Interrogation of the S. pombe transcriptome using strand specific poly-A enriched RNA sequencing, with the aim to identify and quantify regulatory lncRNA under various physiological conditions and genetic perturbations.

Long non-coding RNAs (lncRNAs) are emerging as important regulators of gene expression, although it remains unclear to what extent they contribute to the information flow from genotype to phenotype. Using strand-specific RNA-sequencing, we identify thousands of unstable, or cryptic, lncRNAs in Schizosaccharomyces pombe. These transcripts are degraded by both overlapping and specific pathways involving the core exosome, the nuclear exosome, the cytoplasmic exonuclease Exo2, and the RNAi machinery. Such cryptic lncRNAs are transcribed both from intergenic regions and antisense to protein-coding genes, and are enriched at centromeric and sub-telomeric regions. We describe a group of antisense lncRNAs that are up-regulated in meiotic cells, and regulated by the exosome, the RNAi machinery and Exo2. We additionally uncover a distinct group of lncRNAs that are up-regulated in nitrogen-starved cells. In contrast to the meiotic lncRNAs, the lncRNAs up-regulated during nitrogen starvation arise from bidirectional transcription from mRNA promoters, and are predominantly regulated by the exosome. Importantly, our data implicate Exo2 in regulation of meiotic gene expression.