Extensive characterization of NMD complexes in yeast

Nonsense mediated mRNA decay is a translation-dependent surveillance pathway that detects and eliminates RNA harboring premature termination codon. Our NMD complexes analysis led to the description of strong in vivo interaction between Nmd4, Ebs1 and Upf1, the major factor of NMD. We wondered if these proteins affected the degradation of RNA sensitive to NMD and if they could act on a specific class of targets. We performed RNAseq experiments in strains deleted for NMD4, EBS1 or both in comparison with wild type and upf1∆ strains. Our analysis confirmed that Nmd4 and Ebs1 have a role in the degradation of NMD substrates. The effect of Nmd4 or Ebs1 deletion was weak compared to upf1∆, fold change compared with WT was between -1 and 1 in log2. The double mutant had a global stronger effect. We have not detected any target specificity for Nmd4 or Ebs1, their profiles were very well correlated. We have also compared our data with upf1∆ RNAseq results. Among the more stabilized RNA in ebs1 and nmd4∆ strains, the majority were also stabilized in upf1∆. We observed a good correlation between upf1∆ and ebs1∆ profiles. For nmd4∆ the correlation was weaker, probably due to the low effect of the deletion, on NMD substrates stabilisation. We conclude that Nmd4 and Ebs1 play a specific role in the stabilization of all NMD substrates. body RNAseq of WT and NMD deficient yeast cells (upf1∆, nmd4∆, ebs1∆, nmd4∆/ebs1∆)