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Bodelón A, Fablet M, Siqueira de Oliveira D, Vieira C, García Guerreiro MP. Impact of Heat Stress on Transposable Element Expression and Derived Small RNAs in Drosophila subobscura. Genome Biol Evol 2023; 15:evad189. [PMID: 37847062 PMCID: PMC10627563 DOI: 10.1093/gbe/evad189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 10/02/2023] [Accepted: 10/09/2023] [Indexed: 10/18/2023] Open
Abstract
Global warming is forcing insect populations to move and adapt, triggering adaptive genetic responses. Thermal stress is known to alter gene expression, repressing the transcription of active genes, and inducing others, such as those encoding heat shock proteins. It has also been related to the activation of some specific transposable element (TE) families. However, the actual magnitude of this stress on the whole genome and the factors involved in these genomic changes are still unclear. We studied mRNAs and small RNAs in gonads of two Drosophila subobscura populations, considered a good model to study adaptation to temperature changes. In control conditions, we found that a few genes and TE families were differentially expressed between populations, pointing out their putative involvement in the adaptation of populations to their different environments. Under heat stress, sex-specific changes in gene expression together with a trend toward overexpression, mainly of heat shock response-related genes, were observed. We did not observe large changes of TE expression nor small RNA production due to stress. Only population and sex-specific expression changes of some TE families (mainly retrotransposons), or the amounts of siRNAs and piRNAs, derived from specific TE families were observed, as well as the piRNA production from some piRNA clusters. Changes in small RNA amounts and TE expression could not be clearly correlated, indicating that other factors as chromatin modulation could also be involved. This work provides the first whole transcriptomic study including genes, TEs, and small RNAs after a heat stress in D. subobscura.
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Affiliation(s)
- Alejandra Bodelón
- Grup de Genòmica, Bioinformática i Biologia Evolutiva, Departament de Genètica i Microbiologia (Edifici C), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Marie Fablet
- Laboratoire de Biométrie et Biologie Evolutive, Université de Lyon; Université Lyon 1; CNRS; UMR 5558, Villeurbanne, France
- Institut universitaire de France, Paris, France
| | - Daniel Siqueira de Oliveira
- Laboratoire de Biométrie et Biologie Evolutive, Université de Lyon; Université Lyon 1; CNRS; UMR 5558, Villeurbanne, France
- Institute of Biosciences, Humanities and Exact Sciences, São Paulo State University (Unesp), São Paulo, Brazil
| | - Cristina Vieira
- Laboratoire de Biométrie et Biologie Evolutive, Université de Lyon; Université Lyon 1; CNRS; UMR 5558, Villeurbanne, France
| | - Maria Pilar García Guerreiro
- Grup de Genòmica, Bioinformática i Biologia Evolutiva, Departament de Genètica i Microbiologia (Edifici C), Universitat Autònoma de Barcelona, Barcelona, Spain
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Wierzbicki F, Kofler R. The composition of piRNA clusters in Drosophila melanogaster deviates from expectations under the trap model. BMC Biol 2023; 21:224. [PMID: 37858221 PMCID: PMC10588112 DOI: 10.1186/s12915-023-01727-7] [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: 03/06/2023] [Accepted: 10/06/2023] [Indexed: 10/21/2023] Open
Abstract
BACKGROUND It is widely assumed that the invasion of a transposable element (TE) in mammals and invertebrates is stopped when a copy of the TE jumps into a piRNA cluster (i.e., the trap model). However, recent works, which for example showed that deletion of three major piRNA clusters has no effect on TE activity, cast doubt on the trap model. RESULTS Here, we test the trap model from a population genetics perspective. Our simulations show that the composition of regions that act as transposon traps (i.e., potentially piRNA clusters) ought to deviate from regions that have no effect on TE activity. We investigated TEs in five Drosophila melanogaster strains using three complementary approaches to test whether the composition of piRNA clusters matches these expectations. We found that the abundance of TE families inside and outside of piRNA clusters is highly correlated, although this is not expected under the trap model. Furthermore, the distribution of the number of TE insertions in piRNA clusters is also much broader than expected. CONCLUSIONS We found that the observed composition of piRNA clusters is not in agreement with expectations under the simple trap model. Dispersed piRNA producing TE insertions and temporal as well as spatial heterogeneity of piRNA clusters may account for these deviations.
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Affiliation(s)
- Filip Wierzbicki
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria
- Vienna Graduate School of Population Genetics, Vienna, Austria
| | - Robert Kofler
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria.
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3
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Stunf Pukl S. Are miRNAs Dynamic Biomarkers in Keratoconus? A Review of the Literature. Genes (Basel) 2022; 13:genes13040588. [PMID: 35456395 PMCID: PMC9025197 DOI: 10.3390/genes13040588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/19/2022] [Accepted: 03/23/2022] [Indexed: 02/01/2023] Open
Abstract
Aim: A review of miRNA (microRNA) profiling studies in keratoconus. Methods: Literature search strategy—PubMed central database, using miRNA or microRNA and keratoconus as keywords. Results: Eleven experimental or clinical studies on humans regarding miRNA and keratoconus, published in English between 2009 and 2020 were retrieved. Conclusion: The publications regarding the role of miRNAs in keratoconus are scarce and diverse but provide some valuable information about potential new mechanisms of keratoconus development and progression. The cornea expresses almost 300 different miRNAs, 18 of which are specific, and miR-184 is by far the most abundant, with expression restricted to central basal and suprabasal epithelial cells. Mutations in the seed region of MIR184 were proved to be rare and nonspecific in patients with isolated keratoconus. Overall, in keratoconus, a total of 29 miRNAs were upregulated, and 11 were downregulated. It appeared that miR-143-3p, miR-182-5p, and miR-92a-3p were highly expressed, while the miRNAs connected to cell–cell junction, cell division, and motor activity were downregulated. In less advanced forms, altered expression of four miRNAs—miR-151a-3p, miR-194-5p, miR-195-5p, miR-185-5p—was proved in the cone epithelium; in contrast, in advanced keratoconus, the expression of miR-151a-3p and miR-194-5p remained altered, changes in the expression of miR-195 and miR-185 were not reported, and the expression of miR-138-5p, miR-146b-5p, miR-28-5p, and miR-181a-2-3p was also altered in the corneal epithelium. Keratoconus is a dynamic process of corneal stromal thinning that might result from a dynamic miRNA expression in the corneal epithelium exposed to environmental and behavioral factors causing repetitive traumas. Further experimental studies are needed to prove this hypothesis.
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Affiliation(s)
- Spela Stunf Pukl
- Medical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia; ; Tel.: +386-41-382-487
- Eye Hospital, University Clinical Center Ljubljana, 1000 Ljubljana, Slovenia
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4
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Yildirim E, Curtis R, Hwangbo DS. Roles of peripheral clocks: lessons from the fly. FEBS Lett 2022; 596:263-293. [PMID: 34862983 PMCID: PMC8844272 DOI: 10.1002/1873-3468.14251] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/26/2021] [Accepted: 11/29/2021] [Indexed: 02/03/2023]
Abstract
To adapt to and anticipate rhythmic changes in the environment such as daily light-dark and temperature cycles, internal timekeeping mechanisms called biological clocks evolved in a diverse set of organisms, from unicellular bacteria to humans. These biological clocks play critical roles in organisms' fitness and survival by temporally aligning physiological and behavioral processes to the external cues. The central clock is located in a small subset of neurons in the brain and drives daily activity rhythms, whereas most peripheral tissues harbor their own clock systems, which generate metabolic and physiological rhythms. Since the discovery of Drosophila melanogaster clock mutants in the early 1970s, the fruit fly has become an extensively studied model organism to investigate the mechanism and functions of circadian clocks. In this review, we primarily focus on D. melanogaster to survey key discoveries and progresses made over the past two decades in our understanding of peripheral clocks. We discuss physiological roles and molecular mechanisms of peripheral clocks in several different peripheral tissues of the fly.
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Affiliation(s)
| | - Rachel Curtis
- Department of Biology, University of Louisville, Louisville, KY, USA
| | - Dae-Sung Hwangbo
- Department of Biology, University of Louisville, Louisville, KY, USA
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5
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Ben Youssef M, Christelle Ouédraogo B, Bastarache P, Dumas P, Moffat CE, Vickruck JL, Morin PJ. Exposure to Temperature and Insecticides Modulates the Expression of Small Noncoding RNA-Associated Transcripts in the Colorado Potato Beetle, Leptinotarsa decemlineata (Coleoptera: Chrysomelidae). JOURNAL OF INSECT SCIENCE (ONLINE) 2022; 22:23. [PMID: 35172010 PMCID: PMC8849280 DOI: 10.1093/jisesa/ieac004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Indexed: 06/14/2023]
Abstract
The Colorado potato beetle (Leptinotarsa decemlineata (Say)) is an insect that can adapt to various challenges, including temperature fluctuations or select insecticide treatments. This pest is also an ongoing threat to the potato industry. Small noncoding RNAs such as miRNAs, which can control posttranscriptionally the expression of various genes, and piRNAs, which can notably impact mRNA turnover, are modulated in insects under different conditions. Unfortunately, information regarding the expression status of key players involved in their synthesis and function is for the most part lacking. The current study thus aims at assessing the levels of such targets in L. decemlineata exposed to hot and cold temperatures as well as treated to the insecticides chlorantraniliprole, clothianidin, imidacloprid, and spinosad. Transcript expression levels of Ago1, Ago2, Ago3, Dcr2a, Dcr2b, Expo-5, Siwi-1, and Siwi-2, components of pathways associated with small noncoding RNA production or function, were measured by qRT-PCR and revealed modulation of select transcripts in response to temperature challenges and to select insecticides. RNAi-mediated reduction of Ago2 transcript levels in L. decemlineata injected with Ago2-targeting dsRNA and exposed to cold and warm temperatures was also conducted. Changes in survival rates were observed for the latter condition in dsRNA- versus saline-injected insects. These results showcase the differential expression of select targets involved in small noncoding RNA homeostasis and provide leads for the subsequent assessment of their involvement during stress response in L. decemlineata using RNAi-based approaches.
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Affiliation(s)
- Mariem Ben Youssef
- Department of Chemistry and Biochemistry, Université de Moncton, 18 Antonine-Maillet Avenue, Moncton, New Brunswick, E1A 3E9, Canada
| | - Brigitte Christelle Ouédraogo
- Department of Chemistry and Biochemistry, Université de Moncton, 18 Antonine-Maillet Avenue, Moncton, New Brunswick, E1A 3E9, Canada
| | - Pierre Bastarache
- Department of Chemistry and Biochemistry, Université de Moncton, 18 Antonine-Maillet Avenue, Moncton, New Brunswick, E1A 3E9, Canada
| | - Pascal Dumas
- Department of Chemistry and Biochemistry, Université de Moncton, 18 Antonine-Maillet Avenue, Moncton, New Brunswick, E1A 3E9, Canada
| | - Chandra E Moffat
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, 850 Lincoln Road, Fredericton, New Brunswick, E3B 4Z7, Canada
| | - Jessica L Vickruck
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, 850 Lincoln Road, Fredericton, New Brunswick, E3B 4Z7, Canada
| | - Pier Jr Morin
- Department of Chemistry and Biochemistry, Université de Moncton, 18 Antonine-Maillet Avenue, Moncton, New Brunswick, E1A 3E9, Canada
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6
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Bai Y, Caussinus E, Leo S, Bosshardt F, Myachina F, Rot G, Robinson MD, Lehner CF. A cis-regulatory element promoting increased transcription at low temperature in cultured ectothermic Drosophila cells. BMC Genomics 2021; 22:771. [PMID: 34711176 PMCID: PMC8555087 DOI: 10.1186/s12864-021-08057-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 10/06/2021] [Indexed: 02/06/2023] Open
Abstract
Background Temperature change affects the myriad of concurrent cellular processes in a non-uniform, disruptive manner. While endothermic organisms minimize the challenge of ambient temperature variation by keeping the core body temperature constant, cells of many ectothermic species maintain homeostatic function within a considerable temperature range. The cellular mechanisms enabling temperature acclimation in ectotherms are still poorly understood. At the transcriptional level, the heat shock response has been analyzed extensively. The opposite, the response to sub-optimal temperature, has received lesser attention in particular in animal species. The tissue specificity of transcriptional responses to cool temperature has not been addressed and it is not clear whether a prominent general response occurs. Cis-regulatory elements (CREs), which mediate increased transcription at cool temperature, and responsible transcription factors are largely unknown. Results The ectotherm Drosophila melanogaster with a presumed temperature optimum around 25 °C was used for transcriptomic analyses of effects of temperatures at the lower end of the readily tolerated range (14–29 °C). Comparative analyses with adult flies and cell culture lines indicated a striking degree of cell-type specificity in the transcriptional response to cool. To identify potential cis-regulatory elements (CREs) for transcriptional upregulation at cool temperature, we analyzed temperature effects on DNA accessibility in chromatin of S2R+ cells. Candidate cis-regulatory elements (CREs) were evaluated with a novel reporter assay for accurate assessment of their temperature-dependency. Robust transcriptional upregulation at low temperature could be demonstrated for a fragment from the pastrel gene, which expresses more transcript and protein at reduced temperatures. This CRE is controlled by the JAK/STAT signaling pathway and antagonizing activities of the transcription factors Pointed and Ets97D. Conclusion Beyond a rich data resource for future analyses of transcriptional control within the readily tolerated range of an ectothermic animal, a novel reporter assay permitting quantitative characterization of CRE temperature dependence was developed. Our identification and functional dissection of the pst_E1 enhancer demonstrate the utility of resources and assay. The functional characterization of this CoolUp enhancer provides initial mechanistic insights into transcriptional upregulation induced by a shift to temperatures at the lower end of the readily tolerated range. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08057-4.
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Affiliation(s)
- Yu Bai
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Emmanuel Caussinus
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Stefano Leo
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Fritz Bosshardt
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Faina Myachina
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Gregor Rot
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.,SIB Swiss Institute of Bioinformatics, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Mark D Robinson
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.,SIB Swiss Institute of Bioinformatics, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Christian F Lehner
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.
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7
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Silva WTAF, Otto SP, Immler S. Evolution of plasticity in production and transgenerational inheritance of small RNAs under dynamic environmental conditions. PLoS Genet 2021; 17:e1009581. [PMID: 34038409 PMCID: PMC8186813 DOI: 10.1371/journal.pgen.1009581] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 06/08/2021] [Accepted: 05/05/2021] [Indexed: 01/07/2023] Open
Abstract
In a changing environment, small RNAs (sRNAs) play an important role in the post-transcriptional regulation of gene expression and can vary in abundance depending on the conditions experienced by an individual (phenotypic plasticity) and its parents (non-genetic inheritance). Many sRNAs are unusual in that they can be produced in two ways, either using genomic DNA as the template (primary sRNAs) or existing sRNAs as the template (secondary sRNAs). Thus, organisms can evolve rapid plastic responses to their current environment by adjusting the amplification rate of sRNA templates. sRNA levels can also be transmitted transgenerationally by the direct transfer of either sRNAs or the proteins involved in amplification. Theory is needed to describe the selective forces acting on sRNA levels, accounting for the dual nature of sRNAs as regulatory elements and templates for amplification and for the potential to transmit sRNAs and their amplification agents to offspring. Here, we develop a model to study the dynamics of sRNA production and inheritance in a fluctuating environment. We tested the selective advantage of mutants capable of sRNA-mediated phenotypic plasticity within resident populations with fixed levels of sRNA transcription. Even when the resident was allowed to evolve an optimal constant rate of sRNA production, plastic amplification rates capable of responding to environmental conditions were favored. Mechanisms allowing sRNA transcripts or amplification agents to be inherited were favored primarily when parents and offspring face similar environments and when selection acts before the optimal level of sRNA can be reached within the organism. Our study provides a clear set of testable predictions for the evolution of sRNA-related mechanisms of phenotypic plasticity and transgenerational inheritance.
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Affiliation(s)
| | - Sarah P. Otto
- Department of Zoology, University of British Columbia, Vancouver, Canada
| | - Simone Immler
- Department of Evolutionary Biology, Uppsala University, Uppsala, Sweden
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
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8
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Neumann A, Meinke S, Goldammer G, Strauch M, Schubert D, Timmermann B, Heyd F, Preußner M. Alternative splicing coupled mRNA decay shapes the temperature-dependent transcriptome. EMBO Rep 2020; 21:e51369. [PMID: 33140569 PMCID: PMC7726792 DOI: 10.15252/embr.202051369] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 10/02/2020] [Accepted: 10/08/2020] [Indexed: 11/09/2022] Open
Abstract
Mammalian body temperature oscillates with the time of the day and is altered in diverse pathological conditions. We recently identified a body temperature‐sensitive thermometer‐like kinase, which alters SR protein phosphorylation and thereby globally controls alternative splicing (AS). AS can generate unproductive variants which are recognized and degraded by diverse mRNA decay pathways—including nonsense‐mediated decay (NMD). Here we show extensive coupling of body temperature‐controlled AS to mRNA decay, leading to global control of temperature‐dependent gene expression (GE). Temperature‐controlled, decay‐inducing splicing events are evolutionarily conserved and pervasively found within RNA‐binding proteins, including most SR proteins. AS‐coupled poison exon inclusion is essential for rhythmic GE of SR proteins and has a global role in establishing temperature‐dependent rhythmic GE profiles, both in mammals under circadian body temperature cycles and in plants in response to ambient temperature changes. Together, these data identify body temperature‐driven AS‐coupled mRNA decay as an evolutionary ancient, core clock‐independent mechanism to generate rhythmic GE.
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Affiliation(s)
- Alexander Neumann
- Institute of Chemistry and Biochemistry, Laboratory of RNA Biochemistry, Freie Universität Berlin, Berlin, Germany.,Omiqa Bioinformatics, Berlin, Germany
| | - Stefan Meinke
- Institute of Chemistry and Biochemistry, Laboratory of RNA Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Gesine Goldammer
- Institute of Chemistry and Biochemistry, Laboratory of RNA Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Miriam Strauch
- Institute of Chemistry and Biochemistry, Laboratory of RNA Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Daniel Schubert
- Epigenetics of Plants, Freie Universität Berlin, Berlin, Germany
| | - Bernd Timmermann
- Sequencing Core Facility, Max-Planck-Institute for Molecular Genetics, Berlin, Germany
| | - Florian Heyd
- Institute of Chemistry and Biochemistry, Laboratory of RNA Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Marco Preußner
- Institute of Chemistry and Biochemistry, Laboratory of RNA Biochemistry, Freie Universität Berlin, Berlin, Germany
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9
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Gebert D, Jehn J, Rosenkranz D. Widespread selection for extremely high and low levels of secondary structure in coding sequences across all domains of life. Open Biol 2019; 9:190020. [PMID: 31138098 PMCID: PMC6544989 DOI: 10.1098/rsob.190020] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Codon composition, GC content and local RNA secondary structures can have a profound effect on gene expression, and mutations affecting these parameters, even though they do not alter the protein sequence, are not neutral in terms of selection. Although evidence exists that, in some cases, selection favours more stable RNA secondary structures, we currently lack a concrete idea of how many genes are affected within a species, and whether this is a universal phenomenon in nature. We searched for signs of structural selection in a global manner, analysing a set of 1 million coding sequences from 73 species representing all domains of life, as well as viruses, by means of our newly developed software PACKEIS. We show that codon composition and amino acid identity are main determinants of RNA secondary structure. In addition, we show that the arrangement of synonymous codons within coding sequences is non-random, yielding extremely high, but also extremely low, RNA structuredness significantly more often than expected by chance. Taken together, we demonstrate that selection for high and low levels of secondary structure is a widespread phenomenon. Our results provide another line of evidence that synonymous mutations are less neutral than commonly thought, which is of importance for many evolutionary models.
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Affiliation(s)
- Daniel Gebert
- Institute of Organismic and Molecular Evolution iOME, Anthropology, Johannes Gutenberg University Mainz , Anselm-Franz-von-Bentzel-Weg 7, 55099 Mainz , Germany
| | - Julia Jehn
- Institute of Organismic and Molecular Evolution iOME, Anthropology, Johannes Gutenberg University Mainz , Anselm-Franz-von-Bentzel-Weg 7, 55099 Mainz , Germany
| | - David Rosenkranz
- Institute of Organismic and Molecular Evolution iOME, Anthropology, Johannes Gutenberg University Mainz , Anselm-Franz-von-Bentzel-Weg 7, 55099 Mainz , Germany
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Casier K, Delmarre V, Gueguen N, Hermant C, Viodé E, Vaury C, Ronsseray S, Brasset E, Teysset L, Boivin A. Environmentally-induced epigenetic conversion of a piRNA cluster. eLife 2019; 8:e39842. [PMID: 30875295 PMCID: PMC6420265 DOI: 10.7554/elife.39842] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 03/06/2019] [Indexed: 01/02/2023] Open
Abstract
Transposable element (TE) activity is repressed in animal gonads by PIWI-interacting RNAs (piRNAs) produced by piRNA clusters. Current models in flies propose that germinal piRNA clusters are functionally defined by the maternal inheritance of piRNAs produced during the previous generation. Taking advantage of an inactive, but ready to go, cluster of P-element derived transgene insertions in Drosophila melanogaster, we show here that raising flies at high temperature (29°C) instead of 25°C triggers the stable conversion of this locus from inactive into actively producing functional piRNAs. The increase of antisense transcripts from the cluster at 29°C combined with the requirement of transcription of euchromatic homologous sequences, suggests a role of double stranded RNA in the production of de novo piRNAs. This report describes the first case of the establishment of an active piRNA cluster by environmental changes in the absence of maternal inheritance of homologous piRNAs. Editorial note This article has been through an editorial process in which the authors decide how to respond to the issues raised during peer review. The Reviewing Editor's assessment is that all the issues have been addressed (see decision letter).
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Affiliation(s)
- Karine Casier
- Laboratoire Biologie du Développement, UMR7622Sorbonne Université, CNRS, Institut de Biologie Paris-SeineParisFrance
| | - Valérie Delmarre
- Laboratoire Biologie du Développement, UMR7622Sorbonne Université, CNRS, Institut de Biologie Paris-SeineParisFrance
| | - Nathalie Gueguen
- GReDUniversité Clermont Auvergne, CNRS, INSERM, BP 10448Clermont-FerrandFrance
| | - Catherine Hermant
- Laboratoire Biologie du Développement, UMR7622Sorbonne Université, CNRS, Institut de Biologie Paris-SeineParisFrance
| | - Elise Viodé
- Laboratoire Biologie du Développement, UMR7622Sorbonne Université, CNRS, Institut de Biologie Paris-SeineParisFrance
| | - Chantal Vaury
- GReDUniversité Clermont Auvergne, CNRS, INSERM, BP 10448Clermont-FerrandFrance
| | - Stéphane Ronsseray
- Laboratoire Biologie du Développement, UMR7622Sorbonne Université, CNRS, Institut de Biologie Paris-SeineParisFrance
| | - Emilie Brasset
- GReDUniversité Clermont Auvergne, CNRS, INSERM, BP 10448Clermont-FerrandFrance
| | - Laure Teysset
- Laboratoire Biologie du Développement, UMR7622Sorbonne Université, CNRS, Institut de Biologie Paris-SeineParisFrance
| | - Antoine Boivin
- Laboratoire Biologie du Développement, UMR7622Sorbonne Université, CNRS, Institut de Biologie Paris-SeineParisFrance
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11
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Lehmann M, Knust E, Hebbar S. Drosophila melanogaster: A Valuable Genetic Model Organism to Elucidate the Biology of Retinitis Pigmentosa. Methods Mol Biol 2019; 1834:221-249. [PMID: 30324448 DOI: 10.1007/978-1-4939-8669-9_16] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Retinitis pigmentosa (RP) is a complex inherited disease. It is associated with mutations in a wide variety of genes with many different functions. These mutations impact the integrity of rod photoreceptors and ultimately result in the progressive degeneration of rods and cone photoreceptors in the retina, leading to complete blindness. A hallmark of this disease is the variable degree to which symptoms are manifest in patients. This is indicative of the influence of the environment, and/or of the distinct genetic makeup of the individual.The fruit fly, Drosophila melanogaster, has effectively proven to be a great model system to better understand interconnected genetic networks. Unraveling genetic interactions and thereby different cellular processes is relatively easy because more than a century of research on flies has enabled the creation of sophisticated genetic tools to perturb gene function. A remarkable conservation of disease genes across evolution and the similarity of the general organization of the fly and vertebrate photoreceptor cell had prompted research on fly retinal degeneration. To date six fly models for RP, including RP4, RP11, RP12, RP14, RP25, and RP26, have been established, and have provided useful information on RP disease biology. In this chapter, an outline of approaches and experimental specifications are described to enable utilizing or developing new fly models of RP.
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Affiliation(s)
- Malte Lehmann
- Max-Planck-Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Elisabeth Knust
- Max-Planck-Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
| | - Sarita Hebbar
- Max-Planck-Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
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12
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Kronholm I, Ketola T. Effects of acclimation time and epigenetic mechanisms on growth of Neurospora in fluctuating environments. Heredity (Edinb) 2018; 121:327-341. [PMID: 30143790 PMCID: PMC6133946 DOI: 10.1038/s41437-018-0138-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Revised: 07/17/2018] [Accepted: 07/23/2018] [Indexed: 01/19/2023] Open
Abstract
Reaction norms or tolerance curves have often been used to predict how organisms deal with fluctuating environments. A potential drawback is that reaction norms measured in different constant environments may not capture all aspects of organismal responses to fluctuating environments. We examined growth of the filamentous fungus Neurospora crassa in fluctuating temperatures and tested if growth in fluctuating temperatures can be explained simply by the growth in different constant temperatures or if more complex models are needed. In addition, as previous studies on fluctuating environments have revealed that past temperatures that organisms have experienced can affect their response to current temperature, we tested the roles of different epigenetic mechanisms in response to fluctuating environments using different mutants. We found that growth of Neurospora can be predicted in fluctuating temperatures to some extent if acclimation times are taken into account in the model. Interestingly, while fluctuating environments have been linked with epigenetic responses, we found only some evidence of involvement of epigenetic mechanisms on tolerating fluctuating temperatures. Mutants which lacked H3K4 or H3K36 methylation had slightly impaired response to temperature fluctuations, in addition the H3K4 methylation mutant and a mutant in the RNA interference pathway had altered acclimation times.
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Affiliation(s)
- Ilkka Kronholm
- Centre of Excellence in Biological Interactions, Department of Biological and Environmental Sciences, University of Jyväskylä, FI-40014, Jyväskylä, Finland.
| | - Tarmo Ketola
- Centre of Excellence in Biological Interactions, Department of Biological and Environmental Sciences, University of Jyväskylä, FI-40014, Jyväskylä, Finland
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Murakami A. Non-specific protein modifications may be novel mechanism underlying bioactive phytochemicals. J Clin Biochem Nutr 2018; 62:115-123. [PMID: 29610550 PMCID: PMC5874230 DOI: 10.3164/jcbn.17-113] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 11/27/2017] [Indexed: 12/27/2022] Open
Abstract
In a variety of experimental models, dietary phytochemicals have been demonstrated to exhibit pronounced and versatile bioactivities. Importantly, the possibility of such phytochemicals for human application has been supported in part by epidemiological surveys, which have demonstrated that frequent ingestion of vegetables and fruits containing abundant phytochemicals lowers the risk of onset of various diseases. However, the action mechanisms underlying those dietary phytochemical activities remain to be fully elucidated. For example, even though the anti-oxidant effects of natural polyphenols have long received widespread attention from food scientists, their roles in and contribution to those bioactivities remain controversial because of their poor bioavailability, resulting in extremely low concentrations in the bloodstream. Meanwhile, another important question is why phytochemicals have beneficial effects for animals, including humans, since they are biosynthesized by plants as compounds necessary for adaptation to environmental stress. In regard to that fundamental question, we recently reported novel and unique mechanisms of action of zerumbone, a sesquiterpene with anti-inflammatory and chemopreventive properties. This agent was found to partially exhibit bioactivity through its non-specific interactions with cellular proteins. More strikingly, a non-specific protein binding action of zerumbone was revealed to partially contribute to its anti-inflammatory functions via activation of heat shock factor 1. The present review article highlights and introduces our recent findings regarding the proteo-stress-mediated mechanisms of this phytochemical, along with the concept of hormesis.
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Affiliation(s)
- Akira Murakami
- Food Hormesis Laboratory, Department of Food Science & Nutrition, School of Human Science & Environment, Research Institute for Food and Nutritional Sciences, University of Hyogo, 1-1-12 Shinzaike-Honcho, Himeji, Hyogo 670-0092, Japan
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Abstract
Temperature has a major impact on gene expression in ectotherms. But until recently, it was not clear in which way, if any, small non-coding RNAs such as miRNAs or piRNAs contribute to thermosensitive gene regulation. We have recently shown that temperature-responsive miRNAs in Drosophila drive adaptation to different ambient temperatures on the transcriptome level. Moreover, we demonstrated that higher temperatures lead to a more efficient piRNA-dependent transposon silencing, possibly due to heat-induced unfolding of RNA secondary structures. In this commentary, we will dwell upon particular interesting aspects connected to our findings, hoping that our point of view may encourage other scientists to address some of the questions raised here. We will particularly focus on aspects related to climate-dependent transposon propagation in evolution and putative transgenerational epigenetic effects of altered small RNA transcriptomes. We further briefly indicate how temperature-responsive miRNAs may confound the interpretation of data obtained from experiments comprising heat-shock treatment which is a widely used technique not only in Drosophila genetics.
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Affiliation(s)
- Isabel Fast
- a Institute of Organismic and Molecular Evolution, Johannes Gutenberg University , Mainz , Germany
| | - David Rosenkranz
- a Institute of Organismic and Molecular Evolution, Johannes Gutenberg University , Mainz , Germany
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