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Genome-wide identification of functionally distinct subsets of cellular mRNAs associated with two nucleocytoplasmic-shuttling mammalian splicing factors.
Genome Biol. 2006; 7(11):R113.GB

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.

Authors+Show Affiliations

Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av, Prof, Egas Moniz, 1649-028 Lisboa, Portugal. m.gamacarvalho@fm.ul.ptNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info available

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

17137510

Citation

Gama-Carvalho, Margarida, et al. "Genome-wide Identification of Functionally Distinct Subsets of Cellular mRNAs Associated With Two Nucleocytoplasmic-shuttling Mammalian Splicing Factors." Genome Biology, vol. 7, no. 11, 2006, pp. R113.
Gama-Carvalho M, Barbosa-Morais NL, Brodsky AS, et al. Genome-wide identification of functionally distinct subsets of cellular mRNAs associated with two nucleocytoplasmic-shuttling mammalian splicing factors. Genome Biol. 2006;7(11):R113.
Gama-Carvalho, M., Barbosa-Morais, N. L., Brodsky, A. S., Silver, P. A., & Carmo-Fonseca, M. (2006). Genome-wide identification of functionally distinct subsets of cellular mRNAs associated with two nucleocytoplasmic-shuttling mammalian splicing factors. Genome Biology, 7(11), R113.
Gama-Carvalho M, et al. Genome-wide Identification of Functionally Distinct Subsets of Cellular mRNAs Associated With Two Nucleocytoplasmic-shuttling Mammalian Splicing Factors. Genome Biol. 2006;7(11):R113. PubMed PMID: 17137510.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Genome-wide identification of functionally distinct subsets of cellular mRNAs associated with two nucleocytoplasmic-shuttling mammalian splicing factors. AU - Gama-Carvalho,Margarida, AU - Barbosa-Morais,Nuno L, AU - Brodsky,Alexander S, AU - Silver,Pamela A, AU - Carmo-Fonseca,Maria, PY - 2006/07/31/received PY - 2006/10/18/revised PY - 2006/11/30/accepted PY - 2006/12/2/pubmed PY - 2007/3/3/medline PY - 2006/12/2/entrez SP - R113 EP - R113 JF - Genome biology JO - Genome Biol VL - 7 IS - 11 N2 - 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. SN - 1474-760X UR - https://www.unboundmedicine.com/medline/citation/17137510/Genome_wide_identification_of_functionally_distinct_subsets_of_cellular_mRNAs_associated_with_two_nucleocytoplasmic_shuttling_mammalian_splicing_factors_ L2 - https://genomebiology.biomedcentral.com/articles/10.1186/gb-2006-7-11-r113 DB - PRIME DP - Unbound Medicine ER -