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Genome-wide identification of functionally distinct subsets of cellular mRNAs associated with two nucleocytoplasmic-shuttling mammalian splicing factors

Margarida Gama-Carvalho1*, Nuno L Barbosa-Morais12, Alexander S Brodsky34, Pamela A Silver3 and Maria Carmo-Fonseca1

Author Affiliations

1 Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal

2 Hutchison/MRC Research Centre, Department of Oncology, University of Cambridge, Hills Road, Cambridge CB2 0XZ, UK

3 Department of Systems Biology, Harvard Medical School, 200 Longwood Ave, Alpert 536, Boston, MA 02115, USA

4 Department of Molecular Biology, Cell Biology and Biochemistry and Center for Genomics & Proteomics, Brown University, 69 Brown Street, Providence, Rhode Island 02912, USA

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Genome Biology 2006, 7:R113  doi:10.1186/gb-2006-7-11-r113

Published: 30 November 2006

Abstract

Background

Pre-mRNA splicing is an essential step in gene expression that occurs co-transcriptionally in the cell nucleus, involving a large number of RNA binding protein splicing factors, in addition to core spliceosome components. Several of these proteins are required for the recognition of intronic sequence elements, transiently associating with the primary transcript during splicing. Some protein splicing factors, such as the U2 small nuclear RNP auxiliary factor (U2AF), are known to be exported to the cytoplasm, despite being implicated solely in nuclear functions. This observation raises the question of whether U2AF associates with mature mRNA-ribonucleoprotein particles in transit to the cytoplasm, participating in additional cellular functions.

Results

Here we report the identification of RNAs immunoprecipitated by a monoclonal antibody specific for the U2AF 65 kDa subunit (U2AF65) and demonstrate its association with spliced mRNAs. For comparison, we analyzed mRNAs associated with the polypyrimidine tract binding protein (PTB), a splicing factor that also binds to intronic pyrimidine-rich sequences but additionally participates in mRNA localization, stability, and translation. Our results show that 10% of cellular mRNAs expressed in HeLa cells associate differentially with U2AF65 and PTB. Among U2AF65-associated mRNAs there is a predominance of transcription factors and cell cycle regulators, whereas PTB-associated transcripts are enriched in mRNA species that encode proteins implicated in intracellular transport, vesicle trafficking, and apoptosis.

Conclusion

Our results show that U2AF65 associates with specific subsets of spliced mRNAs, strongly suggesting that it is involved in novel cellular functions in addition to splicing.