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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...

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Autores principales: Rodriguez-Lopez, Maria, Anver, Shajahan, Cotobal, Cristina, Kamrad, Stephan, Malecki, Michal, Correia-Melo, Clara, Hoti, Mimoza, Townsend, StJohn, Marguerat, Samuel, Pong, Sheng Kai, Wu, Mary Y, Montemayor, Luis, Howell, Michael, Ralser, Markus, Bähler, Jürg
Formato: Online Artículo Texto
Lenguaje:English
Publicado: eLife Sciences Publications, Ltd 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8730722/
https://www.ncbi.nlm.nih.gov/pubmed/34984977
http://dx.doi.org/10.7554/eLife.76000
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author Rodriguez-Lopez, Maria
Anver, Shajahan
Cotobal, Cristina
Kamrad, Stephan
Malecki, Michal
Correia-Melo, Clara
Hoti, Mimoza
Townsend, StJohn
Marguerat, Samuel
Pong, Sheng Kai
Wu, Mary Y
Montemayor, Luis
Howell, Michael
Ralser, Markus
Bähler, Jürg
author_facet Rodriguez-Lopez, Maria
Anver, Shajahan
Cotobal, Cristina
Kamrad, Stephan
Malecki, Michal
Correia-Melo, Clara
Hoti, Mimoza
Townsend, StJohn
Marguerat, Samuel
Pong, Sheng Kai
Wu, Mary Y
Montemayor, Luis
Howell, Michael
Ralser, Markus
Bähler, Jürg
author_sort Rodriguez-Lopez, Maria
collection PubMed
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.
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spelling pubmed-87307222022-01-06 Functional profiling of long intergenic non-coding RNAs in fission yeast Rodriguez-Lopez, Maria Anver, Shajahan Cotobal, Cristina Kamrad, Stephan Malecki, Michal Correia-Melo, Clara Hoti, Mimoza Townsend, StJohn Marguerat, Samuel Pong, Sheng Kai Wu, Mary Y Montemayor, Luis Howell, Michael Ralser, Markus Bähler, Jürg eLife Genetics and Genomics 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. eLife Sciences Publications, Ltd 2022-01-05 /pmc/articles/PMC8730722/ /pubmed/34984977 http://dx.doi.org/10.7554/eLife.76000 Text en © 2022, Rodriguez-Lopez et al https://creativecommons.org/licenses/by/4.0/This article is distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use and redistribution provided that the original author and source are credited.
spellingShingle Genetics and Genomics
Rodriguez-Lopez, Maria
Anver, Shajahan
Cotobal, Cristina
Kamrad, Stephan
Malecki, Michal
Correia-Melo, Clara
Hoti, Mimoza
Townsend, StJohn
Marguerat, Samuel
Pong, Sheng Kai
Wu, Mary Y
Montemayor, Luis
Howell, Michael
Ralser, Markus
Bähler, Jürg
Functional profiling of long intergenic non-coding RNAs in fission yeast
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 Genetics and Genomics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8730722/
https://www.ncbi.nlm.nih.gov/pubmed/34984977
http://dx.doi.org/10.7554/eLife.76000
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