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Marešová A, Oravcová M, Rodríguez-López M, Hradilová M, Zemlianski V, Häsler R, Hernández P, Bähler J, Převorovský M. Critical importance of DNA binding for CSL protein functions in fission yeast. J Cell Sci 2024; 137:jcs261568. [PMID: 38482739 DOI: 10.1242/jcs.261568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 03/07/2024] [Indexed: 05/01/2024] Open
Abstract
CSL proteins [named after the homologs CBF1 (RBP-Jκ in mice), Suppressor of Hairless and LAG-1] are conserved transcription factors found in animals and fungi. In the fission yeast Schizosaccharomyces pombe, they regulate various cellular processes, including cell cycle progression, lipid metabolism and cell adhesion. CSL proteins bind to DNA through their N-terminal Rel-like domain and central β-trefoil domain. Here, we investigated the importance of DNA binding for CSL protein functions in fission yeast. We created CSL protein mutants with disrupted DNA binding and found that the vast majority of CSL protein functions depend on intact DNA binding. Specifically, DNA binding is crucial for the regulation of cell adhesion, lipid metabolism, cell cycle progression, long non-coding RNA expression and genome integrity maintenance. Interestingly, perturbed lipid metabolism leads to chromatin structure changes, potentially linking lipid metabolism to the diverse phenotypes associated with CSL protein functions. Our study highlights the critical role of DNA binding for CSL protein functions in fission yeast.
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Affiliation(s)
- Anna Marešová
- Department of Cell Biology, Faculty of Science, Charles University, Viničná 7, 128 00 Prague 2, Czechia
| | - Martina Oravcová
- Department of Cell Biology, Faculty of Science, Charles University, Viničná 7, 128 00 Prague 2, Czechia
| | - María Rodríguez-López
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Miluše Hradilová
- Laboratory of Genomics and Bioinformatics, Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague 4, Czechia
| | - Viacheslav Zemlianski
- Department of Cell Biology, Faculty of Science, Charles University, Viničná 7, 128 00 Prague 2, Czechia
| | - Robert Häsler
- Center for Inflammatory Skin Diseases, Department of Dermatology and Allergy, University Hospital Schleswig-Holstein, Campus Kiel, Rosalind-Franklin-Straße 9, 24105 Kiel, Germany
| | - Pablo Hernández
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Jürg Bähler
- Institute of Healthy Ageing and Department of Genetics, Evolution and Environment , University College London, Gower Street, London WC1E 6BT, UK
| | - Martin Převorovský
- Department of Cell Biology, Faculty of Science, Charles University, Viničná 7, 128 00 Prague 2, Czechia
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Chatfield-Reed K, Marno Jones K, Shah F, Chua G. Genetic-interaction screens uncover novel biological roles and regulators of transcription factors in fission yeast. G3 GENES|GENOMES|GENETICS 2022; 12:6655692. [PMID: 35924983 PMCID: PMC9434175 DOI: 10.1093/g3journal/jkac194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 07/20/2022] [Indexed: 12/05/2022]
Abstract
In Schizosaccharomyces pombe, systematic analyses of single transcription factor deletion or overexpression strains have made substantial advances in determining the biological roles and target genes of transcription factors, yet these characteristics are still relatively unknown for over a quarter of them. Moreover, the comprehensive list of proteins that regulate transcription factors remains incomplete. To further characterize Schizosaccharomyces pombe transcription factors, we performed synthetic sick/lethality and synthetic dosage lethality screens by synthetic genetic array. Examination of 2,672 transcription factor double deletion strains revealed a sick/lethality interaction frequency of 1.72%. Phenotypic analysis of these sick/lethality strains revealed potential cell cycle roles for several poorly characterized transcription factors, including SPBC56F2.05, SPCC320.03, and SPAC3C7.04. In addition, we examined synthetic dosage lethality interactions between 14 transcription factors and a miniarray of 279 deletion strains, observing a synthetic dosage lethality frequency of 4.99%, which consisted of known and novel transcription factor regulators. The miniarray contained deletions of genes that encode primarily posttranslational-modifying enzymes to identify putative upstream regulators of the transcription factor query strains. We discovered that ubiquitin ligase Ubr1 and its E2/E3-interacting protein, Mub1, degrade the glucose-responsive transcriptional repressor Scr1. Loss of ubr1+ or mub1+ increased Scr1 protein expression, which resulted in enhanced repression of flocculation through Scr1. The synthetic dosage lethality screen also captured interactions between Scr1 and 2 of its known repressors, Sds23 and Amk2, each affecting flocculation through Scr1 by influencing its nuclear localization. Our study demonstrates that sick/lethality and synthetic dosage lethality screens can be effective in uncovering novel functions and regulators of Schizosaccharomyces pombe transcription factors.
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Affiliation(s)
- Kate Chatfield-Reed
- Department of Biological Sciences, University of Calgary , Calgary, Alberta T2N 1N4, Canada
| | - Kurtis Marno Jones
- Department of Biological Sciences, University of Calgary , Calgary, Alberta T2N 1N4, Canada
| | - Farah Shah
- Department of Biological Sciences, University of Calgary , Calgary, Alberta T2N 1N4, Canada
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3
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Rodriguez-Lopez M, Anver S, Cotobal C, Kamrad S, Malecki M, Correia-Melo C, Hoti M, Townsend S, Marguerat S, Pong SK, Wu MY, Montemayor L, Howell M, Ralser M, Bähler J. Functional profiling of long intergenic non-coding RNAs in fission yeast. eLife 2022; 11:e76000. [PMID: 34984977 PMCID: PMC8730722 DOI: 10.7554/elife.76000] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 12/02/2021] [Indexed: 12/19/2022] Open
Abstract
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 analysed 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 analysed 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 analysed 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.
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Affiliation(s)
- Maria Rodriguez-Lopez
- University College London, Institute of Healthy Ageing and Department of Genetics, Evolution & EnvironmentLondonUnited Kingdom
| | - Shajahan Anver
- University College London, Institute of Healthy Ageing and Department of Genetics, Evolution & EnvironmentLondonUnited Kingdom
| | - Cristina Cotobal
- University College London, Institute of Healthy Ageing and Department of Genetics, Evolution & EnvironmentLondonUnited Kingdom
| | - Stephan Kamrad
- University College London, Institute of Healthy Ageing and Department of Genetics, Evolution & EnvironmentLondonUnited Kingdom
- The Francis Crick Institute, Molecular Biology of Metabolism LaboratoryLondonUnited Kingdom
- Charité Universitätsmedizin Berlin, Institute of BiochemistryBerlinGermany
| | - Michal Malecki
- University College London, Institute of Healthy Ageing and Department of Genetics, Evolution & EnvironmentLondonUnited Kingdom
| | - Clara Correia-Melo
- The Francis Crick Institute, Molecular Biology of Metabolism LaboratoryLondonUnited Kingdom
| | - Mimoza Hoti
- University College London, Institute of Healthy Ageing and Department of Genetics, Evolution & EnvironmentLondonUnited Kingdom
| | - StJohn Townsend
- University College London, Institute of Healthy Ageing and Department of Genetics, Evolution & EnvironmentLondonUnited Kingdom
- The Francis Crick Institute, Molecular Biology of Metabolism LaboratoryLondonUnited Kingdom
| | - Samuel Marguerat
- University College London, Institute of Healthy Ageing and Department of Genetics, Evolution & EnvironmentLondonUnited Kingdom
| | - Sheng Kai Pong
- University College London, Institute of Healthy Ageing and Department of Genetics, Evolution & EnvironmentLondonUnited Kingdom
| | - Mary Y Wu
- The Francis Crick Institute, High Throughput ScreeningLondonUnited Kingdom
| | - Luis Montemayor
- University College London, Institute of Healthy Ageing and Department of Genetics, Evolution & EnvironmentLondonUnited Kingdom
| | - Michael Howell
- The Francis Crick Institute, High Throughput ScreeningLondonUnited Kingdom
| | - Markus Ralser
- The Francis Crick Institute, Molecular Biology of Metabolism LaboratoryLondonUnited Kingdom
- Charité Universitätsmedizin Berlin, Institute of BiochemistryBerlinGermany
| | - Jürg Bähler
- University College London, Institute of Healthy Ageing and Department of Genetics, Evolution & EnvironmentLondonUnited Kingdom
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4
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Transcription factor stoichiometry in cell fate determination. J Genet 2021. [DOI: 10.1007/s12041-021-01278-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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5
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Deletion of the non-essential Rpb9 subunit of RNA polymerase II results in pleiotropic phenotypes in Schizosaccharomyces pombe. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2021; 1869:140654. [PMID: 33775921 DOI: 10.1016/j.bbapap.2021.140654] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 03/19/2021] [Accepted: 03/22/2021] [Indexed: 10/21/2022]
Abstract
Schizosaccharomyces pombe RNA polymerase II comprises twelve different subunits. Its Rpb9 subunit comprises 113 amino acids, and is the only non-essential subunit of S. pombe RNA polymerase II. However, its functions have not been studied in S. pombe. The results presented in this study demonstrate that Rpb9 is involved in regulating growth under optimum and certain stress conditions in S. pombe. To further address the role (s) of various domains of this subunit in regulating these phenotypes, deletion mutant analysis was done. We observed that the region spanning 1-74 amino acids, encompassing the amino-terminal zinc finger domain and the linker region of Rpb9 was able to rescue the phenotypes associated with rpb9+deletion. We also demonstrate that the functions of this subunit are only partially conserved among yeast and humans. Our computational biology approaches provide a structural basis for the differential role of various Rpb9 domains in S. pombe. Furthermore, using these tools we show that there has been a co-evolution of the interaction residues between the Rpb9 subunit and the two largest subunits of RNA polymerase II, allowing for a more stringent organism-specific packing. Taken together, our results have provided functional and structural insights into the Rpb9 subunit of S. pombe.
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6
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Sweta K, Sharma N. Functional interaction between ELL transcription elongation factor and Epe1 reveals the role of Epe1 in the regulation of transcription outside heterochromatin. Mol Microbiol 2021; 116:80-96. [PMID: 33533152 DOI: 10.1111/mmi.14691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 01/25/2021] [Accepted: 01/27/2021] [Indexed: 11/30/2022]
Abstract
Eleven-nineteen lysine-rich leukemia (ELL) is a eukaryotic RNA polymerase II transcription elongation factor. In Schizosaccharomyces pombe, it is important for survival under genotoxic stress conditions. However, the molecular basis underlying this function of ELL in S. pombe is yet to be deciphered. Here, we carried out a genetic screen to identify multicopy suppressor(s) that could restore normal growth of ell1 deletion mutant in the presence of DNA damaging agent. Sequence analysis of the identified suppressors revealed the anti-silencing protein, Epe1, as one of the suppressors of ell1 deletion associated genotoxic stress sensitivity. Our results further demonstrate that the overexpression of Epe1 could suppress all other phenotypes associated with the absence of Ell1. Moreover, transcriptional defect of ell1Δ strain could also be alleviated by the overexpression of Epe1. Epe1 also showed a physical interaction with Ell1. Interestingly, we also observed that the region of Epe1 encompassing 403-948 amino acids was indispensable for all the above functions. Furthermore, our results show that the overexpression of Epe1 causes increased H3K9 acetylation and RNA polymerase II recruitment. Taken together, our results show a functional interaction between Epe1 and Ell1, and this function is independent of the well-known JmjC and N-terminal transcriptional activation domains of Epe1 in S. pombe.
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Affiliation(s)
- Kumari Sweta
- University School of Biotechnology, G.G.S. Indraprastha University, New Delhi, India
| | - Nimisha Sharma
- University School of Biotechnology, G.G.S. Indraprastha University, New Delhi, India
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7
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Garg A. A lncRNA-regulated gene expression system with rapid induction kinetics in the fission yeast Schizosaccharomyces pombe. RNA (NEW YORK, N.Y.) 2020; 26:1743-1752. [PMID: 32788323 PMCID: PMC7566572 DOI: 10.1261/rna.076000.120] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 08/07/2020] [Indexed: 06/11/2023]
Abstract
The fission yeast Schizosaccharomyces pombe is an excellent model organism for the study of eukaryotic cellular physiology. The organism is genetically tractable and several tools to study the functions of individual genes are available. One such tool is regulatable gene expression and overproduction of proteins. Limitations of currently available overexpression systems include delay in expression after induction, narrow dynamic range, and system-wide changes due to induction conditions. Here I describe a new long noncoding RNA (lncRNA)-regulated, thiamine-inducible expression system that integrates lncRNA-based transcriptional interference at the fission yeast tgp1 promoter with the fast repression kinetics of the thiamine-repressible nmt1 promoter. This hybrid system has rapid induction kinetics, broad dynamic range, and tunable expression via thiamine concentration. The lncRNA-regulated thiamine-inducible system will be advantageous for the study of individual genes and for potential applications in the production of heterologous proteins in fission yeast.
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Affiliation(s)
- Angad Garg
- Molecular Biology Program, Sloan-Kettering Institute, New York, New York 10065, USA
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8
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Furukawa T, van Rhijn N, Fraczek M, Gsaller F, Davies E, Carr P, Gago S, Fortune-Grant R, Rahman S, Gilsenan JM, Houlder E, Kowalski CH, Raj S, Paul S, Cook P, Parker JE, Kelly S, Cramer RA, Latgé JP, Moye-Rowley S, Bignell E, Bowyer P, Bromley MJ. The negative cofactor 2 complex is a key regulator of drug resistance in Aspergillus fumigatus. Nat Commun 2020; 11:427. [PMID: 31969561 PMCID: PMC7194077 DOI: 10.1038/s41467-019-14191-1] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 12/13/2019] [Indexed: 12/13/2022] Open
Abstract
The frequency of antifungal resistance, particularly to the azole class of ergosterol biosynthetic inhibitors, is a growing global health problem. Survival rates for those infected with resistant isolates are exceptionally low. Beyond modification of the drug target, our understanding of the molecular basis of azole resistance in the fungal pathogen Aspergillus fumigatus is limited. We reasoned that clinically relevant antifungal resistance could derive from transcriptional rewiring, promoting drug resistance without concomitant reductions in pathogenicity. Here we report a genome-wide annotation of transcriptional regulators in A. fumigatus and construction of a library of 484 transcription factor null mutants. We identify 12 regulators that have a demonstrable role in itraconazole susceptibility and show that loss of the negative cofactor 2 complex leads to resistance, not only to the azoles but also the salvage therapeutics amphotericin B and terbinafine without significantly affecting pathogenicity. Resistance to primary treatments of invasive aspergillosis is growing. Here, the authors generate a knockout library for 484 transcription factors in Aspergillus fumigatus, and show that loss of the NCT complex leads to cross-resistance to all primary and some salvage therapeutics without affecting pathogenicity.
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Affiliation(s)
- Takanori Furukawa
- Manchester Fungal Infection Group, Division of Infection, Immunity and Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Manchester, CTF Building, 46 Grafton Street, Manchester, M13 9NT, UK.,Lydia Becker Institute of Immunology and Inflammation, Manchester Collaborative Centre for Inflammation Research, Division of Infection, Immunity and Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Norman van Rhijn
- Manchester Fungal Infection Group, Division of Infection, Immunity and Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Manchester, CTF Building, 46 Grafton Street, Manchester, M13 9NT, UK.,Lydia Becker Institute of Immunology and Inflammation, Manchester Collaborative Centre for Inflammation Research, Division of Infection, Immunity and Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Marcin Fraczek
- Manchester Fungal Infection Group, Division of Infection, Immunity and Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Manchester, CTF Building, 46 Grafton Street, Manchester, M13 9NT, UK
| | - Fabio Gsaller
- Manchester Fungal Infection Group, Division of Infection, Immunity and Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Manchester, CTF Building, 46 Grafton Street, Manchester, M13 9NT, UK
| | - Emma Davies
- Manchester Fungal Infection Group, Division of Infection, Immunity and Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Manchester, CTF Building, 46 Grafton Street, Manchester, M13 9NT, UK
| | - Paul Carr
- Manchester Fungal Infection Group, Division of Infection, Immunity and Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Manchester, CTF Building, 46 Grafton Street, Manchester, M13 9NT, UK
| | - Sara Gago
- Manchester Fungal Infection Group, Division of Infection, Immunity and Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Manchester, CTF Building, 46 Grafton Street, Manchester, M13 9NT, UK.,Lydia Becker Institute of Immunology and Inflammation, Manchester Collaborative Centre for Inflammation Research, Division of Infection, Immunity and Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Rachael Fortune-Grant
- Manchester Fungal Infection Group, Division of Infection, Immunity and Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Manchester, CTF Building, 46 Grafton Street, Manchester, M13 9NT, UK.,Lydia Becker Institute of Immunology and Inflammation, Manchester Collaborative Centre for Inflammation Research, Division of Infection, Immunity and Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Sayema Rahman
- Manchester Fungal Infection Group, Division of Infection, Immunity and Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Manchester, CTF Building, 46 Grafton Street, Manchester, M13 9NT, UK.,Lydia Becker Institute of Immunology and Inflammation, Manchester Collaborative Centre for Inflammation Research, Division of Infection, Immunity and Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Jane Mabey Gilsenan
- Manchester Fungal Infection Group, Division of Infection, Immunity and Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Manchester, CTF Building, 46 Grafton Street, Manchester, M13 9NT, UK
| | - Emma Houlder
- Lydia Becker Institute of Immunology and Inflammation, Manchester Collaborative Centre for Inflammation Research, Division of Infection, Immunity and Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Caitlin H Kowalski
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH, 03766, USA
| | - Shriya Raj
- Unité des Aspergillus, Institut Pasteur, 25 rue du Docteur Roux, 75724 Cedex 15, Paris, France
| | - Sanjoy Paul
- Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
| | - Peter Cook
- Lydia Becker Institute of Immunology and Inflammation, Manchester Collaborative Centre for Inflammation Research, Division of Infection, Immunity and Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Josie E Parker
- Institute of Life Science, Swansea University Medical School, Swansea University, Swansea, Wales, SA2 8PP, UK
| | - Steve Kelly
- Institute of Life Science, Swansea University Medical School, Swansea University, Swansea, Wales, SA2 8PP, UK
| | - Robert A Cramer
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH, 03766, USA
| | - Jean-Paul Latgé
- Unité des Aspergillus, Institut Pasteur, 25 rue du Docteur Roux, 75724 Cedex 15, Paris, France
| | - Scott Moye-Rowley
- Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
| | - Elaine Bignell
- Manchester Fungal Infection Group, Division of Infection, Immunity and Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Manchester, CTF Building, 46 Grafton Street, Manchester, M13 9NT, UK.,Lydia Becker Institute of Immunology and Inflammation, Manchester Collaborative Centre for Inflammation Research, Division of Infection, Immunity and Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Paul Bowyer
- Manchester Fungal Infection Group, Division of Infection, Immunity and Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Manchester, CTF Building, 46 Grafton Street, Manchester, M13 9NT, UK. .,Lydia Becker Institute of Immunology and Inflammation, Manchester Collaborative Centre for Inflammation Research, Division of Infection, Immunity and Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK.
| | - Michael J Bromley
- Manchester Fungal Infection Group, Division of Infection, Immunity and Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Manchester, CTF Building, 46 Grafton Street, Manchester, M13 9NT, UK. .,Lydia Becker Institute of Immunology and Inflammation, Manchester Collaborative Centre for Inflammation Research, Division of Infection, Immunity and Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK.
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Checkpoint Regulation of Nuclear Tos4 Defines S Phase Arrest in Fission Yeast. G3-GENES GENOMES GENETICS 2020; 10:255-266. [PMID: 31719112 PMCID: PMC6945033 DOI: 10.1534/g3.119.400726] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
From yeast to humans, the cell cycle is tightly controlled by regulatory networks that regulate cell proliferation and can be monitored by dynamic visual markers in living cells. We have observed S phase progression by monitoring nuclear accumulation of the FHA-containing DNA binding protein Tos4, which is expressed in the G1/S phase transition. We use Tos4 localization to distinguish three classes of DNA replication mutants: those that arrest with an apparent 1C DNA content and accumulate Tos4 at the restrictive temperature; those that arrest with an apparent 2C DNA content, that do not accumulate Tos4; and those that proceed into mitosis despite a 1C DNA content, again without Tos4 accumulation. Our data indicate that Tos4 localization in these conditions is responsive to checkpoint kinases, with activation of the Cds1 checkpoint kinase promoting Tos4 retention in the nucleus, and activation of the Chk1 damage checkpoint promoting its turnover. Tos4 localization therefore allows us to monitor checkpoint-dependent activation that responds to replication failure in early vs. late S phase.
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Targeted Forward Genetics: Population-Scale Analyses of Allele Replacements Spanning Thousands of Base Pairs in Fission Yeast. G3-GENES GENOMES GENETICS 2019; 9:4097-4106. [PMID: 31597677 PMCID: PMC6893178 DOI: 10.1534/g3.119.400805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Precise allele replacement (genome editing), without unwanted changes to the genome, provides a powerful tool to define the functions of DNA elements and encoded factors in their normal biological context. While CRISPR is now used extensively for gene targeting, its utility for precise allele replacement at population scale is limited because: (A) there is a strict requirement for a correctly positioned PAM motif to introduce recombinogenic dsDNA breaks (DSBs); (B) efficient replacements only occur very close to the DSBs; and (C) indels and off-target changes are frequently generated. Here we show, using a saturated mutation library with about 15,000 alleles of the ade6 gene of Schizosaccharomyces pombe, that pop-in, pop-out allele replacement circumvents these problems. Two rounds of selection ensure that clones arise by homologous recombination with the target locus. Moreover, the exceptionally high efficiency allows one to carry out the process in bulk, then screen individual clones for phenotypes and genotypes. Alleles were introduced successfully throughout the region targeted, up to 1,956 base pairs from the DSB. About 11% of mutant alleles were hypomorphic, demonstrating utility for analyses of essential genes and genetic elements. This process of “targeted forward genetics” can be used to analyze comprehensively, across thousands of base pairs within a specific target region, a variety of allelic changes, such as scanning amino acid substitutions, deletions, and epitope tags. The overall approach and optimized workflow are extensible to other organisms that support gene targeting.
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11
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Takenaka K, Tanabe T, Kawamukai M, Matsuo Y. Overexpression of the transcription factor Rst2 in Schizosaccharomyces pombe indicates growth defect, mitotic defects, and microtubule disorder. Biosci Biotechnol Biochem 2018; 82:247-257. [PMID: 29316864 DOI: 10.1080/09168451.2017.1415126] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
In Schizosaccharomyces pombe, the transcription factor Rst2 regulates ste11 in meiosis and fbp1 in glucogenesis downstream of the cyclic adenosine monophosphate (cAMP)-dependent protein kinase (PKA) pathway. Here, we demonstrate that Rst2 regulates additional cellular events. Overexpressed Rst2 elevated the frequency of oval, bent, branched, septated, and multi-septated cells. Cells showed normal nuclear divisions but exhibited abnormal nuclear organization at low frequency. In oval cells, microtubules were curved but they were rescued by the deletion of mal3. Since growth defect was not rescued by mal3 deletion, we argue that it is regulated independently. Loss of functional Pka1 exaggerated growth defect upon Rst2 overexpression because its downregulation by Pka1 was lost. Overexpression of Rst2 also caused sensitivity to KCl and CaCl2. These findings suggest that, in addition to meiosis and glucogenesis, Rst2 is involved in cellular events such as regulation of cell growth, cell morphology, mitosis progression, microtubules structure, nuclear structure, and stress response.
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Affiliation(s)
- Kouhei Takenaka
- a Department of Life Science and Biotechnology, Faculty of Life and Environmental Science , Shimane University , Matsue , Japan
| | - Takuma Tanabe
- a Department of Life Science and Biotechnology, Faculty of Life and Environmental Science , Shimane University , Matsue , Japan
| | - Makoto Kawamukai
- a Department of Life Science and Biotechnology, Faculty of Life and Environmental Science , Shimane University , Matsue , Japan
| | - Yasuhiro Matsuo
- a Department of Life Science and Biotechnology, Faculty of Life and Environmental Science , Shimane University , Matsue , Japan
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12
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Bandyopadhyay S, Ghosh PM, Basu S, Paul M, Alam SB, Das E, Sundaram G. Antagonistic regulation of cyclin expression by the bZIP transcription factors Pcr1 and Atf1 during G2/M transition. FEMS Microbiol Lett 2017. [PMID: 28645196 DOI: 10.1093/femsle/fnx132] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The transcription factor Atf1 is known to promote cell survival during various stress conditions in Schizosaccharomyces pombe by activating the expression of appropriate genes. It can also activate transcription of other important genes responsible for cell cycle progression. An Atf1-dependent increase in the expression of cell division promoting genes will oppose activation of checkpoints necessary to ensure repairs and cell survival during stress. Hence, selective inhibition of the cell cycle-related functions of Atf1 would be indispensable for cellular survival during stress. Here we present evidence in favour of selective inhibition of Atf1's ability to activate cdc13+ transcription. We show that the transcription factor Pcr1 can specifically inhibit the recruitment of Atf1 on cdc13 promoter and thereby prevent Atf1-mediated mitotic acceleration. We also show that this opposition of Atf1 functions by Pcr1 extends to the G1-S transition event as well. Altogether these results suggest a previously unknown antagonistic function of Atf1 and Pcr1 in regulating Cdc13 expression during cell cycle progression.
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Affiliation(s)
- Sushobhana Bandyopadhyay
- Department of Biochemistry and Centre for Research in Nanoscience and Nanotechnology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata-700019, West Bengal, India
| | - Protiti Maiti Ghosh
- Department of Biochemistry and Centre for Research in Nanoscience and Nanotechnology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata-700019, West Bengal, India
| | - Sohini Basu
- Department of Biochemistry and Centre for Research in Nanoscience and Nanotechnology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata-700019, West Bengal, India
| | - Madhurima Paul
- Department of Biochemistry and Centre for Research in Nanoscience and Nanotechnology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata-700019, West Bengal, India
| | - Syed Benazir Alam
- Department of Biochemistry and Centre for Research in Nanoscience and Nanotechnology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata-700019, West Bengal, India
| | - Elizabeth Das
- Department of Biochemistry and Centre for Research in Nanoscience and Nanotechnology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata-700019, West Bengal, India
| | - Geetanjali Sundaram
- Department of Biochemistry and Centre for Research in Nanoscience and Nanotechnology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata-700019, West Bengal, India
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13
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Převorovský M, Oravcová M, Zach R, Jordáková A, Bähler J, Půta F, Folk P. CSL protein regulates transcription of genes required to prevent catastrophic mitosis in fission yeast. Cell Cycle 2016; 15:3082-3093. [PMID: 27687771 DOI: 10.1080/15384101.2016.1235100] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
For every eukaryotic cell to grow and divide, intricately coordinated action of numerous proteins is required to ensure proper cell-cycle progression. The fission yeast Schizosaccharomyces pombe has been instrumental in elucidating the fundamental principles of cell-cycle control. Mutations in S. pombe 'cut' (cell untimely torn) genes cause failed coordination between cell and nuclear division, resulting in catastrophic mitosis. Deletion of cbf11, a fission yeast CSL transcription factor gene, triggers a 'cut' phenotype, but the precise role of Cbf11 in promoting mitotic fidelity is not known. We report that Cbf11 directly activates the transcription of the acetyl-coenzyme A carboxylase gene cut6, and the biotin uptake/biosynthesis genes vht1 and bio2, with the former 2 implicated in mitotic fidelity. Cbf11 binds to a canonical, metazoan-like CSL response element (GTGGGAA) in the cut6 promoter. Expression of Cbf11 target genes shows apparent oscillations during the cell cycle using temperature-sensitive cdc25-22 and cdc10-M17 block-release experiments, but not with other synchronization methods. The penetrance of catastrophic mitosis in cbf11 and cut6 mutants is nutrient-dependent. We also show that drastic decrease in biotin availability arrests cell proliferation but does not cause mitotic defects. Taken together, our results raise the possibility that CSL proteins play conserved roles in regulating cell-cycle progression, and they could guide experiments into mitotic CSL functions in mammals.
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Affiliation(s)
- Martin Převorovský
- a Department of Cell Biology , Faculty of Science, Charles University in Prague , Prague , Czech Republic
| | - Martina Oravcová
- a Department of Cell Biology , Faculty of Science, Charles University in Prague , Prague , Czech Republic
| | - Róbert Zach
- a Department of Cell Biology , Faculty of Science, Charles University in Prague , Prague , Czech Republic
| | - Anna Jordáková
- a Department of Cell Biology , Faculty of Science, Charles University in Prague , Prague , Czech Republic
| | - Jürg Bähler
- b Research Department of Genetics , Evolution & Environment and UCL Cancer Institute, University College London , Gower Street, London , UK
| | - František Půta
- a Department of Cell Biology , Faculty of Science, Charles University in Prague , Prague , Czech Republic
| | - Petr Folk
- a Department of Cell Biology , Faculty of Science, Charles University in Prague , Prague , Czech Republic
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14
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Vishwanatha A, Rallis C, Bevkal Subramanyaswamy S, D'Souza CJM, Bähler J, Schweingruber ME. Identification of nuclear genes affecting 2-Deoxyglucose resistance in Schizosaccharomyces pombe. FEMS Yeast Res 2016; 16:fow061. [PMID: 27481777 PMCID: PMC5452730 DOI: 10.1093/femsyr/fow061] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/25/2016] [Indexed: 01/16/2023] Open
Abstract
2-Deoxyglucose (2-DG) is a toxic glucose analog. To identify genes involved in 2-DG toxicity in Schizosaccharomyces pombe, we screened a wild-type overexpression library for genes which render cells 2-DG resistant. A gene we termed odr1, encoding an uncharacterized hydrolase, led to strong resistance and altered invertase expression when overexpressed. We speculate that Odr1 neutralizes the toxic form of 2-DG, similar to the Saccharomyces cerevisiae Dog1 and Dog2 phosphatases which dephosphorylate 2-DG-6-phosphate synthesized by hexokinase. In a complementary approach, we screened a haploid deletion library to identify 2-DG-resistant mutants. This screen identified the genes snf5, ypa1, pas1 and pho7. In liquid medium, deletions of these genes conferred 2-DG resistance preferentially under glucose-repressed conditions. The deletion mutants expressed invertase activity more constitutively than the control strain, indicating defects in the control of glucose repression. No S. cerevisiae orthologs of the pho7 gene is known, and no 2-DG resistance has been reported for any of the deletion mutants of the other genes identified here. Moreover, 2-DG leads to derepressed invertase activity in S. pombe, while in S. cerevisiae it becomes repressed. Taken together, these findings suggest that mechanisms involved in 2-DG resistance differ between budding and fission yeasts.
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Affiliation(s)
- Akshay Vishwanatha
- Department of Studies in Biochemistry, University of Mysore, Manasagangotri, Mysuru 570 006, Karnataka, India
| | - Charalampos Rallis
- Research Department of Genetics, Evolution and Environment, UCL Institute of Healthy Ageing, University College London, London WC1E 6BT, UK
| | - Shubha Bevkal Subramanyaswamy
- Department of Studies in Biochemistry, University of Mysore, Manasagangotri, Mysuru 570 006, Karnataka, India Institute of Cell Biology, University of Bern, Baltzerstrasse 4, CH-3012 Bern, Switzerland
| | | | - Jürg Bähler
- Research Department of Genetics, Evolution and Environment, UCL Institute of Healthy Ageing, University College London, London WC1E 6BT, UK
| | - Martin Ernst Schweingruber
- Department of Studies in Biochemistry, University of Mysore, Manasagangotri, Mysuru 570 006, Karnataka, India
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15
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Chatfield-Reed K, Vachon L, Kwon EJG, Chua G. Conserved and Diverged Functions of the Calcineurin-Activated Prz1 Transcription Factor in Fission Yeast. Genetics 2016; 202:1365-75. [PMID: 26896331 PMCID: PMC4905549 DOI: 10.1534/genetics.115.184218] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 02/10/2016] [Indexed: 11/23/2022] Open
Abstract
Gene regulation in response to intracellular calcium is mediated by the calcineurin-activated transcription factor Prz1 in the fission yeast Schizosaccharomyces pombe Genome-wide studies of the Crz1 and CrzA fungal orthologs have uncovered numerous target genes involved in conserved and species-specific cellular processes. In contrast, very few target genes of Prz1 have been published. This article identifies an extensive list of genes using transcriptome and ChIP-chip analyses under inducing conditions of Prz1, including CaCl2 and tunicamycin treatment, as well as a ∆pmr1 genetic background. We identified 165 upregulated putative target genes of Prz1 in which the majority contained a calcium-dependent response element in their promoters, similar to that of the Saccharomyces cerevisiae ortholog Crz1 These genes were functionally enriched for Crz1-conserved processes such as cell-wall biosynthesis. Overexpression of prz1(+)increased resistance to the cell-wall degradation enzyme zymolyase, likely from upregulation of theO-mannosyltransferase encoding gene omh1(+) Loss of omh1(+)abrogates this phenotype. We uncovered a novel inhibitory role in flocculation for Prz1. Loss of prz1(+)resulted in constitutive flocculation and upregulation of genes encoding the flocculins Gsf2 and Pfl3, as well as the transcription factor Cbf12. The constitutive flocculation of the ∆prz1 strain was abrogated by the loss of gsf2(+) or cbf12(+) This study reveals that Prz1 functions as a positive and negative transcriptional regulator of genes involved in cell-wall biosynthesis and flocculation, respectively. Moreover, comparison of target genes between Crz1/CrzA and Prz1 indicate some conservation in DNA-binding specificity, but also substantial rewiring of the calcineurin-mediated transcriptional regulatory network.
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Affiliation(s)
- Kate Chatfield-Reed
- Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Lianne Vachon
- Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Eun-Joo Gina Kwon
- Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Gordon Chua
- Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
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16
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Quesnel DM, Oldenburg TBP, Larter SR, Gieg LM, Chua G. Biostimulation of Oil Sands Process-Affected Water with Phosphate Yields Removal of Sulfur-Containing Organics and Detoxification. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:13012-13020. [PMID: 26448451 DOI: 10.1021/acs.est.5b01391] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The ability to mitigate toxicity of oil sands process-affected water (OSPW) for return into the environment is an important issue for effective tailings management in Alberta, Canada. OSPW toxicity has been linked to classical naphthenic acids (NAs), but the toxic contribution of other acid-extractable organics (AEOs) remains unknown. Here, we examine the potential for in situ bioremediation of OSPW AEOs by indigenous algae. Phosphate biostimulation was performed in OSPW to promote the growth of indigenous photosynthetic microorganisms and subsequent toxicity and chemical changes were determined. After 12 weeks, the AEO fraction of phosphate-biostimulated OSPW was significantly less toxic to the fission yeast Schizosaccharomyces pombe than unstimulated OSPW. Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) analysis of the AEO fraction in phosphate-biostimulated OSPW showed decreased levels of SO3 class compounds, including a subset that may represent linear arylsulfonates. A screen with S. pombe transcription factor mutant strains for growth sensitivity to the AEO fraction or sodium dodecylbenzenesulfonate revealed a mode of toxic action consistent with oxidative stress and detrimental effects on cellular membranes. These findings demonstrate a potential algal-based in situ bioremediation strategy for OSPW AEOs and uncover a link between toxicity and AEOs other than classical NAs.
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Affiliation(s)
- Dean M Quesnel
- Department of Biological Sciences, and ‡PRG, Department of Geosciences, University of Calgary , 2500 University Drive NW, Calgary, Alberta Canada T2N 1N4
| | - Thomas B P Oldenburg
- Department of Biological Sciences, and ‡PRG, Department of Geosciences, University of Calgary , 2500 University Drive NW, Calgary, Alberta Canada T2N 1N4
| | - Stephen R Larter
- Department of Biological Sciences, and ‡PRG, Department of Geosciences, University of Calgary , 2500 University Drive NW, Calgary, Alberta Canada T2N 1N4
| | - Lisa M Gieg
- Department of Biological Sciences, and ‡PRG, Department of Geosciences, University of Calgary , 2500 University Drive NW, Calgary, Alberta Canada T2N 1N4
| | - Gordon Chua
- Department of Biological Sciences, and ‡PRG, Department of Geosciences, University of Calgary , 2500 University Drive NW, Calgary, Alberta Canada T2N 1N4
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17
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Převorovský M, Oravcová M, Tvarůžková J, Zach R, Folk P, Půta F, Bähler J. Fission Yeast CSL Transcription Factors: Mapping Their Target Genes and Biological Roles. PLoS One 2015; 10:e0137820. [PMID: 26366556 PMCID: PMC4569565 DOI: 10.1371/journal.pone.0137820] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 08/24/2015] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Cbf11 and Cbf12, the fission yeast CSL transcription factors, have been implicated in the regulation of cell-cycle progression, but no specific roles have been described and their target genes have been only partially mapped. METHODOLOGY/PRINCIPAL FINDINGS Using a combination of transcriptome profiling under various conditions and genome-wide analysis of CSL-DNA interactions, we identify genes regulated directly and indirectly by CSL proteins in fission yeast. We show that the expression of stress-response genes and genes that are expressed periodically during the cell cycle is deregulated upon genetic manipulation of cbf11 and/or cbf12. Accordingly, the coordination of mitosis and cytokinesis is perturbed in cells with genetically manipulated CSL protein levels, together with other specific defects in cell-cycle progression. Cbf11 activity is nutrient-dependent and Δcbf11-associated defects are mitigated by inactivation of the protein kinase A (Pka1) and stress-activated MAP kinase (Sty1p38) pathways. Furthermore, Cbf11 directly regulates a set of lipid metabolism genes and Δcbf11 cells feature a stark decrease in the number of storage lipid droplets. CONCLUSIONS/SIGNIFICANCE Our results provide a framework for a more detailed understanding of the role of CSL proteins in the regulation of cell-cycle progression in fission yeast.
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Affiliation(s)
- Martin Převorovský
- Research Department of Genetics, Evolution & Environment and UCL Cancer Institute, University College London, London, United Kingdom
- Department of Cell Biology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - Martina Oravcová
- Department of Cell Biology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - Jarmila Tvarůžková
- Department of Cell Biology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - Róbert Zach
- Department of Cell Biology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - Petr Folk
- Department of Cell Biology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - František Půta
- Department of Cell Biology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - Jürg Bähler
- Research Department of Genetics, Evolution & Environment and UCL Cancer Institute, University College London, London, United Kingdom
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18
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Systematic genetic analysis of transcription factors to map the fission yeast transcription-regulatory network. Biochem Soc Trans 2013; 41:1696-700. [DOI: 10.1042/bst20130224] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Mapping transcriptional-regulatory networks requires the identification of target genes, binding specificities and signalling pathways of transcription factors. However, the characterization of each transcription factor sufficiently for deciphering such networks remains laborious. The recent availability of overexpression and deletion strains for almost all of the transcription factor genes in the fission yeast Schizosaccharomyces pombe provides a valuable resource to better investigate transcription factors using systematic genetics. In the present paper, I review and discuss the utility of these strain collections combined with transcriptome profiling and genome-wide chromatin immunoprecipitation to identify the target genes of transcription factors.
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