PT  - JOURNAL ARTICLE
AU  - Sophie R Atkinson
AU  - Samuel Marguerat
AU  - Danny A Bitton
AU  - Maria Rodríguez-López
AU  - Charalampos Rallis
AU  - Jean-François Lemay
AU  - Cristina Cotobal
AU  - Michal Malecki
AU  - Juan Mata
AU  - François Bachand
AU  - Jürg Bähler
TI  - Long non-coding RNA repertoire and regulation by nuclear exosome, cytoplasmic exonuclease and RNAi in fission yeast
AID  - 10.1101/158477
DP  - 2017 Jan 01
TA  - bioRxiv
PG  - 158477
4099  - http://biorxiv.org/content/early/2017/08/04/158477.short
4100  - http://biorxiv.org/content/early/2017/08/04/158477.full
AB  - Transcriptomes feature pervasive, but poorly defined long non-coding RNAs (lncRNAs). We identify 5775 novel lncRNAs in Schizosaccharomyces pombe, nearly 4-times the previously annotated lncRNAs. Most lncRNAs become derepressed under genetic and physiological perturbations, especially during late meiosis. These lncRNAs are targeted by three RNA-processing pathways: the nuclear exosome, cytoplasmic exonuclease and RNAi, with substantial coordination and redundancy among pathways. We classify lncRNAs 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 CUTs are often bidirectional and actively translated. The cytoplasmic exonuclease and RNAi repress thousands of meiotically induced RNAs. Antisense lncRNA and sense mRNA expression often negatively correlate in the physiological, but not the genetic conditions. Intergenic and bidirectional lncRNAs emerge from nucleosome-depleted regions, upstream of positioned nucleosomes. This broad survey of the S. pombe lncRNA repertoire and characteristics provides a rich resource for functional analyses.