Tiling Microarray Analysis of NMD and Splicing mutants reveal novel functions for the NMD in the quality control of the splicing process and in subtelomeric gene silencing

Abstract

We have analyzed global transcriptome in yeast strains lacking the NMD component Upf1p or Xrn1p using tiling microarrays. Using these arrays, we showed recently that NMD eliminates many unspliced precursors that arise from inefficient splicing (Sayani, Mol.Cell 2008). We pursued this analysis by generating double mutants where splicing factors and the NMD are both inactivated. Arrays of these double mutants showed that unspliced precursors of many genes are detectable only when both NMD and these splicing factors are inactivated, indicating that NMD eliminates unspliced precursors resulting from splicing factors inactivation. This is a new function for NMD, as the nuclear exosome was thought to be responsible for degrading unspliced RNAs resulting from splicing factors mutations. Finally, we found that many subtelomeric genes accumulate 5′‐extended species in NMD mutants. These extended RNAs function to repress transcription at the normal promoters. NMD mutants are deficient for induction of these genes, but inactivation of the Histone Deacetylase Hda1p is sufficient to rescue this defect, suggesting a connection between silencing due to these 5′‐extended RNAs and chromatin modifications. Overall, these results have revealed novel functions for NMD in quality control of splicing in yeast, and identified an intriguing connection between NMD function and subtelomeric gene silencing.