Identifying mRNA subsets in messenger ribonucleoprotein complexes by usingcDNA arrays

Genomic array technologies provide a means for profiling global changes in gene expression under a variety of conditions. However, it has been difficu lt to assess whether transcriptional or posttranscriptional regulation is r esponsible for these changes. Additionally, fluctuations in gene expression in a single cell type within a complex tissue like a tumor may be masked b y overlapping profiles of all cell types in the population. In this paper, we describe the use of cDNA arrays to identify subsets of mRNAs contained i n endogenous messenger ribonucleoprotein complexes (mRNPs) that are cell ty pe specific. We identified mRNA subsets from P19 embryonal carcinoma stem c ells by using mRNA-binding proteins Nun, elF-4E, and PARR that are known to play a role in translation. The mRNA profiles associated with each of thes e mRNPs were unique and represented gene clusters that differed from total cellular RNA. Additionally, the composition of mRNAs detected in HuB-mRNP c omplexes changed dramatically after induction of neuronal differentiation w ith retinoic acid. We suggest that the association of structurally related mRNAs into mRNP complexes is dynamic and may help regulate posttranscriptio nal events such as mRNA turnover and translation. Recovering proteins speci fically associated with mRNP complexes to identify and profile endogenously clustered mRNAs should provide insight into structural and functional rela tionships among gene transcripts and/or their protein products. We have ter med this approach to functional genomics ribonomics and suggest that it wil l provide a useful paradigm for organizing genomic information in a biologi cally relevant manner.