XUTs are a class of Xrn1-sensitive antisense regulatory non-coding RNA in yeast

Antisense control by ncRNAs Several lines of evidence suggest that non-coding RNAs (ncRNAs) have a significant role in gene regulation in eukaryotes. Genome-wide deep sequencing in the yeast Saccharomyces cerevisiae has now identified antisense ncRNAs that are destabilized by the Xrn1 RNA exonuclease in the 5′ RNA-decay pathway. These Xrn1-sensitive unstable transcripts, or XUTs, seem to function in gene repression and can be antagonized by histone H3K4 trimethylation. Non-coding (nc)RNAs are key players in numerous biological processes such as gene regulation, chromatin domain formation and genome stability 1 , 2 . Large ncRNAs interact with histone modifiers 3 , 4 , 5 and are involved in cancer development 6 , X-chromosome inactivation 7 and autosomal gene imprinting 8 . However, despite recent evidence showing that pervasive transcription is more widespread than previously thought 9 , only a few examples mediating gene regulation in eukaryotes have been described 10 . In Saccharomyces cerevisiae , the bona-fide regulatory ncRNAs are destabilized by the Xrn1 5′–3′ RNA exonuclease 11 , 12 (also known as Kem1), but the genome-wide characterization of the entire regulatory ncRNA family remains elusive. Here, using strand-specific RNA sequencing (RNA-seq), we identify a novel class of 1,658 Xrn1-sensitive unstable transcripts (XUTs) in which 66% are antisense to open reading frames. These transcripts are polyadenylated and RNA polymerase II (RNAPII)-dependent. The majority of XUTs strongly accumulate in lithium-containing media, indicating that they might have a role in adaptive responses to changes in growth conditions. Notably, RNAPII chromatin immunoprecipitation followed by DNA sequencing (ChIP-seq) analysis of Xrn1-deficient strains revealed a significant decrease of RNAPII occupancy over 273 genes with antisense XUTs. These genes show an unusual bias for H3K4me3 marks and require the Set1 histone H3 lysine 4 methyl-transferase for silencing. Furthermore, abolishing H3K4me3 triggers the silencing of other genes with antisense XUTs, supporting a model in which H3K4me3 antagonizes antisense ncRNA repressive activity. Our results demonstrate that antisense ncRNA-mediated regulation is a general regulatory pathway for gene expression in S. cerevisiae .