1
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Erman A, Hawkins LJ, Storey KB. Changes in microRNA expression related to ischemia-reperfusion injury in the kidney of the thirteen-lined ground squirrel during torpor. Biochimie 2024; 225:40-48. [PMID: 38705508 DOI: 10.1016/j.biochi.2024.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Revised: 04/18/2024] [Accepted: 05/02/2024] [Indexed: 05/07/2024]
Abstract
During the hibernation season, the thirteen-lined ground squirrel undergoes cyclical torpor and arousal periods. The decrease and restoration of metabolic rate and oxygen delivery during torpor and arousal, respectively, may cause reperfusion-ischemia injury in the kidneys. In order to maintain the structural integrity of the kidneys necessary for renal function resumption during arousal, the thirteen-lined ground squirrel has developed adaptive methods to prevent and repair kidney injury. In this present study, computational methods were used to clean and analyze sequenced kidney RNA samples. Significantly differentially expressed microRNAs and enriched gene sets were also determined. From the gene set analysis, the results showed an increase in ubiquitin-related processes and p53 signaling pathways which suggested the occurrence of kidney damage during torpor. There was also an observed increase in cell cycle processes and the anchoring junction cellular compartment which may lend to the prevention of kidney injury. From the differentially expressed microRNAs, miR-27a (log2FC = 1.639; p-value = 0.023), miR-129 (log2FC = 2.516; p-value = 0.023), miR-let-7b (log2FC = 2.360; p-value = 0.025), miR-let-7c (log2FC = 2.291; p-value = 0.037) and miR-let-7i (log2FC = 1.564; p-value = 0.039) were found to be significantly upregulated. These biochemical adaptations may allow the thirteen-lined ground squirrel to maintain kidney structure and function during hibernation.
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Affiliation(s)
- Aylin Erman
- Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario, K1S 5B6, Canada.
| | - Liam J Hawkins
- Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario, K1S 5B6, Canada
| | - Kenneth B Storey
- Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario, K1S 5B6, Canada
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2
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Ingelson-Filpula WA, Storey KB. Hibernation-Induced microRNA Expression Promotes Signaling Pathways and Cell Cycle Dysregulation in Ictidomys tridecemlineatus Cardiac Tissue. Metabolites 2023; 13:1096. [PMID: 37887421 PMCID: PMC10608741 DOI: 10.3390/metabo13101096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 10/05/2023] [Accepted: 10/16/2023] [Indexed: 10/28/2023] Open
Abstract
The thirteen-lined ground squirrel Ictidomys tridecemlineatus is a rodent that lives throughout the United States and Canada and uses metabolic rate depression to facilitate circannual hibernation which helps it survive the winter. Metabolic rate depression is the reorganization of cellular physiology and molecular biology to facilitate a global downregulation of nonessential genes and processes, which conserves endogenous fuel resources and prevents the buildup of waste byproducts. Facilitating metabolic rate depression requires a complex interplay of regulatory approaches, including post-transcriptional modes such as microRNA. MicroRNA are short, single-stranded RNA species that bind to mRNA transcripts and target them for degradation or translational suppression. Using next-generation sequencing, we analyzed euthermic vs. hibernating cardiac tissue in I. tridecemlineatus to predict seven miRNAs (let-7e-5p, miR-122-5p, miR-2355-3p, miR-6715b-3p, miR-378i, miR-9851-3p, and miR-454-3p) that may be differentially regulated during hibernation. Gene ontology and KEGG pathway analysis suggested that these miRNAs cause a strong activation of ErbB2 signaling which causes downstream effects, including the activation of MAPK and PI3K/Akt signaling and concurrent decreases in p53 signaling and cell cycle-related processes. Taken together, these results predict critical miRNAs that may change during hibernation in the hearts of I. tridecemlineatus and identify key signaling pathways that warrant further study in this species.
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Affiliation(s)
| | - Kenneth B. Storey
- Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, ON K1S 5B6, Canada;
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3
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Sullivan IR, Adams DM, Greville LJS, Faure PA, Wilkinson GS. Big brown bats experience slower epigenetic ageing during hibernation. Proc Biol Sci 2022; 289:20220635. [PMID: 35946154 PMCID: PMC9364000 DOI: 10.1098/rspb.2022.0635] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Comparative analyses of bats indicate that hibernation is associated with increased longevity among species. However, it is not yet known if hibernation affects biological ageing of individuals. Here, we use DNA methylation (DNAm) as an epigenetic biomarker of ageing to determine the effect of hibernation on the big brown bat, Eptesicus fuscus. First, we compare epigenetic age, as predicted by a multi-species epigenetic clock, between hibernating and non-hibernating animals and find that hibernation is associated with epigenetic age. Second, we identify genomic sites that exhibit hibernation-associated change in DNAm, independent of age, by comparing samples taken from the same individual in hibernating and active seasons. This paired comparison identified over 3000 differentially methylated positions (DMPs) in the genome. Genome-wide association comparisons to tissue-specific functional elements reveals that DMPs with elevated DNAm during winter occur at sites enriched for quiescent chromatin states, whereas DMPs with reduced DNAm during winter occur at sites enriched for transcription enhancers. Furthermore, genes nearest DMPs are involved in regulation of metabolic processes and innate immunity. Finally, significant overlap exists between genes nearest hibernation DMPs and genes nearest previously identified longevity DMPs. Taken together, these results are consistent with hibernation influencing ageing and longevity in bats.
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Affiliation(s)
- Isabel R. Sullivan
- Department of Biology, University of Maryland, College Park, MD 20742, USA
| | - Danielle M. Adams
- Department of Biology, University of Maryland, College Park, MD 20742, USA,Department of Biological Sciences, Towson University, Towson, MD 21252, USA
| | - Lucas J. S. Greville
- Department of Psychology, Neuroscience and Behaviour, McMaster University, Hamilton, ON, Canada L8S 4K1,Department of Biology, University of Waterloo, Waterloo, ON, Canada N3 L 3G1
| | - Paul A. Faure
- Department of Psychology, Neuroscience and Behaviour, McMaster University, Hamilton, ON, Canada L8S 4K1
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4
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Hadj-Moussa H, Hawkins LJ, Storey KB. Role of MicroRNAs in Extreme Animal Survival Strategies. Methods Mol Biol 2022; 2257:311-347. [PMID: 34432286 DOI: 10.1007/978-1-0716-1170-8_16] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The critical role microRNAs play in modulating global functions is emerging, both in the maintenance of homeostatic mechanisms and in the adaptation to diverse environmental stresses. When stressed, cells must divert metabolic requirements toward immediate survival and eventual recovery and the unique features of miRNAs, such as their relatively ATP-inexpensive biogenesis costs, and the quick and reversible nature of their action, renders them excellent "master controllers" for rapid responses. Many animal survival strategies for dealing with extreme environmental pressures involve prolonged retreats into states of suspended animation to extend the time that they can survive on their limited internal fuel reserves until conditions improve. The ability to retreat into such hypometabolic states is only possible by coupling the global suppression of nonessential energy-expensive functions with an activation of prosurvival networks, a process in which miRNAs are now known to play a major role. In this chapter, we discuss the activation, expression, biogenesis, and unique attributes of miRNA regulation required to facilitate profound metabolic rate depression and implement stress-specific metabolic adaptations. We examine the role of miRNA in strategies of biochemical adaptation including mammalian hibernation, freeze tolerance, freeze avoidance, anoxia and hypoxia survival, estivation, and dehydration tolerance. By comparing these seemingly different adaptive programs in traditional and exotic animal models, we highlight both unique and conserved miRNA-meditated mechanisms for survival. Additional topics discussed include transcription factor networks, temperature dependent miRNA-targeting, and novel species-specific and stress-specific miRNAs.
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Affiliation(s)
| | - Liam J Hawkins
- Department of Biology, Carleton University, Ottawa, ON, Canada
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5
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Muscles in Winter: The Epigenetics of Metabolic Arrest. EPIGENOMES 2021; 5:epigenomes5040028. [PMID: 34968252 PMCID: PMC8715459 DOI: 10.3390/epigenomes5040028] [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: 10/08/2021] [Revised: 12/07/2021] [Accepted: 12/13/2021] [Indexed: 12/11/2022] Open
Abstract
The winter months are challenging for many animal species, which often enter a state of dormancy or hypometabolism to “wait out” the cold weather, food scarcity, reduced daylight, and restricted mobility that can characterize the season. To survive, many species use metabolic rate depression (MRD) to suppress nonessential metabolic processes, conserving energy and limiting tissue atrophy particularly of skeletal and cardiac muscles. Mammalian hibernation is the best recognized example of winter MRD, but some turtle species spend the winter unable to breathe air and use MRD to survive with little or no oxygen (hypoxia/anoxia), and various frogs endure the freezing of about two-thirds of their total body water as extracellular ice. These winter survival strategies are highly effective, but create physiological and metabolic challenges that require specific biochemical adaptive strategies. Gene-related processes as well as epigenetic processes can lower the risk of atrophy during prolonged inactivity and limited nutrient stores, and DNA modifications, mRNA storage, and microRNA action are enacted to maintain and preserve muscle. This review article focuses on epigenetic controls on muscle metabolism that regulate MRD to avoid muscle atrophy and support winter survival in model species of hibernating mammals, anoxia-tolerant turtles and freeze-tolerant frogs. Such research may lead to human applications including muscle-wasting disorders such as sarcopenia, or other conditions of limited mobility.
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6
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MicroRNA Cues from Nature: A Roadmap to Decipher and Combat Challenges in Human Health and Disease? Cells 2021; 10:cells10123374. [PMID: 34943882 PMCID: PMC8699674 DOI: 10.3390/cells10123374] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 11/22/2021] [Accepted: 11/27/2021] [Indexed: 12/15/2022] Open
Abstract
MicroRNAs are small non-coding RNA (18–24 nt long) that fine-tune gene expression at the post-transcriptional level. With the advent of “multi-omics” analysis and sequencing approaches, they have now been implicated in every facet of basic molecular networks, including metabolism, homeostasis, and cell survival to aid cellular machinery in adapting to changing environmental cues. Many animals must endure harsh environmental conditions in nature, including cold/freezing temperatures, oxygen limitation (anoxia/hypoxia), and food or water scarcity, often requiring them to revamp their metabolic organization, frequently on a seasonal or life stage basis. MicroRNAs are important regulatory molecules in such processes, just as they are now well-known to be involved in many human responses to stress or disease. The present review outlines the role of miRNAs in natural animal models of environmental stress and adaptation including torpor/hibernation, anoxia/hypoxia tolerance, and freeze tolerance. We also discuss putative medical applications of advances in miRNA biology including organ preservation for transplant, inflammation, ageing, metabolic disorders (e.g., obesity), mitochondrial dysfunction (mitoMirs) as well as specialized miRNA subgroups respective to low temperature (CryomiRs) and low oxygen (OxymiRs). The review also covers differential regulation of conserved and novel miRNAs involved at cell, tissue, and stress specific levels across multiple species and their roles in survival. Ultimately, the species-specific comparison and conserved miRNA responses seen in evolutionarily disparate animal species can help us to understand the complex miRNA network involved in regulating and reorganizing metabolism to achieve diverse outcomes, not just in nature, but in human health and disease.
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7
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Tessier SN, Ingelson-Filpula WA, Storey KB. Epigenetic regulation by DNA methyltransferases during torpor in the thirteen-lined ground squirrel Ictidomys tridecemlineatus. Mol Cell Biochem 2021; 476:3975-3985. [PMID: 34191233 DOI: 10.1007/s11010-021-04214-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 06/21/2021] [Indexed: 12/31/2022]
Abstract
The thirteen-lined ground squirrel, Ictidomys tridecemlineatus, is a mammal capable of lowering its Tb to almost 0 °C while undergoing deep torpor bouts over the winter. To decrease its metabolic rate to such a drastic extent, the squirrel must undergo multiple physiological, biological, and molecular alterations including downregulation of almost all nonessential processes. Epigenetic regulation allows for a dynamic range of transient phenotypes, allowing the squirrel to downregulate energy-expensive and nonessential pathways during torpor. DNA methylation is a prominent form of epigenetic regulation; therefore, the DNA methyltransferase (DNMT) family of enzymes were studied by measuring expression and activity levels of the five major proteins during torpor bouts. Additionally, specific cytosine marks on genomic DNA were quantified to further elucidate DNA methylation during hibernation. A tissue-specific response was observed that highlighted variant degrees of DNA methylation and DNMT expression/activity, demonstrating that DNA methylation is a highly complex form of epigenetic regulation and likely one of many regulatory mechanisms that enables metabolic rate depression in response to torpor.
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Affiliation(s)
- Shannon N Tessier
- Institute of Biochemistry and Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada.,BioMEMS Resource Center & Center for Engineering in Medicine, Massachusetts General Hospital & Harvard Medical School, 114 16th Street, Charlestown, MA, 02129, USA
| | - W Aline Ingelson-Filpula
- Institute of Biochemistry and Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
| | - Kenneth B Storey
- Institute of Biochemistry and Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada.
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8
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Gillen AE, Fu R, Riemondy KA, Jager J, Fang B, Lazar MA, Martin SL. Liver Transcriptome Dynamics During Hibernation Are Shaped by a Shifting Balance Between Transcription and RNA Stability. Front Physiol 2021; 12:662132. [PMID: 34093224 PMCID: PMC8176218 DOI: 10.3389/fphys.2021.662132] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 04/26/2021] [Indexed: 12/12/2022] Open
Abstract
Hibernators dramatically lower metabolism to save energy while fasting for months. Prolonged fasting challenges metabolic homeostasis, yet small-bodied hibernators emerge each spring ready to resume all aspects of active life, including immediate reproduction. The liver is the body’s metabolic hub, processing and detoxifying macromolecules to provide essential fuels to brain, muscle and other organs throughout the body. Here we quantify changes in liver gene expression across several distinct physiological states of hibernation in 13-lined ground squirrels, using RNA-seq to measure the steady-state transcriptome and GRO-seq to measure transcription for the first time in a hibernator. Our data capture key timepoints in both the seasonal and torpor-arousal cycles of hibernation. Strong positive correlation between transcription and the transcriptome indicates that transcriptional control dominates the known seasonal reprogramming of metabolic gene expression in liver for hibernation. During the torpor-arousal cycle, however, discordance develops between transcription and the steady-state transcriptome by at least two mechanisms: 1) although not transcribed during torpor, some transcripts are unusually stable across the torpor bout; and 2) unexpectedly, on some genes, our data suggest continuing, slow elongation with a failure to terminate transcription across the torpor bout. While the steady-state RNAs corresponding to these read through transcripts did not increase during torpor, they did increase shortly after rewarming despite their simultaneously low transcription. Both of these mechanisms would assure the immediate availability of functional transcripts upon rewarming. Integration of transcriptional, post-transcriptional and RNA stability control mechanisms, all demonstrated in these data, likely initiate a serial gene expression program across the short euthermic period that restores the tissue and prepares the animal for the next bout of torpor.
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Affiliation(s)
- Austin E Gillen
- RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO, United States
| | - Rui Fu
- RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO, United States
| | - Kent A Riemondy
- RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO, United States
| | - Jennifer Jager
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, and The Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States.,Division of Endocrinology, Diabetes, and Metabolism, Department of Genetics, and The Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Bin Fang
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, and The Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States.,Division of Endocrinology, Diabetes, and Metabolism, Department of Genetics, and The Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Mitchell A Lazar
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, and The Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States.,Division of Endocrinology, Diabetes, and Metabolism, Department of Genetics, and The Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Sandra L Martin
- RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO, United States.,Department of Cell and Developmental Biology, University of Colorado School of Medicine, Aurora, CO, United States
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9
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Wu CW, Storey KB. mTOR Signaling in Metabolic Stress Adaptation. Biomolecules 2021; 11:biom11050681. [PMID: 34062764 PMCID: PMC8147357 DOI: 10.3390/biom11050681] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 04/28/2021] [Accepted: 04/30/2021] [Indexed: 12/30/2022] Open
Abstract
The mechanistic target of rapamycin (mTOR) is a central regulator of cellular homeostasis that integrates environmental and nutrient signals to control cell growth and survival. Over the past two decades, extensive studies of mTOR have implicated the importance of this protein complex in regulating a broad range of metabolic functions, as well as its role in the progression of various human diseases. Recently, mTOR has emerged as a key signaling molecule in regulating animal entry into a hypometabolic state as a survival strategy in response to environmental stress. Here, we review current knowledge of the role that mTOR plays in contributing to natural hypometabolic states such as hibernation, estivation, hypoxia/anoxia tolerance, and dauer diapause. Studies across a diverse range of animal species reveal that mTOR exhibits unique regulatory patterns in an environmental stressor-dependent manner. We discuss how key signaling proteins within the mTOR signaling pathways are regulated in different animal models of stress, and describe how each of these regulations uniquely contribute to promoting animal survival in a hypometabolic state.
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Affiliation(s)
- Cheng-Wei Wu
- Department of Veterinary Biomedical Sciences, Western College of Veterinary Medicine, 52 Campus Drive, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK S7N 5B3, Canada
- Correspondence:
| | - Kenneth B. Storey
- Institute of Biochemistry and Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, ON K1S 5B6, Canada;
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10
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Nishida K, Shimozuru M, Okamatsu-Ogura Y, Miyazaki M, Soma T, Sashika M, Tsubota T. Changes in liver microRNA expression and their possible regulatory role in energy metabolism-related genes in hibernating black bears. J Comp Physiol B 2021; 191:397-409. [PMID: 33459845 DOI: 10.1007/s00360-020-01337-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 12/22/2020] [Accepted: 12/30/2020] [Indexed: 01/12/2023]
Abstract
Hibernating bears survive up to 6 months without feeding while yet maintaining metabolic homeostasis. We previously reported expression changes in energy metabolism-related genes in the liver of hibernating Japanese black bears. The present study examined the role of microRNAs in the regulation of hepatic gene expression during hibernation. The quantitative analyses revealed significant increases in the expression of 4 microRNAs (miR-221-3p, miR-222-3p, miR-455-3p, and miR-195a-5p) and decreases of 2 microRNAs (miR-122-5p and miR-7a-1-5p) during hibernation. RNA sequencing and in silico target prediction regarding 3 upregulated microRNAs (miR-221-3p, miR-222-3p and miR-455-3p) found 13 target mRNAs with significantly decreased expression during hibernation. The transfection of microRNA mimics into cells showed that miR-222 and miR-455 reduced solute carrier family 16 member 4 (SLC16A4) and fatty acid synthase (FASN) mRNA expression, respectively. Our results suggest that the increased levels of hepatic miRNA during hibernation (miR-222-3p and miR-455-3p) negatively regulate the expression of targeted genes predicted to be involved in the transport of energy source and de novo fatty acid synthesis, is consistent with a regulatory role of these miRNAs in energy metabolism in hibernating black bears.
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Affiliation(s)
- Kazuhei Nishida
- Laboratory of Wildlife Biology and Medicine, Faculty of Veterinary Medicine, Hokkaido University, Kita 18 Nishi 9, Kita-ku, Sapporo, Hokkaido, 060-0818, Japan
| | - Michito Shimozuru
- Laboratory of Wildlife Biology and Medicine, Faculty of Veterinary Medicine, Hokkaido University, Kita 18 Nishi 9, Kita-ku, Sapporo, Hokkaido, 060-0818, Japan.
| | - Yuko Okamatsu-Ogura
- Laboratory of Biochemistry, Faculty of Veterinary Medicine, Hokkaido University, Kita 18 Nishi 9, Kita-ku, Sapporo, Hokkaido, 060-0818, Japan
| | - Mitsunori Miyazaki
- Department of Physical Therapy, School of Rehabilitation Sciences, Health Sciences University of Hokkaido, Hokkaido, 061-0293, Japan
| | - Tsukasa Soma
- Laboratory of Wildlife Biology and Medicine, Faculty of Veterinary Medicine, Hokkaido University, Kita 18 Nishi 9, Kita-ku, Sapporo, Hokkaido, 060-0818, Japan
| | - Mariko Sashika
- Laboratory of Wildlife Biology and Medicine, Faculty of Veterinary Medicine, Hokkaido University, Kita 18 Nishi 9, Kita-ku, Sapporo, Hokkaido, 060-0818, Japan
| | - Toshio Tsubota
- Laboratory of Wildlife Biology and Medicine, Faculty of Veterinary Medicine, Hokkaido University, Kita 18 Nishi 9, Kita-ku, Sapporo, Hokkaido, 060-0818, Japan
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11
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Capraro A, O'Meally D, Waters SA, Patel HR, Georges A, Waters PD. MicroRNA dynamics during hibernation of the Australian central bearded dragon (Pogona vitticeps). Sci Rep 2020; 10:17854. [PMID: 33082398 PMCID: PMC7576210 DOI: 10.1038/s41598-020-73706-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 09/17/2020] [Indexed: 11/12/2022] Open
Abstract
Hibernation is a physiological state employed by many animals that are exposed to limited food and adverse winter conditions. Controlling tissue-specific and organism wide changes in metabolism and cellular function requires precise regulation of gene expression, including by microRNAs (miRNAs). Here we profile miRNA expression in the central bearded dragon (Pogona vitticeps) using small RNA sequencing of brain, heart, and skeletal muscle from individuals in late hibernation and four days post-arousal. A total of 1295 miRNAs were identified in the central bearded dragon genome; 664 of which were novel to central bearded dragon. We identified differentially expressed miRNAs (DEmiRs) in all tissues and correlated mRNA expression with known and predicted target mRNAs. Functional analysis of DEmiR targets revealed an enrichment of differentially expressed mRNA targets involved in metabolic processes. However, we failed to reveal biologically relevant tissue-specific processes subjected to miRNA-mediated regulation in heart and skeletal muscle. In brain, neuroprotective pathways were identified as potential targets regulated by miRNAs. Our data suggests that miRNAs are necessary for modulating the shift in cellular metabolism during hibernation and regulating neuroprotection in the brain. This study is the first of its kind in a hibernating reptile and provides key insight into this ephemeral phenotype.
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Affiliation(s)
- Alexander Capraro
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, UNSW Sydney, Kensington, NSW, 2052, Australia.
| | - Denis O'Meally
- Institute for Applied Ecology, University of Canberra, Canberra, ACT, 2601, Australia
- Center for Gene Therapy, Beckman Research Institute of the City of Hope, Duarte, CA, 91010, USA
| | - Shafagh A Waters
- School of Women's & Children's Health, Faculty of Medicine, UNSW Sydney, Kensington, NSW, 2052, Australia
| | - Hardip R Patel
- John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia
| | - Arthur Georges
- Institute for Applied Ecology, University of Canberra, Canberra, ACT, 2601, Australia
| | - Paul D Waters
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, UNSW Sydney, Kensington, NSW, 2052, Australia
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12
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Popova S, Ulanova A, Gritsyna Y, Salmov N, Rogachevsky V, Mikhailova G, Bobylev A, Bobyleva L, Yutskevich Y, Morenkov O, Zakharova N, Vikhlyantsev I. Predominant synthesis of giant myofibrillar proteins in striated muscles of the long-tailed ground squirrel Urocitellus undulatus during interbout arousal. Sci Rep 2020; 10:15185. [PMID: 32938992 PMCID: PMC7495002 DOI: 10.1038/s41598-020-72127-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 08/24/2020] [Indexed: 12/11/2022] Open
Abstract
Molecular mechanisms underlying muscle-mass retention during hibernation have been extensively discussed in recent years. This work tested the assumption that protein synthesis hyperactivation during interbout arousal of the long-tailed ground squirrel Urocitellus undulatus should be accompanied by increased calpain-1 activity in striated muscles. Calpain-1 is known to be autolysed and activated in parallel. Western blotting detected increased amounts of autolysed calpain-1 fragments in the heart (1.54-fold, p < 0.05) and m. longissimus dorsi (1.8-fold, p < 0.01) of ground squirrels during interbout arousal. The total protein synthesis rate determined by SUnSET declined 3.67-fold in the heart (p < 0.01) and 2.96-fold in m. longissimus dorsi (p < 0.01) during interbout arousal. The synthesis rates of calpain-1 substrates nebulin and titin in muscles did not differ during interbout arousal from those in active summer animals. A recovery of the volume of m. longissimus dorsi muscle fibres, a trend towards a heart-muscle mass increase and a restoration of the normal titin content (reduced in the muscles during hibernation) were observed. The results indicate that hyperactivation of calpain-1 in striated muscles of long-tailed ground squirrels during interbout arousal is accompanied by predominant synthesis of giant sarcomeric cytoskeleton proteins. These changes may contribute to muscle mass retention during hibernation.
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Affiliation(s)
- Svetlana Popova
- Laboratory of the Structure and Functions of Muscle Proteins, Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - Anna Ulanova
- Laboratory of the Structure and Functions of Muscle Proteins, Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - Yulia Gritsyna
- Laboratory of the Structure and Functions of Muscle Proteins, Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - Nikolay Salmov
- Laboratory of the Structure and Functions of Muscle Proteins, Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - Vadim Rogachevsky
- Laboratory of Signal Perception Mechanisms, Institute of Cell Biophysics, FRC PSCBR, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - Gulnara Mikhailova
- Laboratory of the Structure and Functions of Muscle Proteins, Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - Alexander Bobylev
- Laboratory of the Structure and Functions of Muscle Proteins, Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - Liya Bobyleva
- Laboratory of the Structure and Functions of Muscle Proteins, Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - Yana Yutskevich
- Kuban State University, Krasnodar, Krasnodar Krai, 350040, Russia
| | - Oleg Morenkov
- Laboratory of Cell Culture and Tissue Engineering, Institute of Cell Biophysics, FRC PSCBR, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - Nadezda Zakharova
- Laboratory of Natural and Artificial Hypobiosis Mechanisms, Institute of Cell Biophysics, FRC PSCBR, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - Ivan Vikhlyantsev
- Laboratory of the Structure and Functions of Muscle Proteins, Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia.
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13
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Al-Attar R, Storey KB. Suspended in time: Molecular responses to hibernation also promote longevity. Exp Gerontol 2020; 134:110889. [PMID: 32114078 DOI: 10.1016/j.exger.2020.110889] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 02/20/2020] [Accepted: 02/21/2020] [Indexed: 12/16/2022]
Abstract
Aging in most animals is an inevitable process that causes or is a result of physiological, biochemical, and molecular changes in the body, and has a strong influence on an organism's lifespan. Although advancement in medicine has allowed humans to live longer, the prevalence of age-associated medical complications is continuously burdening older adults worldwide. Current animal models used in research to study aging have provided novel information that has helped investigators understand the aging process; however, these models are limiting. Aging is a complex process that is regulated at multiple biological levels, and while a single manipulation in these models can provide information on a process, it is not enough to understand the global regulation of aging. Some mammalian hibernators live up to 9.8-times higher than their expected average lifespan, and new research attributes this increase to their ability to hibernate. A common theme amongst these mammalian hibernators is their ability to greatly reduce their metabolic rate to a fraction of their normal rate and initiate cytoprotective responses that enable their survival. Metabolic rate depression is strictly regulated at different biological levels in order to enable the animal to not only survive, but to also do so by relying mainly on their limited internal fuels. As such, understanding both the global and specific regulatory mechanisms used to promote survival during hibernation could, in theory, allow investigators to have a better understanding of the aging process. This can also allow pharmaceutical industries to find therapeutics that could delay or reverse age-associated medical complications and promote healthy aging and longevity in humans.
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Affiliation(s)
- Rasha Al-Attar
- Institute of Biochemistry and Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario K1S 5B6, Canada.
| | - Kenneth B Storey
- Institute of Biochemistry and Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario K1S 5B6, Canada.
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14
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Hadj-Moussa H, Zhang J, Pifferi F, Perret M, Storey KB. Profiling torpor-responsive microRNAs in muscles of the hibernating primate Microcebus murinus. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1863:194473. [DOI: 10.1016/j.bbagrm.2019.194473] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 12/09/2019] [Accepted: 12/09/2019] [Indexed: 12/25/2022]
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15
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Reynolds JA. Noncoding RNA Regulation of Dormant States in Evolutionarily Diverse Animals. THE BIOLOGICAL BULLETIN 2019; 237:192-209. [PMID: 31714856 DOI: 10.1086/705484] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Dormancy is evolutionarily widespread and can take many forms, including diapause, dauer formation, estivation, and hibernation. Each type of dormancy is characterized by distinct features; but accumulating evidence suggests that each is regulated by some common processes, often referred to as a common "toolkit" of regulatory mechanisms, that likely include noncoding RNAs that regulate gene expression. Noncoding RNAs, especially microRNAs, are well-known regulators of biological processes associated with numerous dormancy-related processes, including cell cycle progression, cell growth and proliferation, developmental timing, metabolism, and environmental stress tolerance. This review provides a summary of our current understanding of noncoding RNAs and their involvement in regulating dormancy.
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16
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Biggar KK, Storey KB. Functional impact of microRNA regulation in models of extreme stress adaptation. J Mol Cell Biol 2019; 10:93-101. [PMID: 29206937 DOI: 10.1093/jmcb/mjx053] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2017] [Accepted: 11/30/2017] [Indexed: 01/12/2023] Open
Abstract
When confronted with severe environmental stress, some animals are able to undergo a substantial reorganization of their cellular environment that enables long-term survival. One molecular mechanism of adaptation that has received considerable attention in recent years has been the action of reversible transcriptome regulation by microRNA. The implementation of new computational and high-throughput experimental approaches has started to uncover the vital contributions of microRNA towards stress adaptation. Indeed, recent studies have suggested that microRNA may have a major regulatory influence over a number of cellular processes that are essential to prolonged environmental stress survival. To date, a number of studies have highlighted the role of microRNA in the regulation of a metabolically depressed state, documenting stress-responsive microRNA expression during mammalian hibernation, frog and insect freeze tolerance, and turtle and marine snail anoxia tolerance. These studies collectively indicate a conserved principle of microRNA stress response across phylogeny. As we are on the verge of dissecting the role of microRNA in environmental stress adaptation, this review summarizes recent research advances and the hallmark expression patterns that facilitate stress survival.
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Affiliation(s)
- Kyle K Biggar
- Institute of Biochemistry & Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Kenneth B Storey
- Institute of Biochemistry & Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
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17
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Nakipova OV, Averin AS, Kosarsky LS, Ignatiev DA. The Force-Frequency Dependence in the Heart Papillary Muscle of Ground Squirrel as a Reflection of Changes in the Functional State of Animals during the Annual Cycle. Biophysics (Nagoya-shi) 2019. [DOI: 10.1134/s0006350919050191] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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18
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Capraro A, O'Meally D, Waters SA, Patel HR, Georges A, Waters PD. Waking the sleeping dragon: gene expression profiling reveals adaptive strategies of the hibernating reptile Pogona vitticeps. BMC Genomics 2019; 20:460. [PMID: 31170930 PMCID: PMC6555745 DOI: 10.1186/s12864-019-5750-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 04/29/2019] [Indexed: 12/30/2022] Open
Abstract
Background Hibernation is a physiological state exploited by many animals exposed to prolonged adverse environmental conditions associated with winter. Large changes in metabolism and cellular function occur, with many stress response pathways modulated to tolerate physiological challenges that might otherwise be lethal. Many studies have sought to elucidate the molecular mechanisms of mammalian hibernation, but detailed analyses are lacking in reptiles. Here we examine gene expression in the Australian central bearded dragon (Pogona vitticeps) using mRNA-seq and label-free quantitative mass spectrometry in matched brain, heart and skeletal muscle samples from animals at late hibernation, 2 days post-arousal and 2 months post-arousal. Results We identified differentially expressed genes in all tissues between hibernation and post-arousal time points; with 4264 differentially expressed genes in brain, 5340 differentially expressed genes in heart, and 5587 differentially expressed genes in skeletal muscle. Furthermore, we identified 2482 differentially expressed genes across all tissues. Proteomic analysis identified 743 proteins (58 differentially expressed) in brain, 535 (57 differentially expressed) in heart, and 337 (36 differentially expressed) in skeletal muscle. Tissue-specific analyses revealed enrichment of protective mechanisms in all tissues, including neuroprotective pathways in brain, cardiac hypertrophic processes in heart, and atrophy protective pathways in skeletal muscle. In all tissues stress response pathways were induced during hibernation, as well as evidence for gene expression regulation at transcription, translation and post-translation. Conclusions These results reveal critical stress response pathways and protective mechanisms that allow for maintenance of both tissue-specific function, and survival during hibernation in the central bearded dragon. Furthermore, we provide evidence for multiple levels of gene expression regulation during hibernation, particularly enrichment of miRNA-mediated translational repression machinery; a process that would allow for rapid and energy efficient reactivation of translation from mature mRNA molecules at arousal. This study is the first molecular investigation of its kind in a hibernating reptile, and identifies strategies not yet observed in other hibernators to cope stress associated with this remarkable state of metabolic depression. Electronic supplementary material The online version of this article (10.1186/s12864-019-5750-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alexander Capraro
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, UNSW Sydney, Sydney, NSW, 2052, Australia.
| | - Denis O'Meally
- Institute for Applied Ecology, University of Canberra, Canberra, ACT, 2601, Australia.,Present address: Center for Gene Therapy, Beckman Research Institute of the City of Hope, Duarte, CA, 91010, USA
| | - Shafagh A Waters
- School of Women's & Children's Health, Faculty of Medicine, UNSW Sydney, Sydney, NSW, 2052, Australia
| | - Hardip R Patel
- John Curtin School of Medical Research, Australian National University, Canberra, 2601, ACT, Australia
| | - Arthur Georges
- Institute for Applied Ecology, University of Canberra, Canberra, ACT, 2601, Australia
| | - Paul D Waters
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, UNSW Sydney, Sydney, NSW, 2052, Australia
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19
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Hoyeck MP, Hadj-Moussa H, Storey KB. Estivation-responsive microRNAs in a hypometabolic terrestrial snail. PeerJ 2019; 7:e6515. [PMID: 30809463 PMCID: PMC6387573 DOI: 10.7717/peerj.6515] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 01/25/2019] [Indexed: 01/01/2023] Open
Abstract
When faced with extreme environmental conditions, the milk snail (Otala lactea) enters a state of dormancy known as estivation. This is characterized by a strong reduction in metabolic rate to <30% of normal resting rate that is facilitated by various behavioural, physiological, and molecular mechanisms. Herein, we investigated the regulation of microRNA in the induction of estivation. Changes in the expression levels of 75 highly conserved microRNAs were analysed in snail foot muscle, of which 26 were significantly upregulated during estivation compared with controls. These estivation-responsive microRNAs were linked to cell functions that are crucial for long-term survival in a hypometabolic state including anti-apoptosis, cell-cycle arrest, and maintenance of muscle functionality. Several of the microRNA responses by snail foot muscle also characterize hypometabolism in other species and support the existence of a conserved suite of miRNA responses that regulate environmental stress responsive metabolic rate depression across phylogeny.
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Affiliation(s)
- Myriam P Hoyeck
- Institute of Biochemistry, Departments of Biology and Chemistry, Carleton University, Ottawa, Ontario, Canada
| | - Hanane Hadj-Moussa
- Institute of Biochemistry, Departments of Biology and Chemistry, Carleton University, Ottawa, Ontario, Canada
| | - Kenneth B Storey
- Institute of Biochemistry, Departments of Biology and Chemistry, Carleton University, Ottawa, Ontario, Canada
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20
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Hadj‐Moussa H, Storey KB. Bringing nature back: using hibernation to reboot organ preservation. FEBS J 2018; 286:1094-1100. [DOI: 10.1111/febs.14683] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 09/14/2018] [Accepted: 10/17/2018] [Indexed: 12/19/2022]
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21
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Biggar K, Luu B, Wu C, Pifferi F, Perret M, Storey K. Identification of novel and conserved microRNA and their expression in the gray mouse lemur, Microcebus murinus, a primate capable of daily torpor. Gene 2018; 677:332-339. [DOI: 10.1016/j.gene.2018.08.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 07/10/2018] [Accepted: 08/04/2018] [Indexed: 12/13/2022]
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22
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Luu BE, Storey KB. Solving Donor Organ Shortage with Insights from Freeze Tolerance in Nature. Bioessays 2018; 40:e1800092. [DOI: 10.1002/bies.201800092] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 08/02/2018] [Indexed: 01/06/2023]
Affiliation(s)
- Bryan E. Luu
- Institute of Biochemistry and Department of BiologyCarleton University1125 Colonel By DriveOttawaON, K1S 5B6
| | - Kenneth B. Storey
- Institute of Biochemistry and Department of BiologyCarleton University1125 Colonel By DriveOttawaON, K1S 5B6
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23
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Hawkins LJ, Al-Attar R, Storey KB. Transcriptional regulation of metabolism in disease: From transcription factors to epigenetics. PeerJ 2018; 6:e5062. [PMID: 29922517 PMCID: PMC6005171 DOI: 10.7717/peerj.5062] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 06/04/2018] [Indexed: 12/13/2022] Open
Abstract
Every cell in an individual has largely the same genomic sequence and yet cells in different tissues can present widely different phenotypes. This variation arises because each cell expresses a specific subset of genomic instructions. Control over which instructions, or genes, are expressed is largely controlled by transcriptional regulatory pathways. Each cell must assimilate a huge amount of environmental input, and thus it is of no surprise that transcription is regulated by many intertwining mechanisms. This large regulatory landscape means there are ample possibilities for problems to arise, which in a medical context means the development of disease states. Metabolism within the cell, and more broadly, affects and is affected by transcriptional regulation. Metabolism can therefore contribute to improper transcriptional programming, or pathogenic metabolism can be the result of transcriptional dysregulation. Here, we discuss the established and emerging mechanisms for controling transcription and how they affect metabolism in the context of pathogenesis. Cis- and trans-regulatory elements, microRNA and epigenetic mechanisms such as DNA and histone methylation, all have input into what genes are transcribed. Each has also been implicated in diseases such as metabolic syndrome, various forms of diabetes, and cancer. In this review, we discuss the current understanding of these areas and highlight some natural models that may inspire future therapeutics.
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Affiliation(s)
- Liam J Hawkins
- Institute of Biochemistry, Department of Biology, Carleton University, Ottawa, ON, Canada
| | - Rasha Al-Attar
- Institute of Biochemistry, Department of Biology, Carleton University, Ottawa, ON, Canada
| | - Kenneth B Storey
- Institute of Biochemistry, Department of Biology, Carleton University, Ottawa, ON, Canada
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24
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Lopez MS, Dempsey RJ, Vemuganti R. The microRNA miR-21 conditions the brain to protect against ischemic and traumatic injuries. CONDITIONING MEDICINE 2017; 1:35-46. [PMID: 34268484 PMCID: PMC8279043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Ischemic and traumatic injuries to CNS remain leading causes of death and disability worldwide, despite decades of research into risk factors, therapies, and preventative measures. Recent studies showed that CNS injuries significantly alter the cerebral microRNAome that impact the secondary brain damage as well as plasticity and recovery. Many microRNA based therapies are currently in various clinical trials for different pathologic conditions indicating their therapeutic potential. In the present review, we discuss the role of miR-21 in acute CNS injuries which is currently thought to be a potent neuroprotective microRNA. We emphasize on the potential of miR-21 in promoting cell and tissue survival and preventing inflammation and apoptosis. We also discussed the role of miR-21 in conditioning the brain to promote ischemic tolerance. Finally, we discussed some of the challenges and difficulties to develop miR-21 as a neuroprotective therapy in humans.
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Affiliation(s)
- Mary S Lopez
- Cellular and Molecular Pathology Program, University of Wisconsin, Madison, WI, USA
- Department of Neurological Surgery, University of Wisconsin, Madison, WI, USA
| | - Robert J Dempsey
- Cellular and Molecular Pathology Program, University of Wisconsin, Madison, WI, USA
- Department of Neurological Surgery, University of Wisconsin, Madison, WI, USA
| | - Raghu Vemuganti
- Cellular and Molecular Pathology Program, University of Wisconsin, Madison, WI, USA
- Department of Neurological Surgery, University of Wisconsin, Madison, WI, USA
- William S. Middleton Veteran's Administration Hospital, Madison, WI, USA
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25
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Wu CW, Storey KB. Regulation of Smad mediated microRNA transcriptional response in ground squirrels during hibernation. Mol Cell Biochem 2017; 439:151-161. [PMID: 28780752 DOI: 10.1007/s11010-017-3144-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 08/02/2017] [Indexed: 11/25/2022]
Abstract
Mammalian hibernation is a state of dormancy that is used by some animals to survive through the unfavorable conditions of winter, and is characterized by coordinated suppression of basal metabolism that is supported by global inhibition of energy/ATP-consuming processes. In this study, we examine the regulation of the anti-proliferatory TGF-β/Smad transcription factor signaling pathway in the liver tissue of the hibernating 13-lined ground squirrel Ictidomys tridecemlineatus. The TGF-β/Smad signaling pathway is known to mediate cell cycle arrest through induction of cell cycle dependent kinase inhibitors, and more recently, has been shown to regulate a wide range of cellular processes via its control of microRNA biosynthesis. We show that phosphorylation levels of the Smad3 protein at its activation residue is increased by ~1.5-fold during torpor, and this is associated with an increase in nuclear localization and DNA binding activity of Smad3. Expression levels of several TGF-β induced microRNAs previously described in human cells were also activated in ground squirrel during torpor. Among these were miR-21, miR-23a, and miR-107, which contain either the conserved R-SBE or R-SBE related motif found in microRNAs that are post-transcriptionally processed by Smad proteins. We show that levels of miR-21 were highly elevated at multiple stages of torpor, and predicted gene targets of miR-21 were enriched to multiple pro-growth cellular processes. Overall, we provide evidence that show the Smad3 transcription factor is activated in ground squirrels during torpor, and suggest a role for this signaling pathway in mediating anti-proliferatory signals via its transcriptional control of cell cycle inhibitors and downstream microRNAs.
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Affiliation(s)
- Cheng-Wei Wu
- Institute of Biochemistry and Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
- Department of Biology, Genetics Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Kenneth B Storey
- Institute of Biochemistry and Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada.
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26
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Exploration of low temperature microRNA function in an anoxia tolerant vertebrate ectotherm, the red eared slider turtle ( Trachemys scripta elegans ). J Therm Biol 2017; 68:139-146. [DOI: 10.1016/j.jtherbio.2016.09.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 09/07/2016] [Accepted: 09/12/2016] [Indexed: 12/14/2022]
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27
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Reynolds JA, Peyton JT, Denlinger DL. Changes in microRNA abundance may regulate diapause in the flesh fly, Sarcophaga bullata. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2017; 84:1-14. [PMID: 28300610 DOI: 10.1016/j.ibmb.2017.03.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 03/03/2017] [Accepted: 03/06/2017] [Indexed: 06/06/2023]
Abstract
Diapause, an alternative developmental pathway characterized by changes in developmental timing and metabolism, is coordinated by molecular mechanisms that are not completely understood. MicroRNA (miRNA) mediated gene silencing is emerging as a key component of animal development and may have a significant role in initiating, maintaining, and terminating insect diapause. In the present study, we test this possibility by using high-throughput sequencing and qRT-PCR to discover diapause-related shifts in miRNA abundance in the flesh fly, Sarcophaga bullata. We identified ten evolutionarily conserved miRNAs that were differentially expressed in diapausing pupae compared to their nondiapausing counterparts. miR-289-5p and miR-1-3p were overexpressed in diapausing pupae and may be responsible for silencing expression of candidate genes during diapause. miR-9c-5p, miR-13b-3p, miR-31a-5p, miR-92b-3p, miR-275-3p, miR-276a-3p, miR-277-3p, and miR-305-5p were underexpressed in diapausing pupae and may contribute to increased expression of heat shock proteins and other factors necessary for the enhanced environmental stress-response that is a feature of diapause. In S. bullata, a maternal effect blocks the programming of diapause in progeny of females that have experienced pupal diapause, and in this study we report that several miRNAs, including miR-263a-5p, miR-100-5p, miR-125-5p, and let-7-5p were significantly overexpressed in such nondiapausing flies and may prevent entry into diapause. Together these miRNAs appear to be integral to the molecular processes that mediate entry into diapause.
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Affiliation(s)
- Julie A Reynolds
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus OH 43210, USA.
| | - Justin T Peyton
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus OH 43210, USA
| | - David L Denlinger
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus OH 43210, USA; Department of Entomology, The Ohio State University, Columbus OH 43210, USA
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28
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Tarahovsky YS, Fadeeva IS, Komelina NP, Khrenov MO, Zakharova NM. Antipsychotic inductors of brain hypothermia and torpor-like states: perspectives of application. Psychopharmacology (Berl) 2017; 234:173-184. [PMID: 27933367 DOI: 10.1007/s00213-016-4496-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 11/26/2016] [Indexed: 12/12/2022]
Abstract
Hypothermia and hypometabolism (hypometabothermia) normally observed during natural hibernation and torpor, allow animals to protect their body and brain against the damaging effects of adverse environment. A similar state of hypothermia can be achieved under artificial conditions through physical cooling or pharmacological effects directed at suppression of metabolism and the processes of thermoregulation. In these conditions called torpor-like states, the mammalian ability to recover from stroke, heart attack, and traumatic injuries greatly increases. Therefore, the development of therapeutic methods for different pathologies is a matter of great concern. With the discovery of the antipsychotic drug chlorpromazine in the 1950s of the last century, the first attempts to create a pharmacologically induced state of hibernation for therapeutic purposes were made. That was the beginning of numerous studies in animals and the broad use of therapeutic hypothermia in medicine. Over the last years, many new agents have been discovered which were capable of lowering the body temperature and inhibiting the metabolism. The psychotropic agents occupy a significant place among them, which, in our opinion, is not sufficiently recognized in the contemporary literature. In this review, we summarized the latest achievements related to the ability of modern antipsychotics to target specific receptors in the brain, responsible for the initiation of hypometabothermia.
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Affiliation(s)
- Yury S Tarahovsky
- Institute of Cell Biophysics RAS, Pushchino, Moscow Region, Russian Federation, 142290. .,Institute of Theoretical and Experimental Biophysics RAS, Pushchino, Moscow Region, Russian Federation, 142290.
| | - Irina S Fadeeva
- Institute of Cell Biophysics RAS, Pushchino, Moscow Region, Russian Federation, 142290.,Institute of Theoretical and Experimental Biophysics RAS, Pushchino, Moscow Region, Russian Federation, 142290
| | - Natalia P Komelina
- Institute of Cell Biophysics RAS, Pushchino, Moscow Region, Russian Federation, 142290
| | - Maxim O Khrenov
- Institute of Cell Biophysics RAS, Pushchino, Moscow Region, Russian Federation, 142290
| | - Nadezhda M Zakharova
- Institute of Cell Biophysics RAS, Pushchino, Moscow Region, Russian Federation, 142290
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29
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Frigault JJ, Morin MD, Morin PJ. Differential expression and emerging functions of non-coding RNAs in cold adaptation. J Comp Physiol B 2016; 187:19-28. [PMID: 27866230 DOI: 10.1007/s00360-016-1049-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 10/07/2016] [Accepted: 10/26/2016] [Indexed: 01/16/2023]
Abstract
Several species undergo substantial physiological and biochemical changes to confront the harsh conditions associated with winter. Small mammalian hibernators and cold-hardy insects are examples of natural models of cold adaptation that have been amply explored. While the molecular picture associated with cold adaptation has started to become clearer in recent years, notably through the use of high-throughput experimental approaches, the underlying cold-associated functions attributed to several non-coding RNAs, including microRNAs (miRNAs) and long non-coding RNAs (lncRNAs), remain to be better characterized. Nevertheless, key pioneering work has provided clues on the likely relevance of these molecules in cold adaptation. With an emphasis on mammalian hibernation and insect cold hardiness, this work first reviews various molecular changes documented so far in these processes. The cascades leading to miRNA and lncRNA production as well as the mechanisms of action of these non-coding RNAs are subsequently described. Finally, we present examples of differentially expressed non-coding RNAs in models of cold adaptation and elaborate on the potential significance of this modulation with respect to low-temperature adaptation.
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Affiliation(s)
- Jacques J Frigault
- Department of Chemistry and Biochemistry, Université de Moncton, 18 Antonine-Maillet Avenue, Moncton, NB, E1A 3E9, Canada
| | - Mathieu D Morin
- Department of Chemistry and Biochemistry, Université de Moncton, 18 Antonine-Maillet Avenue, Moncton, NB, E1A 3E9, Canada
| | - Pier Jr Morin
- Department of Chemistry and Biochemistry, Université de Moncton, 18 Antonine-Maillet Avenue, Moncton, NB, E1A 3E9, Canada.
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30
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Luu BE, Biggar KK, Wu CW, Storey KB. Torpor-responsive expression of novel microRNA regulating metabolism and other cellular pathways in the thirteen-lined ground squirrel,Ictidomys tridecemlineatus. FEBS Lett 2016; 590:3574-3582. [DOI: 10.1002/1873-3468.12435] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Revised: 09/07/2016] [Accepted: 09/08/2016] [Indexed: 11/08/2022]
Affiliation(s)
- Bryan E. Luu
- Institute of Biochemistry and Department of Biology; Carleton University; Ottawa Canada
| | - Kyle K. Biggar
- Institute of Biochemistry and Department of Biology; Carleton University; Ottawa Canada
| | - Cheng-Wei Wu
- Institute of Biochemistry and Department of Biology; Carleton University; Ottawa Canada
| | - Kenneth B. Storey
- Institute of Biochemistry and Department of Biology; Carleton University; Ottawa Canada
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