Translating Ribosome Affinity Purification (TRAP) for Cell-Specific Translation Profiling in Developing Flowers

  • Ying Wang
  • Yuling Jiao
Part of the Methods in Molecular Biology book series (MIMB, volume 1110)


The development of a multicellular organism is accompanied by cell differentiation. In fact, many biological processes have cell specificity, such that distinct cell types respond differently to endogenous or environmental cues. To obtain cell-specific gene expression profiles, translating ribosome affinity purification (TRAP) has been developed to label polysomes containing translating mRNAs in genetically defined cell types. Here, we describe the immunopurification of epitope-labeled polysomes and associated RNAs from target cell types. TRAP has the additional advantage of obtaining only translating mRNAs, which are a better proxy to the proteome than a standard mRNA preparation.


mRNA Cell type Posttranscriptional regulation Transcriptome 



We thank J. Bailey-Serres for sharing protocols. This work was supported by the National Natural Science Foundation of China Grants 31222033 and 31171159, by the National Basic Research Program of China (973 Program) Grant 2012CB910902, and by the Hundred Talents Program of CAS.


  1. 1.
    Wang Y, Jiao Y (2011) Advances in plant cell type-specific genome-wide studies of gene expression. Front Biol 6:384–389CrossRefGoogle Scholar
  2. 2.
    Rogers ED, Jackson T, Moussaieff A, Aharoni A, Benfey PN (2012) Cell type-specific transcriptional profiling: implications for metabolite profiling. Plant J 70:5–17PubMedCentralPubMedCrossRefGoogle Scholar
  3. 3.
    Kerk NM, Ceserani T, Tausta SL, Sussex IM, Nelson TM (2003) Laser capture microdissection of cells from plant tissues. Plant Physiol 132:27–35PubMedCentralPubMedCrossRefGoogle Scholar
  4. 4.
    Birnbaum K, Shasha DE, Wang JY, Jung JW, Lambert GM, Galbraith DW, Benfey PN (2003) A gene expression map of the Arabidopsis root. Science 302:1956–1960PubMedCrossRefGoogle Scholar
  5. 5.
    Zhang C, Barthelson RA, Lambert GM, Galbraith DW (2008) Global characterization of cell-specific gene expression through fluorescence-activated sorting of nuclei. Plant Physiol 147:30–40PubMedCentralPubMedCrossRefGoogle Scholar
  6. 6.
    Deal RB, Henikoff S (2010) A simple method for gene expression and chromatin profiling of individual cell types within a tissue. Dev Cell 18:1030–1040PubMedCentralPubMedCrossRefGoogle Scholar
  7. 7.
    Mustroph A, Zanetti ME, Jang CJ, Holtan HE, Repetti PP, Galbraith DW, Girke T, Bailey-Serres J (2009) Profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis. Proc Natl Acad Sci USA 106:18843–18848PubMedCrossRefGoogle Scholar
  8. 8.
    Jiao Y, Meyerowitz EM (2010) Cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control. Mol Syst Biol 6:419PubMedCentralPubMedCrossRefGoogle Scholar
  9. 9.
    Juntawong P, Bailey-Serres J (2012) Dynamic light regulation of translation status in Arabidopsis thaliana. Front Plant Sci 3:66PubMedCentralPubMedCrossRefGoogle Scholar
  10. 10.
    Ribeiro DM, Araujo WL, Fernie AR, Schippers JH, Mueller-Roeber B (2012) Translatome and metabolome effects triggered by gibberellins during rosette growth in Arabidopsis. J Exp Bot 63:2769–2786PubMedCrossRefGoogle Scholar
  11. 11.
    Sanz E, Yang L, Su T, Morris DR, McKnight GS, Amieux PS (2009) Cell-type-specific isolation of ribosome-associated mRNA from complex tissues. Proc Natl Acad Sci USA 106:13939–13944PubMedCrossRefGoogle Scholar
  12. 12.
    Heiman M, Schaefer A, Gong S, Peterson JD, Day M, Ramsey KE, Suarez-Farinas M, Schwarz C, Stephan DA, Surmeier DJ, Greengard P, Heintz N (2008) A translational profiling approach for the molecular characterization of CNS cell types. Cell 135: 738–748PubMedCentralPubMedCrossRefGoogle Scholar
  13. 13.
    Thomas A, Lee PJ, Dalton JE, Nomie KJ, Stoica L, Costa-Mattioli M, Chang P, Nuzhdin S, Arbeitman MN, Dierick HA (2012) A versatile method for cell-specific profiling of translated mRNAs in Drosophila. PLoS ONE 7:e40276PubMedCentralPubMedCrossRefGoogle Scholar
  14. 14.
    Krizek BA, Fletcher JC (2005) Molecular mechanisms of flower development: an armchair guide. Nat Rev Genet 6:688–698PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, New York 2014

Authors and Affiliations

  1. 1.State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina

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