Abstract
Genomes are pervasively transcribed with a profusion of non-coding transcripts. Long non-coding RNAs (lncRNAs), which are longer than 200 nucleotides but often unstable, contribute a substantial and diverse portion to non-coding transcriptomes. Most lncRNAs are poorly annotated and understood, although several play defined roles in gene regulation and diseases. Here we systematically uncover and analyse lncRNAs in Schizosaccharomyces pombe. Based on RNA-seq data from RNA-processing mutants and physiological conditions, we identify 5775 novel lncRNAs, nearly 4-times the previously annotated lncRNAs in S. pombe. These lncRNAs show strong changes in expression, mainly derepression, under the genetic and physiological perturbations, most notably during late meiosis. Most lncRNAs are cryptic and targeted by three RNA-processing pathways: the nuclear exosome, cytoplasmic exonuclease, and RNAi. Double-mutant analyses reveal substantial coordination and redundancy among these pathways. We classify lncRNAs by their dominant pathway into cryptic unstable transcripts (CUTs), Xrn1-sensitive unstable transcripts (XUTs), and Dicer-sensitive unstable transcripts (DUTs). XUTs and DUTs are enriched for antisense lncRNAs, while bidirectional lncRNAs are often CUTs and actively translated. The cytoplasmic exonuclease, along with RNAi, functions in dampening the expression of thousands of lncRNAs and mRNAs that become derepressed during meiosis. Antisense lncRNA expression mostly negatively correlates with sense mRNA expression in the physiological, but not in the genetic conditions. Intergenic and bidirectional lncRNAs emerge from nucleosome-depleted regions, upstream of positioned nucleosomes. This broad survey of the lncRNA repertoire and characteristics in S. pombe, and the interwoven regulatory pathways that target lncRNAs, provides a rich framework for their further functional analyses.