Genome-wide analysis of RNA-protein interactions illustrates specificity of the mRNA export machinery

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Method for the Isolation and Identification of mRNAs, microRNAs and Protein Components of Ribonucleoprotein Complexes from Cell Extracts using RIP-Chip
13:34

Method for the Isolation and Identification of mRNAs, microRNAs and Protein Components of Ribonucleoprotein Complexes from Cell Extracts using RIP-Chip

Published on: September 29, 2012

Haley Hieronymus1, Pamela A Silver

  • 1Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School and the Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA.

Nature Genetics
|January 14, 2003
PubMed

Insights

Researchers identified specific messenger RNA (mRNA) export factors, Yra1 and Mex67, binding nearly 20% of yeast genes. This reveals a coordinated export process for co-regulated functional mRNA transcripts.

Area of Science:

  • Molecular Biology
  • Genetics
  • Cell Biology

Background:

  • Nuclear export of messenger RNA (mRNA) relies on RNA-binding proteins forming a messenger ribonucleoprotein (mRNP) network.
  • The complete set of mRNA targets for specific export factors remains largely uncharacterized.

Purpose of the Study:

  • To identify, on a genome-wide scale, the specific mRNAs bound by two conserved yeast mRNA export factors, Yra1 and Mex67.
  • To determine the binding levels and functional relevance of these mRNA-export factor interactions.

Main Methods:

  • Genome-wide identification of mRNA targets for Yra1 and Mex67 in yeast.
  • Analysis of the relationship between mRNA binding levels, transcriptional frequency, and functional classes of proteins encoded by the bound mRNAs.
  • Investigation of potential interactions between mRNA export factors and transcription factors.

Main Results:

  • Yra1 and Mex67 bind approximately 1,000 and 1,150 different mRNAs, respectively, representing about 20% of the yeast genome.
  • Yra1 binding correlates with transcriptional frequency, while Mex67 binding does not.
  • Yra1-bound transcripts are enriched for mRNAs regulated by specific transcription factors, including Abf1, and encode distinct functional protein classes.

Conclusions:

  • mRNA export factors exhibit previously unrecognized specificity in binding distinct mRNA populations.
  • These factors coordinate the export of transcriptionally co-regulated, functionally related mRNA classes.
  • Potential interactions with the transcriptional machinery may mediate this coordination.

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