Gene Expression Analysis of Messenger RNP Complexes

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