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. doi: 10.1016/s1097-2765(03)00446-5.


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.

Publication types

  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Cluster Analysis
  • Codon, Nonsense*
  • Endoribonucleases / genetics
  • Endoribonucleases / metabolism
  • Exoribonucleases / genetics
  • Exoribonucleases / metabolism
  • Gene Expression Profiling
  • Gene Expression Regulation, Fungal*
  • Genome, Fungal*
  • Oligonucleotide Array Sequence Analysis
  • Open Reading Frames
  • RNA Cap-Binding Proteins
  • RNA, Fungal / metabolism*
  • RNA, Messenger / chemistry
  • RNA, Messenger / metabolism*
  • RNA-Binding Proteins / genetics
  • RNA-Binding Proteins / metabolism
  • Reproducibility of Results
  • Saccharomyces cerevisiae / genetics
  • Saccharomyces cerevisiae / metabolism
  • Saccharomyces cerevisiae Proteins / genetics
  • Saccharomyces cerevisiae Proteins / metabolism


  • Codon, Nonsense
  • RNA Cap-Binding Proteins
  • RNA, Fungal
  • RNA, Messenger
  • RNA-Binding Proteins
  • Saccharomyces cerevisiae Proteins
  • DCP1 protein, S cerevisiae
  • Endoribonucleases
  • Exoribonucleases
  • XRN1 protein, S cerevisiae