A global non-coding RNA system modulates fission yeast protein levels in response to stress.
Non-coding RNAs (ncRNAs) are frequent and prevalent across the taxa. Although individual non-coding loci have been assigned a function, most are uncharacterized. Their global biological significance is unproven and remains controversial. Here we investigate the role played by ncRNAs in the stress response of Schizosaccharomyces pombe. We integrate global proteomics and RNA sequencing data to identify a systematic programme in which elevated antisense RNA arising both from ncRNAs and from 3'-overlapping convergent gene pairs is directly associated with substantial reductions in protein levels throughout the genome. We describe an extensive array of ncRNAs with trans associations that have the potential to influence multiple pathways. Deletion of one such locus reduces levels of atf1, a transcription factor downstream of the stress-activated mitogen-activated protein kinase (MAPK) pathway, and alters sensitivity to oxidative stress. These non-coding transcripts therefore regulate specific stress responses, adding unanticipated information-processing capacity to the MAPK signalling system.
1] Applied Computational Biology and Bioinformatics Group, Cancer Research UK Manchester Institute, University of Manchester, Wilmslow Road, Manchester M20 4BX, UK [2].
Hui Sun
HS
Leong
1] Applied Computational Biology and Bioinformatics Group, Cancer Research UK Manchester Institute, University of Manchester, Wilmslow Road, Manchester M20 4BX, UK [2].
Keren
K
Dawson
Applied Computational Biology and Bioinformatics Group, Cancer Research UK Manchester Institute, University of Manchester, Wilmslow Road, Manchester M20 4BX, UK.
Chris
C
Wirth
Applied Computational Biology and Bioinformatics Group, Cancer Research UK Manchester Institute, University of Manchester, Wilmslow Road, Manchester M20 4BX, UK.
Yaoyong
Y
Li
Biological Mass Spectrometry Facility, Cancer Research UK Manchester Institute, University of Manchester, Wilmslow Road, Manchester M20 4BX, UK.
Yvonne
Y
Connolly
Biological Mass Spectrometry Facility, Cancer Research UK Manchester Institute, University of Manchester, Wilmslow Road, Manchester M20 4BX, UK.
Duncan L
DL
Smith
Cell Regulation Group, Cancer Research UK Manchester Institute, University of Manchester, Wilmslow Road, Manchester M20 4BX, UK.
Caroline R M
CR
Wilkinson
Applied Computational Biology and Bioinformatics Group, Cancer Research UK Manchester Institute, University of Manchester, Wilmslow Road, Manchester M20 4BX, UK.
Crispin J
CJ
Miller
D015966:Gene Expression Regulation, Fungal; D005800:Genes, Fungal; D016366:Open Reading Frames / Q000235:genetics; D009997:Osmotic Pressure; D018384:Oxidative Stress / Q000235:genetics; D020543:Proteome / Q000378:metabolism; D016372:RNA, Antisense / Q000378:metabolism; D012331:RNA, Fungal / Q000235:genetics* / Q000378:metabolism; D022661:RNA, Untranslated / Q000235:genetics* / Q000378:metabolism; D012568:Schizosaccharomyces / Q000235:genetics*; D029702:Schizosaccharomyces pombe Proteins / Q000235:genetics / Q000378:metabolism*; D013312:Stress, Physiological / Q000235:genetics*; D059467:Transcriptome / Q000235:genetics
D020543:Proteome; D016372:RNA, Antisense; D012331:RNA, Fungal; D022661:RNA, Untranslated; D029702:Schizosaccharomyces pombe Proteins