Functional profiling of long intergenic non-coding RNAs in fission yeast
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...
| Main Authors: | , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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eLife Sciences Publications Ltd
2022-01-01
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| Series: | eLife |
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| Online Access: | https://elifesciences.org/articles/76000 |
| _version_ | 1818026461412458496 |
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| author | Maria Rodriguez-Lopez Shajahan Anver Cristina Cotobal Stephan Kamrad Michal Malecki Clara Correia-Melo Mimoza Hoti StJohn Townsend Samuel Marguerat Sheng Kai Pong Mary Y Wu Luis Montemayor Michael Howell Markus Ralser Jürg Bähler |
| author_facet | Maria Rodriguez-Lopez Shajahan Anver Cristina Cotobal Stephan Kamrad Michal Malecki Clara Correia-Melo Mimoza Hoti StJohn Townsend Samuel Marguerat Sheng Kai Pong Mary Y Wu Luis Montemayor Michael Howell Markus Ralser Jürg Bähler |
| author_sort | Maria Rodriguez-Lopez |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-10T04:32:22Z |
| format | Article |
| id | doaj.art-817fde84c4244994a2ac74da02dfcfb1 |
| institution | Directory Open Access Journal |
| issn | 2050-084X |
| language | English |
| last_indexed | 2024-12-10T04:32:22Z |
| publishDate | 2022-01-01 |
| publisher | eLife Sciences Publications Ltd |
| record_format | Article |
| series | eLife |
| spelling | doaj.art-817fde84c4244994a2ac74da02dfcfb12022-12-22T02:02:06ZengeLife Sciences Publications LtdeLife2050-084X2022-01-011110.7554/eLife.76000Functional profiling of long intergenic non-coding RNAs in fission yeastMaria Rodriguez-Lopez0https://orcid.org/0000-0002-2066-0589Shajahan Anver1https://orcid.org/0000-0002-7582-5125Cristina Cotobal2Stephan Kamrad3https://orcid.org/0000-0002-5957-4661Michal Malecki4https://orcid.org/0000-0002-1525-5036Clara Correia-Melo5https://orcid.org/0000-0001-6062-1472Mimoza Hoti6StJohn Townsend7Samuel Marguerat8https://orcid.org/0000-0002-2402-3165Sheng Kai Pong9https://orcid.org/0000-0002-9940-1175Mary Y Wu10https://orcid.org/0000-0002-2074-6171Luis Montemayor11Michael Howell12https://orcid.org/0000-0003-0912-0079Markus Ralser13Jürg Bähler14https://orcid.org/0000-0003-4036-1532University College London, Institute of Healthy Ageing and Department of Genetics, Evolution & Environment, London, United KingdomUniversity College London, Institute of Healthy Ageing and Department of Genetics, Evolution & Environment, London, United KingdomUniversity College London, Institute of Healthy Ageing and Department of Genetics, Evolution & Environment, London, United KingdomUniversity 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, GermanyUniversity College London, Institute of Healthy Ageing and Department of Genetics, Evolution & Environment, London, United KingdomThe Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London, United KingdomUniversity College London, Institute of Healthy Ageing and Department of Genetics, Evolution & Environment, London, United KingdomUniversity 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 KingdomUniversity College London, Institute of Healthy Ageing and Department of Genetics, Evolution & Environment, London, United KingdomUniversity College London, Institute of Healthy Ageing and Department of Genetics, Evolution & Environment, London, United KingdomThe Francis Crick Institute, High Throughput Screening, London, United KingdomUniversity College London, Institute of Healthy Ageing and Department of Genetics, Evolution & Environment, London, United KingdomThe Francis Crick Institute, High Throughput Screening, London, United KingdomThe Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London, United Kingdom; Charité Universitätsmedizin Berlin, Institute of Biochemistry, Berlin, GermanyUniversity College London, Institute of Healthy Ageing and Department of Genetics, Evolution & Environment, London, United KingdomEukaryotic 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.https://elifesciences.org/articles/76000long non-coding RNAphenomicsgene regulationS. pombehigh-throughput phenotypingRNA function |
| spellingShingle | Maria Rodriguez-Lopez Shajahan Anver Cristina Cotobal Stephan Kamrad Michal Malecki Clara Correia-Melo Mimoza Hoti StJohn Townsend Samuel Marguerat Sheng Kai Pong Mary Y Wu Luis Montemayor Michael Howell Markus Ralser Jürg Bähler Functional profiling of long intergenic non-coding RNAs in fission yeast eLife long non-coding RNA phenomics gene regulation S. pombe high-throughput phenotyping RNA function |
| title | Functional profiling of long intergenic non-coding RNAs in fission yeast |
| title_full | Functional profiling of long intergenic non-coding RNAs in fission yeast |
| title_fullStr | Functional profiling of long intergenic non-coding RNAs in fission yeast |
| title_full_unstemmed | Functional profiling of long intergenic non-coding RNAs in fission yeast |
| title_short | Functional profiling of long intergenic non-coding RNAs in fission yeast |
| title_sort | functional profiling of long intergenic non coding rnas in fission yeast |
| topic | long non-coding RNA phenomics gene regulation S. pombe high-throughput phenotyping RNA function |
| url | https://elifesciences.org/articles/76000 |
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