Functional profiling of long intergenic non-coding RNAs in fission yeast

eLife

Michael Howell¹  Mary Y Wu¹  Clara Correia-Melo²  Markus Ralser³  Samuel Marguerat⁴  Shajahan Anver⁴  Michal Malecki⁴  Sheng Kai Pong⁴  Luis Montemayor⁴  Maria Rodriguez-Lopez⁴  Mimoza Hoti⁴  Jürg Bähler⁴  Cristina Cotobal⁴  StJohn Townsend⁵  Stephan Kamrad⁶ 

[1] The Francis Crick Institute, High Throughput Screening, London, United Kingdom;The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London, United Kingdom;The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London, United Kingdom;Charité Universitätsmedizin Berlin, Institute of Biochemistry, Berlin, Germany;University College London, Institute of Healthy Ageing and Department of Genetics, Evolution & Environment, London, United Kingdom;University College London, Institute of Healthy Ageing and Department of Genetics, Evolution & Environment, London, United Kingdom;The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London, United Kingdom;University College London, Institute of Healthy Ageing and Department of Genetics, Evolution & Environment, London, United Kingdom;The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London, United Kingdom;Charité Universitätsmedizin Berlin, Institute of Biochemistry, Berlin, Germany;

关键词: long non-coding RNA;    phenomics;    gene regulation;    S. pombe;    high-throughput phenotyping;    RNA function;    S. pombe;   

DOI  :  10.7554/eLife.76000

来源: eLife Sciences Publications, Ltd

【 摘 要 】

Eukaryotic genomes express numerous long intergenic non-coding RNAs (lincRNAs) that do not overlap any coding genes. Some lincRNAs function in various aspects of gene regulation, but it is not clear in general to what extent lincRNAs contribute to the information flow from genotype to phenotype. To explore this question, we systematically analysed cellular roles of lincRNAs in Schizosaccharomyces pombe. Using seamless CRISPR/Cas9-based genome editing, we deleted 141 lincRNA genes to broadly phenotype these mutants, together with 238 diverse coding-gene mutants for functional context. We applied high-throughput colony-based assays to determine mutant growth and viability in benign conditions and in response to 145 different nutrient, drug, and stress conditions. These analyses uncovered phenotypes for 47.5% of the lincRNAs and 96% of the protein-coding genes. For 110 lincRNA mutants, we also performed high-throughput microscopy and flow cytometry assays, linking 37% of these lincRNAs with cell-size and/or cell-cycle control. With all assays combined, we detected phenotypes for 84 (59.6%) of all lincRNA deletion mutants tested. For complementary functional inference, we analysed colony growth of strains ectopically overexpressing 113 lincRNA genes under 47 different conditions. Of these overexpression strains, 102 (90.3%) showed altered growth under certain conditions. Clustering analyses provided further functional clues and relationships for some of the lincRNAs. These rich phenomics datasets associate lincRNA mutants with hundreds of phenotypes, indicating that most of the lincRNAs analysed exert cellular functions in specific environmental or physiological contexts. This study provides groundwork to further dissect the roles of these lincRNAs in the relevant conditions.

【 授权许可】

CC BY