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General and miRNA-mediated mRNA degradation occurs on ribosome complexes in Drosophila cells

Sanja Antic, Michael T. Wolfinger, Anna Skucha, Stefanie Hosiner and Silke Dorner

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Mol. Cell. Biol. 01346-14

The translation and degradation of mRNAs are two key steps in gene expression that are highly regulated and targeted by many factors including miRNAs. While it is well established that translation and mRNA degradation are tightly coupled, it is still not entirely clear where in the cell mRNA degradation takes place. In this study, we have investigated the possibility of mRNA degradation on the ribosome in Drosophila cells. Using polysome profiles and ribosome affinity purification we could demonstrate the co-purification of various deadenylation and decapping factors with ribosome complexes. Also AGO1 and GW182, two key factors in the miRNA-mediated mRNA degradation pathway, were associated with ribosome complexes. Their co-purification was dependent on intact mRNAs suggesting the association of these factors with the mRNA rather than the ribosome itself. Furthermore, we isolated decapped mRNA degradation intermediates from ribosome complexes and performed HiSeq analysis. Interestingly, 93 % of decapped mRNA fragments (approx. 12,000) could be detected with the same relative abundance on ribosome complexes as in cell lysates. In summary, our findings strongly indicate the association of the majority of bulk mRNAs but also mRNAs targeted by miRNAs with the ribosome during their degradation.

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