Protocol

mRNA Processing and Metabolism

Volume 257 of the series Methods in Molecular Biology™ pp 125-134

Gene Expression Analysis of Messenger RNP Complexes

  • Luiz O. F. PenalvaAffiliated withThe Center for RNA Biology, Department of Molecular Genetics and Microbiology, Duke University Medical Center
  • , Scott A. TenenbaumAffiliated withThe Center for RNA Biology, Department of Molecular Genetics and Microbiology, Duke University Medical Center
  • , Jack D. KeeneAffiliated withDepartment of Molecular Genetics and Microbiology, The Center for RNA Biology, Duke University Medical Center

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Abstract

RNA-binding proteins can organize messenger RNAs (mRNAs) into structurally and functionally related subsets, thus facilitating the coordinate production of gene classes necessary for complex cellular processes. Historically, in vitro methods primarily have been used to identify individual targets of mRNA-binding proteins. However, more direct methods are required for the identification of endogenously associated RNAs and their cognate proteins. To better understand posttranscriptional mRNA organization within the cell, we developed a systems biology approach to identify multiple-endogenous mRNA transcripts associated with RNA-binding proteins. This approach, termed ribonomics, takes advantage of high-throughput genomic array technologies that have greatly advanced the study of global gene expression changes. This chapter describes techniques for purifying mRNA–protein complexes (mRNPs) and identifying the associated mRNAs

Key Words

Genomics microarrays poly A binding protein (PABP) RNA-binding proteins ribonomics mRNA tagging RNP ribonucleoprotein mRNA–protein complexes posttranscriptional gene regulation