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He F, et al.  (2003) Genome-wide analysis of mRNAs regulated by the nonsense-mediated and 5' to 3' mRNA decay pathways in yeast. Mol Cell 12(6):1439-52

Abstract: 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.

Status: Published Type: Journal Article PubMed ID: 14690598

Topics addressed in this paper

Number of different genes curated to this paper: 67

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Topics Topics not linked to Genes Genes linked to topics (#1 - 10 )
AMD2 APN2 ARG81 BRR1 CAT2 CDC40 CPA1 CUS1 DAL2 DAL3
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Topics Genes linked to topics (#11 - 20 )
DAL7 DBR1 DCI1 DCP1 DNL4 DUR1,2 DUR3 ECI1 EST1 EST2
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Topics Genes linked to topics (#21 - 30 )
EST3 FAA2 FOX2 GDH2 GZF3 IDP3 LYS5 MEC3 MEP2 MLH3
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Topics Genes linked to topics (#31 - 40 )
MSL1 NAM7 NIT2 NKP2 NMD2 NTG2 PEX10 PEX4 PEX6 PPT2
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Topics Genes linked to topics (#41 - 50 )
PXA1 PXA2 RAD1 RAD57 REV3 RGM1 RNR3 SAD1 SEO1 SPP2
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Topics Genes linked to topics (#51 - 60 )
STN1 TEL1 THI11 THI20 THI21 THI22 THI4 THI6 THI72 UGA3
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Topics Genes linked to topics (#61 - 67 )
UPF3 XRN1 YJR149W YKU70 YLR317W YMR181C YOL153C
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