Genomic Identification and Functional Characterization of Essential Genes in Caenorhabditis elegans
Using combined genetic mapping, Illumina sequencing, bioinformatics analyses, and experimental validation, we identified 60 essential genes from 104 lethal mutations in two genomic regions of Caenorhabditis elegans totaling ∼14 Mb on chromosome III(mid) and chromosome V(left). Five of the 60 genes h...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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Oxford University Press
2018-03-01
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| Series: | G3: Genes, Genomes, Genetics |
| Subjects: | |
| Online Access: | http://g3journal.org/lookup/doi/10.1534/g3.117.300338 |
| _version_ | 1818571352368480256 |
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| author | Zhaozhao Qin Robert Johnsen Shicheng Yu Jeffrey Shih-Chieh Chu David L. Baillie Nansheng Chen |
| author_facet | Zhaozhao Qin Robert Johnsen Shicheng Yu Jeffrey Shih-Chieh Chu David L. Baillie Nansheng Chen |
| author_sort | Zhaozhao Qin |
| collection | DOAJ |
| description | Using combined genetic mapping, Illumina sequencing, bioinformatics analyses, and experimental validation, we identified 60 essential genes from 104 lethal mutations in two genomic regions of Caenorhabditis elegans totaling ∼14 Mb on chromosome III(mid) and chromosome V(left). Five of the 60 genes had not previously been shown to have lethal phenotypes by RNA interference depletion. By analyzing the regions around the lethal missense mutations, we identified four putative new protein functional domains. Furthermore, functional characterization of the identified essential genes shows that most are enzymes, including helicases, tRNA synthetases, and kinases in addition to ribosomal proteins. Gene Ontology analysis indicated that essential genes often encode for enzymes that conduct nucleic acid binding activities during fundamental processes, such as intracellular DNA replication, transcription, and translation. Analysis of essential gene shows that they have fewer paralogs, encode proteins that are in protein interaction hubs, and are highly expressed relative to nonessential genes. All these essential gene traits in C. elegans are consistent with those of human disease genes. Most human orthologs (90%) of the essential genes in this study are related to human diseases. Therefore, functional characterization of essential genes underlines their importance as proxies for understanding the biological functions of human disease genes. |
| first_indexed | 2024-12-14T13:54:34Z |
| format | Article |
| id | doaj.art-a8ab8c9e46394a52ab04ff57da9b797c |
| institution | Directory Open Access Journal |
| issn | 2160-1836 |
| language | English |
| last_indexed | 2024-12-14T13:54:34Z |
| publishDate | 2018-03-01 |
| publisher | Oxford University Press |
| record_format | Article |
| series | G3: Genes, Genomes, Genetics |
| spelling | doaj.art-a8ab8c9e46394a52ab04ff57da9b797c2022-12-21T22:58:53ZengOxford University PressG3: Genes, Genomes, Genetics2160-18362018-03-018398199710.1534/g3.117.30033822Genomic Identification and Functional Characterization of Essential Genes in Caenorhabditis elegansZhaozhao QinRobert JohnsenShicheng YuJeffrey Shih-Chieh ChuDavid L. BaillieNansheng ChenUsing combined genetic mapping, Illumina sequencing, bioinformatics analyses, and experimental validation, we identified 60 essential genes from 104 lethal mutations in two genomic regions of Caenorhabditis elegans totaling ∼14 Mb on chromosome III(mid) and chromosome V(left). Five of the 60 genes had not previously been shown to have lethal phenotypes by RNA interference depletion. By analyzing the regions around the lethal missense mutations, we identified four putative new protein functional domains. Furthermore, functional characterization of the identified essential genes shows that most are enzymes, including helicases, tRNA synthetases, and kinases in addition to ribosomal proteins. Gene Ontology analysis indicated that essential genes often encode for enzymes that conduct nucleic acid binding activities during fundamental processes, such as intracellular DNA replication, transcription, and translation. Analysis of essential gene shows that they have fewer paralogs, encode proteins that are in protein interaction hubs, and are highly expressed relative to nonessential genes. All these essential gene traits in C. elegans are consistent with those of human disease genes. Most human orthologs (90%) of the essential genes in this study are related to human diseases. Therefore, functional characterization of essential genes underlines their importance as proxies for understanding the biological functions of human disease genes.http://g3journal.org/lookup/doi/10.1534/g3.117.300338essential genelethalgenetic balancerwhole genome sequencing (WGS)functional characterization |
| spellingShingle | Zhaozhao Qin Robert Johnsen Shicheng Yu Jeffrey Shih-Chieh Chu David L. Baillie Nansheng Chen Genomic Identification and Functional Characterization of Essential Genes in Caenorhabditis elegans G3: Genes, Genomes, Genetics essential gene lethal genetic balancer whole genome sequencing (WGS) functional characterization |
| title | Genomic Identification and Functional Characterization of Essential Genes in Caenorhabditis elegans |
| title_full | Genomic Identification and Functional Characterization of Essential Genes in Caenorhabditis elegans |
| title_fullStr | Genomic Identification and Functional Characterization of Essential Genes in Caenorhabditis elegans |
| title_full_unstemmed | Genomic Identification and Functional Characterization of Essential Genes in Caenorhabditis elegans |
| title_short | Genomic Identification and Functional Characterization of Essential Genes in Caenorhabditis elegans |
| title_sort | genomic identification and functional characterization of essential genes in caenorhabditis elegans |
| topic | essential gene lethal genetic balancer whole genome sequencing (WGS) functional characterization |
| url | http://g3journal.org/lookup/doi/10.1534/g3.117.300338 |
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