An in vitro assay to study regulated mRNA stability.

The examination of posttranscriptional regulation of mRNA in mammalian cells is critical to discovering the role that mRNA plays in the initiation and maintenance of cellular processes. The complexity of the system defies a holistic approach and, therefore, we have devised an in vitro mRNA turnover assay that enables us to elucidate the factors involved in mRNA deadenylation and degradation. Our system, using an S100 HeLa extract and in vitro transcribed RNAs, accurately mimics the end products of mRNA turnover, which have been previously described using in vivo studies and, in addition, allows for the detailed study of factors that may play a role in regulated deadenylation and degradation. Another important aspect of our system is the ease with which it can be manipulated. We can provide any synthetic RNA molecule to the assay to test for specific sequence activity. Furthermore, the results are clear and accurately interpretable. We have demonstrated that our in vitro system accurately deadenylates and decays a capped and polyadenylated RNA molecule in a processive manner without nonspecific nuclease activity. Finally, we have demonstrated regulated instability in vitro using the AU-rich elements (AREs) from tumor necrosis factor-alpha (TNF-alpha) and granulocyte macrophage colony stimulating factor (GM-CSF) embedded within the RNA molecule. The presence of the AREs increased the deadenylation and the decay rates seen in vivo. We feel that this system can be expanded and adapted to examine a variety of mRNA regulatory events in mammalian cells.

Adenovirus VAI-RNA regulates gene expression by controlling stability of ribosome-bound RNAs.

Adenovirus VAI-RNA is a small virally encoded RNA that is required for efficient protein synthesis at late times of adenoviral infection. We show that in transient transfection assays VAI-RNA promotes not only an increased level of protein encoded by a co-transfected marker (CAT) plasmid, but also a marked accumulation of its transcript. The increases in CAT protein and RNA levels reflect an enhanced stability of the cytoplasmic RNA as shown by primer extension analyses of RNA isolated from transfected cells upon transcriptional arrest. Surprisingly, the ability of VAI to activate expression of CAT requires the translation of a substantial portion of the RNA: when translation is prevented by elimination of the initiator AUG codon or by introduction of stop codons 5' to codon 107, VAI-RNA is no longer capable of increasing CAT RNA levels; the introduction of stop codons 3' of codon-135, on the other hand, does not significantly impair VAI-RNA function. We conclude that in addition to its role as a specific activator of translation, adenovirus VA genes function to regulate the stability of ribosome-bound RNA.

Interaction between a poly(A)-specific ribonuclease and the 5' cap influences mRNA deadenylation rates in vitro.

We have used an in vitro system that reproduces in vivo aspects of mRNA turnover to elucidate mechanisms of deadenylation. DAN, the major enzyme responsible for poly(A) tail shortening in vitro, specifically interacts with the 5' cap structure of RNA substrates, and this interaction is greatly stimulated by a poly(A) tail. Several observations suggest that cap-DAN interactions are functionally important for the networking between regulated mRNA stability and translation. First, uncapped RNA substrates are inefficiently deadenylated. Second, a stem-loop structure in the 5' UTR dramatically reduces deadenylation by interfering with cap-DAN interactions. Third, the addition of cap binding protein eIF4E inhibits deadenylation in vitro. These data provide insights into the early steps of substrate recognition that target an mRNA for degradation.