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Gritsyna YV, Grabarskaya MA, Mikhailova GZ, Popova SS, Bobyleva LG, Ermakov AM, Zakharova NM, Vikhlyantsev IM. Differential Expression of Titin and Obscurin mRNA in Striated Muscles of the Long-Tailed Ground Squirrel Urocitellus undulatus. J EVOL BIOCHEM PHYS+ 2022. [DOI: 10.1134/s0022093022050052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Hyams Y, Panov J, Rosner A, Brodsky L, Rinkevich Y, Rinkevich B. Transcriptome landscapes that signify Botrylloides leachi (Ascidiacea) torpor states. Dev Biol 2022; 490:22-36. [PMID: 35809632 DOI: 10.1016/j.ydbio.2022.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 06/10/2022] [Accepted: 06/12/2022] [Indexed: 11/18/2022]
Abstract
Harsh environments enforce the expression of behavioural, morphological, physiological, and reproductive rejoinders, including torpor. Here we study the morphological, cellular, and molecular alterations in torpor architype in the colonial urochordate Botrylloides aff. leachii by employing whole organism Transmission electron (TEM) and light microscope observations, RNA sequencing, real-time polymerase chain reaction (qPCR) quantification of selected genes, and immunolocalization of WNT, SMAD and SOX2 gene expressions. On the morphological level, torpor starts with gradual regression of all zooids and buds which leaves the colony surviving as condensed vasculature remnants that may be 'aroused' to regenerate fully functional colonies upon changes in the environment. Simultaneously, we observed altered distributions of hemolymph cell types. Phagocytes doubled in number, while the number of morula cells declined by half. In addition, two new circulating cell types were observed, multi-nucleated and bacteria-bearing cells. RNA sequencing technology revealed marked differences in gene expression between different organism compartments and states: active zooids and ampullae, and between mid-torpor and naive colonies, or naive and torpid colonies. Gene Ontology term enrichment analyses further showed disparate biological processes. In torpid colonies, we observed overall 233 up regulated genes. These genes included NR4A2, EGR1, MUC5AC, HMCN2 and. Also, 27 transcription factors were upregulated in torpid colonies including ELK1, HDAC3, RBMX, MAZ, STAT1, STAT4 and STAT6. Interestingly, genes involved in developmental processes such as SPIRE1, RHOA, SOX11, WNT5A and SNX18 were also upregulated in torpid colonies. We further validated the dysregulation of 22 genes during torpor by utilizing qPCR. Immunohistochemistry of representative genes from three signaling pathways revealed high expression of these genes in circulated cells along torpor. WNT agonist administration resulted in early arousal from torpor in 80% of the torpid colonies while in active colonies WNT agonist triggered the torpor state. Abovementioned results thus connote unique transcriptome landscapes associated with Botrylloides leachii torpor.
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Affiliation(s)
- Yosef Hyams
- Israel Oceanographic and Limnological Research, National Institute of Oceanography, P.O. Box 9753, Tel Shikmona, Haifa, 3109701, Israel; Marine Biology Department, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, 31905, Israel.
| | - Julia Panov
- Tauber Bioinformatics Research Center, University of Haifa, Haifa, 31905, Israel; Sagol Department of Neurobiology, University of Haifa, Haifa, 3498838, Israel
| | - Amalia Rosner
- Israel Oceanographic and Limnological Research, National Institute of Oceanography, P.O. Box 9753, Tel Shikmona, Haifa, 3109701, Israel
| | - Leonid Brodsky
- Tauber Bioinformatics Research Center, University of Haifa, Haifa, 31905, Israel
| | - Yuval Rinkevich
- Comprehensive Pneumology Center, Institute of Lung Biology and Disease, Helmholtz Zentrum Munchen, Max-Lebsche-Platz 31, 81377, München, Germany
| | - Baruch Rinkevich
- Israel Oceanographic and Limnological Research, National Institute of Oceanography, P.O. Box 9753, Tel Shikmona, Haifa, 3109701, Israel
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Integrative transcription start site analysis and physiological phenotyping reveal torpor-specific expression program in mouse skeletal muscle. Commun Biol 2021; 4:1290. [PMID: 34782710 PMCID: PMC8592991 DOI: 10.1038/s42003-021-02819-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 10/28/2021] [Indexed: 11/30/2022] Open
Abstract
Mice enter an active hypometabolic state, called daily torpor when they experience a lowered caloric intake under cold ambient temperature. During torpor, the oxygen consumption rate in some animals drops to less than 30% of the normal rate without harming the body. This safe but severe reduction in metabolism is attractive for various clinical applications; however, the mechanism and molecules involved are unclear. Therefore, here we systematically analyzed the gene expression landscape on the level of the RNA transcription start sites in mouse skeletal muscles under various metabolic states to identify torpor-specific transcribed regulatory patterns. We analyzed the soleus muscles from 38 mice in torpid and non-torpid conditions and identified 287 torpor-specific promoters out of 12,862 detected promoters. Furthermore, we found that the transcription factor ATF3 is highly expressed during torpor deprivation and its binding motif is enriched in torpor-specific promoters. Atf3 was also highly expressed in the heart and brown adipose tissue during torpor and systemically knocking out Atf3 affected the torpor phenotype. Our results demonstrate that mouse torpor combined with powerful genetic tools is useful for studying active hypometabolism.
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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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Sun H, Wang J, Xing Y, Pan YH, Mao X. Gut transcriptomic changes during hibernation in the greater horseshoe bat ( Rhinolophus ferrumequinum). Front Zool 2020; 17:21. [PMID: 32690984 PMCID: PMC7366455 DOI: 10.1186/s12983-020-00366-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 07/10/2020] [Indexed: 11/10/2022] Open
Abstract
Background The gut is the major organ for nutrient absorption and immune response in the body of animals. Although effects of fasting on the gut functions have been extensively studied in model animals (e.g. mice), little is known about the response of the gut to fasting in a natural condition (e.g. hibernation). During hibernation, animals endure the long term of fasting and hypothermia. Results Here we generated the first gut transcriptome in a wild hibernating bat (Rhinolophus ferrumequinum). We identified 1614 differentially expressed genes (DEGs) during four physiological states (Torpor, Arousal, Winter Active and Summer Active). Gene co-expression network analysis assigns 926 DEGs into six modules associated with Torpor and Arousal. Our results reveal that in response to the stress of luminal nutrient deficiency during hibernation, the gut helps to reduce food intake by overexpressing genes (e.g. CCK and GPR17) that regulate the sensitivity to insulin and leptin. At the same time, the gut contributes energy supply by overexpressing genes that increase capacity for ketogenesis (HMGCS2) and selective autophagy (TEX264). Furthermore, we identified separate sets of multiple DEGs upregulated in Torpor and Arousal whose functions are involved in innate immunity. Conclusion This is the first gut transcriptome of a hibernating mammal. Our study identified candidate genes associated with regulation of food intake and enhance of innate immunity in the gut during hibernation. By comparing with previous studies, we found that two DEGs (CPE and HSPA8) were also significantly elevated during torpor in liver and brain of R. ferrumequinum and several DEGs (e.g. TXNIP and PDK1/4) were commonly upregulated during torpor in multiple tissues of different mammals. Our results support that shared expression changes may underlie the hibernation phenotype by most mammals.
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Affiliation(s)
- Haijian Sun
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai, 200062 China
| | - Jiaying Wang
- Institute of Estuarine and Coastal Research, East China Normal University, Shanghai, 200062 China
| | - Yutong Xing
- Institute of Estuarine and Coastal Research, East China Normal University, Shanghai, 200062 China
| | - Yi-Hsuan Pan
- Key Laboratory of Brain Functional Genomics of Ministry of Education, School of Life Science, East China Normal University, Shanghai, 200062 China
| | - Xiuguang Mao
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai, 200062 China.,Institute of Eco-Chongming (IEC), East China Normal University, Shanghai, 200062 China
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Grabek KR, Cooke TF, Epperson LE, Spees KK, Cabral GF, Sutton SC, Merriman DK, Martin SL, Bustamante CD. Genetic variation drives seasonal onset of hibernation in the 13-lined ground squirrel. Commun Biol 2019; 2:478. [PMID: 31886416 PMCID: PMC6925185 DOI: 10.1038/s42003-019-0719-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 11/28/2019] [Indexed: 01/23/2023] Open
Abstract
Hibernation in sciurid rodents is a dynamic phenotype timed by a circannual clock. When housed in an animal facility, 13-lined ground squirrels exhibit variation in seasonal onset of hibernation, which is not explained by environmental or biological factors. We hypothesized that genetic factors instead drive variation in timing. After increasing genome contiguity, here, we employ a genotype-by-sequencing approach to characterize genetic variation in 153 ground squirrels. Combined with datalogger records (n = 72), we estimate high heritability (61-100%) for hibernation onset. Applying a genome-wide scan with 46,996 variants, we identify 2 loci significantly (p < 7.14 × 10-6), and 12 loci suggestively (p < 2.13 × 10-4), associated with onset. At the most significant locus, whole-genome resequencing reveals a putative causal variant in the promoter of FAM204A. Expression quantitative trait loci (eQTL) analyses further reveal gene associations for 8/14 loci. Our results highlight the power of applying genetic mapping to hibernation and present new insight into genetics driving its onset.
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Affiliation(s)
- Katharine R. Grabek
- Department of Genetics and Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA USA
- Fauna Bio Incorporated, Berkeley, CA USA
| | - Thomas F. Cooke
- Department of Genetics, Stanford University School of Medicine, Stanford, CA USA
- Whitehead Institute for Biomedical Research, Cambridge, MA USA
| | - L. Elaine Epperson
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO, USA
| | - Kaitlyn K. Spees
- Department of Genetics, Stanford University School of Medicine, Stanford, CA USA
| | - Gleyce F. Cabral
- Department of Genetics, Stanford University School of Medicine, Stanford, CA USA
- Laboratório de Genética Humana e Médica, Universidade Federal do Pará, Rua Augusto Corrêa, 1 - 66.075-110, Belem, PA Brazil
| | - Shirley C. Sutton
- Department of Genetics and Department of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA USA
| | - Dana K. Merriman
- Department of Biology, University of Wisconsin Oshkosh, Oshkosh, WI USA
| | - Sandra L. Martin
- Department of Cell and Developmental Biology, University of Colorado School of Medicine, Aurora, CO USA
| | - Carlos D. Bustamante
- Department of Genetics and Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA USA
- Chan Zuckerberg Biohub, San Francisco, CA USA
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Field KA, Sewall BJ, Prokkola JM, Turner GG, Gagnon MF, Lilley TM, Paul White J, Johnson JS, Hauer CL, Reeder DM. Effect of torpor on host transcriptomic responses to a fungal pathogen in hibernating bats. Mol Ecol 2018; 27:3727-3743. [PMID: 30080945 DOI: 10.1111/mec.14827] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 07/25/2018] [Accepted: 07/28/2018] [Indexed: 01/07/2023]
Abstract
Hibernation, the use of prolonged torpor to depress metabolism, is employed by mammals to conserve resources during extended periods of extreme temperatures and/or resource limitation. Mammalian hibernators arouse to euthermy periodically during torpor for reasons that are not well understood, and these arousals may facilitate immune processes. To determine whether arousals enable host responses to pathogens, we used dual RNA-Seq and a paired sampling approach to examine gene expression in a hibernating bat, the little brown myotis (Myotis lucifugus). During torpor, transcript levels differed in only a few genes between uninfected wing tissue and adjacent tissue infected with Pseudogymnoascus destructans, the fungal pathogen that causes white-nose syndrome. Within 70-80 min after emergence from torpor, large changes in gene expression were observed due to local infection, particularly in genes involved in pro-inflammatory host responses to fungal pathogens, but also in many genes involved in immune responses and metabolism. These results support the hypothesis that torpor is a period of relative immune dormancy and arousals allow for local immune responses in infected tissues during hibernation. Host-pathogen interactions were also found to regulate gene expression in the pathogen differently depending on the torpor state of the host. Hibernating species must balance the benefits of energy and water conservation achieved during torpor with the costs of decreased immune competence. Interbout arousals allow hibernators to optimize these, and other, trade-offs during prolonged hibernation by enabling host responses to pathogens within brief, periodic episodes of euthermy.
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Affiliation(s)
- Kenneth A Field
- Department of Biology, Bucknell University, Lewisburg, Pennsylvania
| | - Brent J Sewall
- Department of Biology, Temple University, Philadelphia, Pennsylvania
| | - Jenni M Prokkola
- Department of Biology, Bucknell University, Lewisburg, Pennsylvania
| | - Gregory G Turner
- Wildlife Diversity Division, Pennsylvania Game Commission, Harrisburg, Pennsylvania
| | - Marianne F Gagnon
- Department of Biology, Temple University, Philadelphia, Pennsylvania
| | - Thomas M Lilley
- Department of Biology, Bucknell University, Lewisburg, Pennsylvania
| | - J Paul White
- Wisconsin Department of Natural Resources, Madison, Wisconsin
| | - Joseph S Johnson
- Department of Biology, Bucknell University, Lewisburg, Pennsylvania
| | | | - DeeAnn M Reeder
- Department of Biology, Bucknell University, Lewisburg, Pennsylvania
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