Antisense long non-coding (aslnc)RNAs represent a substantial part of eukaryotic 
transcriptomes that are, in yeast, controlled by the Xrn1 exonuclease. 
Nonsense-Mediated Decay (NMD) destabilizes the Xrn1-sensitive aslncRNAs (XUT), 
but what determines their sensitivity remains unclear. We report that 3' 
single-stranded (3'-ss) extension mediates XUTs degradation by NMD, assisted by 
the Mtr4 and Dbp2 helicases. Single-gene investigation, genome-wide RNA 
analyses, and double-stranded (ds)RNA mapping revealed that 3'-ss extensions 
discriminate the NMD-targeted XUTs from stable lncRNAs. Ribosome profiling 
showed that XUT are translated, locking them for NMD activity. Interestingly, 
mutants of the Mtr4 and Dbp2 helicases accumulated XUTs, suggesting that dsRNA 
unwinding is a critical step for degradation. Indeed, expression of 
anticomplementary transcripts protects cryptic intergenic lncRNAs from NMD. Our 
results indicate that aslncRNAs form dsRNA that are only translated and targeted 
to NMD if dissociated by Mtr4 and Dbp2. We propose that NMD buffers genome 
expression by discarding pervasive regulatory transcripts.