Hotel Estoril Eden, Monte Estoril,
5-8 October 2005



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issecting RNA-Protein Interactions at the Genome Wide Level

Margarida Gama-Carvalho1, N. Barbosa-Morais1, A. Brodsky2, P. Silver2 and M. Carmo-Fonseca1
Institute of Molecular Medicine, Faculty of Medicine, University of Lisbon, Portugal
Department of Systems Biology, Harvard Medical School and Department of Cancer Biology, Dana Farber Cancer Institute, USA

Work from the past few years has begun to reveal mRNA binding proteins as multifunctional entities that act on the mRNA biogenesis pathway from transcription initiation through translation and decay. Several pre-mRNA splicing factors have been identified as nucleocytoplasmic binding proteins and in some cases unexpectedly shown to influence downstream events in the gene expression pathway. Association of mRNA binding proteins with mRNA through untranslated sequence elements for regulation (USER codes) has been proposed to constitute a mechanism that allows for the coordination of gene expression at the post-transcriptional level, defining so called post-transcriptional operons (Keen and Tenenbaum (2002). Mol Cell 9: 1161-1167). This coordination  would be expected to be particularly useful in pathways that require rapid activation or shutdown of the expression of specific sets of genes.

Through a genome wide approach coupling RNA immunoprecipitation and microarray analysis, we have identified a subset of mRNA molecules that interact with the pre-mRNA splicing factors U2AF65 and PTB, also known to be nucleocytoplasmic mRNA binding proteins. Classification of the mRNAs associated with each protein into GO groups suggests that each protein associates with functionally coherent mRNA populations, supporting a coordinating role in gene expression. To understand whether these RNA populations contain distinctive sequence elements we have performed sequence motif search for consensus U2AF and PTB binding sites in the whole transcript, coding sequence and UTRs and compared to a non-associated mRNA population. The results support the model of a differential interaction between functionally related mRNA populations and specific regulatory RNA binding proteins through the presence of USER codes.