Mapping DNA damage‐dependent genetic interactions in yeast via party mating and barcode fusion genetics
Abstract Condition‐dependent genetic interactions can reveal functional relationships between genes that are not evident under standard culture conditions. State‐of‐the‐art yeast genetic interaction mapping, which relies on robotic manipulation of arrays of double‐mutant strains, does not scale read...
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| Format: | Article |
| Language: | English |
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Springer Nature
2018-05-01
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| Series: | Molecular Systems Biology |
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| Online Access: | https://doi.org/10.15252/msb.20177985 |
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| author | J Javier Díaz‐Mejía Albi Celaj Joseph C Mellor Atina Coté Attila Balint Brandon Ho Pritpal Bansal Fatemeh Shaeri Marinella Gebbia Jochen Weile Marta Verby Anna Karkhanina YiFan Zhang Cassandra Wong Justin Rich D'Arcy Prendergast Gaurav Gupta Sedide Öztürk Daniel Durocher Grant W Brown Frederick P Roth |
| author_facet | J Javier Díaz‐Mejía Albi Celaj Joseph C Mellor Atina Coté Attila Balint Brandon Ho Pritpal Bansal Fatemeh Shaeri Marinella Gebbia Jochen Weile Marta Verby Anna Karkhanina YiFan Zhang Cassandra Wong Justin Rich D'Arcy Prendergast Gaurav Gupta Sedide Öztürk Daniel Durocher Grant W Brown Frederick P Roth |
| author_sort | J Javier Díaz‐Mejía |
| collection | DOAJ |
| description | Abstract Condition‐dependent genetic interactions can reveal functional relationships between genes that are not evident under standard culture conditions. State‐of‐the‐art yeast genetic interaction mapping, which relies on robotic manipulation of arrays of double‐mutant strains, does not scale readily to multi‐condition studies. Here, we describe barcode fusion genetics to map genetic interactions (BFG‐GI), by which double‐mutant strains generated via en masse “party” mating can also be monitored en masse for growth to detect genetic interactions. By using site‐specific recombination to fuse two DNA barcodes, each representing a specific gene deletion, BFG‐GI enables multiplexed quantitative tracking of double mutants via next‐generation sequencing. We applied BFG‐GI to a matrix of DNA repair genes under nine different conditions, including methyl methanesulfonate (MMS), 4‐nitroquinoline 1‐oxide (4NQO), bleomycin, zeocin, and three other DNA‐damaging environments. BFG‐GI recapitulated known genetic interactions and yielded new condition‐dependent genetic interactions. We validated and further explored a subnetwork of condition‐dependent genetic interactions involving MAG1, SLX4, and genes encoding the Shu complex, and inferred that loss of the Shu complex leads to an increase in the activation of the checkpoint protein kinase Rad53. |
| format | Article |
| id | doaj-art-2cc42bd94f72421daa7d032148d66de4 |
| institution | Kabale University |
| issn | 1744-4292 |
| language | English |
| publishDate | 2018-05-01 |
| publisher | Springer Nature |
| record_format | Article |
| series | Molecular Systems Biology |
| spelling | doaj-art-2cc42bd94f72421daa7d032148d66de42025-08-20T03:46:32ZengSpringer NatureMolecular Systems Biology1744-42922018-05-0114511710.15252/msb.20177985Mapping DNA damage‐dependent genetic interactions in yeast via party mating and barcode fusion geneticsJ Javier Díaz‐Mejía0Albi Celaj1Joseph C Mellor2Atina Coté3Attila Balint4Brandon Ho5Pritpal Bansal6Fatemeh Shaeri7Marinella Gebbia8Jochen Weile9Marta Verby10Anna Karkhanina11YiFan Zhang12Cassandra Wong13Justin Rich14D'Arcy Prendergast15Gaurav Gupta16Sedide Öztürk17Daniel Durocher18Grant W Brown19Frederick P Roth20Donnelly Centre, University of TorontoDonnelly Centre, University of TorontoDonnelly Centre, University of TorontoDonnelly Centre, University of TorontoDonnelly Centre, University of TorontoDonnelly Centre, University of TorontoDonnelly Centre, University of TorontoDonnelly Centre, University of TorontoDonnelly Centre, University of TorontoDonnelly Centre, University of TorontoDonnelly Centre, University of TorontoDonnelly Centre, University of TorontoDonnelly Centre, University of TorontoLunenfeld‐Tanenbaum Research Institute, Mt. Sinai HospitalDonnelly Centre, University of TorontoDonnelly Centre, University of TorontoDonnelly Centre, University of TorontoDepartment of Biological Chemistry and Molecular Pharmacology, Harvard Medical SchoolDepartment of Molecular Genetics, University of TorontoDonnelly Centre, University of TorontoDonnelly Centre, University of TorontoAbstract Condition‐dependent genetic interactions can reveal functional relationships between genes that are not evident under standard culture conditions. State‐of‐the‐art yeast genetic interaction mapping, which relies on robotic manipulation of arrays of double‐mutant strains, does not scale readily to multi‐condition studies. Here, we describe barcode fusion genetics to map genetic interactions (BFG‐GI), by which double‐mutant strains generated via en masse “party” mating can also be monitored en masse for growth to detect genetic interactions. By using site‐specific recombination to fuse two DNA barcodes, each representing a specific gene deletion, BFG‐GI enables multiplexed quantitative tracking of double mutants via next‐generation sequencing. We applied BFG‐GI to a matrix of DNA repair genes under nine different conditions, including methyl methanesulfonate (MMS), 4‐nitroquinoline 1‐oxide (4NQO), bleomycin, zeocin, and three other DNA‐damaging environments. BFG‐GI recapitulated known genetic interactions and yielded new condition‐dependent genetic interactions. We validated and further explored a subnetwork of condition‐dependent genetic interactions involving MAG1, SLX4, and genes encoding the Shu complex, and inferred that loss of the Shu complex leads to an increase in the activation of the checkpoint protein kinase Rad53.https://doi.org/10.15252/msb.20177985condition‐dependentDNA barcodeen massegenetic interactionsequencing |
| spellingShingle | J Javier Díaz‐Mejía Albi Celaj Joseph C Mellor Atina Coté Attila Balint Brandon Ho Pritpal Bansal Fatemeh Shaeri Marinella Gebbia Jochen Weile Marta Verby Anna Karkhanina YiFan Zhang Cassandra Wong Justin Rich D'Arcy Prendergast Gaurav Gupta Sedide Öztürk Daniel Durocher Grant W Brown Frederick P Roth Mapping DNA damage‐dependent genetic interactions in yeast via party mating and barcode fusion genetics Molecular Systems Biology condition‐dependent DNA barcode en masse genetic interaction sequencing |
| title | Mapping DNA damage‐dependent genetic interactions in yeast via party mating and barcode fusion genetics |
| title_full | Mapping DNA damage‐dependent genetic interactions in yeast via party mating and barcode fusion genetics |
| title_fullStr | Mapping DNA damage‐dependent genetic interactions in yeast via party mating and barcode fusion genetics |
| title_full_unstemmed | Mapping DNA damage‐dependent genetic interactions in yeast via party mating and barcode fusion genetics |
| title_short | Mapping DNA damage‐dependent genetic interactions in yeast via party mating and barcode fusion genetics |
| title_sort | mapping dna damage dependent genetic interactions in yeast via party mating and barcode fusion genetics |
| topic | condition‐dependent DNA barcode en masse genetic interaction sequencing |
| url | https://doi.org/10.15252/msb.20177985 |
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