title: Natural genetic variation impacts expression levels of coding, non-coding, and antisense transcripts in fission yeast.
abstract: Our current understanding of how natural genetic variation affects gene expression beyond well-annotated coding genes is still limited. The use of deep sequencing technologies for the study of expression quantitative trait loci (eQTLs) has the potential to close this gap. Here, we generated the first recombinant strain library for fission yeast and conducted an RNA-seq-based QTL study of the coding, non-coding, and antisense transcriptomes. We show that the frequency of distal effects (trans-eQTLs) greatly exceeds the number of local effects (cis-eQTLs) and that non-coding RNAs are as likely to be affected by eQTLs as protein-coding RNAs. We identified a genetic variation of swc5 that modifies the levels of 871 RNAs, with effects on both sense and antisense transcription, and show that this effect most likely goes through a compromised deposition of the histone variant H2A.Z. The strains, methods, and datasets generated here provide a rich resource for future studies.
authors.affiliation: Biotechnology Centre, Technische Universität Dresden, Dresden, Germany Cologne Cluster of Excellence in Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne, Germany.
authors.forename: Mathieu
authors.initials: M
authors.lastname: Clément-Ziza
authors.affiliation: Department of Genetics, Evolution & Environment and UCL Genetics Institute, University College London, London, UK.
authors.forename: Francesc X
authors.initials: FX
authors.lastname: Marsellach
authors.affiliation: Department of Genetics, Evolution & Environment and UCL Genetics Institute, University College London, London, UK.
authors.forename: Sandra
authors.initials: S
authors.lastname: Codlin
authors.affiliation: Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark.
authors.forename: Manos A
authors.initials: MA
authors.lastname: Papadakis
authors.affiliation: Biotechnology Centre, Technische Universität Dresden, Dresden, Germany.
authors.forename: Susanne
authors.initials: S
authors.lastname: Reinhardt
authors.affiliation: Department of Genetics, Evolution & Environment and UCL Genetics Institute, University College London, London, UK.
authors.forename: María
authors.initials: M
authors.lastname: Rodríguez-López
authors.affiliation: Department of Genetics, Evolution & Environment and UCL Genetics Institute, University College London, London, UK.
authors.forename: Stuart
authors.initials: S
authors.lastname: Martin
authors.affiliation: Department of Genetics, Evolution & Environment and UCL Genetics Institute, University College London, London, UK.
authors.forename: Samuel
authors.initials: S
authors.lastname: Marguerat
authors.affiliation: Biozentrum, University of Basel, Basel, Switzerland.
authors.forename: Alexander
authors.initials: A
authors.lastname: Schmidt
authors.affiliation: Department of Genetics, Evolution & Environment and UCL Genetics Institute, University College London, London, UK.
authors.forename: Eunhye
authors.initials: E
authors.lastname: Lee
authors.affiliation: Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark.
authors.forename: Christopher T
authors.initials: CT
authors.lastname: Workman
authors.affiliation: Department of Genetics, Evolution & Environment and UCL Genetics Institute, University College London, London, UK j.bahler@ucl.ac.uk andreas.beyer@uni-koeln.de.
authors.forename: Jürg
authors.initials: J
authors.lastname: Bähler
authors.affiliation: Biotechnology Centre, Technische Universität Dresden, Dresden, Germany Cologne Cluster of Excellence in Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne, Germany j.bahler@ucl.ac.uk andreas.beyer@uni-koeln.de.
authors.forename: Andreas
authors.initials: A
authors.lastname: Beyer
mesh_terms: D018797:Cell Cycle Proteins / Q000235:genetics / Q000378:metabolism*; D044127:Epigenesis, Genetic; D015966:Gene Expression Regulation, Fungal; D014644:Genetic Variation; D040641:Quantitative Trait Loci; D012331:RNA, Fungal / Q000378:metabolism*; D012568:Schizosaccharomyces / Q000235:genetics*; D029702:Schizosaccharomyces pombe Proteins / Q000235:genetics* / Q000378:metabolism; D059467:Transcriptome
chemical_list: D018797:Cell Cycle Proteins; D012331:RNA, Fungal; D029702:Schizosaccharomyces pombe Proteins; C486628:Smc5 protein, S pombe
keywords: QTL; Schizosaccharomyces pombe; antisense transcription; histone variant; non‐coding RNA