Widespread impact of nonsense-mediated mRNA decay on the yeast intronome.
Nonsense-mediated mRNA decay (NMD) eliminates transcripts carrying premature translation termination codons, but the role of NMD on yeast unspliced pre-mRNA degradation is controversial. Using tiling arrays, we show that many unspliced yeast pre-mRNAs accumulate in strains mutated for the NMD component Upf1p and the exonuclease Xrn1p. Intron identity and suboptimal splicing signals resulting in weak splicing were found to be important determinants in NMD targeting. In the absence of functional NMD, unspliced precursors accumulate in the cytoplasm, possibly in P-bodies. NMD can also complement RNase III-mediated nuclear degradation of unspliced RPS22B pre-mRNAs, degrades most unspliced precursors generated by a 5' splice site mutation in RPS10B, and limits RPS29B unspliced precursors accumulation during amino acid starvation. These results show that NMD has a wider impact than previously thought on the degradation of yeast-unspliced transcripts and plays an important role in discarding precursors of regulated or suboptimally spliced transcripts.
Sayani
Shakir
S
Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095-1569, USA.
Janis
Michael
M
Lee
Chrissie Young
CY
Toesca
Isabelle
I
Chanfreau
Guillaume F
GF
D000596:Amino Acids / Q000172:deficiency; D015152:Blotting, Northern; D002467:Cell Nucleus / Q000378:metabolism; D018389:Codon, Nonsense / Q000235:genetics*; D016384:Consensus Sequence; D005091:Exons / Q000235:genetics; D017353:Gene Deletion; D017404:In Situ Hybridization, Fluorescence; D007438:Introns / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis; D012322:RNA Precursors / Q000378:metabolism; D022821:RNA Splice Sites; D012326:RNA Splicing; D020871:RNA Stability; D012333:RNA, Messenger / Q000378:metabolism; D015203:Reproducibility of Results; D012441:Saccharomyces cerevisiae / Q000235:genetics* / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000378:metabolism
D000596:Amino Acids; D018389:Codon, Nonsense; D012322:RNA Precursors; D022821:RNA Splice Sites; D012333:RNA, Messenger; D029701:Saccharomyces cerevisiae Proteins