1
|
García-Ruano D, Hsu I, Leray B, Billard B, Liti G, Coudreuse D. Engineering heterothallic strains in fission yeast. Yeast 2024; 41:87-94. [PMID: 38099423 DOI: 10.1002/yea.3914] [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: 09/13/2023] [Revised: 10/18/2023] [Accepted: 11/15/2023] [Indexed: 02/24/2024] Open
Abstract
In poor nitrogen conditions, fission yeast cells mate, undergo meiosis and form spores that are resistant to deleterious environments. Natural isolates of Schizosaccharomyces pombe are homothallic. This allows them to naturally switch between the two h- and h+ mating types with a high frequency, thereby ensuring the presence of both mating partners in a population of cells. However, alteration of the mating type locus can abolish mating type switching or reduce it to a very low frequency. Such heterothallic strains have been isolated and are common in research laboratories due to the simplicity of their use for Mendelian genetics. In addition to the standard laboratory strains, a large collection of natural S. pombe isolates is now available, representing a powerful resource for investigating the genetic diversity and biology of fission yeast. However, most of these strains are homothallic, and only tedious or mutagenic strategies have been described to obtain heterothallic cells from a homothallic parent. Here, we describe a simple approach to generate heterothallic strains. It takes advantage of an alteration of the mating type locus that was previously identified in a mating type switching-deficient strain and the CRISPR-Cas9 editing tool, allowing for a one-step engineering of heterothallic cells with high efficiency.
Collapse
Affiliation(s)
- Daniel García-Ruano
- Institute of Biochemistry and Cellular Genetics, CNRS UMR 5095, University of Bordeaux, Bordeaux, France
| | - Ian Hsu
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Nice, France
| | - Baptiste Leray
- Institute of Biochemistry and Cellular Genetics, CNRS UMR 5095, University of Bordeaux, Bordeaux, France
| | | | - Gianni Liti
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Nice, France
| | - Damien Coudreuse
- Institute of Biochemistry and Cellular Genetics, CNRS UMR 5095, University of Bordeaux, Bordeaux, France
| |
Collapse
|
2
|
García A, Durán L, Sánchez M, González S, Santamaría R, Antequera F. Asymmetrical nucleosomal DNA signatures regulate transcriptional directionality. Cell Rep 2024; 43:113605. [PMID: 38127622 DOI: 10.1016/j.celrep.2023.113605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 10/03/2023] [Accepted: 12/05/2023] [Indexed: 12/23/2023] Open
Abstract
Despite the symmetrical structure of nucleosomes, in vitro studies have shown that transcription proceeds with different efficiency depending on the orientation of the DNA sequence around them. However, it is unclear whether this functional asymmetry is present in vivo and whether it could regulate transcriptional directionality. Here, we report that the proximal and distal halves of nucleosomal DNA contribute differentially to nucleosome stability in the genome. In +1 nucleosomes, this asymmetry facilitates or hinders transcription depending on the orientation of its underlying DNA, and this difference is associated with an asymmetrical interaction between DNA and histones. These properties are encoded in the DNA signature of +1 nucleosomes, since its incorporation in the two orientations into downstream nucleosomes renders them asymmetrically accessible to MNase and inverts the balance between sense and antisense transcription. Altogether, our results show that nucleosomal DNA endows nucleosomes with asymmetrical properties that modulate the directionality of transcription.
Collapse
Affiliation(s)
- Alicia García
- Instituto de Biología Funcional y Genómica (IBFG), CSIC-Universidad de Salamanca, Campus Miguel de Unamuno, 37007 Salamanca, Spain
| | - Laura Durán
- Instituto de Biología Funcional y Genómica (IBFG), CSIC-Universidad de Salamanca, Campus Miguel de Unamuno, 37007 Salamanca, Spain
| | - Mar Sánchez
- Instituto de Biología Funcional y Genómica (IBFG), CSIC-Universidad de Salamanca, Campus Miguel de Unamuno, 37007 Salamanca, Spain
| | - Sara González
- Instituto de Biología Funcional y Genómica (IBFG), CSIC-Universidad de Salamanca, Campus Miguel de Unamuno, 37007 Salamanca, Spain
| | - Rodrigo Santamaría
- Departamento de Informática y Automática, Universidad de Salamanca/Facultad de Ciencias, Plaza de los Caídos s/n, 37007 Salamanca, Spain
| | - Francisco Antequera
- Instituto de Biología Funcional y Genómica (IBFG), CSIC-Universidad de Salamanca, Campus Miguel de Unamuno, 37007 Salamanca, Spain.
| |
Collapse
|
3
|
Nguyen LAC, Mori M, Yasuda Y, Galipon J. Functional Consequences of Shifting Transcript Boundaries in Glucose Starvation. Mol Cell Biol 2023; 43:611-628. [PMID: 37937348 PMCID: PMC10761120 DOI: 10.1080/10985549.2023.2270406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 10/10/2023] [Indexed: 11/09/2023] Open
Abstract
Glucose is a major source of carbon and essential for the survival of many organisms, ranging from yeast to human. A sudden 60-fold reduction of glucose in exponentially growing fission yeast induces transcriptome-wide changes in gene expression. This regulation is multilayered, and the boundaries of transcripts are known to vary, with functional consequences at the protein level. By combining direct RNA sequencing with 5'-CAGE and short-read sequencing, we accurately defined the 5'- and 3'-ends of transcripts that are both poly(A) tailed and 5'-capped in glucose starvation, followed by proteome analysis. Our results confirm previous experimentally validated loci with alternative isoforms and reveal several transcriptome-wide patterns. First, we show that sense-antisense gene pairs are more strongly anticorrelated when a time lag is taken into account. Second, we show that the glucose starvation response initially elicits a shortening of 3'-UTRs and poly(A) tails, followed by a shortening of the 5'-UTRs at later time points. These result in domain gains and losses in proteins involved in the stress response. Finally, the relatively poor overlap both between differentially expressed genes (DEGs), differential transcript usage events (DTUs), and differentially detected proteins (DDPs) highlight the need for further study on post-transcriptional regulation mechanisms in glucose starvation.
Collapse
Affiliation(s)
- Lan Anh Catherine Nguyen
- Institute for Advanced Biosciences, Keio University, Yamagata, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Kanagawa, Fujisawa, Japan
| | - Masaru Mori
- Institute for Advanced Biosciences, Keio University, Yamagata, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Kanagawa, Fujisawa, Japan
- Institute of Innovation for Future Society, Nagoya University, Aichi, Nagoya, Japan
| | - Yuji Yasuda
- Institute for Advanced Biosciences, Keio University, Yamagata, Tsuruoka, Japan
- Faculty of Environment and Information Studies, Keio University, Kanagawa, Fujisawa, Japan
| | - Josephine Galipon
- Institute for Advanced Biosciences, Keio University, Yamagata, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Kanagawa, Fujisawa, Japan
- Graduate School of Science and Engineering, Yamagata University, Yamagata, Yonezawa, Japan
| |
Collapse
|
4
|
Lian Q, Maestroni L, Gaudin M, Llorente B, Mercier R. Meiotic recombination is confirmed to be unusually high in the fission yeast Schizosaccharomyces pombe. iScience 2023; 26:107614. [PMID: 37664590 PMCID: PMC10474467 DOI: 10.1016/j.isci.2023.107614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 03/20/2023] [Accepted: 08/09/2023] [Indexed: 09/05/2023] Open
Abstract
In most eukaryotes, meiotic crossovers (COs) are limited to 1-3 per chromosome, and are prevented from occurring close to one another by CO interference. The fission yeast Schizosaccharomyces pombe, an exception to these general rules, was reported to have the highest CO number per chromosome and no or weak interference. However, global CO frequency was indirectly estimated, calling for confirmation. Here, we used an innovative strategy to determine COs genome-wide in S. pombe. We confirmed weak CO interference, acting at physical distances compatible with the patterning of recombination precursors. We revealed a slight co-variation in CO number between chromosomes, suggesting that a limiting pro-CO factor varies between meiocytes. CO number per chromosome varies proportionally with chromosome size, with the three chromosomes having, on average, 15.9, 12.5, and 7.0 COs, respectively. This reinforces S. pombe's status as the eukaryote with the highest CO number per chromosome described to date.
Collapse
Affiliation(s)
- Qichao Lian
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, Cologne, Germany
| | - Laetitia Maestroni
- CNRS UMR7258, INSERM U1068, Aix Marseille Université UM105, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Maxime Gaudin
- CNRS UMR7258, INSERM U1068, Aix Marseille Université UM105, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Bertrand Llorente
- CNRS UMR7258, INSERM U1068, Aix Marseille Université UM105, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Raphael Mercier
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, Cologne, Germany
| |
Collapse
|
5
|
Weith M, Großbach J, Clement‐Ziza M, Gillet L, Rodríguez‐López M, Marguerat S, Workman CT, Picotti P, Bähler J, Aebersold R, Beyer A. Genetic effects on molecular network states explain complex traits. Mol Syst Biol 2023; 19:e11493. [PMID: 37485750 PMCID: PMC10407735 DOI: 10.15252/msb.202211493] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 06/29/2023] [Accepted: 07/04/2023] [Indexed: 07/25/2023] Open
Abstract
The complexity of many cellular and organismal traits results from the integration of genetic and environmental factors via molecular networks. Network structure and effect propagation are best understood at the level of functional modules, but so far, no concept has been established to include the global network state. Here, we show when and how genetic perturbations lead to molecular changes that are confined to small parts of a network versus when they lead to modulation of network states. Integrating multi-omics profiling of genetically heterogeneous budding and fission yeast strains with an array of cellular traits identified a central state transition of the yeast molecular network that is related to PKA and TOR (PT) signaling. Genetic variants affecting this PT state globally shifted the molecular network along a single-dimensional axis, thereby modulating processes including energy and amino acid metabolism, transcription, translation, cell cycle control, and cellular stress response. We propose that genetic effects can propagate through large parts of molecular networks because of the functional requirement to centrally coordinate the activity of fundamental cellular processes.
Collapse
Affiliation(s)
- Matthias Weith
- Excellence Cluster on Cellular Stress Responses in Aging Associated DiseasesUniversity of CologneCologneGermany
| | - Jan Großbach
- Excellence Cluster on Cellular Stress Responses in Aging Associated DiseasesUniversity of CologneCologneGermany
| | | | - Ludovic Gillet
- Department of BiologyInstitute of Molecular Systems Biology, ETH ZürichZürichSwitzerland
| | - María Rodríguez‐López
- Institute of Healthy Ageing and Department of Genetics, Evolution & EnvironmentUniversity College LondonLondonUK
| | - Samuel Marguerat
- Institute of Healthy Ageing and Department of Genetics, Evolution & EnvironmentUniversity College LondonLondonUK
| | - Christopher T Workman
- Department of Biotechnology and BiomedicineTechnical University of DenmarkLyngbyDenmark
| | - Paola Picotti
- Department of BiologyInstitute of Molecular Systems Biology, ETH ZürichZürichSwitzerland
| | - Jürg Bähler
- Institute of Healthy Ageing and Department of Genetics, Evolution & EnvironmentUniversity College LondonLondonUK
| | - Ruedi Aebersold
- Department of BiologyInstitute of Molecular Systems Biology, ETH ZürichZürichSwitzerland
| | - Andreas Beyer
- Excellence Cluster on Cellular Stress Responses in Aging Associated DiseasesUniversity of CologneCologneGermany
| |
Collapse
|
6
|
Offei B, Braun-Galleani S, Venkatesh A, Casey WT, O’Connor KE, Byrne KP, Wolfe KH. Identification of genetic variants of the industrial yeast Komagataella phaffii (Pichia pastoris) that contribute to increased yields of secreted heterologous proteins. PLoS Biol 2022; 20:e3001877. [PMID: 36520709 PMCID: PMC9754263 DOI: 10.1371/journal.pbio.3001877] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 10/13/2022] [Indexed: 12/23/2022] Open
Abstract
The yeast Komagataella phaffii (formerly called Pichia pastoris) is used widely as a host for secretion of heterologous proteins, but only a few isolates of this species exist and all the commonly used expression systems are derived from a single genetic background, CBS7435 (NRRL Y-11430). We hypothesized that other genetic backgrounds could harbor variants that affect yields of secreted proteins. We crossed CBS7435 with 2 other K. phaffii isolates and mapped quantitative trait loci (QTLs) for secretion of a heterologous protein, β-glucosidase, by sequencing individual segregant genomes. A major QTL mapped to a frameshift mutation in the mannosyltransferase gene HOC1, which gives CBS7435 a weaker cell wall and higher protein secretion than the other isolates. Inactivation of HOC1 in the other isolates doubled β-glucosidase secretion. A second QTL mapped to an amino acid substitution in IRA1 that tripled β-glucosidase secretion in 1-week batch cultures but reduced cell viability, and its effects are specific to this heterologous protein. Our results demonstrate that QTL analysis is a powerful method for dissecting the basis of biotechnological traits in nonconventional yeasts, and a route to improving their industrial performance.
Collapse
Affiliation(s)
- Benjamin Offei
- UCD Conway Institute and School of Medicine, University College Dublin, Dublin, Ireland
| | - Stephanie Braun-Galleani
- UCD Conway Institute and School of Medicine, University College Dublin, Dublin, Ireland
- School of Biochemical Engineering, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Anjan Venkatesh
- UCD Conway Institute and School of Medicine, University College Dublin, Dublin, Ireland
| | - William T. Casey
- Bioplastech Ltd., NovaUCD, Belfield Innovation Park, University College Dublin, Dublin, Ireland
| | - Kevin E. O’Connor
- UCD Earth Institute and School of Biomolecular & Biomedical Science, University College Dublin, Dublin, Ireland
- BiOrbic Bioeconomy SFI Research Centre, University College Dublin, Dublin, Ireland
| | - Kevin P. Byrne
- UCD Conway Institute and School of Medicine, University College Dublin, Dublin, Ireland
| | - Kenneth H. Wolfe
- UCD Conway Institute and School of Medicine, University College Dublin, Dublin, Ireland
- * E-mail:
| |
Collapse
|
7
|
Grossbach J, Gillet L, Clément‐Ziza M, Schmalohr CL, Schubert OT, Schütter M, Mawer JSP, Barnes CA, Bludau I, Weith M, Tessarz P, Graef M, Aebersold R, Beyer A. The impact of genomic variation on protein phosphorylation states and regulatory networks. Mol Syst Biol 2022; 18:e10712. [PMID: 35574625 PMCID: PMC9109056 DOI: 10.15252/msb.202110712] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 04/08/2022] [Accepted: 04/12/2022] [Indexed: 12/11/2022] Open
Abstract
Genomic variation impacts on cellular networks by affecting the abundance (e.g., protein levels) and the functional states (e.g., protein phosphorylation) of their components. Previous work has focused on the former, while in this context, the functional states of proteins have largely remained neglected. Here, we generated high‐quality transcriptome, proteome, and phosphoproteome data for a panel of 112 genomically well‐defined yeast strains. Genetic effects on transcripts were generally transmitted to the protein layer, but specific gene groups, such as ribosomal proteins, showed diverging effects on protein levels compared with RNA levels. Phosphorylation states proved crucial to unravel genetic effects on signaling networks. Correspondingly, genetic variants that cause phosphorylation changes were mostly different from those causing abundance changes in the respective proteins. Underscoring their relevance for cell physiology, phosphorylation traits were more strongly correlated with cell physiological traits such as chemical compound resistance or cell morphology, compared with transcript or protein abundance. This study demonstrates how molecular networks mediate the effects of genomic variants to cellular traits and highlights the particular importance of protein phosphorylation.
Collapse
Affiliation(s)
- Jan Grossbach
- Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases University of Cologne Cologne Germany
| | - Ludovic Gillet
- Department of Biology Institute of Molecular Systems Biology ETH Zurich Zurich Switzerland
| | - Mathieu Clément‐Ziza
- Center for Molecular Medicine Cologne (CMMC) Medical Faculty, University of Cologne Cologne Germany
- Lesaffre International Marcq‐en‐Barœul France
| | - Corinna L Schmalohr
- Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases University of Cologne Cologne Germany
| | - Olga T Schubert
- Department of Human Genetics University of California, Los Angeles Los Angeles CA USA
| | | | | | | | - Isabell Bludau
- Department of Biology Institute of Molecular Systems Biology ETH Zurich Zurich Switzerland
- Department of Proteomics and Signal Transduction Max Planck Institute of Biochemistry Martinsried Germany
| | - Matthias Weith
- Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases University of Cologne Cologne Germany
| | - Peter Tessarz
- Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases University of Cologne Cologne Germany
- Max Planck Institute for Biology of Ageing Cologne Germany
| | - Martin Graef
- Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases University of Cologne Cologne Germany
- Max Planck Institute for Biology of Ageing Cologne Germany
| | - Ruedi Aebersold
- Department of Biology Institute of Molecular Systems Biology ETH Zurich Zurich Switzerland
- Faculty of Science University of Zurich Zurich Switzerland
| | - Andreas Beyer
- Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases University of Cologne Cologne Germany
- Center for Molecular Medicine Cologne (CMMC) Medical Faculty, University of Cologne Cologne Germany
- Institute for Genetics Faculty of Mathematics and Natural Sciences University of Cologne Cologne Germany
| |
Collapse
|
8
|
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.
Collapse
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
| |
Collapse
|
9
|
Peltier E, Bibi-Triki S, Dutreux F, Caradec C, Friedrich A, Llorente B, Schacherer J. Dissection of quantitative trait loci in the Lachancea waltii yeast species highlights major hotspots. G3 (BETHESDA, MD.) 2021; 11:jkab242. [PMID: 34544138 PMCID: PMC8496267 DOI: 10.1093/g3journal/jkab242] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 07/06/2021] [Indexed: 11/30/2022]
Abstract
Dissecting the genetic basis of complex trait remains a real challenge. The budding yeast Saccharomyces cerevisiae has become a model organism for studying quantitative traits, successfully increasing our knowledge in many aspects. However, the exploration of the genotype-phenotype relationship in non-model yeast species could provide a deeper insight into the genetic basis of complex traits. Here, we have studied this relationship in the Lachancea waltii species which diverged from the S. cerevisiae lineage prior to the whole-genome duplication. By performing linkage mapping analyses in this species, we identified 86 quantitative trait loci (QTL) impacting the growth in a large number of conditions. The distribution of these loci across the genome has revealed two major QTL hotspots. A first hotspot corresponds to a general growth QTL, impacting a wide range of conditions. By contrast, the second hotspot highlighted a trade-off with a disadvantageous allele for drug-free conditions which proved to be advantageous in the presence of several drugs. Finally, a comparison of the detected QTL in L. waltii with those which had been previously identified for the same trait in a closely related species, Lachancea kluyveri was performed. This analysis clearly showed the absence of shared QTL across these species. Altogether, our results represent a first step toward the exploration of the genetic architecture of quantitative trait across different yeast species.
Collapse
Affiliation(s)
- Emilien Peltier
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | | | - Fabien Dutreux
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - Claudia Caradec
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - Anne Friedrich
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - Bertrand Llorente
- CNRS UMR7258, INSERM U1068, Aix Marseille Université UM105, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Joseph Schacherer
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
- Institut Universitaire de France (IUF), Paris, France
| |
Collapse
|
10
|
Van Dyke K, Lutz S, Mekonnen G, Myers CL, Albert FW. Trans-acting genetic variation affects the expression of adjacent genes. Genetics 2021; 217:6126816. [PMID: 33789351 DOI: 10.1093/genetics/iyaa051] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 12/16/2020] [Indexed: 11/13/2022] Open
Abstract
Gene expression differences among individuals are shaped by trans-acting expression quantitative trait loci (eQTLs). Most trans-eQTLs map to hotspot locations that influence many genes. The molecular mechanisms perturbed by hotspots are often assumed to involve "vertical" cascades of effects in pathways that can ultimately affect the expression of thousands of genes. Here, we report that trans-eQTLs can affect the expression of adjacent genes via "horizontal" mechanisms that extend along a chromosome. Genes affected by trans-eQTL hotspots in the yeast Saccharomyces cerevisiae were more likely to be located next to each other than expected by chance. These paired hotspot effects tended to occur at adjacent genes that also show coexpression in response to genetic and environmental perturbations, suggesting shared mechanisms. Physical proximity and shared chromatin state, in addition to regulation of adjacent genes by similar transcription factors, were independently associated with paired hotspot effects among adjacent genes. Paired effects of trans-eQTLs can occur at neighboring genes even when these genes do not share a common function. This phenomenon could result in unexpected connections between regulatory genetic variation and phenotypes.
Collapse
Affiliation(s)
- Krisna Van Dyke
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Sheila Lutz
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Gemechu Mekonnen
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Chad L Myers
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Frank W Albert
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA
| |
Collapse
|
11
|
Ellis DA, Reyes-Martín F, Rodríguez-López M, Cotobal C, Sun XM, Saintain Q, Jeffares DC, Marguerat S, Tallada VA, Bähler J. R-loops and regulatory changes in chronologically ageing fission yeast cells drive non-random patterns of genome rearrangements. PLoS Genet 2021; 17:e1009784. [PMID: 34464389 PMCID: PMC8437301 DOI: 10.1371/journal.pgen.1009784] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 09/13/2021] [Accepted: 08/18/2021] [Indexed: 12/03/2022] Open
Abstract
Aberrant repair of DNA double-strand breaks can recombine distant chromosomal breakpoints. Chromosomal rearrangements compromise genome function and are a hallmark of ageing. Rearrangements are challenging to detect in non-dividing cell populations, because they reflect individually rare, heterogeneous events. The genomic distribution of de novo rearrangements in non-dividing cells, and their dynamics during ageing, remain therefore poorly characterized. Studies of genomic instability during ageing have focussed on mitochondrial DNA, small genetic variants, or proliferating cells. To characterize genome rearrangements during cellular ageing in non-dividing cells, we interrogated a single diagnostic measure, DNA breakpoint junctions, using Schizosaccharomyces pombe as a model system. Aberrant DNA junctions that accumulated with age were associated with microhomology sequences and R-loops. Global hotspots for age-associated breakpoint formation were evident near telomeric genes and linked to remote breakpoints elsewhere in the genome, including the mitochondrial chromosome. Formation of breakpoint junctions at global hotspots was inhibited by the Sir2 histone deacetylase and might be triggered by an age-dependent de-repression of chromatin silencing. An unexpected mechanism of genomic instability may cause more local hotspots: age-associated reduction in an RNA-binding protein triggering R-loops at target loci. This result suggests that biological processes other than transcription or replication can drive genome rearrangements. Notably, we detected similar signatures of genome rearrangements that accumulated in old brain cells of humans. These findings provide insights into the unique patterns and possible mechanisms of genome rearrangements in non-dividing cells, which can be promoted by ageing-related changes in gene-regulatory proteins.
Collapse
Affiliation(s)
- David A. Ellis
- Institute of Healthy Ageing, Department of Genetics, Evolution & Environment, University College London, London, United Kingdom
| | - Félix Reyes-Martín
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide/Consejo Superior de Investigaciones Científicas, Seville, Spain
| | - María Rodríguez-López
- Institute of Healthy Ageing, Department of Genetics, Evolution & Environment, University College London, London, United Kingdom
| | - Cristina Cotobal
- Institute of Healthy Ageing, Department of Genetics, Evolution & Environment, University College London, London, United Kingdom
| | - Xi-Ming Sun
- MRC London Institute of Medical Sciences, London, United Kingdom
- Institute of Clinical Sciences, Imperial College London, London, United Kingdom
| | - Quentin Saintain
- Institute of Healthy Ageing, Department of Genetics, Evolution & Environment, University College London, London, United Kingdom
| | - Daniel C. Jeffares
- Institute of Healthy Ageing, Department of Genetics, Evolution & Environment, University College London, London, United Kingdom
| | - Samuel Marguerat
- MRC London Institute of Medical Sciences, London, United Kingdom
- Institute of Clinical Sciences, Imperial College London, London, United Kingdom
| | - Víctor A. Tallada
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide/Consejo Superior de Investigaciones Científicas, Seville, Spain
| | - Jürg Bähler
- Institute of Healthy Ageing, Department of Genetics, Evolution & Environment, University College London, London, United Kingdom
| |
Collapse
|
12
|
Romila CA, Townsend S, Malecki M, Kamrad S, Rodríguez-López M, Hillson O, Cotobal C, Ralser M, Bähler J. Barcode sequencing and a high-throughput assay for chronological lifespan uncover ageing-associated genes in fission yeast. MICROBIAL CELL (GRAZ, AUSTRIA) 2021; 8:146-160. [PMID: 34250083 PMCID: PMC8246024 DOI: 10.15698/mic2021.07.754] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 04/20/2021] [Accepted: 04/26/2021] [Indexed: 12/15/2022]
Abstract
Ageing-related processes are largely conserved, with simple organisms remaining the main platform to discover and dissect new ageing-associated genes. Yeasts provide potent model systems to study cellular ageing owing their amenability to systematic functional assays under controlled conditions. Even with yeast cells, however, ageing assays can be laborious and resource-intensive. Here we present improved experimental and computational methods to study chronological lifespan in Schizosaccharomyces pombe. We decoded the barcodes for 3206 mutants of the latest gene-deletion library, enabling the parallel profiling of ~700 additional mutants compared to previous screens. We then applied a refined method of barcode sequencing (Bar-seq), addressing technical and statistical issues raised by persisting DNA in dead cells and sampling bottlenecks in aged cultures, to screen for mutants showing altered lifespan during stationary phase. This screen identified 341 long-lived mutants and 1246 short-lived mutants which point to many previously unknown ageing-associated genes, including 46 conserved but entirely uncharacterized genes. The ageing-associated genes showed coherent enrichments in processes also associated with human ageing, particularly with respect to ageing in non-proliferative brain cells. We also developed an automated colony-forming unit assay to facilitate medium- to high-throughput chronological-lifespan studies by saving time and resources compared to the traditional assay. Results from the Bar-seq screen showed good agreement with this new assay. This study provides an effective methodological platform and identifies many new ageing-associated genes as a framework for analysing cellular ageing in yeast and beyond.
Collapse
Affiliation(s)
- Catalina A. Romila
- Institute of Healthy Ageing and Department of Genetics, Evolution & Environment, University College London, London WC1E 6BT, UK
- These authors contributed equally
| | - StJohn Townsend
- Institute of Healthy Ageing and Department of Genetics, Evolution & Environment, University College London, London WC1E 6BT, UK
- The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London, NW1 1AT, UK
- These authors contributed equally
| | - Michal Malecki
- Institute of Healthy Ageing and Department of Genetics, Evolution & Environment, University College London, London WC1E 6BT, UK
- Current address: Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Poland
| | - Stephan Kamrad
- Institute of Healthy Ageing and Department of Genetics, Evolution & Environment, University College London, London WC1E 6BT, UK
- The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London, NW1 1AT, UK
- Current address: Charité Universitätsmedizin Berlin, Department of Biochemistry, Germany
| | - María Rodríguez-López
- Institute of Healthy Ageing and Department of Genetics, Evolution & Environment, University College London, London WC1E 6BT, UK
| | - Olivia Hillson
- Institute of Healthy Ageing and Department of Genetics, Evolution & Environment, University College London, London WC1E 6BT, UK
| | - Cristina Cotobal
- Institute of Healthy Ageing and Department of Genetics, Evolution & Environment, University College London, London WC1E 6BT, UK
| | - Markus Ralser
- The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London, NW1 1AT, UK
- Charité Universitätsmedizin Berlin, Department of Biochemistry, Germany
| | - Jürg Bähler
- Institute of Healthy Ageing and Department of Genetics, Evolution & Environment, University College London, London WC1E 6BT, UK
| |
Collapse
|
13
|
Tognetti M, Gabor A, Yang M, Cappelletti V, Windhager J, Rueda OM, Charmpi K, Esmaeilishirazifard E, Bruna A, de Souza N, Caldas C, Beyer A, Picotti P, Saez-Rodriguez J, Bodenmiller B. Deciphering the signaling network of breast cancer improves drug sensitivity prediction. Cell Syst 2021; 12:401-418.e12. [PMID: 33932331 DOI: 10.1016/j.cels.2021.04.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 12/16/2020] [Accepted: 04/07/2021] [Indexed: 02/06/2023]
Abstract
One goal of precision medicine is to tailor effective treatments to patients' specific molecular markers of disease. Here, we used mass cytometry to characterize the single-cell signaling landscapes of 62 breast cancer cell lines and five lines from healthy tissue. We quantified 34 markers in each cell line upon stimulation by the growth factor EGF in the presence or absence of five kinase inhibitors. These data-on more than 80 million single cells from 4,000 conditions-were used to fit mechanistic signaling network models that provide insight into how cancer cells process information. Our dynamic single-cell-based models accurately predicted drug sensitivity and identified genomic features associated with drug sensitivity, including a missense mutation in DDIT3 predictive of PI3K-inhibition sensitivity. We observed similar trends in genotype-drug sensitivity associations in patient-derived xenograft mouse models. This work provides proof of principle that patient-specific single-cell measurements and modeling could inform effective precision medicine strategies.
Collapse
Affiliation(s)
- Marco Tognetti
- Department of Quantitative Biomedicine, University of Zürich, 8057 Zurich, Switzerland; Institute of Molecular Life Sciences, University of Zürich, 8057 Zurich, Switzerland; Institute of Molecular Systems Biology, ETH Zürich, 8093 Zurich, Switzerland; Molecular Life Science PhD Program, Life Science Zürich Graduate School, ETH Zürich and University of Zürich, 8057 Zurich, Switzerland
| | - Attila Gabor
- Institute for Computational Biomedicine, Faculty of Medicine, Heidelberg University, 69117 Heidelberg, Germany; Joint Research Centre for Computational Biomedicine (JRC-COMBINE), Faculty of Medicine, RWTH Aachen University, 52074 Aachen, Germany
| | - Mi Yang
- Joint Research Centre for Computational Biomedicine (JRC-COMBINE), Faculty of Medicine, RWTH Aachen University, 52074 Aachen, Germany; Faculty of Biosciences, Heidelberg University, 69117 Heidelberg, Germany
| | | | - Jonas Windhager
- Department of Quantitative Biomedicine, University of Zürich, 8057 Zurich, Switzerland; Institute of Molecular Life Sciences, University of Zürich, 8057 Zurich, Switzerland; Systems Biology PhD Program, Life Science Zürich Graduate School, ETH Zürich and University of Zürich, 8093 Zürich, Switzerland
| | - Oscar M Rueda
- Department of Oncology and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, UK
| | - Konstantina Charmpi
- Cologne Excellence Cluster Cellular Stress Response in Aging-Associated Diseases (CECAD), Medical Faculty and Faculty of Mathematics and Natural Sciences, University of Cologne, 50923 Cologne, Germany
| | - Elham Esmaeilishirazifard
- Department of Oncology and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, UK; Bioscience, R&D Oncology, Astra Zeneca, Cancer Research UK Cambridge Institute, Cambridge CB2 0RE, UK
| | - Alejandra Bruna
- Department of Oncology and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, UK
| | - Natalie de Souza
- Department of Quantitative Biomedicine, University of Zürich, 8057 Zurich, Switzerland; Institute of Molecular Systems Biology, ETH Zürich, 8093 Zurich, Switzerland
| | - Carlos Caldas
- Department of Oncology and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, UK; Cambridge Breast Unit, NIHR Cambridge Biomedical Research Centre and Cambridge Experimental Cancer Medicine Centre at Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
| | - Andreas Beyer
- Cologne Excellence Cluster Cellular Stress Response in Aging-Associated Diseases (CECAD), Medical Faculty and Faculty of Mathematics and Natural Sciences, University of Cologne, 50923 Cologne, Germany; Center for Molecular Medicine (CMMC), University of Cologne, 50923 Cologne, Germany; Institute for Genetics, Faculty of Mathematics and Natural Sciences, University of Cologne, 50923 Cologne, Germany
| | - Paola Picotti
- Institute of Molecular Systems Biology, ETH Zürich, 8093 Zurich, Switzerland
| | - Julio Saez-Rodriguez
- Institute for Computational Biomedicine, Faculty of Medicine, Heidelberg University, 69117 Heidelberg, Germany; Joint Research Centre for Computational Biomedicine (JRC-COMBINE), Faculty of Medicine, RWTH Aachen University, 52074 Aachen, Germany
| | - Bernd Bodenmiller
- Department of Quantitative Biomedicine, University of Zürich, 8057 Zurich, Switzerland; Institute of Molecular Life Sciences, University of Zürich, 8057 Zurich, Switzerland.
| |
Collapse
|
14
|
Brion C, Caradec C, Pflieger D, Friedrich A, Schacherer J. Pervasive Phenotypic Impact of a Large Nonrecombining Introgressed Region in Yeast. Mol Biol Evol 2021; 37:2520-2530. [PMID: 32359150 PMCID: PMC7475044 DOI: 10.1093/molbev/msaa101] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
To explore the origin of the diversity observed in natural populations, many studies have investigated the relationship between genotype and phenotype. In yeast species, especially in Saccharomyces cerevisiae, these studies are mainly conducted using recombinant offspring derived from two genetically diverse isolates, allowing to define the phenotypic effect of genetic variants. However, large genomic variants such as interspecies introgressions are usually overlooked even if they are known to modify the genotype–phenotype relationship. To have a better insight into the overall phenotypic impact of introgressions, we took advantage of the presence of a 1-Mb introgressed region, which lacks recombination and contains the mating-type determinant in the Lachancea kluyveri budding yeast. By performing linkage mapping analyses in this species, we identified a total of 89 loci affecting growth fitness in a large number of conditions and 2,187 loci affecting gene expression mostly grouped into two major hotspots, one being the introgressed region carrying the mating-type locus. Because of the absence of recombination, our results highlight the presence of a sexual dimorphism in a budding yeast for the first time. Overall, by describing the phenotype–genotype relationship in the Lachancea kluyveri species, we expanded our knowledge on how genetic characteristics of large introgression events can affect the phenotypic landscape.
Collapse
Affiliation(s)
- Christian Brion
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - Claudia Caradec
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - David Pflieger
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - Anne Friedrich
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - Joseph Schacherer
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France.,Institut Universitaire de France (IUF), Paris, France
| |
Collapse
|
15
|
Overcoming off-targets: assessing Western blot signals for Bcnt/Cfdp1, a tentative component of the chromatin remodeling complex. Biosci Rep 2021; 40:224894. [PMID: 32432658 PMCID: PMC7284322 DOI: 10.1042/bsr20194012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 05/15/2020] [Accepted: 05/20/2020] [Indexed: 01/03/2023] Open
Abstract
The Bucentaur (BCNT) protein family is characterized by a conserved amino acid sequence at the C-terminus (BCNT-C domain) and plays an essential role in gene expression and chromosomal maintenance in yeast and Drosophila. The mammalian Bucentaur/Craniofacial developmental protein 1 (Bcnt/Cfdp1) is also a tentative component of the SNF2-related CBP activator protein (Srcap) chromatin remodeling complex, but little is known about its properties, partly because few antibodies are available to examine the endogenous protein. In this paper, we assigned the Western blot signal against the mouse Bcnt/Cfdp1 as a doublet of approximately 45 kDa using anti-Bcnt/Cfdp1 antibodies, which were generated against either of two unrelated immunogens, BCNT-C domain or mouse N-terminal peptide, and in addition, the Cfdp1 knockdown mouse ES cell line and bovine tissue were used as potential negative controls. Moreover, LC-MS/MS analysis of the corresponding doublet to the Flag-tagged mouse Bcnt/Cfdp1 that was constitutively expressed in a HEK293 cell exhibited that the upper band was much more phosphorylated than the lower band with preferential Ser phosphorylation in the WESF motif of BCNT-C domain. Western blot analysis with these evaluated antibodies indicated a preferential expression of Bcnt/Cfdp1 in the early stages of brain development of mouse and rat, which is consistent with a data file of the expression of Bcnt/Cfdp1 mRNA.
Collapse
|
16
|
Brion C, Lutz SM, Albert FW. Simultaneous quantification of mRNA and protein in single cells reveals post-transcriptional effects of genetic variation. eLife 2020; 9:60645. [PMID: 33191917 PMCID: PMC7707838 DOI: 10.7554/elife.60645] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 11/14/2020] [Indexed: 01/27/2023] Open
Abstract
Trans-acting DNA variants may specifically affect mRNA or protein levels of genes located throughout the genome. However, prior work compared trans-acting loci mapped in separate studies, many of which had limited statistical power. Here, we developed a CRISPR-based system for simultaneous quantification of mRNA and protein of a given gene via dual fluorescent reporters in single, live cells of the yeast Saccharomyces cerevisiae. In large populations of recombinant cells from a cross between two genetically divergent strains, we mapped 86 trans-acting loci affecting the expression of ten genes. Less than 20% of these loci had concordant effects on mRNA and protein of the same gene. Most loci influenced protein but not mRNA of a given gene. One locus harbored a premature stop variant in the YAK1 kinase gene that had specific effects on protein or mRNA of dozens of genes. These results demonstrate complex, post-transcriptional genetic effects on gene expression.
Collapse
Affiliation(s)
- Christian Brion
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, United States
| | - Sheila M Lutz
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, United States
| | - Frank Wolfgang Albert
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, United States
| |
Collapse
|
17
|
Sansó M, Parua PK, Pinto D, Svensson JP, Pagé V, Bitton DA, MacKinnon S, Garcia P, Hidalgo E, Bähler J, Tanny JC, Fisher RP. Cdk9 and H2Bub1 signal to Clr6-CII/Rpd3S to suppress aberrant antisense transcription. Nucleic Acids Res 2020; 48:7154-7168. [PMID: 32496538 PMCID: PMC7367204 DOI: 10.1093/nar/gkaa474] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 05/26/2020] [Indexed: 12/13/2022] Open
Abstract
Mono-ubiquitylation of histone H2B (H2Bub1) and phosphorylation of elongation factor Spt5 by cyclin-dependent kinase 9 (Cdk9) occur during transcription by RNA polymerase II (RNAPII), and are mutually dependent in fission yeast. It remained unclear whether Cdk9 and H2Bub1 cooperate to regulate the expression of individual genes. Here, we show that Cdk9 inhibition or H2Bub1 loss induces intragenic antisense transcription of ∼10% of fission yeast genes, with each perturbation affecting largely distinct subsets; ablation of both pathways de-represses antisense transcription of over half the genome. H2Bub1 and phospho-Spt5 have similar genome-wide distributions; both modifications are enriched, and directly proportional to each other, in coding regions, and decrease abruptly around the cleavage and polyadenylation signal (CPS). Cdk9-dependence of antisense suppression at specific genes correlates with high H2Bub1 occupancy, and with promoter-proximal RNAPII pausing. Genetic interactions link Cdk9, H2Bub1 and the histone deacetylase Clr6-CII, while combined Cdk9 inhibition and H2Bub1 loss impair Clr6-CII recruitment to chromatin and lead to decreased occupancy and increased acetylation of histones within gene coding regions. These results uncover novel interactions between co-transcriptional histone modification pathways, which link regulation of RNAPII transcription elongation to suppression of aberrant initiation.
Collapse
Affiliation(s)
- Miriam Sansó
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Cancer Genomics Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Pabitra K Parua
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Daniel Pinto
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Canada
| | - J Peter Svensson
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Viviane Pagé
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Canada
| | - Danny A Bitton
- Research Department of Genetics, Evolution & Environment, University College, London, UK
| | - Sarah MacKinnon
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Canada
| | - Patricia Garcia
- Departament de Ciènces Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | - Elena Hidalgo
- Departament de Ciènces Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | - Jürg Bähler
- Research Department of Genetics, Evolution & Environment, University College, London, UK
| | - Jason C Tanny
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Canada
| | - Robert P Fisher
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| |
Collapse
|
18
|
Kamrad S, Grossbach J, Rodríguez‐López M, Mülleder M, Townsend S, Cappelletti V, Stojanovski G, Correia‐Melo C, Picotti P, Beyer A, Ralser M, Bähler J. Pyruvate kinase variant of fission yeast tunes carbon metabolism, cell regulation, growth and stress resistance. Mol Syst Biol 2020; 16:e9270. [PMID: 32319721 PMCID: PMC7175467 DOI: 10.15252/msb.20199270] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 03/12/2020] [Accepted: 03/18/2020] [Indexed: 12/11/2022] Open
Abstract
Cells balance glycolysis with respiration to support their metabolic needs in different environmental or physiological contexts. With abundant glucose, many cells prefer to grow by aerobic glycolysis or fermentation. Using 161 natural isolates of fission yeast, we investigated the genetic basis and phenotypic effects of the fermentation-respiration balance. The laboratory and a few other strains depended more on respiration. This trait was associated with a single nucleotide polymorphism in a conserved region of Pyk1, the sole pyruvate kinase in fission yeast. This variant reduced Pyk1 activity and glycolytic flux. Replacing the "low-activity" pyk1 allele in the laboratory strain with the "high-activity" allele was sufficient to increase fermentation and decrease respiration. This metabolic rebalancing triggered systems-level adjustments in the transcriptome and proteome and in cellular traits, including increased growth and chronological lifespan but decreased resistance to oxidative stress. Thus, low Pyk1 activity does not lead to a growth advantage but to stress tolerance. The genetic tuning of glycolytic flux may reflect an adaptive trade-off in a species lacking pyruvate kinase isoforms.
Collapse
Affiliation(s)
- Stephan Kamrad
- Molecular Biology of Metabolism LaboratoryThe Francis Crick InstituteLondonUK
- Department of Genetics, Evolution & EnvironmentInstitute of Healthy AgeingUniversity College LondonLondonUK
| | - Jan Grossbach
- CECADMedical Faculty & Faculty of Mathematics and Natural SciencesUniversity of CologneCologneGermany
| | - Maria Rodríguez‐López
- Department of Genetics, Evolution & EnvironmentInstitute of Healthy AgeingUniversity College LondonLondonUK
| | - Michael Mülleder
- Molecular Biology of Metabolism LaboratoryThe Francis Crick InstituteLondonUK
- Charité University MedicineBerlinGermany
| | - StJohn Townsend
- Molecular Biology of Metabolism LaboratoryThe Francis Crick InstituteLondonUK
- Department of Genetics, Evolution & EnvironmentInstitute of Healthy AgeingUniversity College LondonLondonUK
| | - Valentina Cappelletti
- Department of BiologyInstitute of Molecular Systems BiologyETH ZurichZurichSwitzerland
| | - Gorjan Stojanovski
- Department of Genetics, Evolution & EnvironmentInstitute of Healthy AgeingUniversity College LondonLondonUK
| | - Clara Correia‐Melo
- Molecular Biology of Metabolism LaboratoryThe Francis Crick InstituteLondonUK
| | - Paola Picotti
- Department of BiologyInstitute of Molecular Systems BiologyETH ZurichZurichSwitzerland
| | - Andreas Beyer
- CECADMedical Faculty & Faculty of Mathematics and Natural SciencesUniversity of CologneCologneGermany
- Center for Molecular Medicine CologneCologneGermany
| | - Markus Ralser
- Molecular Biology of Metabolism LaboratoryThe Francis Crick InstituteLondonUK
- Charité University MedicineBerlinGermany
| | - Jürg Bähler
- Department of Genetics, Evolution & EnvironmentInstitute of Healthy AgeingUniversity College LondonLondonUK
| |
Collapse
|
19
|
Rodríguez-López M, Gonzalez S, Hillson O, Tunnacliffe E, Codlin S, Tallada VA, Bähler J, Rallis C. The GATA Transcription Factor Gaf1 Represses tRNAs, Inhibits Growth, and Extends Chronological Lifespan Downstream of Fission Yeast TORC1. Cell Rep 2020; 30:3240-3249.e4. [PMID: 32160533 PMCID: PMC7068653 DOI: 10.1016/j.celrep.2020.02.058] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 12/17/2019] [Accepted: 02/13/2020] [Indexed: 12/13/2022] Open
Abstract
Target of Rapamycin Complex 1 (TORC1) signaling promotes growth and aging. Inhibition of TORC1 leads to reduced protein translation, which promotes longevity. TORC1-dependent post-transcriptional regulation of protein translation has been well studied, while analogous transcriptional regulation is less understood. Here we screen fission yeast mutants for resistance to Torin1, which inhibits TORC1 and cell growth. Cells lacking the GATA factor Gaf1 (gaf1Δ) grow normally even in high doses of Torin1. The gaf1Δ mutation shortens the chronological lifespan of non-dividing cells and diminishes Torin1-mediated longevity. Expression profiling and genome-wide binding experiments show that upon TORC1 inhibition, Gaf1 directly upregulates genes for small-molecule metabolic pathways and indirectly represses genes for protein translation. Surprisingly, Gaf1 binds to and downregulates the tRNA genes, so it also functions as a transcription factor for RNA polymerase III. Thus, Gaf1 controls the transcription of both protein-coding and tRNA genes to inhibit translation and growth downstream of TORC1.
Collapse
Affiliation(s)
- María Rodríguez-López
- Institute of Healthy Ageing and Department of Genetics, Evolution & Environment, University College London, London WC1E 6BT, UK
| | - Suam Gonzalez
- School of Health, Sport and Bioscience, University of East London, Stratford Campus, London E14 4LZ, UK
| | - Olivia Hillson
- School of Health, Sport and Bioscience, University of East London, Stratford Campus, London E14 4LZ, UK
| | - Edward Tunnacliffe
- Institute of Healthy Ageing and Department of Genetics, Evolution & Environment, University College London, London WC1E 6BT, UK
| | - Sandra Codlin
- Institute of Healthy Ageing and Department of Genetics, Evolution & Environment, University College London, London WC1E 6BT, UK
| | - Victor A Tallada
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide/CSIC, 41013 Sevilla, Spain
| | - Jürg Bähler
- Institute of Healthy Ageing and Department of Genetics, Evolution & Environment, University College London, London WC1E 6BT, UK.
| | - Charalampos Rallis
- Institute of Healthy Ageing and Department of Genetics, Evolution & Environment, University College London, London WC1E 6BT, UK; School of Health, Sport and Bioscience, University of East London, Stratford Campus, London E14 4LZ, UK; School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK.
| |
Collapse
|
20
|
Tao YT, Suo F, Tusso S, Wang YK, Huang S, Wolf JBW, Du LL. Intraspecific Diversity of Fission Yeast Mitochondrial Genomes. Genome Biol Evol 2020; 11:2312-2329. [PMID: 31364709 PMCID: PMC6736045 DOI: 10.1093/gbe/evz165] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/18/2019] [Indexed: 02/07/2023] Open
Abstract
The fission yeast Schizosaccharomyces pombe is an important model organism, but its natural diversity and evolutionary history remain under-studied. In particular, the population genomics of the S. pombe mitochondrial genome (mitogenome) has not been thoroughly investigated. Here, we assembled the complete circular-mapping mitogenomes of 192 S. pombe isolates de novo, and found that these mitogenomes belong to 69 nonidentical sequence types ranging from 17,618 to 26,910 bp in length. Using the assembled mitogenomes, we identified 20 errors in the reference mitogenome and discovered two previously unknown mitochondrial introns. Analyzing sequence diversity of these 69 types of mitogenomes revealed two highly distinct clades, with only three mitogenomes exhibiting signs of inter-clade recombination. This diversity pattern suggests that currently available S. pombe isolates descend from two long-separated ancestral lineages. This conclusion is corroborated by the diversity pattern of the recombination-repressed K-region located between donor mating-type loci mat2 and mat3 in the nuclear genome. We estimated that the two ancestral S. pombe lineages diverged about 31 million generations ago. These findings shed new light on the evolution of S. pombe and the data sets generated in this study will facilitate future research on genome evolution.
Collapse
Affiliation(s)
- Yu-Tian Tao
- National Institute of Biological Sciences, Beijing, China.,Graduate School of Peking Union Medical College, Beijing, China
| | - Fang Suo
- National Institute of Biological Sciences, Beijing, China
| | - Sergio Tusso
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Planegg-Martinsried, Germany.,Science for Life Laboratories, Department of Evolutionary Biology, Uppsala University, Sweden
| | - Yan-Kai Wang
- National Institute of Biological Sciences, Beijing, China
| | - Song Huang
- National Institute of Biological Sciences, Beijing, China.,Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China
| | - Jochen B W Wolf
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Planegg-Martinsried, Germany.,Science for Life Laboratories, Department of Evolutionary Biology, Uppsala University, Sweden
| | - Li-Lin Du
- National Institute of Biological Sciences, Beijing, China.,Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China
| |
Collapse
|
21
|
Braun-Galleani S, Dias JA, Coughlan AY, Ryan AP, Byrne KP, Wolfe KH. Genomic diversity and meiotic recombination among isolates of the biotech yeast Komagataella phaffii (Pichia pastoris). Microb Cell Fact 2019; 18:211. [PMID: 31801527 PMCID: PMC6894112 DOI: 10.1186/s12934-019-1260-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 11/25/2019] [Indexed: 12/17/2022] Open
Abstract
Background Komagataella phaffii is a yeast widely used in the pharmaceutical and biotechnology industries, and is one of the two species that were previously called Pichia pastoris. However, almost all laboratory work on K. phaffii has utilized strains derived from a single natural isolate, CBS7435. There is little information about the sequence diversity of K. phaffii or the genetic properties of this species. Results We sequenced the genomes of all the known isolates of K. phaffii. We made a genetic cross between derivatives of two isolates that differ at 44,000 single nucleotide polymorphism sites, and used this cross to analyze the rate and landscape of meiotic recombination. We conducted tetrad analysis by making use of the property that K. phaffii haploids do not mate in rich media, which enabled us to isolate and sequence the four types of haploid cell that are present in the colony that forms when a tetra-type ascus germinates. Conclusions We found that only four distinct natural isolates of K. phaffii exist in public yeast culture collections. The meiotic recombination rate in K. phaffii is approximately 3.5 times lower than in Saccharomyces cerevisiae, with an average of 25 crossovers per meiosis. Recombination is suppressed, and genetic diversity among natural isolates is low, in a region around centromeres that is much larger than the centromeres themselves. Our work lays a foundation for future quantitative trait locus analysis in K. phaffii.
Collapse
Affiliation(s)
| | - Julie A Dias
- UCD Conway Institute, School of Medicine, University College Dublin, Dublin, Ireland.,Department of Mathematics and Statistics, McGill University, Montreal, QC, Canada
| | - Aisling Y Coughlan
- UCD Conway Institute, School of Medicine, University College Dublin, Dublin, Ireland
| | - Adam P Ryan
- UCD Conway Institute, School of Medicine, University College Dublin, Dublin, Ireland
| | - Kevin P Byrne
- UCD Conway Institute, School of Medicine, University College Dublin, Dublin, Ireland
| | - Kenneth H Wolfe
- UCD Conway Institute, School of Medicine, University College Dublin, Dublin, Ireland.
| |
Collapse
|
22
|
Sakhanenko NA, Cromie GA, Dudley AM, Galas DJ. Computational Inference Software for Tetrad Assembly from Randomly Arrayed Yeast Colonies. G3 (BETHESDA, MD.) 2019; 9:2071-2088. [PMID: 31109921 PMCID: PMC6643883 DOI: 10.1534/g3.119.400166] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 05/12/2019] [Indexed: 11/23/2022]
Abstract
We describe an information-theory-based method and associated software for computationally identifying sister spores derived from the same meiotic tetrad. The method exploits specific DNA sequence features of tetrads that result from meiotic centromere and allele segregation patterns. Because the method uses only the genomic sequence, it alleviates the need for tetrad-specific barcodes or other genetic modifications to the strains. Using this method, strains derived from randomly arrayed spores can be efficiently grouped back into tetrads.
Collapse
Affiliation(s)
| | | | | | - David J Galas
- Pacific Northwest Research Institute, Seattle, WA 98122
| |
Collapse
|
23
|
Hu Y, Zhao T, Zang T, Zhang Y, Cheng L. Identification of Alzheimer's Disease-Related Genes Based on Data Integration Method. Front Genet 2019; 9:703. [PMID: 30740125 PMCID: PMC6355707 DOI: 10.3389/fgene.2018.00703] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 12/14/2018] [Indexed: 01/18/2023] Open
Abstract
Alzheimer disease (AD) is the fourth major cause of death in the elderly following cancer, heart disease and cerebrovascular disease. Finding candidate causal genes can help in the design of Gene targeted drugs and effectively reduce the risk of the disease. Complex diseases such as AD are usually caused by multiple genes. The Genome-wide association study (GWAS), has identified the potential genetic variants for most diseases. However, because of linkage disequilibrium (LD), it is difficult to identify the causative mutations that directly cause diseases. In this study, we combined expression quantitative trait locus (eQTL) studies with the GWAS, to comprehensively define the genes that cause Alzheimer disease. The method used was the Summary Mendelian randomization (SMR), which is a novel method to integrate summarized data. Two GWAS studies and five eQTL studies were referenced in this paper. We found several candidate SNPs that have a strong relationship with AD. Most of these SNPs overlap in different data sets, providing relatively strong reliability. We also explain the function of the novel AD-related genes we have discovered.
Collapse
Affiliation(s)
- Yang Hu
- Department of Computer Science and Technology, School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Tianyi Zhao
- Department of Computer Science and Technology, School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Tianyi Zang
- Department of Computer Science and Technology, School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Ying Zhang
- Department of Rehabilitation, Heilongjiang Province Land Reclamation Headquarters General Hospital, Harbin, China
| | - Liang Cheng
- Department of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| |
Collapse
|
24
|
Atkinson SR, Marguerat S, Bitton DA, Rodríguez-López M, Rallis C, Lemay JF, Cotobal C, Malecki M, Smialowski P, Mata J, Korber P, Bachand F, Bähler J. Long noncoding RNA repertoire and targeting by nuclear exosome, cytoplasmic exonuclease, and RNAi in fission yeast. RNA (NEW YORK, N.Y.) 2018; 24:1195-1213. [PMID: 29914874 PMCID: PMC6097657 DOI: 10.1261/rna.065524.118] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 06/14/2018] [Indexed: 05/31/2023]
Abstract
Long noncoding RNAs (lncRNAs), which are longer than 200 nucleotides but often unstable, contribute a substantial and diverse portion to pervasive noncoding transcriptomes. Most lncRNAs are poorly annotated and understood, although several play important roles in gene regulation and diseases. Here we systematically uncover and analyze lncRNAs in Schizosaccharomyces pombe. Based on RNA-seq data from twelve RNA-processing mutants and nine physiological conditions, we identify 5775 novel lncRNAs, nearly 4× the previously annotated lncRNAs. The expression of most lncRNAs becomes strongly induced under the genetic and physiological perturbations, most notably during late meiosis. Most lncRNAs are cryptic and suppressed by three RNA-processing pathways: the nuclear exosome, cytoplasmic exonuclease, and RNAi. Double-mutant analyses reveal substantial coordination and redundancy among these pathways. We classify lncRNAs by their dominant pathway into cryptic unstable transcripts (CUTs), Xrn1-sensitive unstable transcripts (XUTs), and Dicer-sensitive unstable transcripts (DUTs). XUTs and DUTs are enriched for antisense lncRNAs, while CUTs are often bidirectional and actively translated. The cytoplasmic exonuclease, along with RNAi, dampens the expression of thousands of lncRNAs and mRNAs that become induced during meiosis. Antisense lncRNA expression mostly negatively correlates with sense mRNA expression in the physiological, but not the genetic conditions. Intergenic and bidirectional lncRNAs emerge from nucleosome-depleted regions, upstream of positioned nucleosomes. Our results highlight both similarities and differences to lncRNA regulation in budding yeast. This broad survey of the lncRNA repertoire and characteristics in S. pombe, and the interwoven regulatory pathways that target lncRNAs, provides a rich framework for their further functional analyses.
Collapse
Affiliation(s)
- Sophie R Atkinson
- Research Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London WC1E 6BT, United Kingdom
| | - Samuel Marguerat
- Research Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London WC1E 6BT, United Kingdom
- MRC London Institute of Medical Sciences (LMS), London W12 0NN, United Kingdom
- Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London W12 0NN, United Kingdom
| | - Danny A Bitton
- Research Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London WC1E 6BT, United Kingdom
| | - Maria Rodríguez-López
- Research Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London WC1E 6BT, United Kingdom
| | - Charalampos Rallis
- Research Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London WC1E 6BT, United Kingdom
| | - Jean-François Lemay
- Department of Biochemistry, Sherbrooke, Université de Sherbrooke, Quebec J1H 5N4, Canada
| | - Cristina Cotobal
- Research Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London WC1E 6BT, United Kingdom
| | - Michal Malecki
- Research Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London WC1E 6BT, United Kingdom
| | - Pawel Smialowski
- LMU Munich, Biomedical Center, 82152 Planegg-Martinsried near Munich, Germany
| | - Juan Mata
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom
| | - Philipp Korber
- LMU Munich, Biomedical Center, 82152 Planegg-Martinsried near Munich, Germany
| | - François Bachand
- Department of Biochemistry, Sherbrooke, Université de Sherbrooke, Quebec J1H 5N4, Canada
| | - Jürg Bähler
- Research Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London WC1E 6BT, United Kingdom
| |
Collapse
|
25
|
Uncovering Natural Longevity Alleles from Intercrossed Pools of Aging Fission Yeast Cells. Genetics 2018; 210:733-744. [PMID: 30072377 PMCID: PMC6216586 DOI: 10.1534/genetics.118.301262] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 07/31/2018] [Indexed: 01/24/2023] Open
Abstract
Chronological lifespan of non-dividing yeast cells is a quantitative trait that reflects cellular aging. By monitoring allele frequencies in aging segregant pools, Ellis et al. uncover regulatory variants in the 5'-untranslated regions of two genes... Quantitative traits often show large variation caused by multiple genetic factors . One such trait is the chronological lifespan of non-dividing yeast cells, serving as a model for cellular aging. Screens for genetic factors involved in aging typically assay mutants of protein-coding genes. To identify natural genetic variants contributing to cellular aging, we exploited two strains of the fission yeast, Schizosaccharomyces pombe, that differ in chronological lifespan. We generated segregant pools from these strains and subjected them to advanced intercrossing over multiple generations to break up linkage groups. We chronologically aged the intercrossed segregant pool, followed by genome sequencing at different times to detect genetic variants that became reproducibly enriched as a function of age. A region on Chromosome II showed strong positive selection during aging. Based on expected functions, two candidate variants from this region in the long-lived strain were most promising to be causal: small insertions and deletions in the 5′-untranslated regions of ppk31 and SPBC409.08. Ppk31 is an ortholog of Rim15, a conserved kinase controlling cell proliferation in response to nutrients, while SPBC409.08 is a predicted spermine transmembrane transporter. Both Rim15 and the spermine-precursor, spermidine, are implicated in aging as they are involved in autophagy-dependent lifespan extension. Single and double allele replacement suggests that both variants, alone or combined, have subtle effects on cellular longevity. Furthermore, deletion mutants of both ppk31 and SPBC409.08 rescued growth defects caused by spermidine. We propose that Ppk31 and SPBC409.08 may function together to modulate lifespan, thus linking Rim15/Ppk31 with spermidine metabolism.
Collapse
|
26
|
Jeffares DC. The natural diversity and ecology of fission yeast. Yeast 2018; 35:253-260. [PMID: 29084364 DOI: 10.1002/yea.3293] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 10/12/2017] [Accepted: 10/13/2017] [Indexed: 12/17/2022] Open
Abstract
While the fission yeast is a powerful model of eukaryote biology, there have been few studies of quantitative genetics, phenotypic or genetic diversity. Here I survey the small collection of fission yeast diversity research. I discuss what we can infer about the ecology and origins of Schizosaccharomyces pombe from microbiology field studies and the few strains that have been collected.
Collapse
Affiliation(s)
- Daniel C Jeffares
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| |
Collapse
|
27
|
Nissen KE, Homer CM, Ryan CJ, Shales M, Krogan NJ, Patrick KL, Guthrie C. The histone variant H2A.Z promotes splicing of weak introns. Genes Dev 2017; 31:688-701. [PMID: 28446597 PMCID: PMC5411709 DOI: 10.1101/gad.295287.116] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 03/22/2017] [Indexed: 12/12/2022]
Abstract
In this study, Nissen et al. investigated the function of the highly conserved histone variant H2A.Z in pre-mRNA splicing using the intron-rich model yeast S. pombe. The findings suggest that H2A.Z occupancy promotes cotranscriptional splicing of suboptimal introns that may otherwise be discarded via proofreading ATPases. Multiple lines of evidence implicate chromatin in the regulation of premessenger RNA (pre-mRNA) splicing. However, the influence of chromatin factors on cotranscriptional splice site usage remains unclear. Here we investigated the function of the highly conserved histone variant H2A.Z in pre-mRNA splicing using the intron-rich model yeast Schizosaccharomyces pombe. Using epistatic miniarray profiles (EMAPs) to survey the genetic interaction landscape of the Swr1 nucleosome remodeling complex, which deposits H2A.Z, we uncovered evidence for functional interactions with components of the spliceosome. In support of these genetic connections, splicing-specific microarrays show that H2A.Z and the Swr1 ATPase are required during temperature stress for the efficient splicing of a subset of introns. Notably, affected introns are enriched for H2A.Z occupancy and more likely to contain nonconsensus splice sites. To test the significance of the latter correlation, we mutated the splice sites in an affected intron to consensus and found that this suppressed the requirement for H2A.Z in splicing of that intron. These data suggest that H2A.Z occupancy promotes cotranscriptional splicing of suboptimal introns that may otherwise be discarded via proofreading ATPases. Consistent with this model, we show that overexpression of splicing ATPase Prp16 suppresses both the growth and splicing defects seen in the absence of H2A.Z.
Collapse
Affiliation(s)
- Kelly E Nissen
- Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco 94158, California, USA
| | - Christina M Homer
- Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco 94158, California, USA
| | - Colm J Ryan
- Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, Ireland
| | - Michael Shales
- Department of Cellular and Molecular Pharmacology, University of California at San Francisco, San Francisco 94158, California, USA.,California Institute for Quantitative Biosciences (QB3), San Francisco 94158, California, USA
| | - Nevan J Krogan
- Department of Cellular and Molecular Pharmacology, University of California at San Francisco, San Francisco 94158, California, USA.,California Institute for Quantitative Biosciences (QB3), San Francisco 94158, California, USA.,J. David Gladstone Institutes, San Francisco 94158, California, USA
| | - Kristin L Patrick
- Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco 94158, California, USA.,Department of Microbial Pathogenesis and Immunology, Texas A&M Health Science Center, Bryan, Texas 77807, USA
| | - Christine Guthrie
- Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco 94158, California, USA
| |
Collapse
|
28
|
Brion C, Legrand S, Peter J, Caradec C, Pflieger D, Hou J, Friedrich A, Llorente B, Schacherer J. Variation of the meiotic recombination landscape and properties over a broad evolutionary distance in yeasts. PLoS Genet 2017; 13:e1006917. [PMID: 28763437 PMCID: PMC5554000 DOI: 10.1371/journal.pgen.1006917] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 08/11/2017] [Accepted: 07/10/2017] [Indexed: 11/19/2022] Open
Abstract
Meiotic recombination is a major factor of genome evolution, deeply characterized in only a few model species, notably the yeast Saccharomyces cerevisiae. Consequently, little is known about variations of its properties across species. In this respect, we explored the recombination landscape of Lachancea kluyveri, a protoploid yeast species that diverged from the Saccharomyces genus more than 100 million years ago and we found striking differences with S. cerevisiae. These variations include a lower recombination rate, a higher frequency of chromosomes segregating without any crossover and the absence of recombination on the chromosome arm containing the sex locus. In addition, although well conserved within the Saccharomyces clade, the S. cerevisiae recombination hotspots are not conserved over a broader evolutionary distance. Finally and strikingly, we found evidence of frequent reversal of commitment to meiosis, resulting in return to mitotic growth after allele shuffling. Identification of this major but underestimated evolutionary phenomenon illustrates the relevance of exploring non-model species. Meiotic recombination promotes accurate chromosome segregation and genetic diversity. To date, the mechanisms and rules lying behind recombination were dissected using model organisms such as the budding yeast Saccharomyces cerevisiae. To assess the conservation and variation of this process over a broad evolutionary distance, we explored the meiotic recombination landscape in Lachancea kluyveri, a budding yeast species that diverged from S. cerevisiae more than 100 million years ago. The meiotic recombination map we generated revealed that the meiotic recombination landscape and properties significantly vary across distantly related yeast species, raising the yet to confirm possibility that recombination hotspots conservation across yeast species depends on synteny conservation. Finally, the frequent meiotic reversions we observed led us to re-evaluate their evolutionary importance.
Collapse
Affiliation(s)
- Christian Brion
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - Sylvain Legrand
- CNRS UMR7258, INSERM U1068, Aix Marseille Université UM105, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Jackson Peter
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - Claudia Caradec
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - David Pflieger
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - Jing Hou
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - Anne Friedrich
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - Bertrand Llorente
- CNRS UMR7258, INSERM U1068, Aix Marseille Université UM105, Institut Paoli-Calmettes, CRCM, Marseille, France
- * E-mail: (JS); (BL)
| | - Joseph Schacherer
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
- * E-mail: (JS); (BL)
| |
Collapse
|
29
|
Regulatory Architecture of Gene Expression Variation in the Threespine Stickleback Gasterosteus aculeatus. G3-GENES GENOMES GENETICS 2017; 7:165-178. [PMID: 27836907 PMCID: PMC5217106 DOI: 10.1534/g3.116.033241] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Much adaptive evolutionary change is underlain by mutational variation in regions of the genome that regulate gene expression rather than in the coding regions of the genes themselves. An understanding of the role of gene expression variation in facilitating local adaptation will be aided by an understanding of underlying regulatory networks. Here, we characterize the genetic architecture of gene expression variation in the threespine stickleback (Gasterosteus aculeatus), an important model in the study of adaptive evolution. We collected transcriptomic and genomic data from 60 half-sib families using an expression microarray and genotyping-by-sequencing, and located expression quantitative trait loci (eQTL) underlying the variation in gene expression in liver tissue using an interval mapping approach. We identified eQTL for several thousand expression traits. Expression was influenced by polymorphism in both cis- and trans-regulatory regions. Trans-eQTL clustered into hotspots. We did not identify master transcriptional regulators in hotspot locations: rather, the presence of hotspots may be driven by complex interactions between multiple transcription factors. One observed hotspot colocated with a QTL recently found to underlie salinity tolerance in the threespine stickleback. However, most other observed hotspots did not colocate with regions of the genome known to be involved in adaptive divergence between marine and freshwater habitats.
Collapse
|
30
|
Huang X, Li Y, Pan J, Li M, Lai Y, Gao J, Li X. RNA-Seq identifies redox balance related gene expression alterations under acute cadmium exposure in yeast. ENVIRONMENTAL MICROBIOLOGY REPORTS 2016; 8:1038-1047. [PMID: 27718328 DOI: 10.1111/1758-2229.12484] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 09/29/2016] [Indexed: 06/06/2023]
Abstract
The nonessential metal cadmium can cause cell toxicity and is associated with a range of human diseases including cardiovascular diseases, neurodegenerative diseases and cancers. In this study, cadmium-induced global gene expression profile of yeast was obtained using RNA Sequencing (RNA-Seq) and further analyzed by means of informatics and experiments. A total of 912 Differentially Expressed Genes (DEGs) (FDR of q < 0.01), including 415 Cd-inducible and 497 Cd-repressed genes were identified. Based on the DEGs, 25 cadmium responsive Clusters of Orthologous Group (COG) and three types of cadmium-induced Gene Ontology (GO) including cellular components, molecular functions and biological processes were analyzed in details. Thereafter, 79 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways under cadmium exposure were assigned. Collectively, 108 redox balance related genes were extracted under cadmium exposure. Meanwhile, cadmium exposure lowered cellular Mitochondrial Membrane Potential (MMP) and increased Reactive Oxygen Species (ROS) levels significantly in the context of mitochondrial dysfunction. Furthermore, cadmium exposure increased cellular GSH levels and decreased GSSG levels and also lowered GSSG/GSH ratio of cells, which supports experimentally our claim that the redox balance is the primary mechanism for cadmium toxicity. The results present in this study may provide new strategies for cadmium detoxification and prevention or therapies of cadmium-associated diseases.
Collapse
Affiliation(s)
- Xinhe Huang
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, 610031, China
| | - Yuxing Li
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, 610031, China
| | - Jingmei Pan
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, 610031, China
| | - Ming Li
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, 610031, China
| | - Yongqin Lai
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, 610031, China
| | - Jie Gao
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, 610031, China
| | - Xueru Li
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, 610031, China
| |
Collapse
|
31
|
Big data mining powers fungal research: recent advances in fission yeast systems biology approaches. Curr Genet 2016; 63:427-433. [PMID: 27730285 DOI: 10.1007/s00294-016-0657-4] [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] [Received: 09/23/2016] [Revised: 10/04/2016] [Accepted: 10/05/2016] [Indexed: 01/05/2023]
Abstract
Biology research has entered into big data era. Systems biology approaches therefore become the powerful tools to obtain the whole landscape of how cell separate, grow, and resist the stresses. Fission yeast Schizosaccharomyces pombe is wonderful unicellular eukaryote model, especially studying its division and metabolism can facilitate to understanding the molecular mechanism of cancer and discovering anticancer agents. In this perspective, we discuss the recent advanced fission yeast systems biology tools, mainly focus on metabolomics profiling and metabolic modeling, protein-protein interactome and genetic interaction network, DNA sequencing and applications, and high-throughput phenotypic screening. We therefore hope this review can be useful for interested fungal researchers as well as bioformaticians.
Collapse
|
32
|
Valenzano DR, Benayoun BA, Singh PP, Zhang E, Etter PD, Hu CK, Clément-Ziza M, Willemsen D, Cui R, Harel I, Machado BE, Yee MC, Sharp SC, Bustamante CD, Beyer A, Johnson EA, Brunet A. The African Turquoise Killifish Genome Provides Insights into Evolution and Genetic Architecture of Lifespan. Cell 2016; 163:1539-54. [PMID: 26638078 DOI: 10.1016/j.cell.2015.11.008] [Citation(s) in RCA: 141] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Revised: 09/07/2015] [Accepted: 11/02/2015] [Indexed: 01/19/2023]
Abstract
Lifespan is a remarkably diverse trait ranging from a few days to several hundred years in nature, but the mechanisms underlying the evolution of lifespan differences remain elusive. Here we de novo assemble a reference genome for the naturally short-lived African turquoise killifish, providing a unique resource for comparative and experimental genomics. The identification of genes under positive selection in this fish reveals potential candidates to explain its compressed lifespan. Several aging genes are under positive selection in this short-lived fish and long-lived species, raising the intriguing possibility that the same gene could underlie evolution of both compressed and extended lifespans. Comparative genomics and linkage analysis identify candidate genes associated with lifespan differences between various turquoise killifish strains. Remarkably, these genes are clustered on the sex chromosome, suggesting that short lifespan might have co-evolved with sex determination. Our study provides insights into the evolutionary forces that shape lifespan in nature.
Collapse
Affiliation(s)
| | | | | | - Elisa Zhang
- Department of Genetics, Stanford University, California 94305, USA
| | - Paul D Etter
- Institute of Molecular Biology, University of Oregon, Oregon 97403, USA
| | - Chi-Kuo Hu
- Department of Genetics, Stanford University, California 94305, USA
| | | | - David Willemsen
- Max Planck Institute for Biology of Ageing, Cologne, 50931, Germany
| | - Rongfeng Cui
- Max Planck Institute for Biology of Ageing, Cologne, 50931, Germany
| | - Itamar Harel
- Department of Genetics, Stanford University, California 94305, USA
| | - Ben E Machado
- Department of Genetics, Stanford University, California 94305, USA
| | - Muh-Ching Yee
- Department of Genetics, Stanford University, California 94305, USA
| | - Sabrina C Sharp
- Department of Genetics, Stanford University, California 94305, USA
| | | | - Andreas Beyer
- Cellular Networks and Systems Biology, CECAD, University of Cologne, Cologne, 50931, Germany
| | - Eric A Johnson
- Institute of Molecular Biology, University of Oregon, Oregon 97403, USA
| | - Anne Brunet
- Department of Genetics, Stanford University, California 94305, USA; Glenn Laboratories for the Biology of Aging, Stanford University, California 94305, USA.
| |
Collapse
|
33
|
Eser P, Wachutka L, Maier KC, Demel C, Boroni M, Iyer S, Cramer P, Gagneur J. Determinants of RNA metabolism in the Schizosaccharomyces pombe genome. Mol Syst Biol 2016; 12:857. [PMID: 26883383 PMCID: PMC4770384 DOI: 10.15252/msb.20156526] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
To decrypt the regulatory code of the genome, sequence elements must be defined that determine the kinetics of RNA metabolism and thus gene expression. Here, we attempt such decryption in an eukaryotic model organism, the fission yeast S. pombe. We first derive an improved genome annotation that redefines borders of 36% of expressed mRNAs and adds 487 non‐coding RNAs (ncRNAs). We then combine RNA labeling in vivo with mathematical modeling to obtain rates of RNA synthesis and degradation for 5,484 expressed RNAs and splicing rates for 4,958 introns. We identify functional sequence elements in DNA and RNA that control RNA metabolic rates and quantify the contributions of individual nucleotides to RNA synthesis, splicing, and degradation. Our approach reveals distinct kinetics of mRNA and ncRNA metabolism, separates antisense regulation by transcription interference from RNA interference, and provides a general tool for studying the regulatory code of genomes.
Collapse
Affiliation(s)
- Philipp Eser
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany Gene Center Munich and Department of Biochemistry, Center for Integrated Protein Science CIPSM, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Leonhard Wachutka
- Gene Center Munich and Department of Biochemistry, Center for Integrated Protein Science CIPSM, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Kerstin C Maier
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Carina Demel
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Mariana Boroni
- Gene Center Munich and Department of Biochemistry, Center for Integrated Protein Science CIPSM, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Srignanakshi Iyer
- Gene Center Munich and Department of Biochemistry, Center for Integrated Protein Science CIPSM, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Patrick Cramer
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Julien Gagneur
- Gene Center Munich and Department of Biochemistry, Center for Integrated Protein Science CIPSM, Ludwig-Maximilians-Universität München, Munich, Germany
| |
Collapse
|
34
|
Hu W, Suo F, Du LL. Bulk Segregant Analysis Reveals the Genetic Basis of a Natural Trait Variation in Fission Yeast. Genome Biol Evol 2015; 7:3496-510. [PMID: 26615217 PMCID: PMC4700965 DOI: 10.1093/gbe/evv238] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Although the fission yeast Schizosaccharomyces pombe is a well-established model organism, studies of natural trait variations in this species remain limited. To assess the feasibility of segregant-pool-based mapping of phenotype-causing genes in natural strains of fission yeast, we investigated the cause of a maltose utilization defect (Mal(-)) of the S. pombe strain CBS5557 (originally known as Schizosaccharomyces malidevorans). Analyzing the genome sequence of CBS5557 revealed 955 nonconservative missense substitutions, and 61 potential loss-of-function variants including 47 frameshift indels, 13 early stop codons, and 1 splice site mutation. As a side benefit, our analysis confirmed 146 sequence errors in the reference genome and improved annotations of 27 genes. We applied bulk segregant analysis to map the causal locus of the Mal(-) phenotype. Through sequencing the segregant pools derived from a cross between CBS5557 and the laboratory strain, we located the locus to within a 2.23-Mb chromosome I inversion found in most S. pombe isolates including CBS5557. To map genes within the inversion region that occupies 18% of the genome, we created a laboratory strain containing the same inversion. Analyzing segregants from a cross between CBS5557 and the inversion-containing laboratory strain narrowed down the locus to a 200-kb interval and led us to identify agl1, which suffers a 5-bp deletion in CBS5557, as the causal gene. Interestingly, loss of agl1 through a 34-kb deletion underlies the Mal(-) phenotype of another S. pombe strain CGMCC2.1628. This work adapts and validates the bulk segregant analysis method for uncovering trait-gene relationship in natural fission yeast strains.
Collapse
Affiliation(s)
- Wen Hu
- PTN Graduate Program, School of Life Sciences, Tsinghua University, Beijing, China National Institute of Biological Sciences, Beijing, China
| | - Fang Suo
- National Institute of Biological Sciences, Beijing, China
| | - Li-Lin Du
- National Institute of Biological Sciences, Beijing, China
| |
Collapse
|
35
|
Skelly DA, Magwene PM. Population perspectives on functional genomic variation in yeast. Brief Funct Genomics 2015; 15:138-46. [PMID: 26467711 DOI: 10.1093/bfgp/elv044] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Advances in high-throughput sequencing have facilitated large-scale surveys of genomic variation in the budding yeast,Saccharomyces cerevisiae These surveys have revealed extensive sequence variation between yeast strains. However, much less is known about how such variation influences the amount and nature of variation for functional genomic traits within and between yeast lineages. We review population-level studies of functional genomic variation, with a particular focus on how population functional genomic approaches can provide insights into both genome function and the evolutionary process. Although variation in functional genomics phenotypes is pervasive, our understanding of the consequences of this variation, either in physiological or evolutionary terms, is still rudimentary and thus motivates increased attention to appropriate null models. To date, much of the focus of population functional genomic studies has been on gene expression variation, but other functional genomic data types are just as likely to reveal important insights at the population level, suggesting a pressing need for more studies that go beyond transcription. Finally, we discuss how a population functional genomic perspective can be a powerful approach for developing a mechanistic understanding of the processes that link genomic variation to organismal phenotypes through gene networks.
Collapse
|
36
|
Jeffares DC, Rallis C, Rieux A, Speed D, Převorovský M, Mourier T, Marsellach FX, Iqbal Z, Lau W, Cheng TM, Pracana R, Mülleder M, Lawson JL, Chessel A, Bala S, Hellenthal G, O’Fallon B, Keane T, Simpson JT, Bischof L, Tomiczek B, Bitton DA, Sideri T, Codlin S, Hellberg JE, van Trigt L, Jeffery L, Li JJ, Atkinson S, Thodberg M, Febrer M, McLay K, Drou N, Brown W, Hayles J, Carazo Salas RE, Ralser M, Maniatis N, Balding DJ, Balloux F, Durbin R, Bähler J. The genomic and phenotypic diversity of Schizosaccharomyces pombe. Nat Genet 2015; 47:235-41. [PMID: 25665008 PMCID: PMC4645456 DOI: 10.1038/ng.3215] [Citation(s) in RCA: 120] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Accepted: 01/14/2015] [Indexed: 12/14/2022]
Abstract
Natural variation within species reveals aspects of genome evolution and function. The fission yeast Schizosaccharomyces pombe is an important model for eukaryotic biology, but researchers typically use one standard laboratory strain. To extend the usefulness of this model, we surveyed the genomic and phenotypic variation in 161 natural isolates. We sequenced the genomes of all strains, finding moderate genetic diversity (π = 3 × 10(-3) substitutions/site) and weak global population structure. We estimate that dispersal of S. pombe began during human antiquity (∼340 BCE), and ancestors of these strains reached the Americas at ∼1623 CE. We quantified 74 traits, finding substantial heritable phenotypic diversity. We conducted 223 genome-wide association studies, with 89 traits showing at least one association. The most significant variant for each trait explained 22% of the phenotypic variance on average, with indels having larger effects than SNPs. This analysis represents a rich resource to examine genotype-phenotype relationships in a tractable model.
Collapse
Affiliation(s)
- Daniel C. Jeffares
- Department of Genetics, Evolution & Environment, University College London, London, UK
| | - Charalampos Rallis
- Department of Genetics, Evolution & Environment, University College London, London, UK
| | - Adrien Rieux
- Department of Genetics, Evolution & Environment, University College London, London, UK
- UCL Genetics Institute, University College London, London, UK
| | - Doug Speed
- Department of Genetics, Evolution & Environment, University College London, London, UK
- UCL Genetics Institute, University College London, London, UK
| | - Martin Převorovský
- Department of Cell Biology, Charles University in Prague, Prague, Czech Republic
| | - Tobias Mourier
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | | | - Zamin Iqbal
- Wellcome Trust Centre for Human Genetics, Oxford, UK
| | - Winston Lau
- Department of Genetics, Evolution & Environment, University College London, London, UK
| | - Tammy M.K. Cheng
- Cell Cycle Laboratory, Cancer Research UK London Research Institute, London, UK
| | - Rodrigo Pracana
- Department of Genetics, Evolution & Environment, University College London, London, UK
| | - Michael Mülleder
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Jonathan L.D. Lawson
- Department of Genetics, University of Cambridge, Cambridge, UK
- The Gurdon Institute, University of Cambridge, Cambridge, UK
| | - Anatole Chessel
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Sendu Bala
- Wellcome Trust Sanger Institute, Cambridge, UK
| | - Garrett Hellenthal
- Department of Genetics, Evolution & Environment, University College London, London, UK
- UCL Genetics Institute, University College London, London, UK
| | | | | | | | - Leanne Bischof
- CSIRO Mathematics, Informatics and Statistics, North Ryde, Australia; The Genome Analysis Centre, Norwich, UK
| | - Bartlomiej Tomiczek
- Department of Genetics, Evolution & Environment, University College London, London, UK
| | - Danny A. Bitton
- Department of Genetics, Evolution & Environment, University College London, London, UK
| | - Theodora Sideri
- Department of Genetics, Evolution & Environment, University College London, London, UK
| | - Sandra Codlin
- Department of Genetics, Evolution & Environment, University College London, London, UK
| | | | - Laurent van Trigt
- Department of Genetics, Evolution & Environment, University College London, London, UK
| | - Linda Jeffery
- Cell Cycle Laboratory, Cancer Research UK London Research Institute, London, UK
| | - Juan-Juan Li
- Cell Cycle Laboratory, Cancer Research UK London Research Institute, London, UK
| | - Sophie Atkinson
- Department of Genetics, Evolution & Environment, University College London, London, UK
| | - Malte Thodberg
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Melanie Febrer
- CSIRO Mathematics, Informatics and Statistics, North Ryde, Australia; The Genome Analysis Centre, Norwich, UK
| | - Kirsten McLay
- CSIRO Mathematics, Informatics and Statistics, North Ryde, Australia; The Genome Analysis Centre, Norwich, UK
| | - Nizar Drou
- CSIRO Mathematics, Informatics and Statistics, North Ryde, Australia; The Genome Analysis Centre, Norwich, UK
| | - William Brown
- Centre for Genetics and Genomics, The University of Nottingham, Nottingham, UK
| | - Jacqueline Hayles
- Cell Cycle Laboratory, Cancer Research UK London Research Institute, London, UK
| | - Rafael E. Carazo Salas
- Department of Genetics, University of Cambridge, Cambridge, UK
- The Gurdon Institute, University of Cambridge, Cambridge, UK
| | - Markus Ralser
- Department of Biochemistry, University of Cambridge, Cambridge, UK
- Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
- Division of Physiology and Metabolism, MRC National Institute for Medical Research, London, UK
| | - Nikolas Maniatis
- Department of Genetics, Evolution & Environment, University College London, London, UK
| | - David J. Balding
- Department of Genetics, Evolution & Environment, University College London, London, UK
- UCL Genetics Institute, University College London, London, UK
| | - Francois Balloux
- Department of Genetics, Evolution & Environment, University College London, London, UK
- UCL Genetics Institute, University College London, London, UK
| | | | - Jürg Bähler
- Department of Genetics, Evolution & Environment, University College London, London, UK
- UCL Genetics Institute, University College London, London, UK
| |
Collapse
|
37
|
Albert FW, Kruglyak L. The role of regulatory variation in complex traits and disease. Nat Rev Genet 2015; 16:197-212. [DOI: 10.1038/nrg3891] [Citation(s) in RCA: 684] [Impact Index Per Article: 76.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|