GSBS Student Publications

Title

Genome-wide analysis of mRNAs regulated by the nonsense-mediated and 5' to 3' mRNA decay pathways in yeast

Student Author(s)

Shuyun Dong

GSBS Program

Biochemistry & Molecular Pharmacology

UMMS Affiliation

Graduate School of Biomedical Sciences; Department of Molecular Genetics and Microbiology

Date

12-24-2003

Document Type

Article

Medical Subject Headings

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 Proteins

Disciplines

Biochemistry | Bioinformatics | Genetics | Genomics | Molecular Biology | Molecular Genetics

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.

Comments

Citation: 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.

Related Resources

Link to article in PubMed

PubMed ID

14690598

Figure 1S.tif (2016 kB)
Figure 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

Figure 2S.tif (10859 kB)
Figure 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

Table 1S.doc (124 kB)
Table 1S. Putative uORF-containing genes regulated by NMD

Table 2S.doc (381 kB)
Table 2S. Major classes of transcripts up-regulated by inactivation of NMD

Table 3S.doc (37 kB)
Table 3S. Functional categories of genes up-regulated by inactivation of NMD

Table 4S.doc (27 kB)
Table 4S. Number of probe sets differentially expressed in the xrn1Delta, xrn1Delta upf1Delta, xrn1Delta nmd2Delta, and xrn1Delta upf3Delta strains

Table 5S.doc (32 kB)
Table 5S. Yeast strains used in this study

Table 6S.doc (115 kB)
Table 6S. Oligonucleotides used in this study

NMD(26)-Figure 1A(Avg-Norm-Data-2271).txt (311 kB)
NMD(26)-Figure 1B(Avg-Norm-Data-2063).txt (120 kB)
NMD(26)-Figure 2(Avg-Norm-Data-1184).txt (144 kB)
NMD(26)-Figure 3B(Avg-Norm-log-FU-1791).txt (110 kB)
NMD(26)-Figure 3D(Avg-Norm-log-FD-306).txt (21 kB)
NMD(26)-Figure 4A(AD-distribution).txt (1 kB)
NMD(26)-Figure 4B(ORFs up-regulated in nmd strains).txt (19 kB)
NMD(26)-R130-9335.txt (2762 kB)
NMD(26)-Raw Data-9335.txt (2835 kB)
NMD-XRN1(20)-R20-9335.txt (1056 kB)
NMD-XRN1(20)-Raw Data-9335.txt (2141 kB)
NMD(26)-Figure 1A(Avg-Norm-Data-2271).xls (594 kB)
NMD(26)-Figure 1B(Avg-Norm-Data-2063).xls (333 kB)
NMD(26)-Figure 2(Avg-Norm-Data-1184).xls (264 kB)
NMD(26)-Figure 3B(Avg-Norm-log-FU-1791).xls (463 kB)
NMD(26)-Figure 3D(Avg-Norm-log-FD-306).xls (90 kB)
NMD(26)-Figure 4A(AD-distribution).xls (13 kB)
NMD(26)-Figure 4B(ORFs up-regulated in nmd strains).xls (60 kB)
Probe sets not changed in nmd-dcp1-xrn1 strains-4540T-4956P.xls (1133 kB)