Functional Profiling of Transcription Factor Genes in Neurospora crassa
Regulation of gene expression by DNA-binding transcription factors is essential for proper control of growth and development in all organisms. In this study, we annotate and characterize growth and developmental phenotypes for transcription factor genes in the model filamentous fungus Neurospora cra...
| Main Authors: | , , , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Oxford University Press
2017-09-01
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| Series: | G3: Genes, Genomes, Genetics |
| Subjects: | |
| Online Access: | http://g3journal.org/lookup/doi/10.1534/g3.117.043331 |
| _version_ | 1819065352100773888 |
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| author | Alexander J. Carrillo Patrick Schacht Ilva E. Cabrera Johnathon Blahut Loren Prudhomme Sarah Dietrich Thomas Bekman Jennifer Mei Cristian Carrera Vivian Chen Isaiah Clark Gerardo Fierro Logan Ganzen Jose Orellana Shelby Wise Kevin Yang Hui Zhong Katherine A. Borkovich |
| author_facet | Alexander J. Carrillo Patrick Schacht Ilva E. Cabrera Johnathon Blahut Loren Prudhomme Sarah Dietrich Thomas Bekman Jennifer Mei Cristian Carrera Vivian Chen Isaiah Clark Gerardo Fierro Logan Ganzen Jose Orellana Shelby Wise Kevin Yang Hui Zhong Katherine A. Borkovich |
| author_sort | Alexander J. Carrillo |
| collection | DOAJ |
| description | Regulation of gene expression by DNA-binding transcription factors is essential for proper control of growth and development in all organisms. In this study, we annotate and characterize growth and developmental phenotypes for transcription factor genes in the model filamentous fungus Neurospora crassa. We identified 312 transcription factor genes, corresponding to 3.2% of the protein coding genes in the genome. The largest class was the fungal-specific Zn2Cys6 (C6) binuclear cluster, with 135 members, followed by the highly conserved C2H2 zinc finger group, with 61 genes. Viable knockout mutants were produced for 273 genes, and complete growth and developmental phenotypic data are available for 242 strains, with 64% possessing at least one defect. The most prominent defect observed was in growth of basal hyphae (43% of mutants analyzed), followed by asexual sporulation (38%), and the various stages of sexual development (19%). Two growth or developmental defects were observed for 21% of the mutants, while 8% were defective in all three major phenotypes tested. Analysis of available mRNA expression data for a time course of sexual development revealed mutants with sexual phenotypes that correlate with transcription factor transcript abundance in wild type. Inspection of this data also implicated cryptic roles in sexual development for several cotranscribed transcription factor genes that do not produce a phenotype when mutated. |
| first_indexed | 2024-12-21T15:45:06Z |
| format | Article |
| id | doaj.art-a2bd32cbb8ab46568685a52015225ed6 |
| institution | Directory Open Access Journal |
| issn | 2160-1836 |
| language | English |
| last_indexed | 2024-12-21T15:45:06Z |
| publishDate | 2017-09-01 |
| publisher | Oxford University Press |
| record_format | Article |
| series | G3: Genes, Genomes, Genetics |
| spelling | doaj.art-a2bd32cbb8ab46568685a52015225ed62022-12-21T18:58:24ZengOxford University PressG3: Genes, Genomes, Genetics2160-18362017-09-01792945295610.1534/g3.117.0433317Functional Profiling of Transcription Factor Genes in Neurospora crassaAlexander J. CarrilloPatrick SchachtIlva E. CabreraJohnathon BlahutLoren PrudhommeSarah DietrichThomas BekmanJennifer MeiCristian CarreraVivian ChenIsaiah ClarkGerardo FierroLogan GanzenJose OrellanaShelby WiseKevin YangHui ZhongKatherine A. BorkovichRegulation of gene expression by DNA-binding transcription factors is essential for proper control of growth and development in all organisms. In this study, we annotate and characterize growth and developmental phenotypes for transcription factor genes in the model filamentous fungus Neurospora crassa. We identified 312 transcription factor genes, corresponding to 3.2% of the protein coding genes in the genome. The largest class was the fungal-specific Zn2Cys6 (C6) binuclear cluster, with 135 members, followed by the highly conserved C2H2 zinc finger group, with 61 genes. Viable knockout mutants were produced for 273 genes, and complete growth and developmental phenotypic data are available for 242 strains, with 64% possessing at least one defect. The most prominent defect observed was in growth of basal hyphae (43% of mutants analyzed), followed by asexual sporulation (38%), and the various stages of sexual development (19%). Two growth or developmental defects were observed for 21% of the mutants, while 8% were defective in all three major phenotypes tested. Analysis of available mRNA expression data for a time course of sexual development revealed mutants with sexual phenotypes that correlate with transcription factor transcript abundance in wild type. Inspection of this data also implicated cryptic roles in sexual development for several cotranscribed transcription factor genes that do not produce a phenotype when mutated.http://g3journal.org/lookup/doi/10.1534/g3.117.043331filamentous fungitranscription factorsfunctional genomicsgene knockoutstranscriptional profiling |
| spellingShingle | Alexander J. Carrillo Patrick Schacht Ilva E. Cabrera Johnathon Blahut Loren Prudhomme Sarah Dietrich Thomas Bekman Jennifer Mei Cristian Carrera Vivian Chen Isaiah Clark Gerardo Fierro Logan Ganzen Jose Orellana Shelby Wise Kevin Yang Hui Zhong Katherine A. Borkovich Functional Profiling of Transcription Factor Genes in Neurospora crassa G3: Genes, Genomes, Genetics filamentous fungi transcription factors functional genomics gene knockouts transcriptional profiling |
| title | Functional Profiling of Transcription Factor Genes in Neurospora crassa |
| title_full | Functional Profiling of Transcription Factor Genes in Neurospora crassa |
| title_fullStr | Functional Profiling of Transcription Factor Genes in Neurospora crassa |
| title_full_unstemmed | Functional Profiling of Transcription Factor Genes in Neurospora crassa |
| title_short | Functional Profiling of Transcription Factor Genes in Neurospora crassa |
| title_sort | functional profiling of transcription factor genes in neurospora crassa |
| topic | filamentous fungi transcription factors functional genomics gene knockouts transcriptional profiling |
| url | http://g3journal.org/lookup/doi/10.1534/g3.117.043331 |
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