. 7.
    German MA, Pillay M, Jeong DH, Hetawal A, Luo S, Janardhanan P, Kannan V, Rymarquis LA, Nobuta K, German R, De Paoli E, Lu C, Schroth G, Meyers BC, Green PJ (2008) Global identification of microRNA-target RNA pairs by parallel analysis of RNA ends. Nat Biotechnol 26:941–946PubMedCrossRefGoogle Scholar
  8. 8.
    Gregory BD, O'Malley RC, Lister R, Urich MA, Tonti-Filippini J, Chen H, Millar AH, Ecker JR (2008) A link between RNA metabolism and silencing affecting Arabidopsis development. Dev Cell 14:854–866PubMedCrossRefGoogle Scholar
  9. 9.
    Jiao Y, Riechmann JL, Meyerowitz EM (2008) Transcriptome-wide analysis of uncapped mRNAs in Arabidopsis reveals regulation of mRNA degradation. Plant Cell 20:2571–2585PubMedCrossRefGoogle Scholar
  10. 10.
    Franco-Zorrilla JM, Del Toro FJ, Godoy M, Perez-Perez J, Lopez-Vidriero I, Oliveros JC, Garcia-Casado G, Llave C, Solano R (2009) Genome-wide identification of small RNA targets based on target enrichment and microarray hybridizations. Plant J 59:840–850PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2011

Authors and Affiliations

  1. 1.State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
  2. 2.Division of Biology 156-29California Institute of TechnologyPasadenaUSA
  3. 3.Center for Research in Agricultural Genomics (CRAG)BarcelonaSpain
  4. 4.Institució Catalana de Recerca i Estudis Avançats (ICREA)BarcelonaSpain

Personalised recommendations