Abstract: Pervasive transcription is now accepted to be a general feature of eukaryotic genomes, generating short and long non-coding RNAs (ncRNAs). Growing number of examples have shown that regulatory ncRNAs can control gene expression and chromatin domain formation. In this review, we discuss recent reports that show that Saccharomyces cerevisiae's genome also supports pervasive transcription, which is strongly controlled by RNA decay pathways and nucleosome positioning. We therefore propose that S. cerevisiae is an excellent model for studying large ncRNAs, which has already provided important examples of antisense-mediated transcriptional silencing.