1
|
Coban I, Lamping JP, Hirsch AG, Wasilewski S, Shomroni O, Giesbrecht O, Salinas G, Krebber H. dsRNA formation leads to preferential nuclear export and gene expression. Nature 2024; 631:432-438. [PMID: 38898279 PMCID: PMC11236707 DOI: 10.1038/s41586-024-07576-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 05/16/2024] [Indexed: 06/21/2024]
Abstract
When mRNAs have been transcribed and processed in the nucleus, they are exported to the cytoplasm for translation. This export is mediated by the export receptor heterodimer Mex67-Mtr2 in the yeast Saccharomyces cerevisiae (TAP-p15 in humans)1,2. Interestingly, many long non-coding RNAs (lncRNAs) also leave the nucleus but it is currently unclear why they move to the cytoplasm3. Here we show that antisense RNAs (asRNAs) accelerate mRNA export by annealing with their sense counterparts through the helicase Dbp2. These double-stranded RNAs (dsRNAs) dominate export compared with single-stranded RNAs (ssRNAs) because they have a higher capacity and affinity for the export receptor Mex67. In this way, asRNAs boost gene expression, which is beneficial for cells. This is particularly important when the expression program changes. Consequently, the degradation of dsRNA, or the prevention of its formation, is toxic for cells. This mechanism illuminates the general cellular occurrence of asRNAs and explains their nuclear export.
Collapse
Affiliation(s)
- Ivo Coban
- Abteilung für Molekulare Genetik, Institut für Mikrobiologie und Genetik, Göttinger Zentrum für Molekulare Biowissenschaften (GZMB), Georg-August Universität Göttingen, Göttingen, Germany
| | - Jan-Philipp Lamping
- Abteilung für Molekulare Genetik, Institut für Mikrobiologie und Genetik, Göttinger Zentrum für Molekulare Biowissenschaften (GZMB), Georg-August Universität Göttingen, Göttingen, Germany
| | - Anna Greta Hirsch
- Abteilung für Molekulare Genetik, Institut für Mikrobiologie und Genetik, Göttinger Zentrum für Molekulare Biowissenschaften (GZMB), Georg-August Universität Göttingen, Göttingen, Germany
| | - Sarah Wasilewski
- Abteilung für Molekulare Genetik, Institut für Mikrobiologie und Genetik, Göttinger Zentrum für Molekulare Biowissenschaften (GZMB), Georg-August Universität Göttingen, Göttingen, Germany
| | - Orr Shomroni
- NGS-Integrative Genomics Core Unit, Institute of Pathology, University Medical Center Göttingen, Göttingen, Germany
| | - Oliver Giesbrecht
- Abteilung für Molekulare Genetik, Institut für Mikrobiologie und Genetik, Göttinger Zentrum für Molekulare Biowissenschaften (GZMB), Georg-August Universität Göttingen, Göttingen, Germany
| | - Gabriela Salinas
- NGS-Integrative Genomics Core Unit, Institute of Pathology, University Medical Center Göttingen, Göttingen, Germany
| | - Heike Krebber
- Abteilung für Molekulare Genetik, Institut für Mikrobiologie und Genetik, Göttinger Zentrum für Molekulare Biowissenschaften (GZMB), Georg-August Universität Göttingen, Göttingen, Germany.
| |
Collapse
|
2
|
Pathania AS, Chava H, Balusu R, Pasupulati AK, Coulter DW, Challagundla KB. The crosstalk between non-coding RNAs and cell-cycle events: A new frontier in cancer therapy. MOLECULAR THERAPY. ONCOLOGY 2024; 32:200785. [PMID: 38595981 PMCID: PMC10973673 DOI: 10.1016/j.omton.2024.200785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
The cell cycle comprises sequential events during which a cell duplicates its genome and divides it into two daughter cells. This process is tightly regulated to ensure that the daughter cell receives identical copied chromosomal DNA and that any errors in the DNA during replication are correctly repaired. Cyclins and their enzyme partners, cyclin-dependent kinases (CDKs), are critical regulators of G- to M-phase transitions during the cell cycle. Mitogenic signals induce the formation of the cyclin/CDK complexes, resulting in phosphorylation and activation of the CDKs. Once activated, cyclin/CDK complexes phosphorylate specific substrates that drive the cell cycle forward. The sequential activation and inactivation of cyclin-CDK complexes are tightly controlled by activating and inactivating phosphorylation events induced by cell-cycle proteins. The non-coding RNAs (ncRNAs), which do not code for proteins, regulate cell-cycle proteins at the transcriptional and translational levels, thereby controlling their expression at different cell-cycle phases. Deregulation of ncRNAs can cause abnormal expression patterns of cell-cycle-regulating proteins, resulting in abnormalities in cell-cycle regulation and cancer development. This review explores how ncRNA dysregulation can disrupt cell division balance and discusses potential therapeutic approaches targeting these ncRNAs to control cell-cycle events in cancer treatment.
Collapse
Affiliation(s)
- Anup S. Pathania
- Department of Biochemistry and Molecular Biology & The Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Haritha Chava
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Ramesh Balusu
- Department of Hematologic Malignancies and Cellular Therapeutics, Kansas University Medical Center, Kansas City, KS 66160, USA
| | - Anil K. Pasupulati
- Department of Biochemistry, University of Hyderabad, Hyderabad, Telangana 500046, India
| | - Don W. Coulter
- Department of Pediatrics, Division of Hematology/Oncology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Kishore B. Challagundla
- Department of Biochemistry and Molecular Biology & The Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
- The Child Health Research Institute, University of Nebraska Medical Center, Omaha, NE 68198, USA
| |
Collapse
|
3
|
Čáp M, Palková Z. Non-Coding RNAs: Regulators of Stress, Ageing, and Developmental Decisions in Yeast? Cells 2024; 13:599. [PMID: 38607038 PMCID: PMC11012152 DOI: 10.3390/cells13070599] [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: 02/15/2024] [Revised: 03/19/2024] [Accepted: 03/27/2024] [Indexed: 04/13/2024] Open
Abstract
Cells must change their properties in order to adapt to a constantly changing environment. Most of the cellular sensing and regulatory mechanisms described so far are based on proteins that serve as sensors, signal transducers, and effectors of signalling pathways, resulting in altered cell physiology. In recent years, however, remarkable examples of the critical role of non-coding RNAs in some of these regulatory pathways have been described in various organisms. In this review, we focus on all classes of non-coding RNAs that play regulatory roles during stress response, starvation, and ageing in different yeast species as well as in structured yeast populations. Such regulation can occur, for example, by modulating the amount and functional state of tRNAs, rRNAs, or snRNAs that are directly involved in the processes of translation and splicing. In addition, long non-coding RNAs and microRNA-like molecules are bona fide regulators of the expression of their target genes. Non-coding RNAs thus represent an additional level of cellular regulation that is gradually being uncovered.
Collapse
Affiliation(s)
- Michal Čáp
- Department of Genetics and Microbiology, Faculty of Science, Charles University, BIOCEV, 128 00 Prague, Czech Republic
| | - Zdena Palková
- Department of Genetics and Microbiology, Faculty of Science, Charles University, BIOCEV, 128 00 Prague, Czech Republic
| |
Collapse
|
4
|
Kang J, Chung A, Suresh S, Bonzi LC, Sourisse JM, Ramirez‐Calero S, Romeo D, Petit‐Marty N, Pegueroles C, Schunter C. Long non-coding RNAs mediate fish gene expression in response to ocean acidification. Evol Appl 2024; 17:e13655. [PMID: 38357358 PMCID: PMC10866067 DOI: 10.1111/eva.13655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 01/18/2024] [Accepted: 01/23/2024] [Indexed: 02/16/2024] Open
Abstract
The majority of the transcribed genome does not have coding potential but these non-coding transcripts play crucial roles in transcriptional and post-transcriptional regulation of protein-coding genes. Regulation of gene expression is important in shaping an organism's response to environmental changes, ultimately impacting their survival and persistence as population or species face global change. However, the roles of long non-coding RNAs (lncRNAs), when confronted with environmental changes, remain largely unclear. To explore the potential role of lncRNAs in fish exposed to ocean acidification (OA), we analyzed publicly available brain RNA-seq data from a coral reef fish Acanthochromis polyacanthus. We annotated the lncRNAs in its genome and examined the expression changes of intergenic lncRNAs (lincRNAs) between A. polyacanthus samples from a natural CO2 seep and a nearby control site. We identified 4728 lncRNAs, including 3272 lincRNAs in this species. Remarkably, 93.03% of these lincRNAs were species-specific. Among the 125 highly expressed lincRNAs and 403 differentially expressed lincRNAs in response to elevated CO2, we observed that lincRNAs were either neighboring or potentially trans-regulating differentially expressed coding genes associated with pH regulation, neural signal transduction, and ion transport, which are known to be important in the response to OA in fish. In summary, lncRNAs may facilitate fish acclimation and mediate the responses of fish to OA by modulating the expression of crucial coding genes, which offers insight into the regulatory mechanisms underlying fish responses to environmental changes.
Collapse
Affiliation(s)
- Jingliang Kang
- Swire Institute of Marine Science, School of Biological SciencesThe University of Hong KongPokfulamHong Kong SAR
| | - Arthur Chung
- Swire Institute of Marine Science, School of Biological SciencesThe University of Hong KongPokfulamHong Kong SAR
| | - Sneha Suresh
- Swire Institute of Marine Science, School of Biological SciencesThe University of Hong KongPokfulamHong Kong SAR
| | - Lucrezia C. Bonzi
- Swire Institute of Marine Science, School of Biological SciencesThe University of Hong KongPokfulamHong Kong SAR
| | - Jade M. Sourisse
- Swire Institute of Marine Science, School of Biological SciencesThe University of Hong KongPokfulamHong Kong SAR
| | - Sandra Ramirez‐Calero
- Swire Institute of Marine Science, School of Biological SciencesThe University of Hong KongPokfulamHong Kong SAR
| | - Daniele Romeo
- Swire Institute of Marine Science, School of Biological SciencesThe University of Hong KongPokfulamHong Kong SAR
| | - Natalia Petit‐Marty
- Swire Institute of Marine Science, School of Biological SciencesThe University of Hong KongPokfulamHong Kong SAR
| | - Cinta Pegueroles
- Department of Genetics, Microbiology and Statistics, Institute for Research on Biodiversity (IRBio)University of BarcelonaBarcelonaSpain
| | - Celia Schunter
- Swire Institute of Marine Science, School of Biological SciencesThe University of Hong KongPokfulamHong Kong SAR
- State Key Laboratory of Marine Pollution and Department of ChemistryCity University of Hong KongHong Kong SARChina
| |
Collapse
|
5
|
Davati N, Ghorbani A. Discovery of long non-coding RNAs in Aspergillus flavus response to water activity, CO 2 concentration, and temperature changes. Sci Rep 2023; 13:10330. [PMID: 37365206 DOI: 10.1038/s41598-023-37236-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 06/19/2023] [Indexed: 06/28/2023] Open
Abstract
Although the role of long non-coding RNAs (lncRNAs) in key biological processes in animals and plants has been confirmed for decades, their identification in fungi remains limited. In this study, we discovered and characterized lncRNAs in Aspergillus flavus in response to changes in water activity, CO2 concentration, and temperature, and predicted their regulatory roles in cellular functions. A total of 472 lncRNAs were identified in the genome of A. flavus, consisting of 470 novel lncRNAs and 2 putative lncRNAs (EFT00053849670 and EFT00053849665). Our analysis of lncRNA expression revealed significant differential expression under stress conditions in A. flavus. Our findings indicate that lncRNAs in A. flavus, particularly down-regulated lncRNAs, may play pivotal regulatory roles in aflatoxin biosynthesis, respiratory activities, cellular survival, and metabolic maintenance under stress conditions. Additionally, we predicted that sense lncRNAs down-regulated by a temperature of 30 °C, osmotic stress, and CO2 concentration might indirectly regulate proline metabolism. Furthermore, subcellular localization analysis revealed that up-and down-regulated lncRNAs are frequently localized in the nucleus under stress conditions, particularly at a water activity of 0.91, while most up-regulated lncRNAs may be located in the cytoplasm under high CO2 concentration.
Collapse
Affiliation(s)
- Nafiseh Davati
- Department of Food Science and Technology, College of Food Industry, Bu-Ali Sina University, Hamedan, 65167-38695, Iran.
| | - Abozar Ghorbani
- Nuclear Agriculture Research School, Nuclear Science and Technology Research Institute (NSTRI), Karaj, Iran.
| |
Collapse
|
6
|
Thiemicke A, Neuert G. Rate thresholds in cell signaling have functional and phenotypic consequences in non-linear time-dependent environments. Front Cell Dev Biol 2023; 11:1124874. [PMID: 37025183 PMCID: PMC10072286 DOI: 10.3389/fcell.2023.1124874] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 03/08/2023] [Indexed: 04/08/2023] Open
Abstract
All cells employ signal transduction pathways to respond to physiologically relevant extracellular cytokines, stressors, nutrient levels, hormones, morphogens, and other stimuli that vary in concentration and rate in healthy and diseased states. A central unsolved fundamental question in cell signaling is whether and how cells sense and integrate information conveyed by changes in the rate of extracellular stimuli concentrations, in addition to the absolute difference in concentration. We propose that different environmental changes over time influence cell behavior in addition to different signaling molecules or different genetic backgrounds. However, most current biomedical research focuses on acute environmental changes and does not consider how cells respond to environments that change slowly over time. As an example of such environmental change, we review cell sensitivity to environmental rate changes, including the novel mechanism of rate threshold. A rate threshold is defined as a threshold in the rate of change in the environment in which a rate value below the threshold does not activate signaling and a rate value above the threshold leads to signal activation. We reviewed p38/Hog1 osmotic stress signaling in yeast, chemotaxis and stress response in bacteria, cyclic adenosine monophosphate signaling in Amoebae, growth factors signaling in mammalian cells, morphogen dynamics during development, temporal dynamics of glucose and insulin signaling, and spatio-temproral stressors in the kidney. These reviewed examples from the literature indicate that rate thresholds are widespread and an underappreciated fundamental property of cell signaling. Finally, by studying cells in non-linear environments, we outline future directions to understand cell physiology better in normal and pathophysiological conditions.
Collapse
Affiliation(s)
- Alexander Thiemicke
- Department of Molecular Physiology and Biophysics, School of Medicine, Vanderbilt University, Nashville, TN, United States
- Program in Chemical and Physical Biology, Vanderbilt University, Nashville, TN, United States
| | - Gregor Neuert
- Department of Molecular Physiology and Biophysics, School of Medicine, Vanderbilt University, Nashville, TN, United States
- Program in Chemical and Physical Biology, Vanderbilt University, Nashville, TN, United States
- Department of Biomedical Engineering, School of Engineering, Vanderbilt University, Nashville, TN, United States
- Department of Pharmacology, School of Medicine, Vanderbilt University, Nashville, TN, United States
- *Correspondence: Gregor Neuert,
| |
Collapse
|
7
|
Villa T, Porrua O. Pervasive transcription: a controlled risk. FEBS J 2022. [PMID: 35587776 DOI: 10.1111/febs.16530] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 04/26/2022] [Accepted: 05/17/2022] [Indexed: 11/30/2022]
Abstract
Transcriptome-wide interrogation of eukaryotic genomes has unveiled the pervasive nature of RNA polymerase II transcription. Virtually, any DNA region with an accessible chromatin structure can be transcribed, resulting in a mass production of noncoding RNAs (ncRNAs) with the potential of interfering with gene expression programs. Budding yeast has proved to be a powerful model organism to understand the mechanisms at play to control pervasive transcription and overcome the risks of hazardous disruption of cellular functions. In this review, we focus on the actors and strategies yeasts employ to govern ncRNA production, and we discuss recent findings highlighting the dangers of losing control over pervasive transcription.
Collapse
Affiliation(s)
- Tommaso Villa
- Institut Jacques Monod CNRS, Université de Paris Cité France
| | - Odil Porrua
- Institut Jacques Monod CNRS, Université de Paris Cité France
| |
Collapse
|
8
|
Adler SO, Spiesser TW, Uschner F, Münzner U, Hahn J, Krantz M, Klipp E. A yeast cell cycle model integrating stress, signaling, and physiology. FEMS Yeast Res 2022; 22:6592118. [PMID: 35617157 PMCID: PMC9246278 DOI: 10.1093/femsyr/foac026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 04/22/2022] [Accepted: 05/23/2022] [Indexed: 11/25/2022] Open
Abstract
The cell division cycle in eukaryotic cells is a series of highly coordinated molecular interactions that ensure that cell growth, duplication of genetic material, and actual cell division are precisely orchestrated to give rise to two viable progeny cells. Moreover, the cell cycle machinery is responsible for incorporating information about external cues or internal processes that the cell must keep track of to ensure a coordinated, timely progression of all related processes. This is most pronounced in multicellular organisms, but also a cardinal feature in model organisms such as baker's yeast. The complex and integrative behavior is difficult to grasp and requires mathematical modeling to fully understand the quantitative interplay of the single components within the entire system. Here, we present a self-oscillating mathematical model of the yeast cell cycle that comprises all major cyclins and their main regulators. Furthermore, it accounts for the regulation of the cell cycle machinery by a series of external stimuli such as mating pheromones and changes in osmotic pressure or nutrient quality. We demonstrate how the external perturbations modify the dynamics of cell cycle components and how the cell cycle resumes after adaptation to or relief from stress.
Collapse
Affiliation(s)
- Stephan O Adler
- Theoretical Biophysics, Humboldt-Universität zu Berlin, Invalidenstr. 42, 10115 Berlin, Germany
| | - Thomas W Spiesser
- Theoretical Biophysics, Humboldt-Universität zu Berlin, Invalidenstr. 42, 10115 Berlin, Germany
| | - Friedemann Uschner
- Theoretical Biophysics, Humboldt-Universität zu Berlin, Invalidenstr. 42, 10115 Berlin, Germany.,Institute for Medical Informatics and Biometry, Technische Universität Dresden, Fetscherstr. 74, 01307 Dresden, Sachsen, Germany
| | - Ulrike Münzner
- Theoretical Biophysics, Humboldt-Universität zu Berlin, Invalidenstr. 42, 10115 Berlin, Germany.,Laboratory of Cell Systems, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, 565-0871, Suita, Osaka, Japan
| | - Jens Hahn
- Theoretical Biophysics, Humboldt-Universität zu Berlin, Invalidenstr. 42, 10115 Berlin, Germany
| | - Marcus Krantz
- Theoretical Biophysics, Humboldt-Universität zu Berlin, Invalidenstr. 42, 10115 Berlin, Germany
| | - Edda Klipp
- Theoretical Biophysics, Humboldt-Universität zu Berlin, Invalidenstr. 42, 10115 Berlin, Germany
| |
Collapse
|
9
|
Jiang N, Wang L, Jiang D, Wang M, Liu H, Yu H, Yao W. Transcriptomic analysis of inhibition by eugenol of ochratoxin A biosynthesis and growth of Aspergillus carbonarius. Food Control 2022. [DOI: 10.1016/j.foodcont.2021.108788] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
|
10
|
Kalem MC, Panepinto JC. Long Non-Coding RNAs in Cryptococcus neoformans: Insights Into Fungal Pathogenesis. Front Cell Infect Microbiol 2022; 12:858317. [PMID: 35372111 PMCID: PMC8968117 DOI: 10.3389/fcimb.2022.858317] [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: 01/19/2022] [Accepted: 02/18/2022] [Indexed: 12/18/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are highly expressed and can modulate multiple cellular processes including transcription, splicing, translation, and many diverse signaling events. LncRNAs can act as sponges for miRNAs, RNA and DNA binding proteins, functioning as competitive endogenous RNAs. The contribution of lncRNAs to microbial pathogenesis is largely neglected in eukaryotic pathogens despite the abundance of RNA sequencing datasets encompassing conditions of stress, gene deletions and conditions that mimic the host environment. The human fungal pathogen Cryptococcus neoformans encodes 6975 (84%) protein-coding and 1359 (16%) non-protein-coding RNAs, of which 1182 (14.2%) are lncRNAs defined by a threshold of greater than 200 nucleotides in length. Here, we discuss the current state of knowledge in C. neoformans lncRNA biology. Utilizing existing RNA seq datasets, we examine trends in lncRNA expression and discuss potential implications for pathogenesis.
Collapse
Affiliation(s)
- Murat C. Kalem
- Department of Microbiology and Immunology, Witebsky Center for Microbial Pathogenesis and Immunology, Jacobs School of Medicine and Biomedical Sciences, State University of New York (SUNY), University at Buffalo, Buffalo, NY, United States
| | - John C. Panepinto
- Department of Microbiology and Immunology, Witebsky Center for Microbial Pathogenesis and Immunology, Jacobs School of Medicine and Biomedical Sciences, State University of New York (SUNY), University at Buffalo, Buffalo, NY, United States
| |
Collapse
|
11
|
Latorre P, Böttcher R, Nadal-Ribelles M, Li CH, Solé C, Martínez-Cebrián G, Boutros PC, Posas F, de Nadal E. Data-driven identification of inherent features of eukaryotic stress-responsive genes. NAR Genom Bioinform 2022; 4:lqac018. [PMID: 35265837 PMCID: PMC8900196 DOI: 10.1093/nargab/lqac018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 12/20/2021] [Accepted: 02/15/2022] [Indexed: 11/13/2022] Open
Abstract
Living organisms are continuously challenged by changes in their environment that can propagate to stresses at the cellular level, such as rapid changes in osmolarity or oxygen tension. To survive these sudden changes, cells have developed stress-responsive mechanisms that tune cellular processes. The response of Saccharomyces cerevisiae to osmostress includes a massive reprogramming of gene expression. Identifying the inherent features of stress-responsive genes is of significant interest for understanding the basic principles underlying the rewiring of gene expression upon stress. Here, we generated a comprehensive catalog of osmostress-responsive genes from 5 independent RNA-seq experiments. We explored 30 features of yeast genes and found that 25 (83%) were distinct in osmostress-responsive genes. We then identified 13 non-redundant minimal osmostress gene traits and used statistical modeling to rank the most stress-predictive features. Intriguingly, the most relevant features of osmostress-responsive genes are the number of transcription factors targeting them and gene conservation. Using data on HeLa samples, we showed that the same features that define yeast osmostress-responsive genes can predict osmostress-responsive genes in humans, but with changes in the rank-ordering of feature-importance. Our study provides a holistic understanding of the basic principles of the regulation of stress-responsive gene expression across eukaryotes.
Collapse
Affiliation(s)
- Pablo Latorre
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - René Böttcher
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Mariona Nadal-Ribelles
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Constance H Li
- Departments of Human Genetics and Urology, Jonsson Comprehensive Cancer Center and Institute for Precision Health, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | - Carme Solé
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Gerard Martínez-Cebrián
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Paul C Boutros
- Departments of Human Genetics and Urology, Jonsson Comprehensive Cancer Center and Institute for Precision Health, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | - Francesc Posas
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Eulàlia de Nadal
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| |
Collapse
|
12
|
Haidara N, Giannini M, Porrua O. Modulated termination of non-coding transcription partakes in the regulation of gene expression. Nucleic Acids Res 2022; 50:1430-1448. [PMID: 35037029 PMCID: PMC8860598 DOI: 10.1093/nar/gkab1304] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 12/17/2021] [Accepted: 12/27/2021] [Indexed: 12/25/2022] Open
Abstract
Pervasive transcription is a universal phenomenon leading to the production of a plethora of non-coding RNAs. If left uncontrolled, pervasive transcription can be harmful for genome expression and stability. However, non-coding transcription can also play important regulatory roles, for instance by promoting the repression of specific genes by a mechanism of transcriptional interference. The efficiency of transcription termination can strongly influence the regulatory capacity of non-coding transcription events, yet very little is known about the mechanisms modulating the termination of non-coding transcription in response to environmental cues. Here, we address this question by investigating the mechanisms that regulate the activity of the main actor in termination of non-coding transcription in budding yeast, the helicase Sen1. We identify a phosphorylation at a conserved threonine of the catalytic domain of Sen1 and we provide evidence that phosphorylation at this site reduces the efficiency of Sen1-mediated termination. Interestingly, we find that this phosphorylation impairs termination at an unannotated non-coding gene, thus repressing the expression of a downstream gene encoding the master regulator of Zn homeostasis, Zap1. Consequently, many additional genes exhibit an expression pattern mimicking conditions of Zn excess, where ZAP1 is naturally repressed. Our findings provide a novel paradigm of gene regulatory mechanism relying on the direct modulation of non-coding transcription termination.
Collapse
Affiliation(s)
- Nouhou Haidara
- Université de Paris, CNRS, Institut Jacques Monod, F-75013 Paris, France.,Université Paris-Saclay, Gif sur Yvette, France
| | - Marta Giannini
- Université de Paris, CNRS, Institut Jacques Monod, F-75013 Paris, France
| | - Odil Porrua
- Université de Paris, CNRS, Institut Jacques Monod, F-75013 Paris, France
| |
Collapse
|
13
|
de Nadal E, Posas F. OUP accepted manuscript. FEMS Yeast Res 2022; 22:6543702. [PMID: 35254447 PMCID: PMC8953452 DOI: 10.1093/femsyr/foac013] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 02/28/2022] [Accepted: 03/03/2022] [Indexed: 11/15/2022] Open
Affiliation(s)
- Eulàlia de Nadal
- Corresponding author: Institute for Research in Biomedicine (IRB Barcelona) Parc Científic de Barcelona c/ Baldiri Reixac, 10. 08028 Barcelona - Spain. E-mail:
| | - Francesc Posas
- Corresponding author: Institute for Research in Biomedicine (IRB Barcelona) Parc Científic de Barcelona c/ Baldiri Reixac, 10. 08028 Barcelona - Spain. E-mail:
| |
Collapse
|
14
|
The signaling pathways involved in metabolic regulation and stress responses of the yeast-like fungi Aureobasidium spp. Biotechnol Adv 2021; 55:107898. [PMID: 34974157 DOI: 10.1016/j.biotechadv.2021.107898] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 12/23/2021] [Accepted: 12/23/2021] [Indexed: 12/22/2022]
Abstract
Aureobasidium spp. can use a wide range of substrates and are widely distributed in different environments, suggesting that they can sense and response to various extracellular signals and be adapted to different environments. It is true that their pullulan, lipid and liamocin biosynthesis and cell growth are regulated by the cAMP-PKA signaling pathway; Polymalate (PMA) and pullulan biosynthesis is controlled by the Ca2+ and TORC1 signaling pathways; the HOG1 signaling pathway determines high osmotic tolerance and high pullulan and liamocin biosynthesis; the Snf1/Mig1 pathway controls glucose repression on pullulan and liamocin biosynthesis; DHN-melanin biosynthesis and stress resistance are regulated by the CWI signaling pathway and TORC1 signaling pathway. In addition, the HSF1 pathway may control cell growth of some novel strains of A. melanogenum at 37 °C. However, the detailed molecular mechanisms of high temperature growth and thermotolerance of some novel strains of A. melanogenum and glucose derepression in A. melanogenum TN3-1 are still unclear.
Collapse
|
15
|
Doughty T, Kerkhoven E. Extracting novel hypotheses and findings from RNA-seq data. FEMS Yeast Res 2021; 20:5721245. [PMID: 32009158 PMCID: PMC7029681 DOI: 10.1093/femsyr/foaa007] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Accepted: 01/31/2020] [Indexed: 12/15/2022] Open
Abstract
Over the past decade, improvements in technology and methods have enabled rapid and relatively inexpensive generation of high-quality RNA-seq datasets. These datasets have been used to characterize gene expression for several yeast species and have provided systems-level insights for basic biology, biotechnology and medicine. Herein, we discuss new techniques that have emerged and existing techniques that enable analysts to extract information from multifactorial yeast RNA-seq datasets. Ultimately, this minireview seeks to inspire readers to query datasets, whether previously published or freshly obtained, with creative and diverse methods to discover and support novel hypotheses.
Collapse
Affiliation(s)
- Tyler Doughty
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 41296, Gothenburg, Sweden
| | - Eduard Kerkhoven
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 41296, Gothenburg, Sweden
| |
Collapse
|
16
|
Li J, Liu X, Yin Z, Hu Z, Zhang KQ. An Overview on Identification and Regulatory Mechanisms of Long Non-coding RNAs in Fungi. Front Microbiol 2021; 12:638617. [PMID: 33995298 PMCID: PMC8113380 DOI: 10.3389/fmicb.2021.638617] [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] [Received: 12/07/2020] [Accepted: 04/06/2021] [Indexed: 01/04/2023] Open
Abstract
For decades, more and more long non-coding RNAs (lncRNAs) have been confirmed to play important functions in key biological processes of different organisms. At present, most identified lncRNAs and those with known functional roles are from mammalian systems. However, lncRNAs have also been found in primitive eukaryotic fungi, and they have different functions in fungal development, metabolism, and pathogenicity. In this review, we highlight some recent researches on lncRNAs in the primitive eukaryotic fungi, particularly focusing on the identification of lncRNAs and their regulatory roles in diverse biological processes.
Collapse
Affiliation(s)
- Juan Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
| | - Xiaoying Liu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
| | - Ziyu Yin
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
| | - Zhihong Hu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
| | - Ke-Qin Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
| |
Collapse
|
17
|
Tran TQ, MacAlpine HK, Tripuraneni V, Mitra S, MacAlpine DM, Hartemink AJ. Linking the dynamics of chromatin occupancy and transcription with predictive models. Genome Res 2021; 31:1035-1046. [PMID: 33893157 PMCID: PMC8168580 DOI: 10.1101/gr.267237.120] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 04/19/2021] [Indexed: 12/30/2022]
Abstract
Though the sequence of the genome within each eukaryotic cell is essentially fixed, it exists within a complex and changing chromatin state. This state is determined, in part, by the dynamic binding of proteins to the DNA. These proteins—including histones, transcription factors (TFs), and polymerases—interact with one another, the genome, and other molecules to allow the chromatin to adopt one of exceedingly many possible configurations. Understanding how changing chromatin configurations associate with transcription remains a fundamental research problem. We sought to characterize at high spatiotemporal resolution the dynamic interplay between transcription and chromatin in response to cadmium stress. Whereas gene regulatory responses to environmental stress in yeast have been studied, how the chromatin state changes and how those changes connect to gene regulation remain unexplored. By combining MNase-seq and RNA-seq data, we found chromatin signatures of transcriptional activation and repression involving both nucleosomal and TF-sized DNA-binding factors. Using these signatures, we identified associations between chromatin dynamics and transcriptional regulation, not only for known cadmium response genes, but across the entire genome, including antisense transcripts. Those associations allowed us to develop generalizable models that predict dynamic transcriptional responses on the basis of dynamic chromatin signatures.
Collapse
Affiliation(s)
- Trung Q Tran
- Department of Computer Science, Duke University, Durham, North Carolina 27708, USA
| | - Heather K MacAlpine
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Vinay Tripuraneni
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Sneha Mitra
- Department of Computer Science, Duke University, Durham, North Carolina 27708, USA
| | - David M MacAlpine
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710, USA.,Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA
| | - Alexander J Hartemink
- Department of Computer Science, Duke University, Durham, North Carolina 27708, USA.,Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA
| |
Collapse
|
18
|
Gowthaman U, García-Pichardo D, Jin Y, Schwarz I, Marquardt S. DNA Processing in the Context of Noncoding Transcription. Trends Biochem Sci 2020; 45:1009-1021. [DOI: 10.1016/j.tibs.2020.07.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 07/17/2020] [Accepted: 07/30/2020] [Indexed: 12/14/2022]
|
19
|
Screening of genes coupled to heat response in Mongolian and Dorper sheep breeds. Biologia (Bratisl) 2020. [DOI: 10.2478/s11756-020-00616-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
20
|
Reca S, Galello F, Ojeda L, Pautasso C, Cañonero L, Moreno S, Portela P, Rossi S. Chromatin remodeling and transcription of the TPK1 subunit of PKA during stress in Saccharomyces cerevisiae. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1863:194599. [DOI: 10.1016/j.bbagrm.2020.194599] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 06/22/2020] [Accepted: 06/22/2020] [Indexed: 01/10/2023]
|
21
|
Cruz de Carvalho MH, Bowler C. Global identification of a marine diatom long noncoding natural antisense transcripts (NATs) and their response to phosphate fluctuations. Sci Rep 2020; 10:14110. [PMID: 32839470 PMCID: PMC7445176 DOI: 10.1038/s41598-020-71002-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 08/06/2020] [Indexed: 11/09/2022] Open
Abstract
Often ignored and regarded as mere transcriptional noise, long noncoding RNAs (lncRNAs) are starting to be considered key regulators of gene expression across the Eukarya domain of life. In the model diatom Phaeodactylum tricornutum, we have previously reported the occurrence of 1,510 intergenic lncRNAs (lincRNAs), many of which displaying specific patterns of expression under phosphate fluctuation (Pi). Using strand-specific RNA-sequencing data we now expand the repertoire of P. tricornutum lncRNAs by identifying 2,628 novel natural antisense transcripts (NATs) that cover 21.5% of the annotated genomic loci. We found that NAT expression is tightly regulated by phosphate depletion and other naturally occurring environmental stresses. Furthermore, we identified 121 phosphate stress responsive NAT-mRNA pairs, the great majority of which showing a positive correlation (concordant pairs) and a small fraction with negative correlation (discordant pairs). Taken together our results show that NATs are highly abundant transcripts in P. tricornutum and that their expression is under tight regulation by nutrient and environmental stresses. Furthermore, our results suggest that in P. tricornutum Pi stress response NAT pairs predominantly regulate positively the expression of their cognate sense genes, the latter being involved in several biological processes underlying the control of cellular homeostasis under stress.
Collapse
Affiliation(s)
- Maria Helena Cruz de Carvalho
- Institut de Biologie de L'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France. .,Faculté des sciences et technologie, Université Paris Est-Créteil (UPEC), 94000, Créteil, France.
| | - Chris Bowler
- Institut de Biologie de L'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
| |
Collapse
|
22
|
Jiménez J, Queralt E, Posas F, de Nadal E. The regulation of Net1/Cdc14 by the Hog1 MAPK upon osmostress unravels a new mechanism regulating mitosis. Cell Cycle 2020; 19:2105-2118. [PMID: 32794416 PMCID: PMC7513861 DOI: 10.1080/15384101.2020.1804222] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
During evolution, cells have developed a plethora of mechanisms to optimize survival in a changing and unpredictable environment. In this regard, they have evolved networks that include environmental sensors, signaling transduction molecules and response mechanisms. Hog1 (yeast) and p38 (mammals) stress-activated protein kinases (SAPKs) are activated upon stress and they drive a full collection of cell adaptive responses aimed to maximize survival. SAPKs are extensively used to learn about the mechanisms through which cells adapt to changing environments. In addition to regulating gene expression and metabolism, SAPKs control cell cycle progression. In this review, we will discuss the latest findings related to the SAPK-driven regulation of mitosis upon osmostress in yeast.
Collapse
Affiliation(s)
- Javier Jiménez
- Departament De Ciències Experimentals I De La Salut, Universitat Pompeu Fabra (UPF) , Barcelona, Spain.,Department of Ciències Bàsiques, Facultat De Medicina I Ciències De La Salut, Universitat Internacional De Catalunya , Barcelona, Spain
| | - Ethel Queralt
- Cell Cycle Group, Institut d'Investigacions Biomèdica De Bellvitge (IDIBELL), L'Hospitalet De Llobregat , Barcelona, Spain
| | - Francesc Posas
- Departament De Ciències Experimentals I De La Salut, Universitat Pompeu Fabra (UPF) , Barcelona, Spain.,Institute for Research in Biomedicine (IRB Barcelona), the Barcelona Institute of Science and Technology , 08028 Barcelona, Spain
| | - Eulàlia de Nadal
- Departament De Ciències Experimentals I De La Salut, Universitat Pompeu Fabra (UPF) , Barcelona, Spain.,Institute for Research in Biomedicine (IRB Barcelona), the Barcelona Institute of Science and Technology , 08028 Barcelona, Spain
| |
Collapse
|
23
|
Quan J, Kang Y, Luo Z, Zhao G, Ma F, Li L, Liu Z. Identification and characterization of long noncoding RNAs provide insight into the regulation of gene expression in response to heat stress in rainbow trout (Oncorhynchus mykiss). COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2020; 36:100707. [PMID: 32693384 DOI: 10.1016/j.cbd.2020.100707] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 06/07/2020] [Accepted: 06/26/2020] [Indexed: 12/22/2022]
Abstract
Rainbow trout are typical cold-water fish species. However, with the intensification of global warming, high temperatures have severely restricted the development of aquaculture during the summer. Understanding the molecular regulatory mechanisms of rainbow trout responses to heat stress will be beneficial for alleviating heat stress-related damage. In this study, we performed RNA-seq of liver tissues from rainbow trout under heat stress (24 °C) and control conditions (18 °C) to identify lncRNAs and target genes by strand-specific library. Changes in nonspecific immune parameters revealed that a strong stress response occurred in rainbow trout at 24 °C. More than 658 million filtered reads and 5916 lncRNAs were identified from six libraries. A total of 927 novel lncRNAs were identified, and 428 differentially expressed lncRNAs were screened with stringent thresholds. The RNA-seq results were verified by RT-qPCR. In addition, a regulatory network of lncRNA-mRNA functional interactions was constructed, and the potential antisense, cis and trans targets of lncRNAs were predicted. GO and KEGG enrichment analyses showed that many target genes involved in maintenance of homeostasis or adaptation to stress and stimuli were highly induced under heat stress. Several regulatory pathways were also found to be involved in heat stress, including the thyroid hormone signaling pathway, the PI3K-Akt signaling pathway, and the estrogen signaling pathway, among others. These results broaden our understanding of lncRNAs associated with heat stress and provide new insights into the lncRNA mediated regulation of the rainbow trout heat stress response.
Collapse
Affiliation(s)
- Jinqiang Quan
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou 730070, PR China
| | - Yujun Kang
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou 730070, PR China
| | - Zhicheng Luo
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou 730070, PR China
| | - Guiyan Zhao
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou 730070, PR China
| | - Fang Ma
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou 730070, PR China; College of Bioengineering and Technology, Tianshui Normal University, Tianshui 741000, PR China
| | - Lanlan Li
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou 730070, PR China
| | - Zhe Liu
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou 730070, PR China.
| |
Collapse
|
24
|
Chen Y, Guo E, Zhang J, Si T. Advances in RNAi-Assisted Strain Engineering in Saccharomyces cerevisiae. Front Bioeng Biotechnol 2020; 8:731. [PMID: 32714914 PMCID: PMC7343710 DOI: 10.3389/fbioe.2020.00731] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 06/10/2020] [Indexed: 12/26/2022] Open
Abstract
Saccharomyces cerevisiae is a widely used eukaryotic model and microbial cell factory. RNA interference (RNAi) is a conserved regulatory mechanism among eukaryotes but absent from S. cerevisiae. Recent reconstitution of RNAi machinery in S. cerevisiae enables the use of this powerful tool for strain engineering. Here we first discuss the introduction of heterologous RNAi pathways in S. cerevisiae, and the design of various expression cassettes of RNAi precursor reagents for tunable, dynamic, and genome-wide regulation. We then summarize notable examples of RNAi-assisted functional genomics and metabolic engineering studies in S. cerevisiae. We conclude with the future challenges and opportunities of RNAi-based approaches, as well as the potential of other regulatory RNAs in advancing yeast engineering.
Collapse
Affiliation(s)
- Yongcan Chen
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Erpeng Guo
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Jianzhi Zhang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Tong Si
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| |
Collapse
|
25
|
Abstract
Proper chromosome segregation is critical for the maintenance of genomic information in every cell division, which is required for cell survival. Cells have orchestrated a myriad of control mechanisms to guarantee proper chromosome segregation. Upon stress, cells induce a number of adaptive responses to maximize survival that range from regulation of gene expression to control of cell-cycle progression. We have found here that in response to osmostress, cells also regulate mitosis to ensure proper telomeric and rDNA segregation during adaptation. Osmostress induces a Hog1-dependent delay of cell-cycle progression in early mitosis by phosphorylating Net1, thereby impairing timely nucleolar release and activation of Cdc14, core elements of mitosis regulation. Thus, Hog1 activation prevents segregation defects to maximize survival. Adaptation to environmental changes is crucial for cell fitness. In Saccharomyces cerevisiae, variations in external osmolarity trigger the activation of the stress-activated protein kinase Hog1 (high-osmolarity glycerol 1), which regulates gene expression, metabolism, and cell-cycle progression. The activation of this kinase leads to the regulation of G1, S, and G2 phases of the cell cycle to prevent genome instability and promote cell survival. Here we show that Hog1 delays mitotic exit when cells are stressed during metaphase. Hog1 phosphorylates the nucleolar protein Net1, altering its affinity for the phosphatase Cdc14, whose activity is essential for mitotic exit and completion of the cell cycle. The untimely release of Cdc14 from the nucleolus upon activation of Hog1 is linked to a defect in ribosomal DNA (rDNA) and telomere segregation, and it ultimately delays cell division. A mutant of Net1 that cannot be phosphorylated by Hog1 displays reduced viability upon osmostress. Thus, Hog1 contributes to maximizing cell survival upon stress by regulating mitotic exit.
Collapse
|
26
|
Viéitez C, Martínez-Cebrián G, Solé C, Böttcher R, Potel CM, Savitski MM, Onnebo S, Fabregat M, Shilatifard A, Posas F, de Nadal E. A genetic analysis reveals novel histone residues required for transcriptional reprogramming upon stress. Nucleic Acids Res 2020; 48:3455-3475. [PMID: 32064518 PMCID: PMC7144942 DOI: 10.1093/nar/gkaa081] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Revised: 01/27/2020] [Accepted: 01/30/2020] [Indexed: 02/06/2023] Open
Abstract
Cells have the ability to sense, respond and adapt to environmental fluctuations. Stress causes a massive reorganization of the transcriptional program. Many examples of histone post-translational modifications (PTMs) have been associated with transcriptional activation or repression under steady-state growth conditions. Comparatively less is known about the role of histone PTMs in the cellular adaptive response to stress. Here, we performed high-throughput genetic screenings that provide a novel global map of the histone residues required for transcriptional reprogramming in response to heat and osmotic stress. Of note, we observed that the histone residues needed depend on the type of gene and/or stress, thereby suggesting a 'personalized', rather than general, subset of histone requirements for each chromatin context. In addition, we identified a number of new residues that unexpectedly serve to regulate transcription. As a proof of concept, we characterized the function of the histone residues H4-S47 and H4-T30 in response to osmotic and heat stress, respectively. Our results uncover novel roles for the kinases Cla4 and Ste20, yeast homologs of the mammalian PAK2 family, and the Ste11 MAPK as regulators of H4-S47 and H4-T30, respectively. This study provides new insights into the role of histone residues in transcriptional regulation under stress conditions.
Collapse
Affiliation(s)
- Cristina Viéitez
- Cell Signaling Research Group, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra (UPF), E-08003 Barcelona, Spain
- European Molecular Biology Laboratory, Genome Biology Unit, 69117 Heidelberg, Germany
| | - Gerard Martínez-Cebrián
- Cell Signaling Research Group, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra (UPF), E-08003 Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Carme Solé
- Cell Signaling Research Group, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra (UPF), E-08003 Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - René Böttcher
- Cell Signaling Research Group, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra (UPF), E-08003 Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Clement M Potel
- European Molecular Biology Laboratory, Genome Biology Unit, 69117 Heidelberg, Germany
| | - Mikhail M Savitski
- European Molecular Biology Laboratory, Genome Biology Unit, 69117 Heidelberg, Germany
| | - Sara Onnebo
- Cell Signaling Research Group, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra (UPF), E-08003 Barcelona, Spain
| | - Marc Fabregat
- Cell Signaling Research Group, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra (UPF), E-08003 Barcelona, Spain
| | - Ali Shilatifard
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, IL 60611, USA
| | - Francesc Posas
- Cell Signaling Research Group, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra (UPF), E-08003 Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Eulàlia de Nadal
- Cell Signaling Research Group, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra (UPF), E-08003 Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| |
Collapse
|
27
|
Wang Z, Jiang Y, Wu H, Xie X, Huang B. Genome-Wide Identification and Functional Prediction of Long Non-coding RNAs Involved in the Heat Stress Response in Metarhizium robertsii. Front Microbiol 2019; 10:2336. [PMID: 31649657 PMCID: PMC6794563 DOI: 10.3389/fmicb.2019.02336] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Accepted: 09/25/2019] [Indexed: 12/11/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) play a significant role in stress responses. To date, only a few studies have reported the role of lncRNAs in insect-pathogenic fungi. Here, we report a genome-wide transcriptional analysis of lncRNAs produced in response to heat stress in Metarhizium robertsii, a model insect-pathogenic fungus, using strand-specific RNA sequencing. A total of 1655 lncRNAs with 1742 isoforms were identified, of which 1081 differentially expressed (DE) lncRNAs were characterized as being heat responsive. By characterizing their genomic structures and expression patterns, we found that the lncRNAs possessed shorter transcripts, fewer exons, and lower expression levels than the protein-coding genes in M. robertsii. Furthermore, target prediction analysis of the lncRNAs revealed thousands of potential DE lncRNA–messenger RNA (mRNA) pairs, among which 5381 pairs function in the cis-regulatory mode. Further pathway enrichment analysis of the corresponding cis-regulated target genes showed that the targets were significantly enriched in the following biological pathways: the Hippo signaling pathway and cell cycle. This finding suggested that these DE lncRNAs control the expression of their corresponding neighboring genes primarily through environmental information processing and cellular processes. Moreover, only 26 trans-regulated lncRNA–mRNA pairs were determined. In addition, among the targets of heat-responsive lncRNAs, two classic genes that may be involved in the response to heat stress were also identified, including hsp70 (XM_007821830 and XM_007825705). These findings expand our knowledge of lncRNAs as important regulators of the response to heat stress in filamentous fungi, including M. robertsii.
Collapse
Affiliation(s)
- Zhangxun Wang
- Anhui Provincial Key Laboratory of Microbial Pest Control, Anhui Agricultural University, Hefei, China.,School of Plant Protection, Anhui Agricultural University, Hefei, China
| | - Yuanyuan Jiang
- Anhui Provincial Key Laboratory of Microbial Pest Control, Anhui Agricultural University, Hefei, China.,School of Plant Protection, Anhui Agricultural University, Hefei, China
| | - Hao Wu
- Anhui Provincial Key Laboratory of Microbial Pest Control, Anhui Agricultural University, Hefei, China
| | - Xiangyun Xie
- Anhui Provincial Key Laboratory of Microbial Pest Control, Anhui Agricultural University, Hefei, China
| | - Bo Huang
- Anhui Provincial Key Laboratory of Microbial Pest Control, Anhui Agricultural University, Hefei, China
| |
Collapse
|
28
|
Nevers A, Doyen A, Malabat C, Néron B, Kergrohen T, Jacquier A, Badis G. Antisense transcriptional interference mediates condition-specific gene repression in budding yeast. Nucleic Acids Res 2019; 46:6009-6025. [PMID: 29788449 PMCID: PMC6158615 DOI: 10.1093/nar/gky342] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 04/23/2018] [Indexed: 12/20/2022] Open
Abstract
Pervasive transcription generates many unstable non-coding transcripts in budding yeast. The transcription of such noncoding RNAs, in particular antisense RNAs (asRNAs), has been shown in a few examples to repress the expression of the associated mRNAs. Yet, such mechanism is not known to commonly contribute to the regulation of a given class of genes. Using a mutant context that stabilized pervasive transcripts, we observed that the least expressed mRNAs during the exponential phase were associated with high levels of asRNAs. These asRNAs also overlapped their corresponding gene promoters with a much higher frequency than average. Interrupting antisense transcription of a subset of genes corresponding to quiescence-enriched mRNAs restored their expression. The underlying mechanism acts in cis and involves several chromatin modifiers. Our results convey that transcription interference represses up to 30% of the 590 least expressed genes, which includes 163 genes with quiescence-enriched mRNAs. We also found that pervasive transcripts constitute a higher fraction of the transcriptome in quiescence relative to the exponential phase, consistent with gene expression itself playing an important role to suppress pervasive transcription. Accordingly, the HIS1 asRNA, normally only present in quiescence, is expressed in exponential phase upon HIS1 mRNA transcription interruption.
Collapse
Affiliation(s)
- Alicia Nevers
- Unité GIM, Institut Pasteur, Paris, France.,Sorbonne Université Pierre et Marie Curie, Paris, France
| | | | - Christophe Malabat
- Unité GIM, Institut Pasteur, Paris, France.,Bioinformatics and Biostatistics Hub, C3BI, Institut Pasteur, USR 3756 IP CNRS, Paris, France
| | - Bertrand Néron
- Bioinformatics and Biostatistics Hub, C3BI, Institut Pasteur, USR 3756 IP CNRS, Paris, France
| | | | - Alain Jacquier
- Unité GIM, Institut Pasteur, Paris, France.,CNRS UMR3525, Paris, France
| | - Gwenael Badis
- Unité GIM, Institut Pasteur, Paris, France.,CNRS UMR3525, Paris, France
| |
Collapse
|
29
|
Dronamraju R, Jha DK, Eser U, Adams AT, Dominguez D, Choudhury R, Chiang YC, Rathmell WK, Emanuele MJ, Churchman LS, Strahl BD. Set2 methyltransferase facilitates cell cycle progression by maintaining transcriptional fidelity. Nucleic Acids Res 2019; 46:1331-1344. [PMID: 29294086 PMCID: PMC5814799 DOI: 10.1093/nar/gkx1276] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 12/18/2017] [Indexed: 12/14/2022] Open
Abstract
Methylation of histone H3 lysine 36 (H3K36me) by yeast Set2 is critical for the maintenance of chromatin structure and transcriptional fidelity. However, we do not know the full range of Set2/H3K36me functions or the scope of mechanisms that regulate Set2-dependent H3K36 methylation. Here, we show that the APC/CCDC20 complex regulates Set2 protein abundance during the cell cycle. Significantly, absence of Set2-mediated H3K36me causes a loss of cell cycle control and pronounced defects in the transcriptional fidelity of cell cycle regulatory genes, a class of genes that are generally long, hence highly dependent on Set2/H3K36me for their transcriptional fidelity. Because APC/C also controls human SETD2, and SETD2 likewise regulates cell cycle progression, our data imply an evolutionarily conserved cell cycle function for Set2/SETD2 that may explain why recurrent mutations of SETD2 contribute to human disease.
Collapse
Affiliation(s)
- Raghuvar Dronamraju
- Department of Biochemistry & Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Deepak Kumar Jha
- Department of Biochemistry & Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Umut Eser
- Department of Genetics, Harvard Medical School, Harvard University, Boston, MA 02115, USA
| | - Alexander T Adams
- Department of Biochemistry & Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Daniel Dominguez
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02115, USA
| | - Rajarshi Choudhury
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Yun-Chen Chiang
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - W Kimryn Rathmell
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Michael J Emanuele
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - L Stirling Churchman
- Department of Genetics, Harvard Medical School, Harvard University, Boston, MA 02115, USA
| | - Brian D Strahl
- Department of Biochemistry & Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA.,Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| |
Collapse
|
30
|
Distribution, Characteristics, and Regulatory Potential of Long Noncoding RNAs in Brown-Rot Fungi. Int J Genomics 2019; 2019:9702342. [PMID: 31192251 PMCID: PMC6525899 DOI: 10.1155/2019/9702342] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Accepted: 03/07/2019] [Indexed: 12/22/2022] Open
Abstract
Long noncoding RNAs have been thoroughly studied in plants, animals, and yeasts, where they play important roles as regulators of transcription. Nevertheless, almost nothing is known about their presence and characteristics in filamentous fungi, especially in basidiomycetes. In the present study, we have carried out an exhaustive annotation and characterization of lncRNAs in two lignin degrader basidiomycetes, Coniophora puteana and Serpula lacrymans. We identified 2,712 putative lncRNAs in the former and 2,242 in the latter, mainly originating from intergenic locations of transposon-sparse genomic regions. The lncRNA length, GC content, expression levels, and stability of the secondary structure differ from coding transcripts but are similar in these two species and resemble that of other eukaryotes. Nevertheless, they lack sequence conservation. Also, we found that lncRNAs are transcriptionally regulated in the same proportion as genes when the fungus actively decomposes soil organic matter. Finally, up to 7% of the upstream gene regions of Coniophora puteana and Serpula lacrymans are transcribed and produce lncRNAs. The study of expression trends in these gene-lncRNA pairs uncovered groups with similar and opposite transcriptional profiles which may be the result of cis-transcriptional regulation.
Collapse
|
31
|
Zhao T, Tao X, Feng S, Wang L, Hong H, Ma W, Shang G, Guo S, He Y, Zhou B, Guan X. LncRNAs in polyploid cotton interspecific hybrids are derived from transposon neofunctionalization. Genome Biol 2018; 19:195. [PMID: 30419941 PMCID: PMC6233382 DOI: 10.1186/s13059-018-1574-2] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 10/23/2018] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Interspecific hybridization and whole genome duplication are driving forces of genomic and organism diversification. But the effect of interspecific hybridization and whole genome duplication on the non-coding portion of the genome in particular remains largely unknown. In this study, we examine the profile of long non-coding RNAs (lncRNAs), comparing them with that of coding genes in allotetraploid cotton (Gossypium hirsutum), its putative diploid ancestors (G. arboreum; G. raimondii), and an F1 hybrid (G. arboreum × G. raimondii, AD). RESULTS We find that most lncRNAs (80%) that were allelic expressed in the allotetraploid genome. Moreover, the genome shock of hybridization reprograms the non-coding transcriptome in the F1 hybrid. Interestingly, the activated lncRNAs are predominantly transcribed from demethylated TE regions, especially from long interspersed nuclear elements (LINEs). The DNA methylation dynamics in the interspecies hybridization are predominantly associated with the drastic expression variation of lncRNAs. Similar trends of lncRNA bursting are also observed in the progress of polyploidization. Additionally, we find that a representative novel lncRNA XLOC_409583 activated after polyploidization from a LINE in the A subgenome of allotetraploid cotton was involved in control of cotton seedling height. CONCLUSION Our results reveal that the processes of hybridization and polyploidization enable the neofunctionalization of lncRNA transcripts, acting as important sources of increased plasticity for plants.
Collapse
Affiliation(s)
- Ting Zhao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- College of Agriculture and Biotechnology, Zhejiang University, Zhejiang, 210058, Hangzhou, China
| | - Xiaoyuan Tao
- College of Agriculture and Biotechnology, Zhejiang University, Zhejiang, 210058, Hangzhou, China
| | - Shouli Feng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Luyao Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Hui Hong
- National Key Laboratory of Plant Molecular Genetics, National Plant Gene Research Center, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Wei Ma
- College of Agriculture and Biotechnology, Zhejiang University, Zhejiang, 210058, Hangzhou, China
| | - Guandong Shang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Shisong Guo
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Yuxin He
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Baoliang Zhou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
| | - Xueying Guan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
- College of Agriculture and Biotechnology, Zhejiang University, Zhejiang, 210058, Hangzhou, China.
| |
Collapse
|
32
|
A current view on long noncoding RNAs in yeast and filamentous fungi. Appl Microbiol Biotechnol 2018; 102:7319-7331. [PMID: 29974182 PMCID: PMC6097775 DOI: 10.1007/s00253-018-9187-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 06/18/2018] [Accepted: 06/20/2018] [Indexed: 02/06/2023]
Abstract
Long noncoding RNAs (lncRNAs) are crucial players in epigenetic regulation. They were initially discovered in human, yet they emerged as common factors involved in a number of central cellular processes in several eukaryotes. For example, in the past decade, research on lncRNAs in yeast has steadily increased. Several examples of lncRNAs were described in Saccharomyces cerevisiae and Schizosaccharomyces pombe. Also, screenings for lncRNAs in ascomycetes were performed and, just recently, the first full characterization of a lncRNA was performed in the filamentous fungus Trichoderma reesei. In this review, we provide a broad overview about currently known fugal lncRNAs. We make an attempt to categorize them according to their functional context, regulatory strategies or special properties. Moreover, the potential of lncRNAs as a biotechnological tool is discussed.
Collapse
|
33
|
Aymoz D, Solé C, Pierre JJ, Schmitt M, de Nadal E, Posas F, Pelet S. Timing of gene expression in a cell-fate decision system. Mol Syst Biol 2018; 14:e8024. [PMID: 29695607 PMCID: PMC5916086 DOI: 10.15252/msb.20178024] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
During development, morphogens provide extracellular cues allowing cells to select a specific fate by inducing complex transcriptional programs. The mating pathway in budding yeast offers simplified settings to understand this process. Pheromone secreted by the mating partner triggers the activity of a MAPK pathway, which results in the expression of hundreds of genes. Using a dynamic expression reporter, we quantified the kinetics of gene expression in single cells upon exogenous pheromone stimulation and in the physiological context of mating. In both conditions, we observed striking differences in the timing of induction of mating‐responsive promoters. Biochemical analyses and generation of synthetic promoter variants demonstrated how the interplay between transcription factor binding and nucleosomes contributes to determine the kinetics of transcription in a simplified cell‐fate decision system.
Collapse
Affiliation(s)
- Delphine Aymoz
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Carme Solé
- Cell Signaling Research Group, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | - Jean-Jerrold Pierre
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Marta Schmitt
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Eulàlia de Nadal
- Cell Signaling Research Group, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | - Francesc Posas
- Cell Signaling Research Group, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | - Serge Pelet
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| |
Collapse
|
34
|
Falcone C, Mazzoni C. RNA stability and metabolism in regulated cell death, aging and diseases. FEMS Yeast Res 2018; 18:4978431. [DOI: 10.1093/femsyr/foy050] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 04/17/2018] [Indexed: 12/13/2022] Open
Affiliation(s)
- Claudio Falcone
- Pasteur Institute-Cenci Bolognetti Foundation, Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185-Rome, Italy
| | - Cristina Mazzoni
- Pasteur Institute-Cenci Bolognetti Foundation, Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185-Rome, Italy
| |
Collapse
|
35
|
Long Noncoding RNAs in Yeast Cells and Differentiated Subpopulations of Yeast Colonies and Biofilms. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2018; 2018:4950591. [PMID: 29765496 PMCID: PMC5889882 DOI: 10.1155/2018/4950591] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 02/07/2018] [Indexed: 02/02/2023]
Abstract
We summarize current knowledge regarding regulatory functions of long noncoding RNAs (lncRNAs) in yeast, with emphasis on lncRNAs identified recently in yeast colonies and biofilms. Potential regulatory functions of these lncRNAs in differentiated cells of domesticated colonies adapted to plentiful conditions versus yeast colony biofilms are discussed. We show that specific cell types differ in their complements of lncRNA, that this complement changes over time in differentiating upper cells, and that these lncRNAs target diverse functional categories of genes in different cell subpopulations and specific colony types.
Collapse
|
36
|
Sun WH, Wang YZ, Xu Y, Yu XW. Genome-wide analysis of long non-coding RNAs in Pichia pastoris during stress by RNA sequencing. Genomics 2018; 111:398-406. [PMID: 29496514 DOI: 10.1016/j.ygeno.2018.02.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 02/07/2018] [Accepted: 02/23/2018] [Indexed: 01/08/2023]
Abstract
Long non-coding RNAs play significant roles in many biological processes. The roles of lncRNAs in Pichia pastoris remain unclear. In this work, we focused on the identification of lncRNAs in P. pastoris and exploration of their potential roles in stress response to PLA2 overexpression and methanol induction. By strand specific RNA sequencing, 208 novel long non-coding RNAs were identified and analyzed. Bioinformatic analysis showed potential trans-target genes and cis-regulated genes of 39 differential lncRNAs. Functional annotation and sequence motif analysis indicated that lncRNAs participate in pathways related to methanol degradation and production of the recombinant protein. The differential expression of lncRNAs was validated by qRT-PCR. Lastly, the potential functions of three lncRNAs were evaluated by knockdown of their expression and analysis of the expression levels of target genes. Our study identifies novel lncRNAs in P. pastoris induced during use as a bioreactor, facilitating future functional research.
Collapse
Affiliation(s)
- Wei-Hong Sun
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, PR China; State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, PR China
| | - Ying-Zheng Wang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, PR China; State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, PR China
| | - Yan Xu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, PR China; State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, PR China.
| | - Xiao-Wei Yu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, PR China; State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, PR China.
| |
Collapse
|
37
|
Vázquez-Ibarra A, Subirana L, Ongay-Larios L, Kawasaki L, Rojas-Ortega E, Rodríguez-González M, de Nadal E, Posas F, Coria R. Activation of the Hog1 MAPK by the Ssk2/Ssk22 MAP3Ks, in the absence of the osmosensors, is not sufficient to trigger osmostress adaptation in Saccharomyces cerevisiae. FEBS J 2018; 285:1079-1096. [PMID: 29341399 DOI: 10.1111/febs.14385] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 12/07/2017] [Accepted: 01/11/2018] [Indexed: 01/13/2023]
Abstract
Yeast cells respond to hyperosmotic stress by activating the high-osmolarity glycerol (HOG) pathway, which consists of two branches, Hkr1/Msb2-Sho1 and Sln1, which trigger phosphorylation and nuclear internalization of the Hog1 mitogen-activated protein kinase. In the nucleus, Hog1 regulates gene transcription and cell cycle progression, which allows the cell to respond and adapt to hyperosmotic conditions. This study demonstrates that the uncoupling of the known sensors of both branches of the pathway at the level of Ssk1 and Ste11 impairs cell growth in hyperosmotic medium. However, under these conditions, Hog1 was still phosphorylated and internalized into the nucleus, suggesting the existence of an alternative Hog1 activation mechanism. In the ssk1ste11 mutant, phosphorylated Hog1 failed to associate with chromatin and to activate transcription of canonical hyperosmolarity-responsive genes. Accordingly, Hog1 also failed to induce glycerol production at the levels of a wild-type strain. Inactivation of the Ptp2 phosphatase moderately rescued growth impairment of the ssk1ste11 mutant under hyperosmotic conditions, indicating that downregulation of the HOG pathway only partially explains the phenotypes displayed by the ssk1ste11 mutant. Cell cycle defects were also observed in response to stress when Hog1 was phosphorylated in the ssk1ste11 mutant. Taken together, these observations indicate that Hog1 phosphorylation by noncanonical upstream mechanisms is not sufficient to trigger a protective response to hyperosmotic stress.
Collapse
Affiliation(s)
- Araceli Vázquez-Ibarra
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Cd de México, México
| | - Laia Subirana
- Cell Signaling Research Group, Departament de Ciències, Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | - Laura Ongay-Larios
- Unidad de Biología Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Cd de México, México
| | - Laura Kawasaki
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Cd de México, México
| | - Eréndira Rojas-Ortega
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Cd de México, México
| | - Miriam Rodríguez-González
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Cd de México, México
| | - Eulàlia de Nadal
- Cell Signaling Research Group, Departament de Ciències, Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | - Francesc Posas
- Cell Signaling Research Group, Departament de Ciències, Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | - Roberto Coria
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Cd de México, México
| |
Collapse
|
38
|
Multiple signaling kinases target Mrc1 to prevent genomic instability triggered by transcription-replication conflicts. Nat Commun 2018; 9:379. [PMID: 29371596 PMCID: PMC5785523 DOI: 10.1038/s41467-017-02756-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 12/21/2017] [Indexed: 02/05/2023] Open
Abstract
Conflicts between replication and transcription machineries represent a major source of genomic instability and cells have evolved strategies to prevent such conflicts. However, little is known regarding how cells cope with sudden increases of transcription while replicating. Here, we report the existence of a general mechanism for the protection of genomic integrity upon transcriptional outbursts in S phase that is mediated by Mrc1. The N-terminal phosphorylation of Mrc1 blocked replication and prevented transcription-associated recombination (TAR) and genomic instability during stress-induced gene expression in S phase. An unbiased kinome screening identified several kinases that phosphorylate Mrc1 at the N terminus upon different environmental stresses. Mrc1 function was not restricted to environmental cues but was also required when unscheduled transcription was triggered by low fitness states such as genomic instability or slow growth. Our data indicate that Mrc1 integrates multiple signals, thereby defining a general safeguard mechanism to protect genomic integrity upon transcriptional outbursts. During S phase of the cell cycle, transcription and replication need to be coordinated in order to avoid conflicts leading to potential genomic instability. Here, the authors find that Mrc1 integrates signals from different kinases to regulate replication during unscheduled transcription events.
Collapse
|
39
|
Stojanovski K, Ferrar T, Benisty H, Uschner F, Delgado J, Jimenez J, Solé C, de Nadal E, Klipp E, Posas F, Serrano L, Kiel C. Interaction Dynamics Determine Signaling and Output Pathway Responses. Cell Rep 2017; 19:136-149. [PMID: 28380353 DOI: 10.1016/j.celrep.2017.03.029] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2016] [Revised: 12/27/2016] [Accepted: 03/08/2017] [Indexed: 12/28/2022] Open
Abstract
The understanding of interaction dynamics in signaling pathways can shed light on pathway architecture and provide insights into targets for intervention. Here, we explored the relevance of kinetic rate constants of a key upstream osmosensor in the yeast high-osmolarity glycerol-mitogen-activated protein kinase (HOG-MAPK) pathway to signaling output responses. We created mutant pairs of the Sln1-Ypd1 complex interface that caused major compensating changes in the association (kon) and dissociation (koff) rate constants (kinetic perturbations) but only moderate changes in the overall complex affinity (Kd). Yeast cells carrying a Sln1-Ypd1 mutant pair with moderate increases in kon and koff displayed a lower threshold of HOG pathway activation than wild-type cells. Mutants with higher kon and koff rates gave rise to higher basal signaling and gene expression but impaired osmoadaptation. Thus, the kon and koff rates of the components in the Sln1 osmosensor determine proper signaling dynamics and osmoadaptation.
Collapse
Affiliation(s)
- Klement Stojanovski
- Cell Signaling Research Group, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Tony Ferrar
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Hannah Benisty
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Friedemann Uschner
- Theoretical Biophysics, Humboldt-Universität zu Berlin, 10115 Berlin, Germany
| | - Javier Delgado
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Javier Jimenez
- Cell Signaling Research Group, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Carme Solé
- Cell Signaling Research Group, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Eulalia de Nadal
- Cell Signaling Research Group, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Edda Klipp
- Theoretical Biophysics, Humboldt-Universität zu Berlin, 10115 Berlin, Germany
| | - Francesc Posas
- Cell Signaling Research Group, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, 08003 Barcelona, Spain.
| | - Luis Serrano
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra, 08003 Barcelona, Spain; ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain.
| | - Christina Kiel
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra, 08003 Barcelona, Spain.
| |
Collapse
|
40
|
Knap P, Tebaldi T, Di Leva F, Biagioli M, Dalla Serra M, Viero G. The Unexpected Tuners: Are LncRNAs Regulating Host Translation during Infections? Toxins (Basel) 2017; 9:E357. [PMID: 29469820 PMCID: PMC5705972 DOI: 10.3390/toxins9110357] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 10/30/2017] [Accepted: 10/31/2017] [Indexed: 12/27/2022] Open
Abstract
Pathogenic bacteria produce powerful virulent factors, such as pore-forming toxins, that promote their survival and cause serious damage to the host. Host cells reply to membrane stresses and ionic imbalance by modifying gene expression at the epigenetic, transcriptional and translational level, to recover from the toxin attack. The fact that the majority of the human transcriptome encodes for non-coding RNAs (ncRNAs) raises the question: do host cells deploy non-coding transcripts to rapidly control the most energy-consuming process in cells-i.e., host translation-to counteract the infection? Here, we discuss the intriguing possibility that membrane-damaging toxins induce, in the host, the expression of toxin-specific long non-coding RNAs (lncRNAs), which act as sponges for other molecules, encoding small peptides or binding target mRNAs to depress their translation efficiency. Unravelling the function of host-produced lncRNAs upon bacterial infection or membrane damage requires an improved understanding of host lncRNA expression patterns, their association with polysomes and their function during this stress. This field of investigation holds a unique opportunity to reveal unpredicted scenarios and novel approaches to counteract antibiotic-resistant infections.
Collapse
Affiliation(s)
- Primoz Knap
- Institute of Biophysics, CNR Unit at Trento, Via Sommarive 18, Povo Trento 38123, Italy.
| | - Toma Tebaldi
- Yale Cancer Center, Yale University School of Medicine, New Haven, CT 06520, USA.
| | - Francesca Di Leva
- Centre for Integrative Biology, University of Trento, Via Sommarive 9, Povo Trento 38123, Italy.
| | - Marta Biagioli
- Centre for Integrative Biology, University of Trento, Via Sommarive 9, Povo Trento 38123, Italy.
| | - Mauro Dalla Serra
- Institute of Biophysics, CNR Unit at Trento, Via Sommarive 18, Povo Trento 38123, Italy.
| | - Gabriella Viero
- Institute of Biophysics, CNR Unit at Trento, Via Sommarive 18, Povo Trento 38123, Italy.
| |
Collapse
|
41
|
Bunina D, Štefl M, Huber F, Khmelinskii A, Meurer M, Barry JD, Kats I, Kirrmaier D, Huber W, Knop M. Upregulation of SPS100 gene expression by an antisense RNA via a switch of mRNA isoforms with different stabilities. Nucleic Acids Res 2017; 45:11144-11158. [PMID: 28977638 PMCID: PMC5737743 DOI: 10.1093/nar/gkx737] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 08/09/2017] [Accepted: 08/21/2017] [Indexed: 12/19/2022] Open
Abstract
Pervasive transcription of genomes generates multiple classes of non-coding RNAs. One of these classes are stable long non-coding RNAs which overlap coding genes in antisense direction (asRNAs). The function of such asRNAs is not fully understood but several cases of antisense-dependent gene expression regulation affecting the overlapping genes have been demonstrated. Using high-throughput yeast genetics and a limited set of four growth conditions we previously reported a regulatory function for ∼25% of asRNAs, most of which repress the expression of the sense gene. To further explore the roles of asRNAs we tested more conditions and identified 15 conditionally antisense-regulated genes, 6 of which exhibited antisense-dependent enhancement of gene expression. We focused on the sporulation-specific gene SPS100, which becomes upregulated upon entry into starvation or sporulation as a function of the antisense transcript SUT169. We demonstrate that the antisense effect is mediated by its 3' intergenic region (3'-IGR) and that this regulation can be transferred to other genes. Genetic analysis revealed that SUT169 functions by changing the relative expression of SPS100 mRNA isoforms from a short and unstable transcript to a long and stable species. These results suggest a novel mechanism of antisense-dependent gene regulation via mRNA isoform switching.
Collapse
Affiliation(s)
- Daria Bunina
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), University of Heidelberg, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
| | - Martin Štefl
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), University of Heidelberg, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
| | - Florian Huber
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), University of Heidelberg, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
| | - Anton Khmelinskii
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), University of Heidelberg, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
| | - Matthias Meurer
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), University of Heidelberg, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
| | - Joseph D. Barry
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Ilia Kats
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), University of Heidelberg, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
| | - Daniel Kirrmaier
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), University of Heidelberg, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
- Deutsches Krebsforschungszentrum (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Wolfgang Huber
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Michael Knop
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), University of Heidelberg, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
- Deutsches Krebsforschungszentrum (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| |
Collapse
|
42
|
Tosato V, West N, Zrimec J, Nikitin DV, Del Sal G, Marano R, Breitenbach M, Bruschi CV. Bridge-Induced Translocation between NUP145 and TOP2 Yeast Genes Models the Genetic Fusion between the Human Orthologs Associated With Acute Myeloid Leukemia. Front Oncol 2017; 7:231. [PMID: 29034209 PMCID: PMC5626878 DOI: 10.3389/fonc.2017.00231] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 09/07/2017] [Indexed: 01/03/2023] Open
Abstract
In mammalian organisms liquid tumors such as acute myeloid leukemia (AML) are related to spontaneous chromosomal translocations ensuing in gene fusions. We previously developed a system named bridge-induced translocation (BIT) that allows linking together two different chromosomes exploiting the strong endogenous homologous recombination system of the yeast Saccharomyces cerevisiae. The BIT system generates a heterogeneous population of cells with different aneuploidies and severe aberrant phenotypes reminiscent of a cancerogenic transformation. In this work, thanks to a complex pop-out methodology of the marker used for the selection of translocants, we succeeded by BIT technology to precisely reproduce in yeast the peculiar chromosome translocation that has been associated with AML, characterized by the fusion between the human genes NUP98 and TOP2B. To shed light on the origin of the DNA fragility within NUP98, an extensive analysis of the curvature, bending, thermostability, and B-Z transition aptitude of the breakpoint region of NUP98 and of its yeast ortholog NUP145 has been performed. On this basis, a DNA cassette carrying homologous tails to the two genes was amplified by PCR and allowed the targeted fusion between NUP145 and TOP2, leading to reproduce the chimeric transcript in a diploid strain of S. cerevisiae. The resulting translocated yeast obtained through BIT appears characterized by abnormal spherical bodies of nearly 500 nm of diameter, absence of external membrane and defined cytoplasmic localization. Since Nup98 is a well-known regulator of the post-transcriptional modification of P53 target genes, and P53 mutations are occasionally reported in AML, this translocant yeast strain can be used as a model to test the constitutive expression of human P53. Although the abnormal phenotype of the translocant yeast was never rescued by its expression, an exogenous P53 was recognized to confer increased vitality to the translocants, in spite of its usual and well-documented toxicity to wild-type yeast strains. These results obtained in yeast could provide new grounds for the interpretation of past observations made in leukemic patients indicating a possible involvement of P53 in cell transformation toward AML.
Collapse
Affiliation(s)
- Valentina Tosato
- Ulisse Biomed S.r.l., AREA Science Park, Trieste, Italy.,Faculty of Health Sciences, University of Primorska, Izola, Slovenia.,Yeast Molecular Genetics, ICGEB, AREA Science Park, Trieste, Italy
| | - Nicole West
- Clinical Pathology, Hospital Maggiore, Trieste, Italy
| | - Jan Zrimec
- Faculty of Health Sciences, University of Primorska, Izola, Slovenia
| | - Dmitri V Nikitin
- Biology Faculty, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Giannino Del Sal
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Roberto Marano
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Michael Breitenbach
- Genetics Division, Department of Cell Biology, University of Salzburg, Salzburg, Austria
| | - Carlo V Bruschi
- Yeast Molecular Genetics, ICGEB, AREA Science Park, Trieste, Italy.,Genetics Division, Department of Cell Biology, University of Salzburg, Salzburg, Austria
| |
Collapse
|
43
|
Nishida K, Kuwano Y, Nishikawa T, Masuda K, Rokutan K. RNA Binding Proteins and Genome Integrity. Int J Mol Sci 2017; 18:E1341. [PMID: 28644387 PMCID: PMC5535834 DOI: 10.3390/ijms18071341] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 06/16/2017] [Accepted: 06/20/2017] [Indexed: 01/10/2023] Open
Abstract
Genome integrity can be threatened by various endogenous or exogenous events. To counteract these stressors, the DNA damage response network contributes to the prevention and/or repair of genomic DNA damage and serves an essential function in cellular survival. DNA binding proteins are involved in this network. Recently, several RNA-binding proteins (RBPs) that are recruited to DNA damage sites have been shown to be direct players in the prevention or repair of DNA damage. In addition, non-coding RNAs, themselves, are involved in the RNA-mediated DNA repair system. Furthermore, RNA modification such as m6A methylation might also contribute to the ultraviolet-responsive DNA damage response. Accumulating evidence suggests that RNA metabolism is more deeply involved in diverse cellular functions than previously expected, and is also intricately associated with the maintenance of genome integrity. In this review, we highlight the roles of RBPs in the maintenance of genome integrity.
Collapse
Affiliation(s)
- Kensei Nishida
- Department of Pathophysiology, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima 770-8503, Japan.
| | - Yuki Kuwano
- Department of Pathophysiology, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima 770-8503, Japan.
| | - Tatsuya Nishikawa
- Department of Pathophysiology, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima 770-8503, Japan.
| | - Kiyoshi Masuda
- Department of Human Genetics, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima 770-8503, Japan.
| | - Kazuhito Rokutan
- Department of Pathophysiology, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima 770-8503, Japan.
| |
Collapse
|
44
|
Yeganeh M, Praz V, Cousin P, Hernandez N. Transcriptional interference by RNA polymerase III affects expression of the Polr3e gene. Genes Dev 2017; 31:413-421. [PMID: 28289142 PMCID: PMC5358760 DOI: 10.1101/gad.293324.116] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 02/15/2017] [Indexed: 01/21/2023]
Abstract
A mammalian interspersed repeat (MIR) nested in antisense orientation within the first intron of the Polr3e gene, encoding an RNA polymerase (Pol) III subunit, is conserved in mammals and highly occupied by Pol III. Here, Yeganeh et al. show that the MIR affects Polr3e expression through transcriptional interference. Overlapping gene arrangements can potentially contribute to gene expression regulation. A mammalian interspersed repeat (MIR) nested in antisense orientation within the first intron of the Polr3e gene, encoding an RNA polymerase III (Pol III) subunit, is conserved in mammals and highly occupied by Pol III. Using a fluorescence assay, CRISPR/Cas9-mediated deletion of the MIR in mouse embryonic stem cells, and chromatin immunoprecipitation assays, we show that the MIR affects Polr3e expression through transcriptional interference. Our study reveals a mechanism by which a Pol II gene can be regulated at the transcription elongation level by transcription of an embedded antisense Pol III gene.
Collapse
Affiliation(s)
- Meghdad Yeganeh
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland
| | - Viviane Praz
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland.,Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Pascal Cousin
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland
| | - Nouria Hernandez
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland
| |
Collapse
|
45
|
Long Noncoding RNAs in the Yeast S. cerevisiae. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1008:119-132. [PMID: 28815538 DOI: 10.1007/978-981-10-5203-3_4] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Long noncoding RNAs have recently been discovered to comprise a sizeable fraction of the RNA World. The scope of their functions, physical organization, and disease relevance remain in the early stages of characterization. Although many thousands of lncRNA transcripts recently have been found to emanate from the expansive DNA between protein-coding genes in animals, there are also hundreds that have been found in simple eukaryotes. Furthermore, lncRNAs have been found in the bacterial and archaeal branches of the tree of life, suggesting they are ubiquitous. In this chapter, we focus primarily on what has been learned so far about lncRNAs from the greatly studied single-celled eukaryote, the yeast Saccharomyces cerevisiae. Most lncRNAs examined in yeast have been implicated in transcriptional regulation of protein-coding genes-often in response to forms of stress-whereas a select few have been ascribed yet other functions. Of those known to be involved in transcriptional regulation of protein-coding genes, the vast majority function in cis. There are also some yeast lncRNAs identified that are not directly involved in regulation of transcription. Examples of these include the telomerase RNA and telomere-encoded transcripts. In addition to its role as a template-encoding telomeric DNA synthesis, telomerase RNA has been shown to function as a flexible scaffold for protein subunits of the RNP holoenzyme. The flexible scaffold model provides a specific mechanistic paradigm that is likely to apply to many other lncRNAs that assemble and orchestrate large RNP complexes, even in humans. Looking to the future, it is clear that considerable fundamental knowledge remains to be obtained about the architecture and functions of lncRNAs. Using genetically tractable unicellular model organisms should facilitate lncRNA characterization. The acquired basic knowledge will ultimately translate to better understanding of the growing list of lncRNAs linked to human maladies.
Collapse
|
46
|
Kyriakou D, Stavrou E, Demosthenous P, Angelidou G, San Luis BJ, Boone C, Promponas VJ, Kirmizis A. Functional characterisation of long intergenic non-coding RNAs through genetic interaction profiling in Saccharomyces cerevisiae. BMC Biol 2016; 14:106. [PMID: 27927215 PMCID: PMC5142380 DOI: 10.1186/s12915-016-0325-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 11/09/2016] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Transcriptome studies have revealed that many eukaryotic genomes are pervasively transcribed producing numerous long non-coding RNAs (lncRNAs). However, only a few lncRNAs have been ascribed a cellular role thus far, with most regulating the expression of adjacent genes. Even less lncRNAs have been annotated as essential hence implying that the majority may be functionally redundant. Therefore, the function of lncRNAs could be illuminated through systematic analysis of their synthetic genetic interactions (GIs). RESULTS Here, we employ synthetic genetic array (SGA) in Saccharomyces cerevisiae to identify GIs between long intergenic non-coding RNAs (lincRNAs) and protein-coding genes. We first validate this approach by demonstrating that the telomerase RNA TLC1 displays a GI network that corresponds to its well-described function in telomere length maintenance. We subsequently performed SGA screens on a set of uncharacterised lincRNAs and uncover their connection to diverse cellular processes. One of these lincRNAs, SUT457, exhibits a GI profile associating it to telomere organisation and we consistently demonstrate that SUT457 is required for telomeric overhang homeostasis through an Exo1-dependent pathway. Furthermore, the GI profile of SUT457 is distinct from that of its neighbouring genes suggesting a function independent to its genomic location. Accordingly, we show that ectopic expression of this lincRNA suppresses telomeric overhang accumulation in sut457Δ cells assigning a trans-acting role for SUT457 in telomere biology. CONCLUSIONS Overall, our work proposes that systematic application of this genetic approach could determine the functional significance of individual lncRNAs in yeast and other complex organisms.
Collapse
Affiliation(s)
- Dimitris Kyriakou
- Department of Biological Sciences, University of Cyprus, Nicosia, CY-1678, Cyprus
| | - Emmanouil Stavrou
- Department of Biological Sciences, University of Cyprus, Nicosia, CY-1678, Cyprus
| | | | - Georgia Angelidou
- Department of Biological Sciences, University of Cyprus, Nicosia, CY-1678, Cyprus
| | - Bryan-Joseph San Luis
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto, Ontario, M5S 3E1, Canada
| | - Charles Boone
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto, Ontario, M5S 3E1, Canada
| | - Vasilis J Promponas
- Department of Biological Sciences, University of Cyprus, Nicosia, CY-1678, Cyprus
| | - Antonis Kirmizis
- Department of Biological Sciences, University of Cyprus, Nicosia, CY-1678, Cyprus.
| |
Collapse
|
47
|
Glucose Starvation Alters Heat Shock Response, Leading to Death of Wild Type Cells and Survival of MAP Kinase Signaling Mutant. PLoS One 2016; 11:e0165980. [PMID: 27870869 PMCID: PMC5117620 DOI: 10.1371/journal.pone.0165980] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 10/20/2016] [Indexed: 12/31/2022] Open
Abstract
A moderate heat shock induces Neurospora crassa to synthesize large quantities of heat shock proteins that are protective against higher, otherwise lethal temperatures. However, wild type cells do not survive when carbohydrate deprivation is added to heat shock. In contrast, a mutant strain defective in a stress-activated protein kinase does survive the combined stresses. In order to understand the basis for this difference in survival, we have determined the relative levels of detected proteins in the mutant and wild type strain during dual stress, and we have identified gene transcripts in both strains whose quantities change in response to heat shock or dual stress. These data and supportive experimental evidence point to reasons for survival of the mutant strain. By using alternative respiratory mechanisms, these cells experience less of the oxidative stress that proves damaging to wild type cells. Of central importance, mutant cells recycle limited resources during dual stress by undergoing autophagy, a process that we find utilized by both wild type and mutant cells during heat shock. Evidence points to inappropriate activation of TORC1, the central metabolic regulator, in wild type cells during dual stress, based upon behavior of an additional signaling mutant and inhibitor studies.
Collapse
|
48
|
Abstract
The survival of all organisms is dependent on complex, coordinated responses to environmental cues. Non-coding RNAs have been identified as major players in regulation of gene expression, with recent evidence supporting roles for long non-coding (lnc)RNAs in both transcriptional and post-transcriptional control. Evidence from our laboratory shows that lncRNAs have the ability to form hybridized structures called R-loops with specific DNA target sequences in S. cerevisiae, thereby modulating gene expression. In this Point of View, we provide an overview of the nature of lncRNA-mediated control of gene expression in the context of our studies using the GAL gene cluster as a model for controlling the timing of transcription.
Collapse
Affiliation(s)
- Zachary T Beck
- a Department of Biochemistry , Purdue University , West Lafayette , IN , USA
| | - Zheng Xing
- a Department of Biochemistry , Purdue University , West Lafayette , IN , USA
| | - Elizabeth J Tran
- a Department of Biochemistry , Purdue University , West Lafayette , IN , USA.,b Purdue University Center for Cancer Research, Purdue University , West Lafayette , IN , USA
| |
Collapse
|
49
|
Gonzalez R, Morales P, Tronchoni J, Cordero-Bueso G, Vaudano E, Quirós M, Novo M, Torres-Pérez R, Valero E. New Genes Involved in Osmotic Stress Tolerance in Saccharomyces cerevisiae. Front Microbiol 2016; 7:1545. [PMID: 27733850 PMCID: PMC5039201 DOI: 10.3389/fmicb.2016.01545] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 09/15/2016] [Indexed: 01/17/2023] Open
Abstract
Adaptation to changes in osmolarity is fundamental for the survival of living cells, and has implications in food and industrial biotechnology. It has been extensively studied in the yeast Saccharomyces cerevisiae, where the Hog1 stress activated protein kinase was discovered about 20 years ago. Hog1 is the core of the intracellular signaling pathway that governs the adaptive response to osmotic stress in this species. The main endpoint of this program is synthesis and intracellular retention of glycerol, as a compatible osmolyte. Despite many details of the signaling pathways and yeast responses to osmotic challenges have already been described, genome-wide approaches are contributing to refine our knowledge of yeast adaptation to hypertonic media. In this work, we used a quantitative fitness analysis approach in order to deepen our understanding of the interplay between yeast cells and the osmotic environment. Genetic requirements for proper growth under osmotic stress showed both common and specific features when hypertonic conditions were induced by either glucose or sorbitol. Tolerance to high-glucose content requires mitochondrial function, while defective protein targeting to peroxisome, GID-complex function (involved in negative regulation of gluconeogenesis), or chromatin dynamics, result in poor survival to sorbitol-induced osmotic stress. On the other side, the competitive disadvantage of yeast strains defective in the endomembrane system is relieved by hypertonic conditions. This finding points to the Golgi-endosome system as one of the main cell components negatively affected by hyperosmolarity. Most of the biological processes highlighted in this analysis had not been previously related to osmotic stress but are probably relevant in an ecological and evolutionary context.
Collapse
Affiliation(s)
- Ramon Gonzalez
- Instituto de Ciencias de la Vid y del Vino - Consejo Superior de Investigaciones Científicas-Universidad de La Rioja-Gobierno de La Rioja Logroño, Spain
| | - Pilar Morales
- Instituto de Ciencias de la Vid y del Vino - Consejo Superior de Investigaciones Científicas-Universidad de La Rioja-Gobierno de La Rioja Logroño, Spain
| | - Jordi Tronchoni
- Instituto de Ciencias de la Vid y del Vino - Consejo Superior de Investigaciones Científicas-Universidad de La Rioja-Gobierno de La Rioja Logroño, Spain
| | - Gustavo Cordero-Bueso
- Departamento de Biomedicina, Biotecnología y Salud Pública, Universidad de Cádiz Cádiz, Spain
| | - Enrico Vaudano
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria-Centro di Ricerca per l'Enologia Asti, Italy
| | | | - Maite Novo
- Departamento de Bioquímica y Biotecnología, Universitat Rovira i Virgili Tarragona, Spain
| | - Rafael Torres-Pérez
- Instituto de Ciencias de la Vid y del Vino - Consejo Superior de Investigaciones Científicas-Universidad de La Rioja-Gobierno de La Rioja Logroño, Spain
| | - Eva Valero
- Departamento de Biología Molecular e Ingeniería Bioquímica, Universidad Pablo de Olavide Sevilla, Spain
| |
Collapse
|
50
|
Wan X, Huang W, Yang S, Zhang Y, Zhang P, Kong Z, Li T, Wu H, Jing F, Li Y. Androgen-induced miR-27A acted as a tumor suppressor by targeting MAP2K4 and mediated prostate cancer progression. Int J Biochem Cell Biol 2016; 79:249-260. [PMID: 27594411 DOI: 10.1016/j.biocel.2016.08.043] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 07/18/2016] [Accepted: 08/29/2016] [Indexed: 11/17/2022]
Abstract
Prostate cancer (PCa) is the most commonly diagnosed and secondly leading cause of cancer death among males. But the precise mechanism of prostate cancer progression, including microRNAs (miRNAs) functioning in it, is still needs further study. We found miR-27a to be down-regulated in prostate cancer, and we investigated the mechanism and role of miRNA-27a in prostate cancer. MiR-27a, a transcriptional target of AR, was an androgen-induced miRNA in LNCaP cells. In castration-resistant prostate cancer (CRPC) cells, we for the first time reported that miR-27a was downregulated by PI3K signaling. MiR-27a functioned as a tumor suppressor in prostate cancer. Over-expression of miR-27a decreased prostate cancer cell proliferation and migration, and induced prostate cancer cell cycle arrest and apoptosis. MAP2K4, miR-27a's direct target gene, functioned as an oncogene in prostate cancer by reducing G1-S phase arrest and inhibiting cell apoptosis of prostate cancer cells. In conclusion, miR-27a functions as a tumor suppressor by suppressing MAP2K4 which acts as an oncogene in prostate cancer cell lines; we also provided a new mechanism of castration-resistant prostate cancer mediated by miR-27a that downregulation of miR-27a caused by aberrant AR signaling and PI3K/Akt signaling after androgen deprivation therapy (ADT) would promote the progression of castration-resistant prostate cancer.
Collapse
Affiliation(s)
- Xuechao Wan
- State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Science, Fudan University, Shanghai 200433, PR China
| | - Wenhua Huang
- State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Science, Fudan University, Shanghai 200433, PR China
| | - Shu Yang
- State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Science, Fudan University, Shanghai 200433, PR China
| | - Yalong Zhang
- State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Science, Fudan University, Shanghai 200433, PR China
| | - Pu Zhang
- State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Science, Fudan University, Shanghai 200433, PR China
| | - Zhe Kong
- State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Science, Fudan University, Shanghai 200433, PR China
| | - Tao Li
- Shanghai Institute of Planned Parenthood Research Hospital, WHO Collaborating Center for Research in Human Reproduction, Shanghai 200433, PR China
| | - Hai Wu
- State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Science, Fudan University, Shanghai 200433, PR China
| | - Fengxiang Jing
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Science, Shanghai 200433, PR China.
| | - Yao Li
- State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Science, Fudan University, Shanghai 200433, PR China.
| |
Collapse
|