1
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Absmeier E, Heyd F. Temperature-controlled molecular switches in mammalian cells. J Biol Chem 2024:107865. [PMID: 39374780 DOI: 10.1016/j.jbc.2024.107865] [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: 05/26/2024] [Revised: 09/27/2024] [Accepted: 09/30/2024] [Indexed: 10/09/2024] Open
Abstract
Temperature is an omnipresent factor impacting on many aspects of life. In bacteria and ectothermic eukaryotes various thermosensors and temperature-controlled switches have been described, ranging from RNA thermometers controlling the heat shock response in prokaryotes to temperature-dependent sex determination in reptiles, likely controlled through protein phosphorylation. However, the impact of subtle changes of human core body temperature are only beginning to be acknowledged. In this review, we will discuss thermosensing mechanisms and their functional implications with a focus on mammalian cells, also in the context of disease conditions. We will point out open questions and possible future directions for this emerging research field, which, in addition to molecular-mechanistic insights, holds the potential for the development of new therapeutic approaches.
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Affiliation(s)
- Eva Absmeier
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Laboratory of mRNA translation and turnover, Takustrasse 6, 14195 Berlin, Germany.
| | - Florian Heyd
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Laboratory of RNA Biochemistry, Takustrasse 6, 14195 Berlin, Germany.
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2
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Flores CC, Pasetto NA, Wang H, Dimitrov AG, Davis JF, Jiang Z, Davis CJ, Gerstner JR. Sleep and diurnal alternative polyadenylation sites associated with human APA-linked brain disorders. RESEARCH SQUARE 2024:rs.3.rs-4707772. [PMID: 39149473 PMCID: PMC11326403 DOI: 10.21203/rs.3.rs-4707772/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Disruption of sleep and circadian rhythms are a comorbid feature of many pathologies, and can negatively influence many health conditions, including neurodegenerative disease, metabolic illness, cancer, and various neurological disorders. Genetic association studies linking sleep and circadian disturbances with disease susceptibility have mainly focused on changes in gene expression due to mutations, such as single-nucleotide polymorphisms. The interaction between sleep and/or circadian rhythms with the use of Alternative Polyadenylation (APA) has been largely undescribed, particularly in the context of other disorders. APA is a process that generates various transcript isoforms of the same gene affecting its mRNA translation, stability, localization, and subsequent function. Here we identified unique APAs expressed in rat brain over time-of-day, immediately following sleep deprivation, and the subsequent recovery period. From these data, we performed a secondary analysis of these sleep- or time-of-day associated PASs with recently described APA-linked human brain disorder susceptibility genes.
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3
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Blake D, Gazzara MR, Breuer I, Ferretti M, Lynch KW. Alternative 3'UTR expression induced by T cell activation is regulated in a temporal and signal dependent manner. Sci Rep 2024; 14:10987. [PMID: 38745101 PMCID: PMC11094061 DOI: 10.1038/s41598-024-61951-1] [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: 11/26/2023] [Accepted: 05/12/2024] [Indexed: 05/16/2024] Open
Abstract
The length of 3' untranslated regions (3'UTR) is highly regulated during many transitions in cell state, including T cell activation, through the process of alternative polyadenylation (APA). However, the regulatory mechanisms and functional consequences of APA remain largely unexplored. Here we present a detailed analysis of the temporal and condition-specific regulation of APA following activation of primary human CD4+ T cells. We find that global APA changes are regulated temporally and CD28 costimulatory signals enhance a subset of these changes. Most APA changes upon T cell activation involve 3'UTR shortening, although a set of genes enriched for function in the mTOR pathway exhibit 3'UTR lengthening. While upregulation of the core polyadenylation machinery likely induces 3'UTR shortening following prolonged T cell stimulation; a significant program of APA changes occur prior to cellular proliferation or upregulation of the APA machinery. Motif analysis suggests that at least a subset of these early changes in APA are driven by upregulation of RBM3, an RNA-binding protein which competes with the APA machinery for binding. Together this work expands our understanding of the impact and mechanisms of APA in response to T cell activation and suggests new mechanisms by which APA may be regulated.
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Affiliation(s)
- Davia Blake
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Immunology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Matthew R Gazzara
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Genomic and Computational Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Isabel Breuer
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Genetics and Epigenetics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Max Ferretti
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Kristen W Lynch
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Immunology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Genomic and Computational Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Genetics and Epigenetics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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4
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Hoekstra MMB, Ness N, Badia-Soteras A, Brancaccio M. Bmal1 integrates circadian function and temperature sensing in the suprachiasmatic nucleus. Proc Natl Acad Sci U S A 2024; 121:e2316646121. [PMID: 38625943 PMCID: PMC11047078 DOI: 10.1073/pnas.2316646121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 03/22/2024] [Indexed: 04/18/2024] Open
Abstract
Circadian regulation and temperature dependency are important orchestrators of molecular pathways. How the integration between these two drivers is achieved, is not understood. We monitored circadian- and temperature-dependent effects on transcription dynamics of cold-response protein RNA Binding Motif 3 (Rbm3). Temperature changes in the mammalian master circadian pacemaker, the suprachiasmatic nucleus (SCN), induced Rbm3 transcription and regulated its circadian periodicity, whereas the core clock gene Per2 was unaffected. Rbm3 induction depended on a full Brain And Muscle ARNT-Like Protein 1 (Bmal1) complement: reduced Bmal1 erased Rbm3 responses and weakened SCN circuit resilience to temperature changes. By focusing on circadian and temperature dependency, we highlight weakened transmission between core clock and downstream pathways as a potential route for reduced circadian resilience.
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Affiliation(s)
- Marieke M. B. Hoekstra
- Department of Brain Science, Imperial College London, LondonW12 0NN, United Kingdom
- Department of Brain Sciences, United Kingdom Dementia Research Institute at Imperial College London, LondonW12 0NN, United Kingdom
| | - Natalie Ness
- Department of Brain Science, Imperial College London, LondonW12 0NN, United Kingdom
- Department of Brain Sciences, United Kingdom Dementia Research Institute at Imperial College London, LondonW12 0NN, United Kingdom
| | - Aina Badia-Soteras
- Department of Brain Science, Imperial College London, LondonW12 0NN, United Kingdom
- Department of Brain Sciences, United Kingdom Dementia Research Institute at Imperial College London, LondonW12 0NN, United Kingdom
| | - Marco Brancaccio
- Department of Brain Science, Imperial College London, LondonW12 0NN, United Kingdom
- Department of Brain Sciences, United Kingdom Dementia Research Institute at Imperial College London, LondonW12 0NN, United Kingdom
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5
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Ma Y, He Z, Wang J, Zheng P, Ma Z, Liang Q, Zhang Q, Zhao X, Huang J, Weng W, Jiang J, Feng J. Mild hypothermia promotes neuronal differentiation of human neural stem cells via RBM3-SOX11 signaling pathway. iScience 2024; 27:109435. [PMID: 38523796 PMCID: PMC10960102 DOI: 10.1016/j.isci.2024.109435] [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: 09/20/2023] [Revised: 01/06/2024] [Accepted: 03/04/2024] [Indexed: 03/26/2024] Open
Abstract
Both therapeutic hypothermia and neural stem cells (NSCs) transplantation have shown promise in neuroprotection and neural repair after brain injury. However, the effects of therapeutic hypothermia on neuronal differentiation of NSCs are not elucidated. In this study, we aimed to investigate whether mild hypothermia promoted neuronal differentiation in cultured and transplanted human NSCs (hNSCs). A significant increase in neuronal differentiation rate of hNSCs was found when exposed to 35°C, from 33% to 45% in vitro and from 7% to 15% in vivo. Additionally, single-cell RNA sequencing identified upregulation of RNA-binding motif protein 3 (RBM3) in neuroblast at 35°C, which stabilized the SRY-box transcription factor 11 (SOX11) mRNA and increased its protein expression, leading to an increase in neuronal differentiation of hNSCs. In conclusion, our study highlights that mild hypothermia at 35°C enhances hNSCs-induced neurogenesis through the novel RBM3-SOX11 signaling pathway, and provides a potential treatment strategy in brain disorders.
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Affiliation(s)
- Yuxiao Ma
- Brain Injury Center, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
- Shanghai Institute of Head Trauma, Shanghai 200127, China
| | - Zhenghui He
- Brain Injury Center, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
- Shanghai Institute of Head Trauma, Shanghai 200127, China
| | - Jiangchang Wang
- Brain Injury Center, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
- Shanghai Institute of Head Trauma, Shanghai 200127, China
| | - Ping Zheng
- Department of Neurosurgery, Shanghai Pudong New Area People’s Hospital, Shanghai 201299, China
| | - Zixuan Ma
- Brain Injury Center, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
- Shanghai Institute of Head Trauma, Shanghai 200127, China
| | - Qian Liang
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Qiao Zhang
- Brain Injury Center, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
- Shanghai Institute of Head Trauma, Shanghai 200127, China
| | - Xiongfei Zhao
- Shanghai Angecon Biotechnology Co., Ltd., Shanghai 201318, China
| | - Jialin Huang
- Brain Injury Center, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
- Shanghai Institute of Head Trauma, Shanghai 200127, China
| | - Weiji Weng
- Brain Injury Center, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
- Shanghai Institute of Head Trauma, Shanghai 200127, China
| | - Jiyao Jiang
- Brain Injury Center, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
- Shanghai Institute of Head Trauma, Shanghai 200127, China
| | - Junfeng Feng
- Brain Injury Center, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
- Shanghai Institute of Head Trauma, Shanghai 200127, China
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Díaz de Cerio M, Oliván S, Ochoa I, García-Sanmartín J, Martínez A. Cold-shock proteins accumulate in centrosomes and their expression and primary cilium morphology are regulated by hypothermia and shear stress. Histol Histopathol 2024; 39:447-462. [PMID: 37694837 DOI: 10.14670/hh-18-656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Primary cilia act as cellular sensors for multiple extracellular stimuli and regulate many intracellular signaling pathways in response. Here we investigate whether the cold-shock proteins (CSPs), CIRP and RBM3, are present in the primary cilia and the physiological consequences of such a relationship. R28, an immortalized retinal precursor cell line, was stained with antibodies against CIRP, RBM3, and ciliary markers. Both CSPs were found in intimate contact with the basal body of the cilium during all stages of the cell cycle, including migrating with the centrosome during mitosis. In addition, the morphological and physiological manifestations of exposing the cells to hypothermia and shear stress were investigated. Exposure to moderately cold (32°C) temperatures, the hypothermia mimetic small molecule zr17-2, or to shear stress resulted in a significant reduction in the number and length of primary cilia. In addition, shear stress induced expression of CIRP and RBM3 in a complex pattern depending on the specific protein, flow intensity, and type of flow (laminar versus oscillatory). Flow-mediated CSP overexpression was detected by qRT-PCR and confirmed by Western blot, at least for CIRP. Furthermore, analysis of public RNA Seq databases on flow experiments confirmed an increase of CIRP and RBM3 expression following exposure to shear stress in renal cell lines. In conclusion, we found that CSPs are integral components of the centrosome and that they participate in cold and shear stress sensing.
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Affiliation(s)
- María Díaz de Cerio
- Angiogenesis Unit, Oncology Area, Center for Biomedical Research of La Rioja (CIBIR), Logroño, Spain
| | - Sara Oliván
- Tissue Microenvironment Lab (TMELab), University of Zaragoza, Aragón Institute of Engineering Research (I3A), Institute for Health Research Aragon (IIS Aragón), Zaragoza, Spain
| | - Ignacio Ochoa
- Tissue Microenvironment Lab (TMELab), University of Zaragoza, Aragón Institute of Engineering Research (I3A), Institute for Health Research Aragon (IIS Aragón), Zaragoza, Spain
- Centro de Investigación Biomédica en Red. Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Institute for Health Research Aragon (IIS Aragón), Zaragoza, Spain
| | - Josune García-Sanmartín
- Angiogenesis Unit, Oncology Area, Center for Biomedical Research of La Rioja (CIBIR), Logroño, Spain
| | - Alfredo Martínez
- Angiogenesis Unit, Oncology Area, Center for Biomedical Research of La Rioja (CIBIR), Logroño, Spain.
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7
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Xu B, Hwangbo DS, Saurabh S, Rosensweig C, Allada R, Kath WL, Braun R. Temperature-driven coordination of circadian transcriptional regulation. PLoS Comput Biol 2024; 20:e1012029. [PMID: 38648221 PMCID: PMC11108206 DOI: 10.1371/journal.pcbi.1012029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 05/21/2024] [Accepted: 03/28/2024] [Indexed: 04/25/2024] Open
Abstract
The circadian clock is an evolutionarily-conserved molecular oscillator that enables species to anticipate rhythmic changes in their environment. At a molecular level, the core clock genes induce circadian oscillations in thousands of genes in a tissue-specific manner, orchestrating myriad biological processes. While previous studies have investigated how the core clock circuit responds to environmental perturbations such as temperature, the downstream effects of such perturbations on circadian regulation remain poorly understood. By analyzing bulk-RNA sequencing of Drosophila fat bodies harvested from flies subjected to different environmental conditions, we demonstrate a highly condition-specific circadian transcriptome: genes are cycling in a temperature-specific manner, and the distributions of their phases also differ between the two conditions. Further employing a reference-based gene regulatory network (Reactome), we find evidence of increased gene-gene coordination at low temperatures and synchronization of rhythmic genes that are network neighbors. We report that the phase differences between cycling genes increase as a function of geodesic distance in the low temperature condition, suggesting increased coordination of cycling on the gene regulatory network. Our results suggest a potential mechanism whereby the circadian clock mediates the fly's response to seasonal changes in temperature.
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Affiliation(s)
- Bingxian Xu
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, United States of America
- NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, Illinois, United States of America
| | - Dae-Sung Hwangbo
- Department of Biology, University of Louisville, Louisville, Kentucky, United States of America
- Department of Neurobiology, Northwestern University, Evanston, Illinois, United States of America
| | - Sumit Saurabh
- Department of Biology, Loyola University, Chicago, Illinois, United States of America
| | - Clark Rosensweig
- NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, Illinois, United States of America
- Department of Neurobiology, Northwestern University, Evanston, Illinois, United States of America
| | - Ravi Allada
- NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, Illinois, United States of America
- Department of Neurobiology, Northwestern University, Evanston, Illinois, United States of America
- Michigan Neuroscience Institute, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Anesthesiology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - William L. Kath
- NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, Illinois, United States of America
- Department of Neurobiology, Northwestern University, Evanston, Illinois, United States of America
- Northwestern Institute on Complex Systems, Northwestern University, Evanston, Illinois, United States of America
- Department of Engineering Sciences and Applied Mathematics, Northwestern University, Evanston, Illinois, United States of America
| | - Rosemary Braun
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, United States of America
- NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, Illinois, United States of America
- Northwestern Institute on Complex Systems, Northwestern University, Evanston, Illinois, United States of America
- Department of Engineering Sciences and Applied Mathematics, Northwestern University, Evanston, Illinois, United States of America
- Department of Physics and Astronomy, Northwestern University, Evanston, Illinois, United States of America
- Santa Fe Institute, Santa Fe, New Mexico, United States of America
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8
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Flores CC, Pasetto NA, Wang H, Dimitrov A, Davis JF, Jiang Z, Davis CJ, Gerstner JR. Identification of sleep and circadian alternative polyadenylation sites associated with APA-linked human brain disorders. RESEARCH SQUARE 2024:rs.3.rs-3867797. [PMID: 38313253 PMCID: PMC10836116 DOI: 10.21203/rs.3.rs-3867797/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2024]
Abstract
Sleep and circadian rhythm disruptions are comorbid features of many pathologies and can negatively influence numerous health conditions, including degenerative diseases, metabolic illnesses, cancer, and various neurological disorders. Genetic association studies linking sleep and circadian disturbances with disease susceptibility have mainly focused on changes in gene expression due to mutations, such as single-nucleotide polymorphisms. Thus, associations between sleep and/or circadian rhythm and alternative polyadenylation (APA), particularly in the context of other health challenges, are largely undescribed. APA is a process that generates various transcript isoforms from the same gene, resulting in effects on mRNA translation, stability, localization, and subsequent function. Here, we have identified unique APAs in rat brain that exhibit time-of-day-dependent oscillations in expression as well as APAs that are altered by sleep deprivation and the subsequent recovery period. Genes affected by APA usage include Mapt/Tau, Ntrk2, Homer1A, Sin3band Sorl. Sorl1 has two APAs which cycle with a 24 h period, one additional APA cycles with a 12 h period and one more that is reduced during recovery sleep. Finally, we compared sleep- or circadian-associated APAs with recently described APA-linked brain disorder susceptibility genes and found 46 genes in common.
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9
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Toyota K, Akashi H, Ishikawa M, Yamaguchi K, Shigenobu S, Sato T, Lange A, Tyler CR, Iguchi T, Miyagawa S. Comparative analysis of gonadal transcriptomes between turtle and alligator identifies common molecular cues activated during the temperature-sensitive period for sex determination. Gene 2023; 888:147763. [PMID: 37666375 DOI: 10.1016/j.gene.2023.147763] [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: 06/12/2023] [Revised: 08/09/2023] [Accepted: 09/01/2023] [Indexed: 09/06/2023]
Abstract
The mode of sex determination in vertebrates can be categorized as genotypic or environmental. In the case of genotypic sex determination (GSD), the sexual fate of an organism is determined by the chromosome composition with some having dominant genes, named sex-determining genes, that drive the sex phenotypes. By contrast, many reptiles exhibit environmental sex determination (ESD), whereby environmental stimuli drive sex determination, and most notably temperature. To date, temperature-dependent sex determination (TSD) has been found in most turtles, some lizards, and all crocodylians, but commonalities in the controlling processes are not well established. Recent innovative sequencing technology has enabled investigations into gonadal transcriptomic profiles during temperature-sensitive periods (TSP) in various TSD species which can help elucidate the controlling mechanisms. In this study, we conducted a time-course analysis of the gonadal transcriptome during the male-producing temperature (26℃) of the Reeve's turtle (Chinese three-keeled pond turtle) Mauremys reevesii. We then compared the transcriptome profiles for this turtle species during the TSP with that for the American alligator Alligator mississippiensis to identify conserved reptilian TSD-related genes. Our transcriptome-based findings provide an opportunity to retrieve the candidate molecular cues that are activated during TSP and compare these target responses between TSD and GSD turtle species, and between TSD species.
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Affiliation(s)
- Kenji Toyota
- Department of Biological Science and Technology, Faculty of Advanced Engineering, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585, Japan; Noto Marine Laboratory, Institute of Nature and Environmental Technology, Kanazawa University, Ogi, Noto-cho, Ishikawa 927-0553, Japan; Department of Biological Sciences, Faculty of Science, Kanagawa University, 2946 Tsuchiya, Hiratsuka, Kanagawa 259-1293, Japan.
| | - Hiroshi Akashi
- Department of Biological Science and Technology, Faculty of Advanced Engineering, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585, Japan; Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
| | - Momoka Ishikawa
- Department of Biological Science and Technology, Faculty of Advanced Engineering, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585, Japan
| | - Katsushi Yamaguchi
- Trans-Omics Facility, National Institute for Basic Biology, 38 Nishigonaka, Myodaiji-cho, Okazaki, Aichi 444-8585, Japan
| | - Shuji Shigenobu
- Trans-Omics Facility, National Institute for Basic Biology, 38 Nishigonaka, Myodaiji-cho, Okazaki, Aichi 444-8585, Japan
| | - Tomomi Sato
- Graduate School of Nanobioscience, Yokohama City University, 22-2 Seto, Kanazawa-ku, Yokohama, Kanagawa 236-0027, Japan
| | - Anke Lange
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK
| | - Charles R Tyler
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK
| | - Taisen Iguchi
- Noto Marine Laboratory, Institute of Nature and Environmental Technology, Kanazawa University, Ogi, Noto-cho, Ishikawa 927-0553, Japan; Graduate School of Nanobioscience, Yokohama City University, 22-2 Seto, Kanazawa-ku, Yokohama, Kanagawa 236-0027, Japan
| | - Shinichi Miyagawa
- Department of Biological Science and Technology, Faculty of Advanced Engineering, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585, Japan.
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10
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Goswami B, Nag S, Ray PS. Fates and functions of RNA-binding proteins under stress. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023:e1825. [PMID: 38014833 DOI: 10.1002/wrna.1825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 10/03/2023] [Accepted: 10/30/2023] [Indexed: 11/29/2023]
Abstract
Exposure to stress activates a well-orchestrated set of changes in gene expression programs that allow the cell to cope with and adapt to the stress, or undergo programmed cell death. RNA-protein interactions, mediating all aspects of post-transcriptional regulation of gene expression, play crucial roles in cellular stress responses. RNA-binding proteins (RBPs), which interact with sequence/structural elements in RNAs to control the steps of RNA metabolism, have therefore emerged as central regulators of post-transcriptional responses to stress. Following exposure to a variety of stresses, the dynamic alterations in the RNA-protein interactome enable cells to respond to intracellular or extracellular perturbations by causing changes in mRNA splicing, polyadenylation, stability, translation, and localization. As RBPs play a central role in determining the cellular proteome both qualitatively and quantitatively, it has become increasingly evident that their abundance, availability, and functions are also highly regulated in response to stress. Exposure to stress initiates a series of signaling cascades that converge on post-translational modifications (PTMs) of RBPs, resulting in changes in their subcellular localization, association with stress granules, extracellular export, proteasomal degradation, and RNA-binding activities. These alterations in the fate and function of RBPs directly impact their post-transcriptional regulatory roles in cells under stress. Adopting the ubiquitous RBP HuR as a prototype, three scenarios illustrating the changes in nuclear-cytoplasmic localization, RNA-binding activity, export and degradation of HuR in response to inflammation, genotoxic stress, and heat shock depict the complex and interlinked regulatory mechanisms that control the fate and functions of RBPs under stress. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
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Affiliation(s)
- Binita Goswami
- Department of Biological Sciences, Indian Institute of Science Education and Research, Mohanpur, West Bengal, India
| | - Sharanya Nag
- Department of Biological Sciences, Indian Institute of Science Education and Research, Mohanpur, West Bengal, India
| | - Partho Sarothi Ray
- Department of Biological Sciences, Indian Institute of Science Education and Research, Mohanpur, West Bengal, India
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11
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Zhou J, Li QQ. Stress responses of plants through transcriptome plasticity by mRNA alternative polyadenylation. MOLECULAR HORTICULTURE 2023; 3:19. [PMID: 37789388 PMCID: PMC10536700 DOI: 10.1186/s43897-023-00066-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 09/07/2023] [Indexed: 10/05/2023]
Abstract
The sessile nature of plants confines their responsiveness to changing environmental conditions. Gene expression regulation becomes a paramount mechanism for plants to adjust their physiological and morphological behaviors. Alternative polyadenylation (APA) is known for its capacity to augment transcriptome diversity and plasticity, thereby furnishing an additional set of tools for modulating gene expression. APA has also been demonstrated to exhibit intimate associations with plant stress responses. In this study, we review APA dynamic features and consequences in plants subjected to both biotic and abiotic stresses. These stresses include adverse environmental stresses, and pathogenic attacks, such as cadmium toxicity, high salt, hypoxia, oxidative stress, cold, heat shock, along with bacterial, fungal, and viral infections. We analyzed the overarching research framework employed to elucidate plant APA response and the alignment of polyadenylation site transitions with the modulation of gene expression levels within the ambit of each stress condition. We also proposed a general APA model where transacting factors, including poly(A) factors, epigenetic regulators, RNA m6A modification factors, and phase separation proteins, assume pivotal roles in APA related transcriptome plasticity during stress response in plants.
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Affiliation(s)
- Jiawen Zhou
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen, 361102, Fujian, China
| | - Qingshun Quinn Li
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen, 361102, Fujian, China.
- Biomedical Sciences, College of Dental Medicine, Western University of Health Sciences, Pomona, CA, 91766, USA.
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12
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Rey-Funes M, Fernández JC, Peláez R, Soliño M, Contartese DS, Ciranna NS, Nakamura R, Sarotto A, Dorfman VB, Zapico JM, Ramos A, de Pascual-Teresa B, López-Costa JJ, Larrayoz IM, Martínez A, Loidl CF. A hypothermia mimetic molecule (zr17-2) reduces ganglion cell death, gliosis, and electroretinogram distortion in male rats subjected to perinatal asphyxia. Front Pharmacol 2023; 14:1252184. [PMID: 37767403 PMCID: PMC10520548 DOI: 10.3389/fphar.2023.1252184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 08/30/2023] [Indexed: 09/29/2023] Open
Abstract
Introduction: Perinatal asphyxia (PA) represents a major problem in perinatology and may cause visual losses, including blindness. We, and others, have shown that hypothermia prevents retinal symptoms associated to PA. In the present work, we evaluate whether a hypothermia mimetic small molecule, zr17-2, has similar effects in the context of PA. Methods: Four experimental groups were studied in male rats: Naturally born rats as controls (CTL), naturally born rats injected s.c. with 50 µL of 330 nmols/L zr17-2 (ZR), animals that were exposed to PA for 20 min at 37°C (PA), and rats that were exposed to PA and injected with zr17-2 (PA-ZR). Forty-five days after treatment, animals were subjected to electroretinography. In addition, morphological techniques (TUNEL, H&E, multiple immunofluorescence) were applied to the retinas. Results: A reduction in the amplitude of the a- and b-wave and oscillatory potentials (OP) of the electroretinogram (ERG) was detected in PA animals. Treatment with zr17-2 resulted in a significant amelioration of these parameters (p < 0.01). In PA animals, a large number of apoptotic cells was found in the GCL. This number was significantly reduced by treatment with the small molecule (p < 0.0001). In a similar way, the thickness of the inner retina and the intensity of GFAP immunoreactivity (gliosis) increased in PA retinas (p < 0.0001). These parameters were corrected by the administration of zr17-2 (p < 0.0001). Furthermore, injection of the small molecule in the absence of PA did not modify the ERG nor the morphological parameters studied, suggesting a lack of toxicity. Discussion: In conclusion, our results indicate that a single s.c. injection of zr17-2 in asphyctic neonates may provide a novel and efficacious method to prevent the visual sequelae of PA.
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Affiliation(s)
- Manuel Rey-Funes
- Laboratorio de Neuropatología Experimental, Instituto de Biología Celular y Neurociencia “Prof. E. De Robertis” (IBCN), Facultad de Medicina, CONICET—Universidad de Buenos Aires, Buenos Aires, Argentina
- Departamento de Biología Celular, Histología, Embriología y Genética, Instituto de Biología Celular y Neurociencia “Prof. E. De Robertis” (IBCN), Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Juan Carlos Fernández
- Laboratorio de Neuropatología Experimental, Instituto de Biología Celular y Neurociencia “Prof. E. De Robertis” (IBCN), Facultad de Medicina, CONICET—Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Rafael Peláez
- Biomarkers and Molecular Signaling Group, Center for Biomedical Research of La Rioja (CIBIR), Logroño, Spain
| | - Manuel Soliño
- Laboratorio de Neuropatología Experimental, Instituto de Biología Celular y Neurociencia “Prof. E. De Robertis” (IBCN), Facultad de Medicina, CONICET—Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Daniela S. Contartese
- Laboratorio de Neuropatología Experimental, Instituto de Biología Celular y Neurociencia “Prof. E. De Robertis” (IBCN), Facultad de Medicina, CONICET—Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Nicolás S. Ciranna
- Laboratorio de Neuropatología Experimental, Instituto de Biología Celular y Neurociencia “Prof. E. De Robertis” (IBCN), Facultad de Medicina, CONICET—Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Ronan Nakamura
- Laboratorio de Neuropatología Experimental, Instituto de Biología Celular y Neurociencia “Prof. E. De Robertis” (IBCN), Facultad de Medicina, CONICET—Universidad de Buenos Aires, Buenos Aires, Argentina
- Departamento de Biología Celular, Histología, Embriología y Genética, Instituto de Biología Celular y Neurociencia “Prof. E. De Robertis” (IBCN), Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Aníbal Sarotto
- Laboratorio de Neuropatología Experimental, Instituto de Biología Celular y Neurociencia “Prof. E. De Robertis” (IBCN), Facultad de Medicina, CONICET—Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Verónica B. Dorfman
- Centro de Estudios Biomédicos Básicos, Aplicados y Desarrollo (CEBBAD), Universidad Maimónides, Buenos Aires, Argentina
| | - José M. Zapico
- Department of Chemistry and Biochemistry, Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Madrid, Spain
| | - Ana Ramos
- Department of Chemistry and Biochemistry, Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Madrid, Spain
| | - Beatriz de Pascual-Teresa
- Department of Chemistry and Biochemistry, Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Madrid, Spain
| | - Juan José López-Costa
- Laboratorio de Neuropatología Experimental, Instituto de Biología Celular y Neurociencia “Prof. E. De Robertis” (IBCN), Facultad de Medicina, CONICET—Universidad de Buenos Aires, Buenos Aires, Argentina
- Departamento de Biología Celular, Histología, Embriología y Genética, Instituto de Biología Celular y Neurociencia “Prof. E. De Robertis” (IBCN), Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Ignacio M. Larrayoz
- Department of Nursing, Biomarkers, Artificial Intelligence, and Signaling (BIAS), University of La Rioja, Logroño, Spain
| | - Alfredo Martínez
- Angiogenesis Group, Oncology Area, Center for Biomedical Research of La Rioja (CIBIR), Logroño, Spain
| | - César Fabián Loidl
- Laboratorio de Neuropatología Experimental, Instituto de Biología Celular y Neurociencia “Prof. E. De Robertis” (IBCN), Facultad de Medicina, CONICET—Universidad de Buenos Aires, Buenos Aires, Argentina
- Departamento de Biología Celular, Histología, Embriología y Genética, Instituto de Biología Celular y Neurociencia “Prof. E. De Robertis” (IBCN), Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina
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13
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Brooks TG, Lahens NF, Grant GR, Sheline YI, FitzGerald GA, Skarke C. Diurnal rhythms of wrist temperature are associated with future disease risk in the UK Biobank. Nat Commun 2023; 14:5172. [PMID: 37620332 PMCID: PMC10449859 DOI: 10.1038/s41467-023-40977-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 08/15/2023] [Indexed: 08/26/2023] Open
Abstract
Many chronic disease symptomatologies involve desynchronized sleep-wake cycles, indicative of disrupted biorhythms. This can be interrogated using body temperature rhythms, which have circadian as well as sleep-wake behavior/environmental evoked components. Here, we investigated the association of wrist temperature amplitudes with a future onset of disease in the UK Biobank one year after actigraphy. Among 425 disease conditions (range n = 200-6728) compared to controls (range n = 62,107-91,134), a total of 73 (17%) disease phenotypes were significantly associated with decreased amplitudes of wrist temperature (Benjamini-Hochberg FDR q < 0.05) and 26 (6.1%) PheCODEs passed a more stringent significance level (Bonferroni-correction α < 0.05). A two-standard deviation (1.8° Celsius) lower wrist temperature amplitude corresponded to hazard ratios of 1.91 (1.58-2.31 95% CI) for NAFLD, 1.69 (1.53-1.88) for type 2 diabetes, 1.25 (1.14-1.37) for renal failure, 1.23 (1.17-1.3) for hypertension, and 1.22 (1.11-1.33) for pneumonia (phenome-wide atlas available at http://bioinf.itmat.upenn.edu/biorhythm_atlas/ ). This work suggests peripheral thermoregulation as a digital biomarker.
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Affiliation(s)
- Thomas G Brooks
- Institute for Translational Medicine and Therapeutics (ITMAT), University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
| | - Nicholas F Lahens
- Institute for Translational Medicine and Therapeutics (ITMAT), University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Gregory R Grant
- Institute for Translational Medicine and Therapeutics (ITMAT), University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Yvette I Sheline
- Department of Radiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Psychiatry, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Neurology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Garret A FitzGerald
- Institute for Translational Medicine and Therapeutics (ITMAT), University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Carsten Skarke
- Institute for Translational Medicine and Therapeutics (ITMAT), University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
- Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
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14
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Haniffa S, Narain P, Hughes MA, Petković A, Šušić M, Mlambo V, Chaudhury D. Chronic social stress blunts core body temperature and molecular rhythms of Rbm3 and Cirbp in mouse lateral habenula. Open Biol 2023; 13:220380. [PMID: 37463657 PMCID: PMC10353891 DOI: 10.1098/rsob.220380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Accepted: 06/29/2023] [Indexed: 07/19/2023] Open
Abstract
Chronic social stress in mice causes behavioural and physiological changes that result in perturbed rhythms of body temperature, activity and sleep-wake cycle. To further understand the link between mood disorders and temperature rhythmicity in mice that are resilient or susceptible to stress, we measured core body temperature (Tcore) before and after exposure to chronic social defeat stress (CSDS). We found that Tcore amplitudes of stress-resilient and susceptible mice are dampened during exposure to CSDS. However, following CSDS, resilient mice recovered temperature amplitude faster than susceptible mice. Furthermore, the interdaily stability (IS) of temperature rhythms was fragmented in stress-exposed mice during CSDS, which recovered to control levels following stress. There were minimal changes in locomotor activity after stress exposure which correlates with regular rhythmic expression of Prok2 - an output signal of the suprachiasmatic nucleus. We also determined that expression of thermosensitive genes Rbm3 and Cirbp in the lateral habenula (LHb) were blunted 1 day after CSDS. Rhythmic expression of these genes recovered 10 days later. Overall, we show that CSDS blunts Tcore and thermosensitive gene rhythms. Tcore rhythm recovery is faster in stress-resilient mice, but Rbm3 and Cirbp recovery is uniform across the phenotypes.
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Affiliation(s)
- Salma Haniffa
- Department of Biology, Science Division, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Priyam Narain
- Centre for Genomics and Systems Biology (CGSB), New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Michelle Ann Hughes
- Department of Biology, Science Division, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Aleksa Petković
- Department of Biology, Science Division, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Marko Šušić
- Department of Biology, Science Division, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Vongai Mlambo
- Department of Biology, Science Division, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Dipesh Chaudhury
- Department of Biology, Science Division, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
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15
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Lyons LC, Vanrobaeys Y, Abel T. Sleep and memory: The impact of sleep deprivation on transcription, translational control, and protein synthesis in the brain. J Neurochem 2023; 166:24-46. [PMID: 36802068 PMCID: PMC10919414 DOI: 10.1111/jnc.15787] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 01/31/2023] [Accepted: 02/07/2023] [Indexed: 02/20/2023]
Abstract
In countries around the world, sleep deprivation represents a widespread problem affecting school-age children, teenagers, and adults. Acute sleep deprivation and more chronic sleep restriction adversely affect individual health, impairing memory and cognitive performance as well as increasing the risk and progression of numerous diseases. In mammals, the hippocampus and hippocampus-dependent memory are vulnerable to the effects of acute sleep deprivation. Sleep deprivation induces changes in molecular signaling, gene expression and may cause changes in dendritic structure in neurons. Genome wide studies have shown that acute sleep deprivation alters gene transcription, although the pool of genes affected varies between brain regions. More recently, advances in research have drawn attention to differences in gene regulation between the level of the transcriptome compared with the pool of mRNA associated with ribosomes for protein translation following sleep deprivation. Thus, in addition to transcriptional changes, sleep deprivation also affects downstream processes to alter protein translation. In this review, we focus on the multiple levels through which acute sleep deprivation impacts gene regulation, highlighting potential post-transcriptional and translational processes that may be affected by sleep deprivation. Understanding the multiple levels of gene regulation impacted by sleep deprivation is essential for future development of therapeutics that may mitigate the effects of sleep loss.
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Affiliation(s)
- Lisa C Lyons
- Program in Neuroscience, Department of Biological Science, Florida State University, Tallahassee, Florida, USA
| | - Yann Vanrobaeys
- Department of Neuroscience and Pharmacology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
- Iowa Neuroscience Institute, Iowa City, Iowa, USA
- Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, Iowa, USA
| | - Ted Abel
- Department of Neuroscience and Pharmacology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
- Iowa Neuroscience Institute, Iowa City, Iowa, USA
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16
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Preußner M, Smith HL, Hughes D, Zhang M, Emmerichs A, Scalzitti S, Peretti D, Swinden D, Neumann A, Haltenhof T, Mallucci GR, Heyd F. ASO targeting RBM3 temperature-controlled poison exon splicing prevents neurodegeneration in vivo. EMBO Mol Med 2023; 15:e17157. [PMID: 36946385 PMCID: PMC10165353 DOI: 10.15252/emmm.202217157] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 02/16/2023] [Accepted: 02/18/2023] [Indexed: 03/23/2023] Open
Abstract
Neurodegenerative diseases are increasingly prevalent in the aging population, yet no disease-modifying treatments are currently available. Increasing the expression of the cold-shock protein RBM3 through therapeutic hypothermia is remarkably neuroprotective. However, systemic cooling poses a health risk, strongly limiting its clinical application. Selective upregulation of RBM3 at normothermia thus holds immense therapeutic potential. Here we identify a poison exon within the RBM3 gene that is solely responsible for its cold-induced expression. Genetic removal or antisense oligonucleotide (ASO)-mediated manipulation of this exon yields high RBM3 levels independent of cooling. Notably, a single administration of ASO to exclude the poison exon, using FDA-approved chemistry, results in long-lasting increased RBM3 expression in mouse brains. In prion-diseased mice, this treatment leads to remarkable neuroprotection, with prevention of neuronal loss and spongiosis despite high levels of disease-associated prion protein. Our promising results in mice support the possibility that RBM3-inducing ASOs might also deliver neuroprotection in humans in conditions ranging from acute brain injury to Alzheimer's disease.
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Affiliation(s)
- Marco Preußner
- Institut für Chemie und Biochemie, RNA BiochemieFreie Universität BerlinBerlinGermany
| | - Heather L Smith
- UK Dementia Research Institute and Department of Clinical NeurosciencesUniversity of CambridgeCambridgeUK
- Altos LabsCambridge Institute of ScienceCambridgeUK
| | - Daniel Hughes
- UK Dementia Research Institute and Department of Clinical NeurosciencesUniversity of CambridgeCambridgeUK
| | - Min Zhang
- Institut für Chemie und Biochemie, RNA BiochemieFreie Universität BerlinBerlinGermany
| | - Ann‐Kathrin Emmerichs
- Institut für Chemie und Biochemie, RNA BiochemieFreie Universität BerlinBerlinGermany
| | - Silvia Scalzitti
- Institut für Chemie und Biochemie, RNA BiochemieFreie Universität BerlinBerlinGermany
| | - Diego Peretti
- UK Dementia Research Institute and Department of Clinical NeurosciencesUniversity of CambridgeCambridgeUK
| | - Dean Swinden
- UK Dementia Research Institute and Department of Clinical NeurosciencesUniversity of CambridgeCambridgeUK
- Altos LabsCambridge Institute of ScienceCambridgeUK
| | - Alexander Neumann
- Institut für Chemie und Biochemie, RNA BiochemieFreie Universität BerlinBerlinGermany
- Omiqa BioinformaticsBerlinGermany
| | - Tom Haltenhof
- Institut für Chemie und Biochemie, RNA BiochemieFreie Universität BerlinBerlinGermany
- Omiqa BioinformaticsBerlinGermany
| | - Giovanna R Mallucci
- UK Dementia Research Institute and Department of Clinical NeurosciencesUniversity of CambridgeCambridgeUK
- Altos LabsCambridge Institute of ScienceCambridgeUK
| | - Florian Heyd
- Institut für Chemie und Biochemie, RNA BiochemieFreie Universität BerlinBerlinGermany
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17
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Winsky-Sommerer R, King HA, Iadevaia V, Möller-Levet C, Gerber AP. A post-transcriptional regulatory landscape of aging in the female mouse hippocampus. Front Aging Neurosci 2023; 15:1119873. [PMID: 37122377 PMCID: PMC10135431 DOI: 10.3389/fnagi.2023.1119873] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 02/27/2023] [Indexed: 05/02/2023] Open
Abstract
Aging is associated with substantial physiological changes and constitutes a major risk factor for neurological disorders including dementia. Alterations in gene expression upon aging have been extensively studied; however, an in-depth characterization of post-transcriptional regulatory events remains elusive. Here, we profiled the age-related changes of the transcriptome and translatome in the female mouse hippocampus by RNA sequencing of total RNA and polysome preparations at four ages (3-, 6-, 12-, 20-month-old); and we implemented a variety of bioinformatics approaches to unravel alterations in transcript abundance, alternative splicing, and polyadenylation site selection. We observed mostly well-coordinated transcriptome and translatome expression signatures across age including upregulation of transcripts related to immune system processes and neuroinflammation, though transcripts encoding ribonucleoproteins or associated with mitochondrial functions, calcium signaling and the cell-cycle displayed substantial discordant profiles, suggesting translational control associated with age-related deficits in hippocampal-dependent behavior. By contrast, alternative splicing was less preserved, increased with age and was associated with distinct functionally-related transcripts encoding proteins acting at synapses/dendrites, RNA-binding proteins; thereby predicting regulatory roles for RBM3 and CIRBP. Only minor changes in polyadenylation site selection were identified, indicating pivotal 3'-end selection in young adults compared to older groups. Overall, our study provides a comprehensive resource of age-associated post-transcriptional regulatory events in the mouse hippocampus, enabling further examination of the molecular features underlying age-associated neurological diseases.
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Affiliation(s)
| | | | | | | | - André P. Gerber
- Faculty of Health and Medical Sciences, School of Biosciences and Medicine, University of Surrey, Guildford, Surrey, United Kingdom
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18
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Skarke C, Brooks T, Lahens N, Grant G, Sheline Y, FitzGerald G. Diurnal rhythmicity of wearable device-measured wrist temperature predicts future disease incidence in the UK Biobank. RESEARCH SQUARE 2023:rs.3.rs-2535978. [PMID: 36824952 PMCID: PMC9949244 DOI: 10.21203/rs.3.rs-2535978/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Many chronic disease symptomatologies involve desynchronized sleep-wake cycles, indicative of disrupted biorhythms. This can be interrogated using body temperature rhythms, which are well-established biomarkers for circadian clock function. Here, we investigated the association of wrist temperature amplitudes with a future onset of disease in the UK Biobank one year after actigraphy. Among 425 disease conditions (range n = 200-6,728) compared to controls (range n = 62,107 - 91,134), a total of 73 (36.5%) disease phenotypes were significantly associated with decreased amplitudes of wrist temperature (Benjamini-Hochberg FDR q < 0.05) and 26 (13%) PheCODEs passed a more stringent significance level (Bonferroni-correction α < 0.05). Here, for example, a two-standard deviation (1.8° Celsius) lower wrist temperature amplitude corresponded to hazard ratios of 1.91 (1.58-2.31 95% CI) for NAFLD, 1.69 (1.53-1.88) for type 2 diabetes, 1.25 (1.14-1.37) for renal failure, 1.23 (1.17-1.3) for hypertension, and 1.22 (1.11-1.33) for pneumonia. A comprehensive phenome-wide atlas of the identified mappings has been made available at http://bioinf.itmat.upenn.edu/biorhythm_atlas/. These findings strongly suggest peripheral thermoregulation as a digital biomarker.
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Affiliation(s)
| | | | | | - Gregory Grant
- Institute of Translational Medicine and Therapeutics (ITMAT), University of Pennsylvania; Department of Genetics, University of Pennsylvania Perelman School of Medicine
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19
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Hettinger ZR, Confides AL, Vanderklish PW, Dupont‐Versteegden EE. The transcript interactome of skeletal muscle RNA binding protein motif 3 (RBM3). Physiol Rep 2023; 11:e15596. [PMID: 36750123 PMCID: PMC9904958 DOI: 10.14814/phy2.15596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 01/13/2023] [Accepted: 01/18/2023] [Indexed: 02/09/2023] Open
Abstract
Post-transcriptional regulation of gene expression represents a critical regulatory step in the production of a functional proteome. Elevated expression of post-transcriptional regulator RNA binding motif protein 3 (RBM3), an RNA binding protein in the cold-shock family, is positively correlated with skeletal muscle growth in adult mice. However, mechanisms through which RBM3 exerts its effects are largely unknown. The purpose of this study was to perform RNA immunoprecipitation followed by RNA sequencing (RIP-seq) and apply a network science approach to understand biological processes (BPs) most associated with RBM3-bound mRNAs. In addition, through nucleotide-sequence-scanning of enriched transcripts, we predicted the motif for skeletal muscle RBM3 binding. Gene set enrichment analysis followed by enrichment mapping of RBM3-bound transcripts (fold change >3; p.adj <0.01) revealed significant enrichment of BPs associated with "Contractile apparatus," "Translation initiation," and "Proteosome complex." Clusters were driven largely by enrichment of Myh1 (FC: 4.43), Eif4b (FC: 5.03), and Trim63 (FC: 5.84), respectively. Motif scanning of enriched sequences revealed a discrete 14 nucleotide-wide motif found most prominently at the junction between the protein coding region's termination sequence and the start of the 3' untranslated region (UTR; E-Value: 1.1 e-015 ). Proof of concept investigation of motif location along enriched transcripts Myh1 and Myl4 revealed 3' UTR binding, suggesting RBM3 involvement in transcript half-life regulation. Together, these results demonstrate the potential influence of RBM3 in reshaping the skeletal muscle proteome through post-transcriptional regulation of mRNAs crucial to muscle adaptations.
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Affiliation(s)
- Zachary R. Hettinger
- Department of Physical Therapy, College of Health SciencesUniversity of KentuckyLexingtonKentuckyUSA
- Center for Muscle BiologyUniversity of KentuckyLexingtonKentuckyUSA
- Present address:
Department of Physical Medicine & RehabilitationHarvard Medical SchoolBostonMassachusettsUSA
| | - Amy L. Confides
- Department of Physical Therapy, College of Health SciencesUniversity of KentuckyLexingtonKentuckyUSA
- Center for Muscle BiologyUniversity of KentuckyLexingtonKentuckyUSA
| | | | - Esther E. Dupont‐Versteegden
- Department of Physical Therapy, College of Health SciencesUniversity of KentuckyLexingtonKentuckyUSA
- Center for Muscle BiologyUniversity of KentuckyLexingtonKentuckyUSA
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20
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Contartese DS, Rey-Funes M, Peláez R, Soliño M, Fernández JC, Nakamura R, Ciranna NS, Sarotto A, Dorfman VB, López-Costa JJ, Zapico JM, Ramos A, de Pascual-Teresa B, Larrayoz IM, Loidl CF, Martínez A. A hypothermia mimetic molecule (zr17-2) reduces ganglion cell death and electroretinogram distortion in a rat model of intraorbital optic nerve crush (IONC). Front Pharmacol 2023; 14:1112318. [PMID: 36755945 PMCID: PMC9899795 DOI: 10.3389/fphar.2023.1112318] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 01/10/2023] [Indexed: 01/24/2023] Open
Abstract
Introduction: Ocular and periocular traumatisms may result in loss of vision. Our previous work showed that therapeutic hypothermia prevents retinal damage caused by traumatic neuropathy. We also generated and characterized small molecules that elicit the beneficial effects of hypothermia at normal body temperature. Here we investigate whether one of these mimetic molecules, zr17-2, is able to preserve the function of eyes exposed to trauma. Methods: Intraorbital optic nerve crush (IONC) or sham manipulation was applied to Sprague-Dawley rats. One hour after surgery, 5.0 µl of 330 nmol/L zr17-2 or PBS, as vehicle, were injected in the vitreum of treated animals. Electroretinograms were performed 21 days after surgery and a- and b-wave amplitude, as well as oscillatory potentials (OP), were calculated. Some animals were sacrificed 6 days after surgery for TUNEL analysis. All animal experiments were approved by the local ethics board. Results: Our previous studies showed that zr17-2 does not cross the blood-ocular barrier, thus preventing systemic treatment. Here we show that intravitreal injection of zr17-2 results in a very significant prevention of retinal damage, providing preclinical support for its pharmacological use in ocular conditions. As previously reported, IONC resulted in a drastic reduction in the amplitude of the b-wave (p < 0.0001) and OPs (p < 0.05), a large decrease in the number of RGCs (p < 0.0001), and a large increase in the number of apoptotic cells in the GCL and the INL (p < 0.0001). Interestingly, injection of zr17-2 largely prevented all these parameters, in a very similar pattern to that elicited by therapeutic hypothermia. The small molecule was also able to reduce oxidative stress-induced retinal cell death in vitro. Discussion: In summary, we have shown that intravitreal injection of the hypothermia mimetic, zr17-2, significantly reduces the morphological and electrophysiological consequences of ocular traumatism and may represent a new treatment option for this cause of visual loss.
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Affiliation(s)
- Daniela S Contartese
- Departamento de Biología Celular, Histología, Embriología y Genética, Instituto de Biología Celular y Neurociencia "Prof. E. De Robertis" (IBCN), UBA-CONICET, Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Manuel Rey-Funes
- Departamento de Biología Celular, Histología, Embriología y Genética, Instituto de Biología Celular y Neurociencia "Prof. E. De Robertis" (IBCN), UBA-CONICET, Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Rafael Peláez
- Biomarkers and Molecular Signaling, Neurodegenerative Diseases Area, Center for Biomedical Research of La Rioja (CIBIR), Logroño, Spain
| | - Manuel Soliño
- Departamento de Biología Celular, Histología, Embriología y Genética, Instituto de Biología Celular y Neurociencia "Prof. E. De Robertis" (IBCN), UBA-CONICET, Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Juan C Fernández
- Departamento de Biología Celular, Histología, Embriología y Genética, Instituto de Biología Celular y Neurociencia "Prof. E. De Robertis" (IBCN), UBA-CONICET, Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Ronan Nakamura
- Departamento de Biología Celular, Histología, Embriología y Genética, Instituto de Biología Celular y Neurociencia "Prof. E. De Robertis" (IBCN), UBA-CONICET, Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Nicolás S Ciranna
- Departamento de Biología Celular, Histología, Embriología y Genética, Instituto de Biología Celular y Neurociencia "Prof. E. De Robertis" (IBCN), UBA-CONICET, Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Aníbal Sarotto
- Departamento de Biología Celular, Histología, Embriología y Genética, Instituto de Biología Celular y Neurociencia "Prof. E. De Robertis" (IBCN), UBA-CONICET, Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Verónica B Dorfman
- Centro de Estudios Biomédicos Básicos, Aplicados y Desarrollo (CEBBAD), Universidad Maimónides, Buenos Aires, Argentina
| | - Juan J López-Costa
- Departamento de Biología Celular, Histología, Embriología y Genética, Instituto de Biología Celular y Neurociencia "Prof. E. De Robertis" (IBCN), UBA-CONICET, Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - José M Zapico
- Department of Chemistry and Biochemistry, Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Madrid, Spain
| | - Ana Ramos
- Department of Chemistry and Biochemistry, Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Madrid, Spain
| | - Beatriz de Pascual-Teresa
- Department of Chemistry and Biochemistry, Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Madrid, Spain
| | - Ignacio M Larrayoz
- Biomarkers and Molecular Signaling, Neurodegenerative Diseases Area, Center for Biomedical Research of La Rioja (CIBIR), Logroño, Spain
| | - César F Loidl
- Departamento de Biología Celular, Histología, Embriología y Genética, Instituto de Biología Celular y Neurociencia "Prof. E. De Robertis" (IBCN), UBA-CONICET, Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Alfredo Martínez
- Angiogenesis Group, Center for Biomedical Research of La Rioja, Logroño, Spain
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21
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Haniffa S, Narain P, Hughes MA, Petković A, Šušić M, Mlambo V, Chaudhury D. Chronic social stress blunts core body temperature and molecular rhythms of Rbm3and Cirbpin mouse lateral habenula.. [DOI: 10.1101/2023.01.02.522528] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/19/2023]
Abstract
AbstractChronic social stress in mice causes behavioral and physiological changes that result in perturbed rhythms of body temperature, activity and sleep-wake cycle. To further understand the link between mood disorders and temperature rhythmicity in mice that are resilient or susceptible to stress, we measured core body temperature (Tcore) before and after exposure to chronic social defeat stress (CSDS). We found that Tcore amplitudes of stress-resilient and susceptible mice are dampened during exposure to CSDS. However, following CSDS, resilient mice recovered temperature amplitude faster than susceptible mice. Furthermore, the interdaily stability (IS) of temperature rhythms was fragmented in stress-exposed mice during CSDS, which recovered to control levels following stress. There were minimal changes in locomotor activity after stress exposure which correlates with regular rhythmic expression ofProk2- an output signal of the suprachiasmatic nucleus. We also determined that expression of thermosensitive genesRbm3andCirbpin the lateral habenula (LHb) were blunted 1-day after CSDS. Rhythmic expression of these genes recovered 10 days later. Overall, we show that CSDS blunts Tcore and thermosensitive gene rhythms. Tcore rhythm recovery is faster in stress-resilient mice, butRbm3andCirbprecovery is uniform across the phenotypes.
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22
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Xie Y, Gao R, Gao Y, Dong Z, Ge J. 11S Proteasome Activator REGγ Promotes Aortic Dissection by Inhibiting RBM3 (RNA Binding Motif Protein 3) Pathway. Hypertension 2023; 80:125-137. [PMID: 36330811 DOI: 10.1161/hypertensionaha.122.19618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND Aortic dissection (AD) is a life-threatening cardiovascular disorder with high mortality and lacking underlying mechanisms or effective treatments. REGγ, the 11S proteasome activator known to promote the degradation of cellular proteins in a ubiquitin- and ATP-independent manner, emerges as a new regulator in the cardiovascular system. METHODS Using β-aminopropionitrile (BAPN)-subjected REGγ knockout AD mice and Ang II (angiotensin II)-treated REGγ deficiency vascular smooth muscle cells (VSMCs) to explore the effect of REGγ in AD progression. RESULTS REGγ was upregulated in mouse aorta of β-aminopropionitrile-induced AD model in vivo and Ang II-treated VSMCs in vitro. REGγ deficiency ameliorated AD progression in β-aminopropionitrile-induced mice by protecting against the switch in VSMCs from contractile to synthetic phenotype through suppressing RBM3 (RNA-binding motif protein 3) decay. Mechanically, REGγ interacted with and degraded the RNA-binding protein RBM3 directly, leading to decreased mRNA stability, lowered expression and transcriptional activity of transcription factor SRF (serum response factor), subsequently reduced transcription of VSMCs-specific contractile genes, α-SMA (alpha-smooth muscle actin) and SM22α (smooth muscle 22 alpha), caused the switch in VSMCs from contractile to synthetic phenotype and associated AD progression. Ablation of endogenous SRF or RBM3, or overexpressing exogenous RBM3 in VSMCs significantly blocked or reestablished the REGγ-dependent action on VSMCs phenotypic switch of Ang II stimulation in vitro. Furthermore, exogenously introducing RBM3 improved the switch in VSMCs from contractile to synthetic phenotype and associated AD features caused by REGγ in vivo. CONCLUSIONS Our results demonstrated that REGγ promoted the switch in VSMCs from contractile to synthetic phenotype and AD progression by inhibiting RBM3-SRF pathway, indicated that modulating REGγ-proteasome activity may be a potential therapeutic approach for AD-associated cardiovascular dysfunction.
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Affiliation(s)
- Yifan Xie
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai, China (Y.X., R.G., Y.G., Z.D., J.G.).,Shanghai Institute of Cardiovascular Diseases' Shanghai' China (Y.X., R.G., Y.G., Z.D., J.G.).,Institutes of Biomedical Science, Fudan University, Shanghai, China (Y.X., J.G.)
| | - Rifeng Gao
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai, China (Y.X., R.G., Y.G., Z.D., J.G.).,Shanghai Institute of Cardiovascular Diseases' Shanghai' China (Y.X., R.G., Y.G., Z.D., J.G.)
| | - Yang Gao
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai, China (Y.X., R.G., Y.G., Z.D., J.G.).,Shanghai Institute of Cardiovascular Diseases' Shanghai' China (Y.X., R.G., Y.G., Z.D., J.G.)
| | - Zheng Dong
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai, China (Y.X., R.G., Y.G., Z.D., J.G.).,Shanghai Institute of Cardiovascular Diseases' Shanghai' China (Y.X., R.G., Y.G., Z.D., J.G.)
| | - Junbo Ge
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai, China (Y.X., R.G., Y.G., Z.D., J.G.).,Shanghai Institute of Cardiovascular Diseases' Shanghai' China (Y.X., R.G., Y.G., Z.D., J.G.).,Institutes of Biomedical Science, Fudan University, Shanghai, China (Y.X., J.G.)
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23
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Nakamura J, Aihara T, Chiba T, Tsuruta F. Cold shock protein RBM3 is upregulated in the autophagy-deficient brain. MICROPUBLICATION BIOLOGY 2022; 2022:10.17912/micropub.biology.000695. [PMID: 36601325 PMCID: PMC9807172 DOI: 10.17912/micropub.biology.000695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/22/2022] [Accepted: 12/05/2022] [Indexed: 01/06/2023]
Abstract
Neural autophagy plays an important role in regulating protein quality control, brain homeostasis, and body temperature. However, the mechanism that links a defect in autophagy to body temperature has not been elucidated. Here, we report that RNA binding motif protein 3 (RBM3) is a potential candidate that regulates body temperature. We found that the body temperatures of Nestin-Cre ; Atg7 f/f conditional KO (cKO) mice were lower than that of wild-type (WT) mice. Moreover, RBM3 was upregulated in the Nestin-Cre ; Atg7 f/f brain. These data suggest that RBM3 is an implicit target that maintains body temperature influenced by neural autophagy.
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Affiliation(s)
- Junnosuke Nakamura
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Takuma Aihara
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Tomoki Chiba
- Master's and Doctoral Program in Biology, Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
,
Ph.D. Program in Human Biology, School of Integrative and Global Majors, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
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Ph.D. Program in Humanics, School of Integrative and Global Majors, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Fuminori Tsuruta
- Master's and Doctoral Program in Biology, Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
,
Ph.D. Program in Human Biology, School of Integrative and Global Majors, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
,
Ph.D. Program in Humanics, School of Integrative and Global Majors, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
,
Master's and Doctoral Program in Neuroscience, Graduate School of Comprehensive Human Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
,
Correspondence to: Fuminori Tsuruta (
)
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24
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Mitschka S, Mayr C. Context-specific regulation and function of mRNA alternative polyadenylation. Nat Rev Mol Cell Biol 2022; 23:779-796. [PMID: 35798852 PMCID: PMC9261900 DOI: 10.1038/s41580-022-00507-5] [Citation(s) in RCA: 99] [Impact Index Per Article: 49.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/02/2022] [Indexed: 02/08/2023]
Abstract
Alternative cleavage and polyadenylation (APA) is a widespread mechanism to generate mRNA isoforms with alternative 3' untranslated regions (UTRs). The expression of alternative 3' UTR isoforms is highly cell type specific and is further controlled in a gene-specific manner by environmental cues. In this Review, we discuss how the dynamic, fine-grained regulation of APA is accomplished by several mechanisms, including cis-regulatory elements in RNA and DNA and factors that control transcription, pre-mRNA cleavage and post-transcriptional processes. Furthermore, signalling pathways modulate the activity of these factors and integrate APA into gene regulatory programmes. Dysregulation of APA can reprogramme the outcome of signalling pathways and thus can control cellular responses to environmental changes. In addition to the regulation of protein abundance, APA has emerged as a major regulator of mRNA localization and the spatial organization of protein synthesis. This role enables the regulation of protein function through the addition of post-translational modifications or the formation of protein-protein interactions. We further discuss recent transformative advances in single-cell RNA sequencing and CRISPR-Cas technologies, which enable the mapping and functional characterization of alternative 3' UTRs in any biological context. Finally, we discuss new APA-based RNA therapeutics, including compounds that target APA in cancer and therapeutic genome editing of degenerative diseases.
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Affiliation(s)
- Sibylle Mitschka
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Christine Mayr
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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25
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Wang N, Langfelder P, Stricos M, Ramanathan L, Richman JB, Vaca R, Plascencia M, Gu X, Zhang S, Tamai TK, Zhang L, Gao F, Ouk K, Lu X, Ivanov LV, Vogt TF, Lu QR, Morton AJ, Colwell CS, Aaronson JS, Rosinski J, Horvath S, Yang XW. Mapping brain gene coexpression in daytime transcriptomes unveils diurnal molecular networks and deciphers perturbation gene signatures. Neuron 2022; 110:3318-3338.e9. [PMID: 36265442 PMCID: PMC9665885 DOI: 10.1016/j.neuron.2022.09.028] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 08/16/2022] [Accepted: 09/22/2022] [Indexed: 01/07/2023]
Abstract
Brain tissue transcriptomes may be organized into gene coexpression networks, but their underlying biological drivers remain incompletely understood. Here, we undertook a large-scale transcriptomic study using 508 wild-type mouse striatal tissue samples dissected exclusively in the afternoons to define 38 highly reproducible gene coexpression modules. We found that 13 and 11 modules are enriched in cell-type and molecular complex markers, respectively. Importantly, 18 modules are highly enriched in daily rhythmically expressed genes that peak or trough with distinct temporal kinetics, revealing the underlying biology of striatal diurnal gene networks. Moreover, the diurnal coexpression networks are a dominant feature of daytime transcriptomes in the mouse cortex. We next employed the striatal coexpression modules to decipher the striatal transcriptomic signatures from Huntington's disease models and heterozygous null mice for 52 genes, uncovering novel functions for Prkcq and Kdm4b in oligodendrocyte differentiation and bipolar disorder-associated Trank1 in regulating anxiety-like behaviors and nocturnal locomotion.
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Affiliation(s)
- Nan Wang
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience & Human Behavior, University of California, Los Angeles, Los Angeles, CA, USA; Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA; UCLA Brain Research Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - Peter Langfelder
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience & Human Behavior, University of California, Los Angeles, Los Angeles, CA, USA; Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA; UCLA Brain Research Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - Matthew Stricos
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience & Human Behavior, University of California, Los Angeles, Los Angeles, CA, USA; Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA; UCLA Brain Research Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - Lalini Ramanathan
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience & Human Behavior, University of California, Los Angeles, Los Angeles, CA, USA; Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA; UCLA Brain Research Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - Jeffrey B Richman
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience & Human Behavior, University of California, Los Angeles, Los Angeles, CA, USA; Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA; UCLA Brain Research Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - Raymond Vaca
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience & Human Behavior, University of California, Los Angeles, Los Angeles, CA, USA; Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA; UCLA Brain Research Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - Mary Plascencia
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience & Human Behavior, University of California, Los Angeles, Los Angeles, CA, USA; Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA; UCLA Brain Research Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - Xiaofeng Gu
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience & Human Behavior, University of California, Los Angeles, Los Angeles, CA, USA; Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA; UCLA Brain Research Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - Shasha Zhang
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience & Human Behavior, University of California, Los Angeles, Los Angeles, CA, USA; Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA; UCLA Brain Research Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - T Katherine Tamai
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA; UCLA Brain Research Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - Liguo Zhang
- Department of Pediatrics, Division of Experimental Hematology and Cancer Biology, Brain Tumor Center, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Fuying Gao
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience & Human Behavior, University of California, Los Angeles, Los Angeles, CA, USA; Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Koliane Ouk
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Xiang Lu
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience & Human Behavior, University of California, Los Angeles, Los Angeles, CA, USA; Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | | | - Thomas F Vogt
- CHDI Management /CHDI Foundation, Princeton, NJ, USA
| | - Qing Richard Lu
- Department of Pediatrics, Division of Experimental Hematology and Cancer Biology, Brain Tumor Center, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - A Jennifer Morton
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Christopher S Colwell
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA; UCLA Brain Research Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | | | - Jim Rosinski
- CHDI Management /CHDI Foundation, Princeton, NJ, USA
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine at UCLA, University of California, Los Angeles, Los Angeles, CA, USA
| | - X William Yang
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience & Human Behavior, University of California, Los Angeles, Los Angeles, CA, USA; Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
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26
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Lv S, Zhou Y, Chen J, Yuan H, Zhang ZN, Luan B. Hepatic ER stress suppresses adipose browning through ATF4-CIRP-ANGPTL3 cascade. Cell Rep 2022; 40:111422. [PMID: 36170814 DOI: 10.1016/j.celrep.2022.111422] [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: 01/06/2022] [Revised: 07/28/2022] [Accepted: 09/07/2022] [Indexed: 12/01/2022] Open
Abstract
Hepatic endoplasmic reticulum (ER) stress is a hallmark of obesity-induced liver steatosis and contributes to the progress of steatosis and insulin resistance in liver. However, its influence on adipose function is still unclear. Here, we identify a hepatic ER stress-induced activating transcription factor 4 (ATF4)-cold-inducible RNA-binding protein (CIRP)-angiopoietin-related protein3 (ANGPTL3) cascade critical for the regulation of adipose browning. We find that obesity increases CIRP expression in liver through ER stress-induced ATF4. CIRP in turn binds to the 3' UTR and increases mRNA stability of ANGPTL3. ANGPTL3 secreted from liver suppresses uncoupling protein 1 expression through integrin αvβ3 and c-Jun N-terminal kinase in adipose tissue. While hepatic expression of either ATF4, CIRP, or ANGPTL3 suppresses adipose browning, knockdown of CIRP and ANGPTL3 in liver or administration of integrin αvβ3 inhibitor cilengitide increases adipose browning process. Taken together, we identify a communication mechanism to link hepatic ER stress and adipose browning that may imply a reciprocal regulation of obesity and liver steatosis.
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Affiliation(s)
- Sihan Lv
- Department of Endocrinology, Tongji Hospital Affiliated to Tongji University, School of Medicine, Tongji University, Shanghai 200072, China
| | - Yingqun Zhou
- Department of Gastroenterology, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai 200072, China
| | - Jiaojiao Chen
- Department of Gastroenterology, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai 200072, China; School of Clinical Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Huiwen Yuan
- Department of Endocrinology, Tongji Hospital Affiliated to Tongji University, School of Medicine, Tongji University, Shanghai 200072, China
| | - Zhen-Ning Zhang
- Translational Medical Center for Stem Cell Therapy & Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200120, China
| | - Bing Luan
- Department of Endocrinology, Tongji Hospital Affiliated to Tongji University, School of Medicine, Tongji University, Shanghai 200072, China.
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27
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Hu Y, Liu Y, Quan X, Fan W, Xu B, Li S. RBM3 is an outstanding cold shock protein with multiple physiological functions beyond hypothermia. J Cell Physiol 2022; 237:3788-3802. [PMID: 35926117 DOI: 10.1002/jcp.30852] [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: 03/16/2022] [Revised: 07/19/2022] [Accepted: 07/25/2022] [Indexed: 11/09/2022]
Abstract
RNA-binding motif protein 3 (RBM3), an outstanding cold shock protein, is rapidly upregulated to ensure homeostasis and survival in a cold environment, which is an important physiological mechanism in response to cold stress. Meanwhile, RBM3 has multiple physiological functions and participates in the regulation of various cellular physiological processes, such as antiapoptosis, circadian rhythm, cell cycle, reproduction, and tumogenesis. The structure, conservation, and tissue distribution of RBM3 in human are demonstrated in this review. Herein, the multiple physiological functions of RBM3 were summarized based on recent research advances. Meanwhile, the cytoprotective mechanism of RBM3 during stress under various adverse conditions and its regulation of transcription were discussed. In addition, the neuroprotection of RBM3 and its oncogenic role and controversy in various cancers were investigated in our review.
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Affiliation(s)
- Yajie Hu
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, National Experimental Teaching Demonstration Center of Animal Medicine Foundation, Daqing, China
| | - Yang Liu
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, National Experimental Teaching Demonstration Center of Animal Medicine Foundation, Daqing, China
| | - Xin Quan
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, National Experimental Teaching Demonstration Center of Animal Medicine Foundation, Daqing, China
| | - Wenxuan Fan
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, National Experimental Teaching Demonstration Center of Animal Medicine Foundation, Daqing, China
| | - Bin Xu
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, National Experimental Teaching Demonstration Center of Animal Medicine Foundation, Daqing, China
| | - Shize Li
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, National Experimental Teaching Demonstration Center of Animal Medicine Foundation, Daqing, China
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28
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Los B, Preußner M, Eschke K, Vidal RM, Abdelgawad A, Olofsson D, Keiper S, Paulo-Pedro M, Grindel A, Meinke S, Trimpert J, Heyd F. Body temperature variation controls pre-mRNA processing and transcription of antiviral genes and SARS-CoV-2 replication. Nucleic Acids Res 2022; 50:6769-6785. [PMID: 35713540 PMCID: PMC9262603 DOI: 10.1093/nar/gkac513] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 05/07/2022] [Accepted: 05/31/2022] [Indexed: 12/24/2022] Open
Abstract
Antiviral innate immunity represents the first defense against invading viruses and is key to control viral infections, including SARS-CoV-2. Body temperature is an omnipresent variable but was neglected when addressing host defense mechanisms and susceptibility to SARS-CoV-2 infection. Here, we show that increasing temperature in a 1.5°C window, between 36.5 and 38°C, strongly increases the expression of genes in two branches of antiviral immunity, nitric oxide production and type I interferon response. We show that alternative splicing coupled to nonsense-mediated decay decreases STAT2 expression in colder conditions and suggest that increased STAT2 expression at elevated temperature induces the expression of diverse antiviral genes and SARS-CoV-2 restriction factors. This cascade is activated in a remarkably narrow temperature range below febrile temperature, which reflects individual, circadian and age-dependent variation. We suggest that decreased body temperature with aging contributes to reduced expression of antiviral genes in older individuals. Using cell culture and in vivo models, we show that higher body temperature correlates with reduced SARS-CoV-2 replication, which may affect the different vulnerability of children versus seniors toward severe SARS-CoV-2 infection. Altogether, our data connect body temperature and pre-mRNA processing to provide new mechanistic insight into the regulation of antiviral innate immunity.
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Affiliation(s)
- Bruna Los
- Laboratory of RNA Biochemistry, Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 6, 14195 Berlin, Germany
| | - Marco Preußner
- Laboratory of RNA Biochemistry, Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 6, 14195 Berlin, Germany
| | - Kathrin Eschke
- Omiqa Bioinformatics, Altensteinstraße 40, 14195 Berlin, Germany
| | | | - Azza Abdelgawad
- Omiqa Bioinformatics, Altensteinstraße 40, 14195 Berlin, Germany
| | - Didrik Olofsson
- Institute of Virology, Freie Universität Berlin, Robert-von-Ostertag-Straße 7-13, 14163 Berlin, Germany
| | - Sandra Keiper
- Laboratory of RNA Biochemistry, Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 6, 14195 Berlin, Germany
| | - Margarida Paulo-Pedro
- Laboratory of RNA Biochemistry, Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 6, 14195 Berlin, Germany
| | - Alica Grindel
- Laboratory of RNA Biochemistry, Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 6, 14195 Berlin, Germany
| | - Stefan Meinke
- Laboratory of RNA Biochemistry, Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 6, 14195 Berlin, Germany
| | - Jakob Trimpert
- Omiqa Bioinformatics, Altensteinstraße 40, 14195 Berlin, Germany
| | - Florian Heyd
- To whom correspondence should be addressed. Tel: +49 30 83862938; Fax: +49 30 838 4 62938;
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29
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Möller-Levet CS, Laing EE, Archer SN, Dijk DJ. Diurnal and circadian rhythmicity of the human blood transcriptome overlaps with organ- and tissue-specific expression of a non-human primate. BMC Biol 2022; 20:63. [PMID: 35264172 PMCID: PMC8905855 DOI: 10.1186/s12915-022-01258-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 02/18/2022] [Indexed: 12/14/2022] Open
Abstract
Background Twenty-four-hour rhythmicity in mammalian tissues and organs is driven by local circadian oscillators, systemic factors, the central circadian pacemaker and light-dark cycles. At the physiological level, the neural and endocrine systems synchronise gene expression in peripheral tissues and organs to the 24-h-day cycle, and disruption of such regulation has been shown to lead to pathological conditions. Thus, monitoring rhythmicity in tissues/organs holds promise for circadian medicine; however, most tissues and organs are not easily accessible in humans and alternative approaches to quantify circadian rhythmicity are needed. We investigated the overlap between rhythmic transcripts in human blood and transcripts shown to be rhythmic in 64 tissues/organs of the baboon, how these rhythms are aligned with light-dark cycles and each other, and whether timing of tissue-specific rhythmicity can be predicted from a blood sample. Results We compared rhythmicity in transcriptomic time series collected from humans and baboons using set logic, circular cross-correlation, circular clustering, functional enrichment analyses, and least squares regression. Of the 759 orthologous genes that were rhythmic in human blood, 652 (86%) were also rhythmic in at least one baboon tissue and most of these genes were associated with basic processes such as transcription and protein homeostasis. In total, 109 (17%) of the 652 overlapping rhythmic genes were reported as rhythmic in only one baboon tissue or organ and several of these genes have tissue/organ-specific functions. The timing of human and baboon rhythmic transcripts displayed prominent ‘night’ and ‘day’ clusters, with genes in the dark cluster associated with translation. Alignment between baboon rhythmic transcriptomes and the overlapping human blood transcriptome was significantly closer when light onset, rather than midpoint of light, or end of light period, was used as phase reference point. The timing of overlapping human and baboon rhythmic transcriptomes was significantly correlated in 25 tissue/organs with an average earlier timing of 3.21 h (SD 2.47 h) in human blood. Conclusions The human blood transcriptome contains sets of rhythmic genes that overlap with rhythmic genes of tissues/organs in baboon. The rhythmic sets vary across tissues/organs, but the timing of most rhythmic genes is similar in human blood and baboon tissues/organs. These results have implications for development of blood transcriptome-based biomarkers for circadian rhythmicity in tissues and organs. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01258-7.
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Affiliation(s)
- Carla S Möller-Levet
- Bioinformatics Core Facility, Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK.
| | - Emma E Laing
- School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
| | - Simon N Archer
- Surrey Sleep Research Centre, Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
| | - Derk-Jan Dijk
- Surrey Sleep Research Centre, Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK. .,UK Dementia Research Institute, Care Research and Technology Centre at Imperial College, London and the University of Surrey, Guildford, UK.
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30
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Dietary Conjugated Linoleic Acid Reduces Body Weight and Fat in Snord116m+/p- and Snord116m-/p- Mouse Models of Prader-Willi Syndrome. Nutrients 2022; 14:nu14040860. [PMID: 35215509 PMCID: PMC8880678 DOI: 10.3390/nu14040860] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 02/07/2022] [Accepted: 02/11/2022] [Indexed: 02/04/2023] Open
Abstract
Prader–Willi Syndrome (PWS) is a human genetic condition that affects up to 1 in 10,000 live births. Affected infants present with hypotonia and developmental delay. Hyperphagia and increasing body weight follow unless drastic calorie restriction is initiated. Recently, our laboratory showed that one of the genes in the deleted locus causative for PWS, Snord116, maintains increased expression of hypothalamic Nhlh2, a basic helix–loop–helix transcription factor. We have previously also shown that obese mice with a deletion of Nhlh2 respond to a conjugated linoleic acid (CLA) diet with weight and fat loss. In this study, we investigated whether mice with a paternal deletion of Snord116 (Snord116m+/p−) would respond similarly. We found that while Snord116m+/p− mice and mice with a deletion of both Snord116 alleles were not significantly obese on a high-fat diet, they did lose body weight and fat on a high-fat/CLA diet, suggesting that the genotype did not interfere with CLA actions. There were no changes in food intake or metabolic rate, and only moderate differences in exercise performance. RNA-seq and microbiome analyses identified hypothalamic mRNAs, and differentially populated gut bacteria, that support future mechanistic analyses. CLA may be useful as a food additive to reduce obesity in humans with PWS.
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Soubise B, Jiang Y, Douet-Guilbert N, Troadec MB. RBM22, a Key Player of Pre-mRNA Splicing and Gene Expression Regulation, Is Altered in Cancer. Cancers (Basel) 2022; 14:cancers14030643. [PMID: 35158909 PMCID: PMC8833553 DOI: 10.3390/cancers14030643] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/19/2022] [Accepted: 01/22/2022] [Indexed: 01/05/2023] Open
Abstract
RNA-Binding Proteins (RBP) are very diverse and cover a large number of functions in the cells. This review focuses on RBM22, a gene encoding an RBP and belonging to the RNA-Binding Motif (RBM) family of genes. RBM22 presents a Zinc Finger like and a Zinc Finger domain, an RNA-Recognition Motif (RRM), and a Proline-Rich domain with a general structure suggesting a fusion of two yeast genes during evolution: Cwc2 and Ecm2. RBM22 is mainly involved in pre-mRNA splicing, playing the essential role of maintaining the conformation of the catalytic core of the spliceosome and acting as a bridge between the catalytic core and other essential protein components of the spliceosome. RBM22 is also involved in gene regulation, and is able to bind DNA, acting as a bona fide transcription factor on a large number of target genes. Undoubtedly due to its wide scope in the regulation of gene expression, RBM22 has been associated with several pathologies and, notably, with the aggressiveness of cancer cells and with the phenotype of a myelodysplastic syndrome. Mutations, enforced expression level, and haploinsufficiency of RBM22 gene are observed in those diseases. RBM22 could represent a potential therapeutic target in specific diseases, and, notably, in cancer.
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Affiliation(s)
- Benoît Soubise
- Université de Brest, Inserm, EFS, UMR 1078, GGB, F-29200 Brest, France; (B.S.); (Y.J.); (N.D.-G.)
| | - Yan Jiang
- Université de Brest, Inserm, EFS, UMR 1078, GGB, F-29200 Brest, France; (B.S.); (Y.J.); (N.D.-G.)
- Department of Hematology, The First Hospital of Jilin University, Changchun 130021, China
| | - Nathalie Douet-Guilbert
- Université de Brest, Inserm, EFS, UMR 1078, GGB, F-29200 Brest, France; (B.S.); (Y.J.); (N.D.-G.)
- CHRU Brest, Service de Génétique, Laboratoire de Génétique Chromosomique, F-29200 Brest, France
| | - Marie-Bérengère Troadec
- Université de Brest, Inserm, EFS, UMR 1078, GGB, F-29200 Brest, France; (B.S.); (Y.J.); (N.D.-G.)
- CHRU Brest, Service de Génétique, Laboratoire de Génétique Chromosomique, F-29200 Brest, France
- Correspondence: ; Tel.: +33-2-98-01-64-55
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Dynamic alternative polyadenylation during iPSC differentiation into cardiomyocytes. Comput Struct Biotechnol J 2022; 20:5859-5869. [DOI: 10.1016/j.csbj.2022.10.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 10/18/2022] [Accepted: 10/18/2022] [Indexed: 11/20/2022] Open
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Lin J, Yu Z, Ye C, Hong L, Chu Y, Shen Y, Li QQ. Alternative polyadenylated mRNAs behave as asynchronous rhythmic transcription in Arabidopsis. RNA Biol 2021; 18:2594-2604. [PMID: 34036876 PMCID: PMC8632115 DOI: 10.1080/15476286.2021.1933732] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 03/03/2021] [Accepted: 05/17/2021] [Indexed: 10/21/2022] Open
Abstract
Alternative polyadenylation (APA) is a widespread post-transcriptional modification method that changes the 3' ends of transcripts by altering poly(A) site usage. However, the longitudinal transcriptomic 3' end profile and its mechanism of action are poorly understood. We applied diurnal time-course poly(A) tag sequencing (PAT-seq) for Arabidopsis and identified 3284 genes that generated both rhythmic and arrhythmic transcripts. These two classes of transcripts appear to exhibit dramatic differences in expression and translation activisty. The asynchronized transcripts derived by APA are embedded with different poly(A) signals, especially for rhythmic transcripts, which contain higher AAUAAA and UGUA signal proportions. The Pol II occupancy maximum is reached upstream of rhythmic poly(A) sites, while it is present directly at arrhythmic poly(A) sites. Integrating H3K9ac and H3K4me3 time-course data analyses revealed that transcriptional activation of histone markers may be involved in the differentiation of rhythmic and arrhythmic APA transcripts. These results implicate an interplay between histone modification and RNA 3'-end processing, shedding light on the mechanism of transcription rhythm and alternative polyadenylation.
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Affiliation(s)
- Juncheng Lin
- Graduate College of Biomedical Sciences, Western University of Health Sciences, Pomona, USA
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Zhibo Yu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Congting Ye
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Liwei Hong
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Yiru Chu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Yingjia Shen
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Qingshun Q. Li
- Graduate College of Biomedical Sciences, Western University of Health Sciences, Pomona, USA
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
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Ruta V, Pagliarini V, Sette C. Coordination of RNA Processing Regulation by Signal Transduction Pathways. Biomolecules 2021; 11:biom11101475. [PMID: 34680108 PMCID: PMC8533259 DOI: 10.3390/biom11101475] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 10/01/2021] [Accepted: 10/05/2021] [Indexed: 02/06/2023] Open
Abstract
Signal transduction pathways transmit the information received from external and internal cues and generate a response that allows the cell to adapt to changes in the surrounding environment. Signaling pathways trigger rapid responses by changing the activity or localization of existing molecules, as well as long-term responses that require the activation of gene expression programs. All steps involved in the regulation of gene expression, from transcription to processing and utilization of new transcripts, are modulated by multiple signal transduction pathways. This review provides a broad overview of the post-translational regulation of factors involved in RNA processing events by signal transduction pathways, with particular focus on the regulation of pre-mRNA splicing, cleavage and polyadenylation. The effects of several post-translational modifications (i.e., sumoylation, ubiquitination, methylation, acetylation and phosphorylation) on the expression, subcellular localization, stability and affinity for RNA and protein partners of many RNA-binding proteins are highlighted. Moreover, examples of how some of the most common signal transduction pathways can modulate biological processes through changes in RNA processing regulation are illustrated. Lastly, we discuss challenges and opportunities of therapeutic approaches that correct RNA processing defects and target signaling molecules.
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Affiliation(s)
- Veronica Ruta
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, 00168 Rome, Italy; (V.R.); (V.P.)
- Organoids Facility, IRCCS Fondazione Policlinico Universitario Agostino Gemelli, 00168 Rome, Italy
| | - Vittoria Pagliarini
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, 00168 Rome, Italy; (V.R.); (V.P.)
- Organoids Facility, IRCCS Fondazione Policlinico Universitario Agostino Gemelli, 00168 Rome, Italy
| | - Claudio Sette
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, 00168 Rome, Italy; (V.R.); (V.P.)
- Laboratory of Neuroembryology, IRCCS Fondazione Santa Lucia, 00143 Rome, Italy
- Correspondence:
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35
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Kim YM, Hong S. Controversial roles of cold‑inducible RNA‑binding protein in human cancer (Review). Int J Oncol 2021; 59:91. [PMID: 34558638 DOI: 10.3892/ijo.2021.5271] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 09/06/2021] [Indexed: 11/05/2022] Open
Abstract
Cold‑inducible RNA‑binding protein (CIRBP) is a cold‑shock protein comprised of an RNA‑binding motif that is induced by several stressors, such as cold shock, UV radiation, nutrient deprivation, reactive oxygen species and hypoxia. CIRBP can modulate post‑transcriptional regulation of target mRNA, which is required to control DNA repair, circadian rhythms, cell growth, telomere integrity and cardiac physiology. In addition, the crucial function of CIRBP in various human diseases, including cancers and inflammatory disease, has been reported. Although CIRBP is primarily considered to be an oncogene, it may also serve a role in tumor suppression. In the present study, the controversial roles of CIRBP in various human cancers is summarized, with a focus on the interconnectivity between CIRBP and its target mRNAs involved in tumorigenesis. CIRBP may represent an important prognostic marker and therapeutic target for cancer therapy.
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Affiliation(s)
- Young-Mi Kim
- Department of Health Sciences and Technology, Gachon Advanced Institute for Health Sciences and Technology, Gachon University, Incheon 21999, Republic of Korea
| | - Suntaek Hong
- Department of Health Sciences and Technology, Gachon Advanced Institute for Health Sciences and Technology, Gachon University, Incheon 21999, Republic of Korea
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36
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Zingone A, Sinha S, Ante M, Nguyen C, Daujotyte D, Bowman ED, Sinha N, Mitchell KA, Chen Q, Yan C, Loher P, Meerzaman D, Ruppin E, Ryan BM. A comprehensive map of alternative polyadenylation in African American and European American lung cancer patients. Nat Commun 2021; 12:5605. [PMID: 34556645 PMCID: PMC8460807 DOI: 10.1038/s41467-021-25763-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 07/22/2021] [Indexed: 11/09/2022] Open
Abstract
Deciphering the post-transcriptional mechanisms (PTM) regulating gene expression is critical to understand the dynamics underlying transcriptomic regulation in cancer. Alternative polyadenylation (APA)-regulation of mRNA 3'UTR length by alternating poly(A) site usage-is a key PTM mechanism whose comprehensive analysis in cancer remains an important open challenge. Here we use a method and analysis pipeline that sequences 3'end-enriched RNA directly to overcome the saturation limitation of traditional 5'-3' based sequencing. We comprehensively map the APA landscape in lung cancer in a cohort of 98 tumor/non-involved tissues derived from European American and African American patients. We identify a global shortening of 3'UTR transcripts in lung cancer, with notable functional implications on the expression of both coding and noncoding genes. We find that APA of non-coding RNA transcripts (long non-coding RNAs and microRNAs) is a recurrent event in lung cancer and discover that the selection of alternative polyA sites is a form of non-coding RNA expression control. Our results indicate that mRNA transcripts from EAs are two times more likely than AAs to undergo APA in lung cancer. Taken together, our findings comprehensively map and identify the important functional role of alternative polyadenylation in determining transcriptomic heterogeneity in lung cancer.
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Affiliation(s)
- Adriana Zingone
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, US
| | - Sanju Sinha
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, US
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, Bethesda, MD, US
| | - Michael Ante
- Lexogen GmbH, Campus Vienna Biocenter 5, 1030, Vienna, Austria
- Ares Genetics GmbH, Karl-Farkas-Gasse 18, 1030, Vienna, Austria
| | - Cu Nguyen
- Computational Genomics Research, Center for Biomedical Informatics and Information Technology (CBIIT), National Cancer Institute, 9609 Medical Center Drive, Rockville, MD, 20850, US
| | - Dalia Daujotyte
- Lexogen GmbH, Campus Vienna Biocenter 5, 1030, Vienna, Austria
| | - Elise D Bowman
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, US
| | - Neelam Sinha
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, Bethesda, MD, US
| | - Khadijah A Mitchell
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, US
| | - Qingrong Chen
- Computational Genomics Research, Center for Biomedical Informatics and Information Technology (CBIIT), National Cancer Institute, 9609 Medical Center Drive, Rockville, MD, 20850, US
| | - Chunhua Yan
- Computational Genomics Research, Center for Biomedical Informatics and Information Technology (CBIIT), National Cancer Institute, 9609 Medical Center Drive, Rockville, MD, 20850, US
| | - Phillipe Loher
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, 19017, US
| | - Daoud Meerzaman
- Computational Genomics Research, Center for Biomedical Informatics and Information Technology (CBIIT), National Cancer Institute, 9609 Medical Center Drive, Rockville, MD, 20850, US
| | - Eytan Ruppin
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, Bethesda, MD, US
| | - Bríd M Ryan
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, US.
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Goh GH, Mark PJ, Blache D, Binks D, Parsons R, Rawashdeh O, Maloney SK. Diet-altered body temperature rhythms are associated with altered rhythms of clock gene expression in peripheral tissues in vivo. J Therm Biol 2021; 100:102983. [PMID: 34503769 DOI: 10.1016/j.jtherbio.2021.102983] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 04/25/2021] [Accepted: 04/26/2021] [Indexed: 10/21/2022]
Abstract
Temperature rhythms can act as potent signals for the modulation of the amplitude and phase of clock gene expression in peripheral organs in vitro, but the relevance of the circadian rhythm of core body temperature (Tc) as a modulating signal in vivo has not yet been investigated. Using calorie restriction and cafeteria feeding, we induced a larger and a dampened Tc amplitude, respectively, in male Wistar rats, and investigated the circadian expression profile of the core clock genes Bmal1, Per2, Cry1, and Rev-erbα, the heat-responsive genes heat shock protein 90 (Hsp90) and cold-inducible RNA binding protein (Cirbp), and Pgc1α, Pparα/γ/δ, Glut1/4, and Chop10 in the liver, skeletal muscle, white adipose tissue (WAT), and adrenal glands. Diet-altered Tc rhythms differentially affected the profiles of clock genes, Hsp90, and Cirbp expression in peripheral tissues. Greater Tc amplitudes elicited by calorie restriction were associated with large amplitudes of Hsp90 and Cirbp expression in the liver and WAT, in which larger amplitudes of clock gene expression were also observed. The amplitudes of metabolic gene expression were greater in the WAT, but not in the liver, in calorie-restricted rats. Conversely, diet-altered Tc rhythms were not translated to distinct changes in the amplitude of Hsp90, Cirbp, or clock or metabolic genes in the skeletal muscle or adrenal glands. While it was not possible to disentangle the effects of diet and temperature in this model, taken together with previous in vitro studies, our study presents novel data consistent with the notion that the circadian Tc rhythm can modulate the amplitude of circadian gene expression in vivo. The different responses of Hsp90 and Cirbp in peripheral tissues may be linked to the tissue-specific responses of peripheral clocks to diet and/or body temperature rhythms, but the association with the amplitude of metabolic gene expression is limited to the WAT.
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Affiliation(s)
- Grace H Goh
- School of Human Biology, University of Western Australia, Crawley, 6009, Australia.
| | - Peter J Mark
- School of Human Biology, University of Western Australia, Crawley, 6009, Australia
| | - Dominique Blache
- School of Agriculture and Environment, University of Western Australia, Crawley, WA, 6009, Australia
| | - Daniel Binks
- School of Human Biology, University of Western Australia, Crawley, 6009, Australia
| | - Rex Parsons
- School of Biomedical Sciences, Faculty of Medicine, University of Queensland, St Lucia, QLD, 4072, Australia
| | - Oliver Rawashdeh
- School of Biomedical Sciences, Faculty of Medicine, University of Queensland, St Lucia, QLD, 4072, Australia
| | - Shane K Maloney
- School of Human Biology, University of Western Australia, Crawley, 6009, Australia
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Anna G, Kannan NN. Post-transcriptional modulators and mediators of the circadian clock. Chronobiol Int 2021; 38:1244-1261. [PMID: 34056966 PMCID: PMC7611477 DOI: 10.1080/07420528.2021.1928159] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 04/26/2021] [Accepted: 05/03/2021] [Indexed: 01/04/2023]
Abstract
The endogenous circadian timekeeping system drives ~24-h rhythms in gene expression and rhythmically coordinates the physiology, metabolism and behavior in a wide range of organisms. Regulation at various levels is important for the accurate functioning of this circadian timing system. The core circadian oscillator consists of an interlocked transcriptional-translational negative feedback loop (TTFL) that imposes a substantial delay between the accumulation of clock gene mRNA and its protein to generate 24-h oscillations. This TTFL mediated daily oscillation of clock proteins is further fine-tuned by post-translational modifications that regulate the clock protein stability, interaction with other proteins and subcellular localization. Emerging evidence from various studies indicates that besides TTFL and post-translational modifications, post-transcriptional regulation plays a key role in shaping the rhythmicity of mRNAs and to delay the accumulation of clock proteins in relation to their mRNAs. In this review, we summarize the current knowledge on the importance of post-transcriptional regulatory mechanisms such as splicing, polyadenylation, the role of RNA-binding proteins, RNA methylation and microRNAs in the context of shaping the circadian rhythmicity in Drosophila and mammals. In particular, we discuss microRNAs, an important player in post-transcriptional regulation of core-clock machinery, circadian neural circuit, clock input, and output pathways. Furthermore, we provide an overview of the microRNAs that exhibit diurnal rhythm in expression and their role in mediating rhythmic physiological processes.
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Affiliation(s)
- Geo Anna
- Chronobiology Laboratory, School of Biology, Indian Institute of Science Education and Research (IISER), Thiruvananthapuram, Kerala 695551, India
| | - Nisha N Kannan
- Chronobiology Laboratory, School of Biology, Indian Institute of Science Education and Research (IISER), Thiruvananthapuram, Kerala 695551, India
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Song Y, Guo Y, Li X, Sun R, Zhu M, Shi J, Tan Z, Zhang L, Huang J. RBM39 Alters Phosphorylation of c-Jun and Binds to Viral RNA to Promote PRRSV Proliferation. Front Immunol 2021; 12:664417. [PMID: 34079549 PMCID: PMC8165236 DOI: 10.3389/fimmu.2021.664417] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 04/23/2021] [Indexed: 01/27/2023] Open
Abstract
As transcriptional co-activator of AP-1/Jun, estrogen receptors and NF-κB, nuclear protein RBM39 also involves precursor mRNA (pre-mRNA) splicing. Porcine reproductive and respiratory syndrome virus (PRRSV) causes sow reproductive disorders and piglet respiratory diseases, which resulted in serious economic losses worldwide. In this study, the up-regulated expression of RBM39 and down-regulated of inflammatory cytokines (IFN-β, TNFα, NF-κB, IL-1β, IL-6) were determined in PRRSV-infected 3D4/21 cells, and accompanied with the PRRSV proliferation. The roles of RBM39 altering phosphorylation of c-Jun to inhibit the AP-1 pathway to promote PRRSV proliferation were further verified. In addition, the nucleocytoplasmic translocation of RBM39 and c-Jun from the nucleus to cytoplasm was enhanced in PRRSV-infected cells. The three RRM domain of RBM39 are crucial to support the proliferation of PRRSV. Several PRRSV RNA (nsp4, nsp5, nsp7, nsp10-12, M and N) binding with RBM39 were determined, which may also contribute to the PRRSV proliferation. Our results revealed a complex mechanism of RBM39 by altering c-Jun phosphorylation and nucleocytoplasmic translocation, and regulating binding of RBM39 with viral RNA to prompt PRRSV proliferation. The results provide new viewpoints to understand the immune escape mechanism of PRRSV infection.
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Affiliation(s)
- Yinna Song
- School of Life Sciences, Tianjin University, Tianjin, China
| | - Yanyu Guo
- School of Life Sciences, Tianjin University, Tianjin, China
| | - Xiaoyang Li
- School of Life Sciences, Tianjin University, Tianjin, China
| | - Ruiqi Sun
- School of Life Sciences, Tianjin University, Tianjin, China
| | - Min Zhu
- School of Life Sciences, Tianjin University, Tianjin, China
| | - Jingxuan Shi
- School of Life Sciences, Tianjin University, Tianjin, China
| | - Zheng Tan
- School of Life Sciences, Tianjin University, Tianjin, China
| | - Lilin Zhang
- School of Life Sciences, Tianjin University, Tianjin, China
- Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, Tianjin University, Tianjin, China
| | - Jinhai Huang
- School of Life Sciences, Tianjin University, Tianjin, China
- Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, Tianjin University, Tianjin, China
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Ahmad SF, Shanaz S, Kumar A, Dar AH, Mohmad A, Bhushan B. Crosstalk of epigenetics with biological rhythmicity in animal kingdom. BIOL RHYTHM RES 2021. [DOI: 10.1080/09291016.2019.1607218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Sheikh Firdous Ahmad
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Bareilly, India
| | - Syed Shanaz
- Department of Animal Genetics and Breeding, Sher-i-Kashmir University of Agricultural Sciences and Technology, Srinagar, India
| | - Abhishek Kumar
- Division of Animal Reproduction, ICAR-Indian Veterinary Research Institute, Bareilly, India
| | - Aashaq Hussain Dar
- Department of Livestock Production and Management, Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, Uttarakhand
| | - Aquil Mohmad
- Division of Parasitology, ICAR-Indian Veterinary Research Institute, Bareilly, India
| | - Bharat Bhushan
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Bareilly, India
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Rey-Funes M, Contartese DS, Peláez R, García-Sanmartín J, Narro-Íñiguez J, Soliño M, Fernández JC, Sarotto A, Ciranna NS, López-Costa JJ, Dorfman VB, Larrayoz IM, Loidl CF, Martínez A. Hypothermic Shock Applied After Perinatal Asphyxia Prevents Retinal Damage in Rats. Front Pharmacol 2021; 12:651599. [PMID: 33897437 PMCID: PMC8060653 DOI: 10.3389/fphar.2021.651599] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 02/22/2021] [Indexed: 01/10/2023] Open
Abstract
Perinatal asphyxia (PA) can cause retinopathy and different degrees of visual loss, including total blindness. In a rat model of PA, we have previously shown a protective effect of hypothermia on the retina when applied simultaneously with the hypoxic insult. In the present work, we evaluated the possible protective effect of hypothermia on the retina of PA rats when applied immediately after delivery. Four experimental groups were studied: Rats born naturally as controls (CTL), animals that were exposed to PA for 20 min at 37°C (PA), animals exposed to PA for 20 min at 15°C (HYP), and animals that were exposed to PA for 20 min at 37°C and, immediately after birth, kept for 15 min at 8°C (HYP-PA). To evaluate the integrity of the visual pathway, animals were subjected to electroretinography at 45 days of age. Molecular (real time PCR) and histological (immunohistochemistry, immunofluorescence, TUNEL assay) techniques were applied to the eyes of all experimental groups collected at 6, 12, 24, and 48 h, and 6 days after birth. PA resulted in a significant reduction in the amplitude of the a- and b-wave and oscillatory potentials (OP) of the electroretinogram. All animals treated with hypothermia had a significant correction of the a-wave and OP, but the b-wave was fully corrected in the HYP group but only partially in the HYP-PA group. The number of TUNEL-positive cells increased sharply in the ganglion cell layer of the PA animals and this increase was significantly prevented by both hypothermia treatments. Expression of the cold-shock proteins, cold-inducible RNA binding protein (CIRP) and RNA binding motif protein 3 (RBM3), was undetectable in retinas of the CTL and PA groups, but they were highly expressed in ganglion neurons and cells of the inner nuclear layer of the HYP and HYP-PA groups. In conclusion, our results suggest that a post-partum hypothermic shock could represent a useful and affordable method to prevent asphyxia-related vision disabling sequelae.
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Affiliation(s)
- Manuel Rey-Funes
- Laboratorio de Neuropatología Experimental, Instituto de Biología Celular y Neurociencia "Prof, E. De Robertis" (IBCN), Facultad de Medicina, CONICET - Universidad de Buenos Aires, Buenos Aires, Argentina.,Departamento de Biología Celular, Histología, Embriología y Genética, Instituto de Biología Celular y Neurociencia "Prof, E. De Robertis" (IBCN), Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Daniela S Contartese
- Laboratorio de Neuropatología Experimental, Instituto de Biología Celular y Neurociencia "Prof, E. De Robertis" (IBCN), Facultad de Medicina, CONICET - Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Rafael Peláez
- Biomarkers and Molecular Signaling Group, Center for Biomedical Research of La Rioja, Logroño, Spain
| | - Josune García-Sanmartín
- Angiogenesis Group, Oncology Area, Center for Biomedical Research of La Rioja, Logroño, Spain
| | - Judit Narro-Íñiguez
- Angiogenesis Group, Oncology Area, Center for Biomedical Research of La Rioja, Logroño, Spain
| | - Manuel Soliño
- Laboratorio de Neuropatología Experimental, Instituto de Biología Celular y Neurociencia "Prof, E. De Robertis" (IBCN), Facultad de Medicina, CONICET - Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Juan Carlos Fernández
- Laboratorio de Neuropatología Experimental, Instituto de Biología Celular y Neurociencia "Prof, E. De Robertis" (IBCN), Facultad de Medicina, CONICET - Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Aníbal Sarotto
- Laboratorio de Neuropatología Experimental, Instituto de Biología Celular y Neurociencia "Prof, E. De Robertis" (IBCN), Facultad de Medicina, CONICET - Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Nicolás S Ciranna
- Laboratorio de Neuropatología Experimental, Instituto de Biología Celular y Neurociencia "Prof, E. De Robertis" (IBCN), Facultad de Medicina, CONICET - Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Juan José López-Costa
- Laboratorio de Neuropatología Experimental, Instituto de Biología Celular y Neurociencia "Prof, E. De Robertis" (IBCN), Facultad de Medicina, CONICET - Universidad de Buenos Aires, Buenos Aires, Argentina.,Departamento de Biología Celular, Histología, Embriología y Genética, Instituto de Biología Celular y Neurociencia "Prof, E. De Robertis" (IBCN), Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Verónica B Dorfman
- Centro de Estudios Biomédicos Básicos, Aplicados y Desarrollo, Universidad Maimónides, Buenos Aires, Argentina
| | - Ignacio M Larrayoz
- Biomarkers and Molecular Signaling Group, Center for Biomedical Research of La Rioja, Logroño, Spain
| | - C Fabián Loidl
- Laboratorio de Neuropatología Experimental, Instituto de Biología Celular y Neurociencia "Prof, E. De Robertis" (IBCN), Facultad de Medicina, CONICET - Universidad de Buenos Aires, Buenos Aires, Argentina.,Departamento de Biología Celular, Histología, Embriología y Genética, Instituto de Biología Celular y Neurociencia "Prof, E. De Robertis" (IBCN), Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Alfredo Martínez
- Angiogenesis Group, Oncology Area, Center for Biomedical Research of La Rioja, Logroño, Spain
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42
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Liu J, Ke X, Wang L, Zhang Y, Yang J. Deficiency of cold-inducible RNA-binding protein exacerbated monocrotaline-induced pulmonary artery hypertension through Caveolin1 and CAVIN1. J Cell Mol Med 2021; 25:4732-4743. [PMID: 33755319 PMCID: PMC8107102 DOI: 10.1111/jcmm.16437] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 02/16/2021] [Accepted: 02/18/2021] [Indexed: 12/18/2022] Open
Abstract
Cold‐inducible RNA‐binding protein (CIRP) was a crucial regulator in multiple diseases. However, its role in pulmonary artery hypertension (PAH) is still unknown. Here, we first established monocrotaline (MCT)‐induced rat PAH model and discovered that CIRP was down‐regulated predominantly in the endothelium of pulmonary artery after MCT injection. We then generated Cirp‐knockout (Cirp‐KO) rats, which manifested severer PAH with exacerbated endothelium damage in response to MCT. Subsequently, Caveolin1 (Cav1) and Cavin1 were identified as downstream targets of CIRP in MCT‐induced PAH, and the decreased expression of these two genes aggravated the injury and apoptosis of pulmonary artery endothelium. Moreover, CIRP deficiency intensified monocrotaline pyrrole (MCTP)‐induced rat pulmonary artery endothelial cells (rPAECs) injuries both in vivo and in vitro, which was counteracted by Cav1 or Cavin1 overexpression. In addition, CIRP regulated the proliferative effect of conditioned media from MCTP‐treated rPAECs on rat pulmonary artery smooth muscle cells, which partially explained the exceedingly thickened pulmonary artery intimal media in Cirp‐KO rats after MCT treatment. These results demonstrated that CIRP acts as a critical protective factor in MCT‐induced rat PAH by directly regulating CAV1 and CAVIN1 expression, which may facilitate the development of new therapeutic targets for the intervention of PAH.
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Affiliation(s)
- Jingjing Liu
- Key Laboratory of Arrhythmias, Ministry of Education, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China.,Department of Cardiology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China.,Institute of Medical Genetics, Tongji University School of Medicine, Shanghai, China
| | - Xianting Ke
- Key Laboratory of Arrhythmias, Ministry of Education, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China.,Department of Cardiology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China.,Institute of Medical Genetics, Tongji University School of Medicine, Shanghai, China
| | - Luxin Wang
- Key Laboratory of Arrhythmias, Ministry of Education, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China.,Department of Cardiology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China.,Institute of Medical Genetics, Tongji University School of Medicine, Shanghai, China
| | - Yangyang Zhang
- Key Laboratory of Arrhythmias, Ministry of Education, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China.,Department of Cardiovascular Surgery, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Jian Yang
- Key Laboratory of Arrhythmias, Ministry of Education, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China.,Department of Cardiology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China.,Institute of Medical Genetics, Tongji University School of Medicine, Shanghai, China
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43
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Ho JJD, Man JHS, Schatz JH, Marsden PA. Translational remodeling by RNA-binding proteins and noncoding RNAs. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 12:e1647. [PMID: 33694288 DOI: 10.1002/wrna.1647] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 02/09/2021] [Accepted: 02/10/2021] [Indexed: 12/14/2022]
Abstract
Responsible for generating the proteome that controls phenotype, translation is the ultimate convergence point for myriad upstream signals that influence gene expression. System-wide adaptive translational reprogramming has recently emerged as a pillar of cellular adaptation. As classic regulators of mRNA stability and translation efficiency, foundational studies established the concept of collaboration and competition between RNA-binding proteins (RBPs) and noncoding RNAs (ncRNAs) on individual mRNAs. Fresh conceptual innovations now highlight stress-activated, evolutionarily conserved RBP networks and ncRNAs that increase the translation efficiency of populations of transcripts encoding proteins that participate in a common cellular process. The discovery of post-transcriptional functions for long noncoding RNAs (lncRNAs) was particularly intriguing given their cell-type-specificity and historical definition as nuclear-functioning epigenetic regulators. The convergence of RBPs, lncRNAs, and microRNAs on functionally related mRNAs to enable adaptive protein synthesis is a newer biological paradigm that highlights their role as "translatome (protein output) remodelers" and reinvigorates the paradigm of "RNA operons." Together, these concepts modernize our understanding of cellular stress adaptation and strategies for therapeutic development. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications Translation > Translation Regulation Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs.
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Affiliation(s)
- J J David Ho
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, Florida, USA.,Division of Hematology, Department of Medicine, Miller School of Medicine, University of Miami, Miami, Florida, USA
| | - Jeffrey H S Man
- Keenan Research Centre, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada.,Department of Medicine, University of Toronto, Toronto, Ontario, Canada.,Department of Respirology, University Health Network, Latner Thoracic Research Laboratories, University of Toronto, Toronto, Ontario, Canada
| | - Jonathan H Schatz
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, Florida, USA.,Division of Hematology, Department of Medicine, Miller School of Medicine, University of Miami, Miami, Florida, USA
| | - Philip A Marsden
- Keenan Research Centre, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada.,Department of Medicine, University of Toronto, Toronto, Ontario, Canada
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44
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Zhang Y, Hamada M. Identification of m 6A-Associated RNA Binding Proteins Using an Integrative Computational Framework. Front Genet 2021; 12:625797. [PMID: 33732286 PMCID: PMC7957075 DOI: 10.3389/fgene.2021.625797] [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: 11/04/2020] [Accepted: 02/05/2021] [Indexed: 12/05/2022] Open
Abstract
N6-methyladenosine (m6A) is an abundant modification on mRNA that plays an important role in regulating essential RNA activities. Several wet lab studies have identified some RNA binding proteins (RBPs) that are related to m6A's regulation. The objective of this study was to identify potential m6A-associated RBPs using an integrative computational framework. The framework was composed of an enrichment analysis and a classification model. Utilizing RBPs' binding data, we analyzed reproducible m6A regions from independent studies using this framework. The enrichment analysis identified known m6A-associated RBPs including YTH domain-containing proteins; it also identified RBM3 as a potential m6A-associated RBP for mouse. Furthermore, a significant correlation for the identified m6A-associated RBPs is observed at the protein expression level rather than the gene expression level. On the other hand, a Random Forest classification model was built for the reproducible m6A regions using RBPs' binding data. The RBP-based predictor demonstrated not only competitive performance when compared with sequence-based predictions but also reflected m6A's action of repelling against RBPs, which suggested that our framework can infer interaction between m6A and m6A-associated RBPs beyond sequence level when utilizing RBPs' binding data. In conclusion, we designed an integrative computational framework for the identification of known and potential m6A-associated RBPs. We hope the analysis will provide more insights on the studies of m6A and RNA modifications.
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Affiliation(s)
- Yiqian Zhang
- Department of Electrical Engineering and Bioscience, Faculty of Science and Engineering, Waseda University, Tokyo, Japan
| | - Michiaki Hamada
- Department of Electrical Engineering and Bioscience, Faculty of Science and Engineering, Waseda University, Tokyo, Japan.,AIST-Waseda University Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), Tokyo, Japan.,Institute for Medical-Oriented Structural Biology, Waseda University, Tokyo, Japan.,Graduate School of Medicine, Nippon Medical School, Tokyo, Japan
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45
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Zhong P, Peng J, Bian Z, Huang H. The Role of Cold Inducible RNA-Binding Protein in Cardiac Physiology and Diseases. Front Pharmacol 2021; 12:610792. [PMID: 33716740 PMCID: PMC7943917 DOI: 10.3389/fphar.2021.610792] [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: 09/28/2020] [Accepted: 01/11/2021] [Indexed: 12/23/2022] Open
Abstract
Cold-inducible RNA-binding protein (CIRP) is an intracellular stress-response protein that can respond to various stress conditions by changing its expression and regulating mRNA stability. As an RNA-binding protein, CIRP modulates gene expression at the post-transcriptional level, including those genes involved in DNA repair, cellular redox metabolism, circadian rhythms, telomere maintenance, and cell survival. CIRP is expressed in a large variety of tissues, including testis, brain, lung, kidney, liver, stomach, bone marrow, and heart. Recent studies have observed the important role of CIRP in cardiac physiology and diseases. CIRP regulates cardiac electrophysiological properties such as the repolarization of cardiomyocytes, the susceptibility of atrial fibrillation, and the function of the sinoatrial node in response to stress. CIRP has also been suggested to protect cardiomyocytes from apoptosis under various stress conditions, including heart failure, high glucose conditions, as well as during extended heart preservation under hypothermic conditions. This review summarizes the findings of CIRP investigations in cardiac physiology and diseases and the underlying molecular mechanism.
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Affiliation(s)
- Peng Zhong
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, China.,Cardiovascular Research Institute of Wuhan University, Wuhan, China.,Hubei Key Laboratory of Cardiology, Wuhan, China
| | - Jianye Peng
- Department of Cardiovascular Medicine, The second Affiliated Hospital of University of South China, Hengyang, China
| | - Zhouyan Bian
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, China.,Cardiovascular Research Institute of Wuhan University, Wuhan, China.,Hubei Key Laboratory of Cardiology, Wuhan, China
| | - He Huang
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, China.,Cardiovascular Research Institute of Wuhan University, Wuhan, China.,Hubei Key Laboratory of Cardiology, Wuhan, China
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46
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Indacochea A, Guerrero S, Ureña M, Araujo F, Coll O, LLeonart ME, Gebauer F. Cold-inducible RNA binding protein promotes breast cancer cell malignancy by regulating Cystatin C levels. RNA (NEW YORK, N.Y.) 2021; 27:190-201. [PMID: 33172965 PMCID: PMC7812870 DOI: 10.1261/rna.076422.120] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 11/05/2020] [Indexed: 06/11/2023]
Abstract
Cold-inducible RNA binding protein (CIRBP) is a stress-responsive protein that promotes cancer development and inflammation. Critical to most CIRBP functions is its capacity to bind and posttranscriptionally modulate mRNA. However, a transcriptome-wide analysis of CIRBP mRNA targets in cancer has not yet been performed. Here, we use an ex vivo breast cancer model to identify CIRBP targets and mechanisms. We find that CIRBP transcript levels correlate with breast cancer subtype and are an indicator of luminal A/B prognosis. Accordingly, overexpression of CIRBP in nontumoral MCF-10A cells promotes cell growth and clonogenicity, while depletion of CIRBP from luminal A MCF-7 cells has opposite effects. We use RNA immunoprecipitation followed by high-throughput sequencing (RIP-seq) to identify a set of 204 high confident CIRBP targets in MCF-7 cells. About 10% of these showed complementary changes after CIRBP manipulation in MCF-10A and MCF-7 cells, and were highly interconnected with known breast cancer genes. To test the potential of CIRBP-mediated regulation of these targets in breast cancer development, we focused on Cystatin C (CST3), one of the most highly interconnected genes, encoding a protein that displays tumor suppressive capacities. CST3 depletion restored the effects of CIRBP depletion in MCF-7 cells, indicating that CIRBP functions, at least in part, by down-regulating CST3 levels. Our data provide a resource of CIRBP targets in breast cancer, and identify CST3 as a novel downstream mediator of CIRBP function.
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Affiliation(s)
- Alberto Indacochea
- Gene Regulation, Stem Cells and Cancer Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain
- Biomedical Research in Cancer Stem Cells, Vall d'Hebron Research Institute (VHIR), 08035 Barcelona, Spain
| | - Santiago Guerrero
- Gene Regulation, Stem Cells and Cancer Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain
| | - Macarena Ureña
- Biomedical Research in Cancer Stem Cells, Vall d'Hebron Research Institute (VHIR), 08035 Barcelona, Spain
| | - Ferrán Araujo
- Biomedical Research in Cancer Stem Cells, Vall d'Hebron Research Institute (VHIR), 08035 Barcelona, Spain
| | - Olga Coll
- Gene Regulation, Stem Cells and Cancer Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain
| | - Matilde E LLeonart
- Biomedical Research in Cancer Stem Cells, Vall d'Hebron Research Institute (VHIR), 08035 Barcelona, Spain
- Spanish Biomedical Research Network Centre in Oncology, CIBERONC, Spain
| | - Fátima Gebauer
- Gene Regulation, Stem Cells and Cancer Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
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47
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The mRNA-Binding Protein RBM3 Regulates Activity Patterns and Local Synaptic Translation in Cultured Hippocampal Neurons. J Neurosci 2020; 41:1157-1173. [PMID: 33310754 PMCID: PMC7888222 DOI: 10.1523/jneurosci.0921-20.2020] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 10/14/2020] [Accepted: 11/12/2020] [Indexed: 12/18/2022] Open
Abstract
The activity and the metabolism of the brain change rhythmically during the day/night cycle. Such rhythmicity is also observed in cultured neurons from the suprachiasmatic nucleus, which is a critical center in rhythm maintenance. However, this issue has not been extensively studied in cultures from areas less involved in timekeeping, as the hippocampus. Using neurons cultured from the hippocampi of newborn rats (both male and female), we observed significant time-dependent changes in global activity, in synaptic vesicle dynamics, in synapse size, and in synaptic mRNA amounts. A transcriptome analysis of the neurons, performed at different times over 24 h, revealed significant changes only for RNA-binding motif 3 (Rbm3). RBM3 amounts changed, especially in synapses. RBM3 knockdown altered synaptic vesicle dynamics and changed the neuronal activity patterns. This procedure also altered local translation in synapses, albeit it left the global cellular translation unaffected. We conclude that hippocampal cultured neurons can exhibit strong changes in their activity levels over 24 h, in an RBM3-dependent fashion. SIGNIFICANCE STATEMENT This work is important in several ways. First, the discovery of relatively regular activity patterns in hippocampal cultures implies that future studies using this common model will need to take the time parameter into account, to avoid misinterpretation. Second, our work links these changes in activity strongly to RBM3, in a fashion that is independent of the canonical clock mechanisms, which is a very surprising observation. Third, we describe here probably the first molecule (RBM3) whose manipulation affects translation specifically in synapses, and not at the whole-cell level. This is a key finding for the rapidly growing field of local synaptic translation.
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48
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Tan YL, Tey SM, Ho HK. Moderate Hypothermia Effectively Alleviates Acetaminophen-Induced Liver Injury With Prolonged Action Beyond Cooling. Dose Response 2020; 18:1559325820970846. [PMID: 33239997 PMCID: PMC7675884 DOI: 10.1177/1559325820970846] [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: 04/30/2020] [Revised: 10/11/2020] [Accepted: 10/13/2020] [Indexed: 12/19/2022] Open
Abstract
Acetaminophen (APAP) overdose accounts for the highest incidence of acute liver failure, despite the availability of an antidote i.e. N-acetylcysteine. This calls for alternative strategies to manage APAP-induced liver injury (AILI). Therapeutic hypothermia has been explored in past studies for hepatoprotection, but these phenomenal reports lack clarification of its optimal window for application, and mechanistic effects in specific AILI. Hence, we conducted an in vitro study with transforming growth factor-α transgenic mouse hepatocytes cell line, TAMH, and human liver hepatocytes cell line, L-02, where cells were conditioned with deep (25°C) or moderate (32°C) hypothermia before, during or after APAP toxicity. Cell viability was evaluated as a hallmark of cytoprotection, along with cell death. Simultaneously, cold shock proteins (CSPs) and heat shock proteins expressions were monitored; key liver functions including drug-metabolizing ability and hepatic clearance were also investigated. Herein, we demonstrated significant hepatoprotection with 24-hour moderate hypothermic conditioning during AILI and this effect sustained for at least 24 hours of rewarming. Such liver preservation was associated with a CSP—RNA-binding motif protein 3 (RBM3) as its knockdown promptly abolished the cytoprotective effects of hypothermia. With mild and reversible liver perturbations, hypothermic therapy appears promising and its RBM3 involvement deserves future exploration.
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Affiliation(s)
- Yeong Lan Tan
- Department of Pharmacy, Faculty of Science, National University of Singapore, Singapore.,NUS Graduate School for Integrative Sciences & Engineering, Centre for Life Sciences, National University of Singapore, Singapore
| | - Siew Min Tey
- Department of Pharmacy, Faculty of Science, National University of Singapore, Singapore
| | - Han Kiat Ho
- Department of Pharmacy, Faculty of Science, National University of Singapore, Singapore.,NUS Graduate School for Integrative Sciences & Engineering, Centre for Life Sciences, National University of Singapore, Singapore
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49
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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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50
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Fischl H, McManus D, Oldenkamp R, Schermelleh L, Mellor J, Jagannath A, Furger A. Cold-induced chromatin compaction and nuclear retention of clock mRNAs resets the circadian rhythm. EMBO J 2020; 39:e105604. [PMID: 33034091 PMCID: PMC7667876 DOI: 10.15252/embj.2020105604] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 08/28/2020] [Accepted: 08/29/2020] [Indexed: 12/22/2022] Open
Abstract
Cooling patients to sub‐physiological temperatures is an integral part of modern medicine. We show that cold exposure induces temperature‐specific changes to the higher‐order chromatin and gene expression profiles of human cells. These changes are particularly dramatic at 18°C, a temperature synonymous with that experienced by patients undergoing controlled deep hypothermia during surgery. Cells exposed to 18°C exhibit largely nuclear‐restricted transcriptome changes. These include the nuclear accumulation of mRNAs encoding components of the negative limbs of the core circadian clock, most notably REV‐ERBα. This response is accompanied by compaction of higher‐order chromatin and hindrance of mRNPs from engaging nuclear pores. Rewarming reverses chromatin compaction and releases the transcripts into the cytoplasm, triggering a pulse of negative limb gene proteins that reset the circadian clock. We show that cold‐induced upregulation of REV‐ERBα is sufficient to trigger this reset. Our findings uncover principles of the cellular cold response that must be considered for current and future applications involving therapeutic deep hypothermia.
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Affiliation(s)
- Harry Fischl
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - David McManus
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Roel Oldenkamp
- Department of Biochemistry, University of Oxford, Oxford, UK
| | | | - Jane Mellor
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Aarti Jagannath
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - André Furger
- Department of Biochemistry, University of Oxford, Oxford, UK
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