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dc.contributor.authorHe, Feng
dc.contributor.authorLi, Xiangrui
dc.contributor.authorSpatrick, Phyllis
dc.contributor.authorCasillo, Ryan
dc.contributor.authorDong, Shuyun
dc.contributor.authorJacobson, Allan
dc.date2022-08-11T08:08:58.000
dc.date.accessioned2022-08-23T16:14:17Z
dc.date.available2022-08-23T16:14:17Z
dc.date.issued2003-12-24
dc.date.submitted2008-09-25
dc.identifier.citation<p>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. <a href="http://dx.doi.org/10.1016/S1097-2765(03)00446-5" target="_blank">Link to article on publisher's website</a></p> <p>See <strong>Additional Files</strong> below for all primary data and supplemental figures and tables. Supplemental data tables are available in both .txt and .xls format.</p>
dc.identifier.issn1097-2765 (Print)
dc.identifier.doi10.1016/S1097-2765(03)00446-5
dc.identifier.pmid14690598
dc.identifier.urihttp://hdl.handle.net/20.500.14038/33827
dc.description.abstractTranscripts 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.
dc.language.isoen_US
dc.relation<a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=14690598&dopt=Abstract">Link to article in PubMed</a>
dc.relation.urlhttp://dx.doi.org/10.1016/S1097-2765(03)00446-5
dc.subjectCluster 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 Proteins
dc.subjectBiochemistry
dc.subjectBioinformatics
dc.subjectGenetics
dc.subjectGenomics
dc.subjectMolecular Biology
dc.subjectMolecular Genetics
dc.titleGenome-wide analysis of mRNAs regulated by the nonsense-mediated and 5' to 3' mRNA decay pathways in yeast
dc.typeJournal Article
dc.source.journaltitleMolecular cell
dc.source.volume12
dc.source.issue6
dc.identifier.legacycoverpagehttps://escholarship.umassmed.edu/gsbs_sp/486
dc.identifier.contextkey638254
dc.file.descriptionTable 1S. Putative uORF-containing genes regulated by NMD
dc.file.descriptionFigure 1S. Probe sets up-regulated in the xrn1Delta strain largely overlap with those up-regulated in the xrn1Delta upf1Delta, xrn1Delta nmd2Delta, or xrn1Delta upf3Delta strains
dc.file.descriptionFigure 2S. Expression patterns of the probe sets up-regulated (A) or down-regulated (B) in the xrn1Delta, xrn1Delta upf1Delta, xrn1Delta nmd2Delta, or xrn1Delta upf3Delta strains
dc.file.descriptionTable 2S. Major classes of transcripts up-regulated by inactivation of NMD
dc.file.descriptionTable 3S. Functional categories of genes up-regulated by inactivation of NMD
dc.file.descriptionTable 4S. Number of probe sets differentially expressed in the xrn1Delta, xrn1Delta upf1Delta, xrn1Delta nmd2Delta, and xrn1Delta upf3Delta strains
dc.file.descriptionTable 5S. Yeast strains used in this study
dc.file.descriptionTable 6S. Oligonucleotides used in this study
refterms.dateFOA2022-08-30T17:34:19Z
html.description.abstract<p>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.</p>
dc.identifier.submissionpathgsbs_sp/486
dc.contributor.departmentDepartment of Molecular Genetics and Microbiology
dc.contributor.departmentGraduate School of Biomedical Sciences
dc.source.pages1439-52
dc.contributor.studentShuyun Dong


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