Skip to main content

In Vivo Cross-Linking Followed by PolyA Enrichment to Identify Yeast mRNA Binding Proteins

  • Protocol
  • First Online:
RNA Remodeling Proteins

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1259))

Abstract

mRNA binding proteins regulate gene expression by controlling the processing, localization, decay, and translation of messenger RNAs (mRNAs). To fully understand this process, it is necessary to identify the complete set of mRNA binding proteins. This work describes a method for the systematic identification of yeast mRNA binding proteins. This method applies in vivo UV cross-linking, affinity pull-down of polyA(+) mRNAs, and analysis by mass spectrometry to identify proteins that directly bind to mRNAs.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Subscribe and save

Springer+ Basic
$34.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or eBook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 139.00
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Similar content being viewed by others

References

  1. Dreyfuss G, Choi YD, Adam SA (1984) Characterization of heterogeneous nuclear RNA–protein complexes in vivo with monoclonal antibodies. Mol Cell Biol 4:1104–1114

    CAS  PubMed Central  PubMed  Google Scholar 

  2. Batisse J, Batisse C, Budd A et al (2009) Purification of nuclear poly(A)-binding protein Nab2 reveals association with the yeast transcriptome and a messenger ribonucleoprotein core structure. J Biol Chem 284:34911–34917

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  3. Klass DM, Scheibe M, Butter F et al (2013) Quantitative proteomic analysis reveals concurrent RNA–protein interactions and identifies new RNA-binding proteins in Saccharomyces cerevisiae. Genome Res 23:1028–1038

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  4. Tsvetanova NG, Klass DM, Salzman J et al (2010) Proteome-wide search reveals unexpected RNA-binding proteins in Saccharomyces cerevisiae. PloS One 5:e12671

    Article  PubMed Central  PubMed  Google Scholar 

  5. Scherrer T, Mittal N, Janga SC et al (2010) A screen for RNA-binding proteins in yeast indicates dual functions for many enzymes. PloS One 5:e15499

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  6. Trcek T, Singer RH (2010) The cytoplasmic fate of an mRNP is determined cotranscriptionally: exception or rule? Genes Dev 24:1827–1831

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  7. Riley KJ, Steitz JA (2013) The “Observer Effect” in genome-wide surveys of protein-RNA interactions. Mol Cell 49:601–604

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  8. Castello A, Fischer B, Eichelbaum K et al (2012) Insights into RNA biology from an atlas of mammalian mRNA-binding proteins. Cell 149:1393–1406

    Article  CAS  PubMed  Google Scholar 

  9. Baltz AG, Munschauer M, Schwanhäusser B et al (2012) The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts. Mol Cell 46:674–690

    Article  CAS  PubMed  Google Scholar 

  10. Mitchell SF, Jain S, She M et al (2013) Global analysis of yeast mRNPs. Nat Struct Mol Biol 20:127–133

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  11. Kwon SC, Yi H, Eichelbaum K et al (2013) The RNA-binding protein repertoire of embryonic stem cells. Nat Struct Mol Biol 20:1122–1130

    Article  CAS  PubMed  Google Scholar 

  12. Teixeira D (2005) Processing bodies require RNA for assembly and contain nontranslating mRNAs. RNA 11:371–382

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  13. Holcik M, Sonenberg N (2005) Translational control in stress and apoptosis. Nat Rev Mol Cell Biol 6:318–327

    Article  CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Sarah F. Mitchell .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2015 Springer Science+Business Media New York

About this protocol

Cite this protocol

Mitchell, S.F., Parker, R. (2015). In Vivo Cross-Linking Followed by PolyA Enrichment to Identify Yeast mRNA Binding Proteins. In: Boudvillain, M. (eds) RNA Remodeling Proteins. Methods in Molecular Biology, vol 1259. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-2214-7_3

Download citation

  • DOI: https://doi.org/10.1007/978-1-4939-2214-7_3

  • Published:

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-2213-0

  • Online ISBN: 978-1-4939-2214-7

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics