Systematic analysis of bypass suppression of essential genes
Abstract Essential genes tend to be highly conserved across eukaryotes, but, in some cases, their critical roles can be bypassed through genetic rewiring. From a systematic analysis of 728 different essential yeast genes, we discovered that 124 (17%) were dispensable essential genes. Through whole‐g...
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| Main Authors: | , , , , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Springer Nature
2020-09-01
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| Series: | Molecular Systems Biology |
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| Online Access: | https://doi.org/10.15252/msb.20209828 |
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| author | Jolanda van Leeuwen Carles Pons Guihong Tan Zi Yang Wang Jing Hou Jochen Weile Marinella Gebbia Wendy Liang Ermira Shuteriqi Zhijian Li Maykel Lopes Matej Ušaj Andreia Dos Santos Lopes Natascha van Lieshout Chad L Myers Frederick P Roth Patrick Aloy Brenda J Andrews Charles Boone |
| author_facet | Jolanda van Leeuwen Carles Pons Guihong Tan Zi Yang Wang Jing Hou Jochen Weile Marinella Gebbia Wendy Liang Ermira Shuteriqi Zhijian Li Maykel Lopes Matej Ušaj Andreia Dos Santos Lopes Natascha van Lieshout Chad L Myers Frederick P Roth Patrick Aloy Brenda J Andrews Charles Boone |
| author_sort | Jolanda van Leeuwen |
| collection | DOAJ |
| description | Abstract Essential genes tend to be highly conserved across eukaryotes, but, in some cases, their critical roles can be bypassed through genetic rewiring. From a systematic analysis of 728 different essential yeast genes, we discovered that 124 (17%) were dispensable essential genes. Through whole‐genome sequencing and detailed genetic analysis, we investigated the genetic interactions and genome alterations underlying bypass suppression. Dispensable essential genes often had paralogs, were enriched for genes encoding membrane‐associated proteins, and were depleted for members of protein complexes. Functionally related genes frequently drove the bypass suppression interactions. These gene properties were predictive of essential gene dispensability and of specific suppressors among hundreds of genes on aneuploid chromosomes. Our findings identify yeast's core essential gene set and reveal that the properties of dispensable essential genes are conserved from yeast to human cells, correlating with human genes that display cell line‐specific essentiality in the Cancer Dependency Map (DepMap) project. |
| format | Article |
| id | doaj-art-27e5a5f4f3414f1c97c8f31d1a196803 |
| institution | Kabale University |
| issn | 1744-4292 |
| language | English |
| publishDate | 2020-09-01 |
| publisher | Springer Nature |
| record_format | Article |
| series | Molecular Systems Biology |
| spelling | doaj-art-27e5a5f4f3414f1c97c8f31d1a1968032024-11-17T12:55:10ZengSpringer NatureMolecular Systems Biology1744-42922020-09-0116912410.15252/msb.20209828Systematic analysis of bypass suppression of essential genesJolanda van Leeuwen0Carles Pons1Guihong Tan2Zi Yang Wang3Jing Hou4Jochen Weile5Marinella Gebbia6Wendy Liang7Ermira Shuteriqi8Zhijian Li9Maykel Lopes10Matej Ušaj11Andreia Dos Santos Lopes12Natascha van Lieshout13Chad L Myers14Frederick P Roth15Patrick Aloy16Brenda J Andrews17Charles Boone18Center for Integrative Genomics, Bâtiment Génopode, University of LausanneInstitute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute for Science and TechnologyDonnelly Centre for Cellular and Biomolecular Research, University of TorontoDonnelly Centre for Cellular and Biomolecular Research, University of TorontoDonnelly Centre for Cellular and Biomolecular Research, University of TorontoDonnelly Centre for Cellular and Biomolecular Research, University of TorontoDonnelly Centre for Cellular and Biomolecular Research, University of TorontoDonnelly Centre for Cellular and Biomolecular Research, University of TorontoDonnelly Centre for Cellular and Biomolecular Research, University of TorontoDonnelly Centre for Cellular and Biomolecular Research, University of TorontoCenter for Integrative Genomics, Bâtiment Génopode, University of LausanneDonnelly Centre for Cellular and Biomolecular Research, University of TorontoCenter for Integrative Genomics, Bâtiment Génopode, University of LausanneDonnelly Centre for Cellular and Biomolecular Research, University of TorontoDepartment of Computer Science and Engineering, University of Minnesota‐Twin CitiesDonnelly Centre for Cellular and Biomolecular Research, University of TorontoInstitute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute for Science and TechnologyDonnelly Centre for Cellular and Biomolecular Research, University of TorontoDonnelly Centre for Cellular and Biomolecular Research, University of TorontoAbstract Essential genes tend to be highly conserved across eukaryotes, but, in some cases, their critical roles can be bypassed through genetic rewiring. From a systematic analysis of 728 different essential yeast genes, we discovered that 124 (17%) were dispensable essential genes. Through whole‐genome sequencing and detailed genetic analysis, we investigated the genetic interactions and genome alterations underlying bypass suppression. Dispensable essential genes often had paralogs, were enriched for genes encoding membrane‐associated proteins, and were depleted for members of protein complexes. Functionally related genes frequently drove the bypass suppression interactions. These gene properties were predictive of essential gene dispensability and of specific suppressors among hundreds of genes on aneuploid chromosomes. Our findings identify yeast's core essential gene set and reveal that the properties of dispensable essential genes are conserved from yeast to human cells, correlating with human genes that display cell line‐specific essentiality in the Cancer Dependency Map (DepMap) project.https://doi.org/10.15252/msb.20209828compensatory evolutiongene essentialitygenetic interactionsgenetic networksgenetic suppression |
| spellingShingle | Jolanda van Leeuwen Carles Pons Guihong Tan Zi Yang Wang Jing Hou Jochen Weile Marinella Gebbia Wendy Liang Ermira Shuteriqi Zhijian Li Maykel Lopes Matej Ušaj Andreia Dos Santos Lopes Natascha van Lieshout Chad L Myers Frederick P Roth Patrick Aloy Brenda J Andrews Charles Boone Systematic analysis of bypass suppression of essential genes Molecular Systems Biology compensatory evolution gene essentiality genetic interactions genetic networks genetic suppression |
| title | Systematic analysis of bypass suppression of essential genes |
| title_full | Systematic analysis of bypass suppression of essential genes |
| title_fullStr | Systematic analysis of bypass suppression of essential genes |
| title_full_unstemmed | Systematic analysis of bypass suppression of essential genes |
| title_short | Systematic analysis of bypass suppression of essential genes |
| title_sort | systematic analysis of bypass suppression of essential genes |
| topic | compensatory evolution gene essentiality genetic interactions genetic networks genetic suppression |
| url | https://doi.org/10.15252/msb.20209828 |
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