Since detection of an RNA molecule is the major criterion to define transcriptional activity, the fraction of the genome that is expressed is generally considered to parallel the complexity of the transcriptome. We show here that several supposedly silent intergenic regions in the genome of S. cerevisiae are actually transcribed by RNA polymerase II, suggesting that the expressed fraction of the genome is higher than anticipated. Surprisingly, however, RNAs originating from these regions are rapidly degraded by the combined action of the exosome and a new poly(A) polymerase activity that is defined by the Trf4 protein and one of two RNA binding proteins, Air1p or Air2p. We show that such a polyadenylation-assisted degradation mechanism is also responsible for the degradation of several Pol I and Pol III transcripts. Our data strongly support the existence of a posttranscriptional quality control mechanism limiting inappropriate expression of genetic information.

Several aspects of eukaryotic mRNA processing are linked to transcription. In Saccharomyces cerevisiae, overexpression of the mRNA export factor Sub2p suppresses the growth defect of hpr1 null cells, yet the protein Hpr1p and the associated THO protein complex are implicated in transcriptional elongation. Indeed, we find that a pool of heat shock HSP104 transcripts are 3-end truncated in THO complex mutant as well as sub2 mutant backgrounds. Surprisingly, however, this defect can be suppressed by deletion of the 3-5 exonuclease Rrp6p. This indicates that incomplete RNAs result from nuclear degradation rather than from a failure to efficiently elongate transcription. RNAs that are not degraded are retained at the transcription site in a Rrp6p-dependent manner. Interestingly, the addition of a RRP6 deletion to sub2 or to THO complex mutants shows a strong synthetic growth phenotype, suggesting that the failure to retain and/or degrade defective mRNAs is deleterious. mRNAs produced in the 3-end processing mutants rna14-3 and rna15-2, as well as an RNA harboring a 3 end generated by a self-cleaving hammerhead ribozyme, are also retained in Rrp6p-dependent transcription site foci. Taken together, our results show that several classes of defective RNPs are subject to a quality control step that impedes release from transcription site foci and suggest that suboptimal messenger ribonucleoprotein assembly leads to RNA degradation by Rrp6p.The physical separation of mRNA biogenesis and bulk protein synthesis in eukaryotic cells necessitates molecular transport between the nuclear and cytoplasmic compartments. To form a mature translatable mRNA, several processing steps must be completed accurately in the nucleus. In successful formation of mature translatable mRNAs, the 5Ј end of the transcript acquires a methylated guanosine cap structure, introns are excised, and the 3Ј end is cleaved and polyadenylated (for a review, see reference 31). These pre-mRNA modifications serve to protect the transcript from the cellular degradation systems as well as prepare it for downstream events. Over the past few years, it has been established that pre-mRNA processing is carefully coordinated with transcription, and processing events are thought to occur mostly while the premRNA is nascent, i.e., still emerging from the transcription machinery (29). Nuclear mRNA export is tightly linked to pre-mRNA processing and, consequently, probably also to transcription. In metazoans, although not strictly required for export, pre-mRNA splicing has been found to make loading of export factors onto the mRNA more efficient: the exon junction complex associates with the mRNA as a consequence of splicing, and the exon junction complex-associated proteins Aly/REF and UAP56 are important for productive mRNA export (14,22,24,25,28,32). The Saccharomyces cerevisiae orthologues of these two proteins (the RNA binding protein Yra1p and the DECD-box RNA helicase Sub2p, respectively) are also involved in mRNA export in this organism (18,37,38,40). Aly/Yra1p is b...

Cryptic unstable transcripts (CUTs) are widely distributed in the genome of S. cerevisiae. These RNAs generally derive from nonannotated regions of the genome and are degraded rapidly and efficiently by the nuclear exosome via a pathway that involves degradative polyadenylation by a new poly(A) polymerase borne by the TRAMP complex. What is the share of significant information that is encrypted in CUTs and what distinguishes a CUT from other Pol II transcripts are unclear to date. Here we report the dissection of the molecular mechanism that leads to degradation of a model CUT, NEL025c. We show that the Nrd1p-Nab3p-dependent pathway, involved in transcription termination of sno/snRNAs, is required, albeit not sufficient, for efficient degradation of NEL025c RNAs and at least a subset of other CUTs. Our results suggest an important role for the Nrd1p-Nab3p pathway in the control of gene expression throughout the genome.

Targeting large transmembrane molecules, including receptor tyrosine kinases, is a major pharmacological challenge. Specific oligonucleotide ligands (aptamers) can be generated for a variety of targets through the iterative evolution of a random pool of sequences (SELEX). Nuclease-resistant aptamers that recognize the human receptor tyrosine kinase RET were obtained using RET-expressing cells as targets in a modified SELEX procedure. Remarkably, one of these aptamers blocked RET-dependent intracellular signaling pathways by interfering with receptor dimerization when the latter was induced by the physiological ligand or by an activating mutation. This strategy is generally applicable to transmembrane receptors and opens the way to targeting other members of this class of proteins that are of major biomedical importance.