Functional profiling of long intergenic non-coding RNAs in fission yeast
Functional profiling of long intergenic non-coding RNAs in fission yeast
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DOI：
10.1101/2021.06.30.450572
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发表时间：
2021-07
期刊：
影响因子：
7.7
通讯作者：
María Rodríguez-López;Shajahan Anver;Cristina Cotobal;S. Kamrad;M. Malecki;Clara Correia-Melo;M. Hoti;StJohn Townsend;S. Marguerat;S. Pong;Mary Y. Wu;Luis Montemayor;M. Howell;M. Ralser;J. Bähler
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作者：
María Rodríguez-López;Shajahan Anver;Cristina Cotobal;S. Kamrad;M. Malecki;Clara Correia-Melo;M. Hoti;StJohn Townsend;S. Marguerat;S. Pong;Mary Y. Wu;Luis Montemayor;M. Howell;M. Ralser;J. Bähler
真核生物基因组表达许多不重叠任何编码基因的长基因间非编码rna （lincRNAs）。一些lincRNAs在基因调控的各个方面发挥作用，但通常不清楚lincRNAs在多大程度上促进了从基因型到表型的信息流。为了探讨这个问题，我们系统地分析了lincrna在pombe Schizosaccharomyces中的细胞作用。使用基于CRISPR/ cas9的无缝基因组编辑，我们删除了141个lincRNA基因，对这些突变体进行了广泛的表型分析，并对238个不同的编码基因突变进行了功能背景分析。我们采用高通量集落法测定突变体在良性条件下以及145种不同营养、药物和应激条件下的生长和活力。这些分析揭示了47.5%的lincrna和96%的蛋白质编码基因的表型。对于110个lincRNA突变体，我们还进行了高通量显微镜和流式细胞术检测，将这些lincRNA中的37%与细胞大小和/或细胞周期控制联系起来。结合所有检测，我们检测了84个（59.6%）lincRNA缺失突变体的表型。为了补充功能推断，我们分析了47种不同条件下异位过表达113个lincRNA基因的菌株的菌落生长。在这些过表达菌株中，102株（90.3%）在一定条件下表现出生长改变。聚类分析为一些lincrna提供了进一步的功能线索和关系。这些丰富的表型组学数据集将lincRNA突变体与数百种表型相关联，表明分析的大多数lincRNA在特定的环境或生理背景下发挥细胞功能。本研究为进一步剖析这些lincrna在相关条件下的作用提供了基础。
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 analyzed 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 analyzed 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 analyzed 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.