Genome-wide analysis of mRNAs regulated by the nonsense-mediated and 5' to 3' mRNA decay pathways in yeast
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Student Authors
Shuyun DongUMass Chan Affiliations
Department of Molecular Genetics and MicrobiologyGraduate School of Biomedical Sciences
Document Type
Journal ArticlePublication Date
2003-12-24Keywords
Cluster Analysis; *Codon, Nonsense; Endoribonucleases; Exoribonucleases; Gene Expression Profiling; *Gene Expression Regulation, Fungal; *Genome, Fungal; Oligonucleotide Array Sequence Analysis; Open Reading Frames; RNA, Fungal; RNA, Messenger; RNA-Binding Proteins; Reproducibility of Results; Saccharomyces cerevisiae; Saccharomyces cerevisiae ProteinsBiochemistry
Bioinformatics
Genetics
Genomics
Molecular Biology
Molecular Genetics
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Show full item recordAbstract
Transcripts regulated by the yeast nonsense-mediated and 5' to 3' mRNA decay pathways were identified by expression profiling of wild-type, upf1Delta, nmd2Delta, upf3Delta, dcp1Delta, and xrn1Delta cells. This analysis revealed that inactivation of Upf1p, Nmd2p, or Upf3p has identical effects on global RNA accumulation; inactivation of Dcp1p or Xrn1p exhibits both common and unique effects on global RNA accumulation but causes upregulation of only a small fraction of transcripts; and the majority of transcripts upregulated in upf/nmd strains are also upregulated to similar extents in dcp1Delta and xrn1Delta strains. Our results define the core transcripts regulated by NMD, identify several novel structural classes of NMD substrates, demonstrate that nonsense-containing mRNAs are primarily degraded by the 5' to 3' decay pathway even in the absence of functional NMD, and indicate that 3' to 5' decay, not 5' to 3' decay, may be the major mRNA decay activity in yeast cells.Source
He F, Li X, Spatrick P, Casillo R, Dong S, Jacobson A. Genome-wide analysis of mRNAs regulated by the nonsense-mediated and 5' to 3' mRNA decay pathways in yeast. Mol Cell. 2003 Dec;12(6):1439-52. PubMed PMID: 14690598. doi:10.1016/S1097-2765(03)00446-5. Link to article on publisher's website
See Additional Files below for all primary data and supplemental figures and tables. Supplemental data tables are available in both .txt and .xls format.
DOI
10.1016/S1097-2765(03)00446-5Permanent Link to this Item
http://hdl.handle.net/20.500.14038/33827PubMed ID
14690598Related Resources
Link to article in PubMedae974a485f413a2113503eed53cd6c53
10.1016/S1097-2765(03)00446-5