Total RNA-Seq in WT and rrp6-delta strains of S. pombe. Total RNA-Seq in WT and rrp6-delta strains of S. pombe

Recent studies have revealed that eukaryotic genomes are pervasively transcribed by RNA polymerase II, producing a plethora of non-coding RNAs which frequently overlap protein-coding genes. Despite the fact that overlapping transcription is well known to repress transcription initiation from downstream promoters, the mechanism behind this phenomenon has remained elusive. It was proposed that transcriptional interference relies on the act of transcription rather than the RNA itself to block access of the transcription machinery to downstream promoters. Here, we use the fission yeast Schizosaccharomyces pombe to demonstrate that an RNA and chromatin-dependent mechanism is responsible for transcriptional interference. This relies on co-transcriptional recruitment of the histone deacetylase Clr3 to nascent non-coding RNA, leading to formation of hypoacetylated chromatin and repression of the downstream protein-coding gene. Our findings highlight the unexpected requirement for RNA as well as trans-acting protein factors in mediating the repressive effects imposed on gene expression through overlapping non-coding transcription. Overall design: Strand-specific total RNA-Seq was prepared for WT and rrp6Δ cells. Both samples were sequenced in duplicates.