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Proteome-wide search reveals unexpected RNA-binding proteins in Saccharomyces cerevisiae.

Publication ,  Journal Article
Tsvetanova, NG; Klass, DM; Salzman, J; Brown, PO
Published in: PLoS One
September 10, 2010

The vast landscape of RNA-protein interactions at the heart of post-transcriptional regulation remains largely unexplored. Indeed it is likely that, even in yeast, a substantial fraction of the regulatory RNA-binding proteins (RBPs) remain to be discovered. Systematic experimental methods can play a key role in discovering these RBPs--most of the known yeast RBPs lack RNA-binding domains that might enable this activity to be predicted. We describe here a proteome-wide approach to identify RNA-protein interactions based on in vitro binding of RNA samples to yeast protein microarrays that represent over 80% of the yeast proteome. We used this procedure to screen for novel RBPs and RNA-protein interactions. A complementary mass spectrometry technique also identified proteins that associate with yeast mRNAs. Both the protein microarray and mass spectrometry methods successfully identify previously annotated RBPs, suggesting that other proteins identified in these assays might be novel RBPs. Of 35 putative novel RBPs identified by either or both of these methods, 12, including 75% of the eight most highly-ranked candidates, reproducibly associated with specific cellular RNAs. Surprisingly, most of the 12 newly discovered RBPs were enzymes. Functional characteristics of the RNA targets of some of the novel RBPs suggest coordinated post-transcriptional regulation of subunits of protein complexes and a possible link between mRNA trafficking and vesicle transport. Our results suggest that many more RBPs still remain to be identified and provide a set of candidates for further investigation.

Duke Scholars

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Published In

PLoS One

DOI

EISSN

1932-6203

Publication Date

September 10, 2010

Volume

5

Issue

9

Location

United States

Related Subject Headings

  • Saccharomyces cerevisiae Proteins
  • Saccharomyces cerevisiae
  • RNA-Binding Proteins
  • RNA, Fungal
  • Proteome
  • Protein Array Analysis
  • General Science & Technology
 

Citation

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Tsvetanova, N. G., Klass, D. M., Salzman, J., & Brown, P. O. (2010). Proteome-wide search reveals unexpected RNA-binding proteins in Saccharomyces cerevisiae. PLoS One, 5(9). https://doi.org/10.1371/journal.pone.0012671
Tsvetanova, Nikoleta G., Daniel M. Klass, Julia Salzman, and Patrick O. Brown. “Proteome-wide search reveals unexpected RNA-binding proteins in Saccharomyces cerevisiae.PLoS One 5, no. 9 (September 10, 2010). https://doi.org/10.1371/journal.pone.0012671.
Tsvetanova NG, Klass DM, Salzman J, Brown PO. Proteome-wide search reveals unexpected RNA-binding proteins in Saccharomyces cerevisiae. PLoS One. 2010 Sep 10;5(9).
Tsvetanova, Nikoleta G., et al. “Proteome-wide search reveals unexpected RNA-binding proteins in Saccharomyces cerevisiae.PLoS One, vol. 5, no. 9, Sept. 2010. Pubmed, doi:10.1371/journal.pone.0012671.
Tsvetanova NG, Klass DM, Salzman J, Brown PO. Proteome-wide search reveals unexpected RNA-binding proteins in Saccharomyces cerevisiae. PLoS One. 2010 Sep 10;5(9).

Published In

PLoS One

DOI

EISSN

1932-6203

Publication Date

September 10, 2010

Volume

5

Issue

9

Location

United States

Related Subject Headings

  • Saccharomyces cerevisiae Proteins
  • Saccharomyces cerevisiae
  • RNA-Binding Proteins
  • RNA, Fungal
  • Proteome
  • Protein Array Analysis
  • General Science & Technology