Nucleic Acids Research Advance Access published online on October 23, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn754
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Identification and characterization of extensive intra-molecular associations between 3'-UTRs and their ORFs
Department of Biology, Technion–Israel Institute of Technology, Haifa 32000, Israel
*To whom correspondence should be addressed. Tel: +972 4 829 3683; Fax: +972 4 822 5153; Email: arava{at}tx.technion.ac.il
Received July 26, 2008. Revised October 6, 2008. Accepted October 6, 2008.
During eukaryotic translation, mRNAs may form intra-molecular interactions between distant domains. The 5'-cap and the polyA tail were shown to interact through their associated proteins, and this can induce physical compaction of the mRNA in vitro. However, the stability of this intra-molecular association in translating mRNAs and whether additional contacts exist in vivo are largely unknown. To explore this, we applied a novel approach in which several endogenous polysomal mRNAs from Saccharomyces cerevisiae were cleaved near their stop codon and the resulting 3'-UTR fragments were tested either for co-sedimentation or co-immunoprecipitation (co-IP) with their ORFs. In all cases a significant fraction of the 3'-UTR fragments sedimented similarly to their ORF-containing fragments, yet the extent of co-sedimentation differed between mRNAs. Similar observations were obtained by a co-IP assay. Interestingly, various treatments that are expected to interfere with the cap to polyA interactions had no effect on the co-sedimentation pattern. Moreover, the 3'-UTR appeared to co-sediment with different regions from within the ORF. Taken together, these results indicate extensive physical associations between 3'-UTRs and their ORFs that vary between genes. This implies that polyribosomal mRNAs are in a compact configuration in vivo.