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

Antisense ncRNAs in yeast control Tyl mobility (12,13) and PHO84 transcription through histone modifications (11,12) in an RNA-interference-independent manner14 (Supplementary Fig. 1). The regulatory ncRNAs are distinct from the canonical [...]
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 (3-5) 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 genomewide 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.