Association of yeast Upf1p with direct substrates of the NMD pathway

UMMS Affiliation

Department of Molecular Genetics and Microbiology

Publication Date


Document Type



Fungal Proteins; *Gene Expression Regulation, Fungal; Models, Genetic; Phenotype; Protein Binding; Protein Biosynthesis; RNA Helicases; RNA Stability; RNA, Fungal; RNA, Messenger; Saccharomyces cerevisiae; Saccharomyces cerevisiae Proteins; Substrate Specificity; Thiamine


Life Sciences | Medicine and Health Sciences


Nonsense-mediated mRNA decay (NMD) is a surveillance mechanism that detects and degrades transcripts containing premature translation termination codons. Gene expression profiling experiments have shown that inactivation of the NMD pathway leads to the accumulation of both aberrant, nonsense-containing mRNAs, and many apparently wild-type transcripts. Such increases in transcript steady-state levels could arise from direct changes in the respective mRNA half-lives, or indirectly, as a consequence of the stabilization of transcripts encoding specific regulatory proteins. Here, we distinguished direct from indirect substrates by virtue of their association with the Saccharomyces cerevisiae Upf1 protein. Analyses of this dataset, and its comparison to the sets of transcripts that respectively increase or decrease in abundance when NMD is either inactivated or reactivated, indicate that the number of direct NMD substrates is larger than previously thought and that low abundance, alternatively transcribed mRNAs, i.e., mRNAs whose 5' ends are derived from previously unannotated 5' flanking sequences, comprise a significant class of direct substrates. Using thiamine metabolism as an example, we also show that apparent NMD-regulated cellular pathways may actually reflect the detection of low-abundance alternative transcripts under conditions where a pathway is repressed.

DOI of Published Version



Proc Natl Acad Sci U S A. 2007 Dec 26;104(52):20872-7. Epub 2007 Dec 17. Link to article on publisher's site

Journal/Book/Conference Title

Proceedings of the National Academy of Sciences of the United States of America

Related Resources

Link to Article in PubMed

PubMed ID