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Gabriel CH, Del Olmo M, Rizki Widini A, Roshanbin R, Woyde J, Hamza E, Gutu NN, Zehtabian A, Ewers H, Granada A, Herzel H, Kramer A. Circadian period is compensated for repressor protein turnover rates in single cells. Proc Natl Acad Sci U S A 2024; 121:e2404738121. [PMID: 39141353 DOI: 10.1073/pnas.2404738121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 07/07/2024] [Indexed: 08/15/2024] Open
Abstract
Most mammalian cells have molecular circadian clocks that generate widespread rhythms in transcript and protein abundance. While circadian clocks are robust to fluctuations in the cellular environment, little is known about the mechanisms by which the circadian period compensates for fluctuating metabolic states. Here, we exploit the heterogeneity of single cells both in circadian period and a metabolic parameter-protein stability-to study their interdependence without the need for genetic manipulation. We generated cells expressing key circadian proteins (CRYPTOCHROME1/2 (CRY1/2) and PERIOD1/2 (PER1/2)) as endogenous fusions with fluorescent proteins and simultaneously monitored circadian rhythms and degradation in thousands of single cells. We found that the circadian period compensates for fluctuations in the turnover rates of circadian repressor proteins and uncovered possible mechanisms using a mathematical model. In addition, the stabilities of the repressor proteins are circadian phase dependent and correlate with the circadian period in a phase-dependent manner, in contrast to the prevailing model.
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Affiliation(s)
- Christian H Gabriel
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Division of Chronobiology, Berlin 10117, Germany
| | - Marta Del Olmo
- Institute for Theoretical Biology, Charité-Universitätsmedizin Berlin, Berlin 10115, Germany
| | - Arunya Rizki Widini
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Division of Chronobiology, Berlin 10117, Germany
| | - Rashin Roshanbin
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Division of Chronobiology, Berlin 10117, Germany
| | - Jonas Woyde
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Division of Chronobiology, Berlin 10117, Germany
| | - Ebrahim Hamza
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Division of Chronobiology, Berlin 10117, Germany
| | - Nica-Nicoleta Gutu
- Charité Comprehensive Cancer Center, Charité-Universitätsmedizin Berlin, Berlin 10117, Germany
| | - Amin Zehtabian
- Department of Biology, Chemistry and Pharmacy, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Berlin 14195, Germany
| | - Helge Ewers
- Department of Biology, Chemistry and Pharmacy, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Berlin 14195, Germany
| | - Adrian Granada
- Charité Comprehensive Cancer Center, Charité-Universitätsmedizin Berlin, Berlin 10117, Germany
| | - Hanspeter Herzel
- Institute for Theoretical Biology, Charité-Universitätsmedizin Berlin, Berlin 10115, Germany
| | - Achim Kramer
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Division of Chronobiology, Berlin 10117, Germany
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2
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Ding L, Weger BD, Liu J, Zhou L, Lim Y, Wang D, Xie Z, Liu J, Ren J, Zheng J, Zhang Q, Yu M, Weger M, Morrison M, Xiao X, Gachon F. Maternal high fat diet induces circadian clock-independent endocrine alterations impacting the metabolism of the offspring. iScience 2024; 27:110343. [PMID: 39045103 PMCID: PMC11263959 DOI: 10.1016/j.isci.2024.110343] [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: 11/24/2023] [Revised: 05/02/2024] [Accepted: 06/19/2024] [Indexed: 07/25/2024] Open
Abstract
Maternal obesity has long-term effects on offspring metabolic health. Among the potential mechanisms, prior research has indicated potential disruptions in circadian rhythms and gut microbiota in the offspring. To challenge this hypothesis, we implemented a maternal high fat diet regimen before and during pregnancy, followed by a standard diet after birth. Our findings confirm that maternal obesity impacts offspring birth weight and glucose and lipid metabolisms. However, we found minimal impact on circadian rhythms and microbiota that are predominantly driven by the feeding/fasting cycle. Notably, maternal obesity altered rhythmic liver gene expression, affecting mitochondrial function and inflammatory response without disrupting the hepatic circadian clock. These changes could be explained by a masculinization of liver gene expression similar to the changes observed in polycystic ovarian syndrome. Intriguingly, such alterations seem to provide the first-generation offspring with a degree of protection against obesity when exposed to a high fat diet.
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Affiliation(s)
- Lu Ding
- Key Laboratory of Endocrinology of National Health Commission, Diabetes Research Center of Chinese Academy of Medical Sciences, Department of Endocrinology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Benjamin D. Weger
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Jieying Liu
- Key Laboratory of Endocrinology of National Health Commission, Diabetes Research Center of Chinese Academy of Medical Sciences, Department of Endocrinology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
- Department of Medical Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China
| | - Liyuan Zhou
- Department of Endocrinology, Beijing Chaoyang Hospital, Capital Medical University, Beijing 100022, China
| | - Yenkai Lim
- Frazer Institute, Faculty of Medicine, The University of Queensland, Woolloongabba, QLD 4102, Australia
| | - Dongmei Wang
- Key Laboratory of Endocrinology of National Health Commission, Diabetes Research Center of Chinese Academy of Medical Sciences, Department of Endocrinology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Ziyan Xie
- Key Laboratory of Endocrinology of National Health Commission, Diabetes Research Center of Chinese Academy of Medical Sciences, Department of Endocrinology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Jing Liu
- Key Laboratory of Endocrinology of National Health Commission, Diabetes Research Center of Chinese Academy of Medical Sciences, Department of Endocrinology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Jing Ren
- Key Laboratory of Endocrinology of National Health Commission, Diabetes Research Center of Chinese Academy of Medical Sciences, Department of Endocrinology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Jia Zheng
- Department of Endocrinology, Peking University First Hospital, Beijing 100034, China
| | - Qian Zhang
- Key Laboratory of Endocrinology of National Health Commission, Diabetes Research Center of Chinese Academy of Medical Sciences, Department of Endocrinology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Miao Yu
- Key Laboratory of Endocrinology of National Health Commission, Diabetes Research Center of Chinese Academy of Medical Sciences, Department of Endocrinology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Meltem Weger
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Mark Morrison
- Frazer Institute, Faculty of Medicine, The University of Queensland, Woolloongabba, QLD 4102, Australia
- Australian Infectious Diseases Research Centre, St. Lucia, QLD 4072, Australia
| | - Xinhua Xiao
- Key Laboratory of Endocrinology of National Health Commission, Diabetes Research Center of Chinese Academy of Medical Sciences, Department of Endocrinology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Frédéric Gachon
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia
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3
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Buijink MR, van Weeghel M, Harms A, Murli DS, Meijer JH, Hankemeier T, Michel S, Kervezee L. Loss of temporal coherence in the circadian metabolome across multiple tissues during ageing in mice. Eur J Neurosci 2024; 60:3843-3857. [PMID: 38802069 DOI: 10.1111/ejn.16428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 05/07/2024] [Accepted: 05/14/2024] [Indexed: 05/29/2024]
Abstract
Circadian clock function declines with ageing, which can aggravate ageing-related diseases such as type 2 diabetes and neurodegenerative disorders. Understanding age-related changes in the circadian system at a systemic level can contribute to the development of strategies to promote healthy ageing. The goal of this study was to investigate the impact of ageing on 24-h rhythms in amine metabolites across four tissues in young (2 months of age) and old (22-25 months of age) mice using a targeted metabolomics approach. Liver, plasma, the suprachiasmatic nucleus (SCN; the location of the central circadian clock in the hypothalamus) and the paraventricular nucleus (PVN; a downstream target of the SCN) were collected from young and old mice every 4 h during a 24-h period (n = 6-7 mice per group). Differential rhythmicity analysis revealed that ageing impacts 24-h rhythms in the amine metabolome in a tissue-specific manner. Most profound changes were observed in the liver, in which rhythmicity was lost in 60% of the metabolites in aged mice. Furthermore, we found strong correlations in metabolite levels between the liver and plasma and between the SCN and the PVN in young mice. These correlations were almost completely abolished in old mice. These results indicate that ageing is accompanied by a severe loss of the circadian coordination between tissues and by disturbed rhythmicity of metabolic processes. The tissue-specific impact of ageing may help to differentiate mechanisms of ageing-related disorders in the brain versus peripheral tissues and thereby contribute to the development of potential therapies for these disorders.
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Affiliation(s)
- M Renate Buijink
- Laboratory for Neurophysiology, Department of Cellular and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - Michel van Weeghel
- Laboratory for Neurophysiology, Department of Cellular and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
- Department of Clinical Chemistry and Pediatrics, Laboratory Genetic Metabolic Diseases, Emma Children's Hospital, Amsterdam UMC location University of Amsterdam, Amsterdam, The Netherlands
- Core Facility Metabolomics, Amsterdam UMC location University of Amsterdam, Amsterdam, The Netherlands
| | - Amy Harms
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands
| | - Devika S Murli
- Laboratory for Neurophysiology, Department of Cellular and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - Johanna H Meijer
- Laboratory for Neurophysiology, Department of Cellular and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - Thomas Hankemeier
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands
| | - Stephan Michel
- Laboratory for Neurophysiology, Department of Cellular and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - Laura Kervezee
- Laboratory for Neurophysiology, Department of Cellular and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
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Seinkmane E, Edmondson A, Peak-Chew SY, Zeng A, Rzechorzek NM, James NR, West J, Munns J, Wong DC, Beale AD, O'Neill JS. Circadian regulation of macromolecular complex turnover and proteome renewal. EMBO J 2024; 43:2813-2833. [PMID: 38778155 PMCID: PMC11217436 DOI: 10.1038/s44318-024-00121-5] [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: 11/03/2023] [Revised: 04/04/2024] [Accepted: 04/15/2024] [Indexed: 05/25/2024] Open
Abstract
Although costly to maintain, protein homeostasis is indispensable for normal cellular function and long-term health. In mammalian cells and tissues, daily variation in global protein synthesis has been observed, but its utility and consequences for proteome integrity are not fully understood. Using several different pulse-labelling strategies, here we gain direct insight into the relationship between protein synthesis and abundance proteome-wide. We show that protein degradation varies in-phase with protein synthesis, facilitating rhythms in turnover rather than abundance. This results in daily consolidation of proteome renewal whilst minimising changes in composition. Coupled rhythms in synthesis and turnover are especially salient to the assembly of macromolecular protein complexes, particularly the ribosome, the most abundant species of complex in the cell. Daily turnover and proteasomal degradation rhythms render cells and mice more sensitive to proteotoxic stress at specific times of day, potentially contributing to daily rhythms in the efficacy of proteasomal inhibitors against cancer. Our findings suggest that circadian rhythms function to minimise the bioenergetic cost of protein homeostasis through temporal consolidation of protein turnover.
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Affiliation(s)
- Estere Seinkmane
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Anna Edmondson
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Sew Y Peak-Chew
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Aiwei Zeng
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Nina M Rzechorzek
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Nathan R James
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - James West
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Jack Munns
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - David Cs Wong
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Andrew D Beale
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
| | - John S O'Neill
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
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5
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Nadimpalli HP, Katsioudi G, Arpa ES, Chikhaoui L, Arpat AB, Liechti A, Palais G, Tessmer C, Hofmann I, Galy B, Gatfield D. Diurnal control of iron responsive element containing mRNAs through iron regulatory proteins IRP1 and IRP2 is mediated by feeding rhythms. Genome Biol 2024; 25:128. [PMID: 38773499 PMCID: PMC11106963 DOI: 10.1186/s13059-024-03270-2] [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: 01/12/2024] [Accepted: 05/09/2024] [Indexed: 05/23/2024] Open
Abstract
BACKGROUND Cellular iron homeostasis is regulated by iron regulatory proteins (IRP1 and IRP2) that sense iron levels (and other metabolic cues) and modulate mRNA translation or stability via interaction with iron regulatory elements (IREs). IRP2 is viewed as the primary regulator in the liver, yet our previous datasets showing diurnal rhythms for certain IRE-containing mRNAs suggest a nuanced temporal control mechanism. The purpose of this study is to gain insights into the daily regulatory dynamics across IRE-bearing mRNAs, specific IRP involvement, and underlying systemic and cellular rhythmicity cues in mouse liver. RESULTS We uncover high-amplitude diurnal oscillations in the regulation of key IRE-containing transcripts in the liver, compatible with maximal IRP activity at the onset of the dark phase. Although IRP2 protein levels also exhibit some diurnal variations and peak at the light-dark transition, ribosome profiling in IRP2-deficient mice reveals that maximal repression of target mRNAs at this timepoint still occurs. We further find that diurnal regulation of IRE-containing mRNAs can continue in the absence of a functional circadian clock as long as feeding is rhythmic. CONCLUSIONS Our findings suggest temporally controlled redundancy in IRP activities, with IRP2 mediating regulation of IRE-containing transcripts in the light phase and redundancy, conceivably with IRP1, at dark onset. Moreover, we highlight the significance of feeding-associated signals in driving rhythmicity. Our work highlights the dynamic nature and regulatory complexity in a metabolic pathway that had previously been considered well-understood.
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Affiliation(s)
| | - Georgia Katsioudi
- Center for Integrative Genomics, University of Lausanne, Lausanne, 1015, Switzerland
| | - Enes Salih Arpa
- Center for Integrative Genomics, University of Lausanne, Lausanne, 1015, Switzerland
| | - Lies Chikhaoui
- Center for Integrative Genomics, University of Lausanne, Lausanne, 1015, Switzerland
| | - Alaaddin Bulak Arpat
- Center for Integrative Genomics, University of Lausanne, Lausanne, 1015, Switzerland
| | - Angelica Liechti
- Center for Integrative Genomics, University of Lausanne, Lausanne, 1015, Switzerland
| | - Gaël Palais
- German Cancer Research Center (DKFZ), Division of Virus-Associated Carcinogenesis, Im Neuenheimer Feld 280, Heidelberg, 69120, Germany
| | - Claudia Tessmer
- German Cancer Research Center (DKFZ), Core Facility Antibodies, Im Neuenheimer Feld 280, Heidelberg, 69120, Germany
| | - Ilse Hofmann
- German Cancer Research Center (DKFZ), Core Facility Antibodies, Im Neuenheimer Feld 280, Heidelberg, 69120, Germany
| | - Bruno Galy
- German Cancer Research Center (DKFZ), Division of Virus-Associated Carcinogenesis, Im Neuenheimer Feld 280, Heidelberg, 69120, Germany
| | - David Gatfield
- Center for Integrative Genomics, University of Lausanne, Lausanne, 1015, Switzerland.
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Nie XY, Menet JS. Circadian regulation of stereotypic chromatin conformations at enhancers. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.24.590818. [PMID: 38712031 PMCID: PMC11071494 DOI: 10.1101/2024.04.24.590818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Cooperation between the circadian transcription factor (TF) CLOCK:BMAL1 and other TFs at cis-regulatory elements (CREs) is critical to daily rhythms of transcription. Yet, the modalities of this cooperation are unclear. Here, we analyzed the co-binding of multiple TFs on single DNA molecules in mouse liver using single molecule footprinting (SMF). We found that SMF reads clustered in stereotypic chromatin states that reflect distinguishable organization of TFs and nucleosomes, and that were remarkably conserved between all samples. DNA protection at CLOCK:BMAL1 binding motif (E-box) varied between CREs, from E-boxes being solely bound by CLOCK:BMAL1 to situations where other TFs competed with CLOCK:BMAL1 for E-box binding. SMF also uncovered CLOCK:BMAL1 cooperative binding at E-boxes separated by 250 bp, which structurally altered the CLOCK:BMAL1-DNA interface. Importantly, we discovered multiple nucleosomes with E-boxes at entry/exit sites that were removed upon CLOCK:BMAL1 DNA binding, thereby promoting the formation of open chromatin states that facilitate DNA binding of other TFs and that were associated with rhythmic transcription. These results demonstrate the utility of SMF for studying how CLOCK:BMAL1 and other TFs regulate stereotypical chromatin states at CREs to promote transcription.
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Affiliation(s)
- Xinyu Y. Nie
- Department of Biology, Center for Biological Clock Research, Texas A&M University, College Station, TX
| | - Jerome S. Menet
- Department of Biology, Center for Biological Clock Research, Texas A&M University, College Station, TX
- Interdisciplinary Program of Genetics, Texas A&M University, College Station, TX
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7
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Unruh BA, Weidemann DE, Miao L, Kojima S. Coordination of rhythmic RNA synthesis and degradation orchestrates 24- and 12-h RNA expression patterns in mouse fibroblasts. Proc Natl Acad Sci U S A 2024; 121:e2314690121. [PMID: 38315868 PMCID: PMC10873638 DOI: 10.1073/pnas.2314690121] [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: 08/24/2023] [Accepted: 01/02/2024] [Indexed: 02/07/2024] Open
Abstract
Circadian RNA expression is essential to ultimately regulate a plethora of downstream rhythmic biochemical, physiological, and behavioral processes. Both transcriptional and posttranscriptional mechanisms are considered important to drive rhythmic RNA expression; however, the extent to which each regulatory process contributes to the rhythmic RNA expression remains controversial. To systematically address this, we monitored RNA dynamics using metabolic RNA labeling technology during a circadian cycle in mouse fibroblasts. We find that rhythmic RNA synthesis is the primary contributor of 24-h RNA rhythms, while rhythmic degradation is more important for 12-h RNA rhythms. These rhythms were predominantly regulated by Bmal1 and/or the core clock mechanism, and the interplay between rhythmic synthesis and degradation has a significant impact in shaping rhythmic RNA expression patterns. Interestingly, core clock RNAs are regulated by multiple rhythmic processes and have the highest amplitude of synthesis and degradation, presumably critical to sustain robust rhythmicity of cell-autonomous circadian rhythms. Our study yields invaluable insights into the temporal dynamics of both 24- and 12-h RNA rhythms in mouse fibroblasts.
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Affiliation(s)
- Benjamin A. Unruh
- Department of Biological Sciences, Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA24061
| | - Douglas E. Weidemann
- Department of Biological Sciences, Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA24061
| | - Lin Miao
- Department of Biological Sciences, Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA24061
| | - Shihoko Kojima
- Department of Biological Sciences, Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA24061
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8
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Berthier A, Gheeraert C, Johanns M, Vinod M, Staels B, Eeckhoute J, Lefebvre P. The Molecular Circadian Clock Is a Target of Anti-cancer Translation Inhibitors. J Biol Rhythms 2024; 39:20-34. [PMID: 37872767 DOI: 10.1177/07487304231202561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Circadian-paced biological processes are key to physiology and required for metabolic, immunologic, and cardiovascular homeostasis. Core circadian clock components are transcription factors whose half-life is precisely regulated, thereby controlling the intrinsic cellular circadian clock. Genetic disruption of molecular clock components generally leads to marked pathological events phenotypically affecting behavior and multiple aspects of physiology. Using a transcriptional signature similarity approach, we identified anti-cancer protein synthesis inhibitors as potent modulators of the cardiomyocyte molecular clock. Eukaryotic protein translation inhibitors, ranging from translation initiation (rocaglates, 4-EGI1, etc.) to ribosomal elongation inhibitors (homoharringtonine, puromycin, etc.), were found to potently ablate protein abundance of REV-ERBα, a repressive nuclear receptor and component of the molecular clock. These inhibitory effects were observed both in vitro and in vivo and could be extended to PER2, another component of the molecular clock. Taken together, our observations suggest that the activity spectrum of protein synthesis inhibitors, whose clinical use is contemplated not only in cancers but also in viral infections, must be extended to circadian rhythm disruption, with potential beneficial or iatrogenic effects upon acute or prolonged administration.
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Affiliation(s)
- Alexandre Berthier
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, Lille, France
| | - Céline Gheeraert
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, Lille, France
| | - Manuel Johanns
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, Lille, France
| | - Manjula Vinod
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, Lille, France
| | - Bart Staels
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, Lille, France
| | - Jérôme Eeckhoute
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, Lille, France
| | - Philippe Lefebvre
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, Lille, France
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9
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Liu X, Cai YD, Chiu JC. Regulation of protein O-GlcNAcylation by circadian, metabolic, and cellular signals. J Biol Chem 2024; 300:105616. [PMID: 38159854 PMCID: PMC10810748 DOI: 10.1016/j.jbc.2023.105616] [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: 07/24/2023] [Revised: 12/12/2023] [Accepted: 12/13/2023] [Indexed: 01/03/2024] Open
Abstract
O-linked β-N-acetylglucosamine (O-GlcNAcylation) is a dynamic post-translational modification that regulates thousands of proteins and almost all cellular processes. Aberrant O-GlcNAcylation has been associated with numerous diseases, including cancer, neurodegenerative diseases, cardiovascular diseases, and type 2 diabetes. O-GlcNAcylation is highly nutrient-sensitive since it is dependent on UDP-GlcNAc, the end product of the hexosamine biosynthetic pathway (HBP). We previously observed daily rhythmicity of protein O-GlcNAcylation in a Drosophila model that is sensitive to the timing of food consumption. We showed that the circadian clock is pivotal in regulating daily O-GlcNAcylation rhythms given its control of the feeding-fasting cycle and hence nutrient availability. Interestingly, we reported that the circadian clock also modulates daily O-GlcNAcylation rhythm by regulating molecular mechanisms beyond the regulation of food consumption time. A large body of work now indicates that O-GlcNAcylation is likely a generalized cellular status effector as it responds to various cellular signals and conditions, such as ER stress, apoptosis, and infection. In this review, we summarize the metabolic regulation of protein O-GlcNAcylation through nutrient availability, HBP enzymes, and O-GlcNAc processing enzymes. We discuss the emerging roles of circadian clocks in regulating daily O-GlcNAcylation rhythm. Finally, we provide an overview of other cellular signals or conditions that impact O-GlcNAcylation. Many of these cellular pathways are themselves regulated by the clock and/or metabolism. Our review highlights the importance of maintaining optimal O-GlcNAc rhythm by restricting eating activity to the active period under physiological conditions and provides insights into potential therapeutic targets of O-GlcNAc homeostasis under pathological conditions.
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Affiliation(s)
- Xianhui Liu
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California, Davis, California, USA
| | - Yao D Cai
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California, Davis, California, USA
| | - Joanna C Chiu
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California, Davis, California, USA.
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10
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Guo Y, Livelo C, Melkani G. Time-restricted feeding regulates lipid metabolism under metabolic challenges. Bioessays 2023; 45:e2300157. [PMID: 37850554 PMCID: PMC10841423 DOI: 10.1002/bies.202300157] [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: 08/22/2023] [Revised: 10/02/2023] [Accepted: 10/04/2023] [Indexed: 10/19/2023]
Abstract
Dysregulation of lipid metabolism is a commonly observed feature associated with metabolic syndrome and leads to the development of negative health outcomes such as obesity, diabetes mellitus, non-alcoholic fatty liver disease, or atherosclerosis. Time-restricted feeding/eating (TRF/TRE), an emerging dietary intervention, has been shown to promote pleiotropic health benefits including the alteration of diurnal expression of genes associated with lipid metabolism, as well as levels of lipid species. Although TRF likely induces a response in multiple organs leading to the modulation of lipid metabolism, a majority of the studies related to TRF effects on lipids have focused only on individual tissues, and furthermore there is a lack of insight into potential underlying mechanisms. In this review, we summarize the current insights regarding TRF effects on lipid metabolism and the potential mechanisms in adipose tissue, liver, skeletal muscle, and heart, and conclude by outlining possible avenues for future exploration.
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Affiliation(s)
- Yiming Guo
- Department of Pathology, Division of Molecular and Cellular Pathology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Christopher Livelo
- Department of Pathology, Division of Molecular and Cellular Pathology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Girish Melkani
- Department of Pathology, Division of Molecular and Cellular Pathology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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Bolshette N, Ibrahim H, Reinke H, Asher G. Circadian regulation of liver function: from molecular mechanisms to disease pathophysiology. Nat Rev Gastroenterol Hepatol 2023; 20:695-707. [PMID: 37291279 DOI: 10.1038/s41575-023-00792-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/27/2023] [Indexed: 06/10/2023]
Abstract
A wide variety of liver functions are regulated daily by the liver circadian clock and via systemic circadian control by other organs and cells within the gastrointestinal tract as well as the microbiome and immune cells. Disruption of the circadian system, as occurs during jetlag, shift work or an unhealthy lifestyle, is implicated in several liver-related pathologies, ranging from metabolic diseases such as obesity, type 2 diabetes mellitus and nonalcoholic fatty liver disease to liver malignancies such as hepatocellular carcinoma. In this Review, we cover the molecular, cellular and organismal aspects of various liver pathologies from a circadian viewpoint, and in particular how circadian dysregulation has a role in the development and progression of these diseases. Finally, we discuss therapeutic and lifestyle interventions that carry health benefits through support of a functional circadian clock that acts in synchrony with the environment.
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Affiliation(s)
- Nityanand Bolshette
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Hussam Ibrahim
- University of Düsseldorf, Medical Faculty, Institute of Clinical Chemistry and Laboratory Diagnostics, Düsseldorf, Germany
| | - Hans Reinke
- University of Düsseldorf, Medical Faculty, Institute of Clinical Chemistry and Laboratory Diagnostics, Düsseldorf, Germany.
| | - Gad Asher
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel.
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12
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Smith JG, Molendijk J, Blazev R, Chen WH, Zhang Q, Litwin C, Zinna VM, Welz PS, Benitah SA, Greco CM, Sassone-Corsi P, Muñoz-Cánoves P, Parker BL, Koronowski KB. Impact of Bmal1 Rescue and Time-Restricted Feeding on Liver and Muscle Proteomes During the Active Phase in Mice. Mol Cell Proteomics 2023; 22:100655. [PMID: 37793502 PMCID: PMC10651687 DOI: 10.1016/j.mcpro.2023.100655] [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: 06/15/2023] [Revised: 09/01/2023] [Accepted: 09/28/2023] [Indexed: 10/06/2023] Open
Abstract
Molecular clocks and daily feeding cycles support metabolism in peripheral tissues. Although the roles of local clocks and feeding are well defined at the transcriptional level, their impact on governing protein abundance in peripheral tissues is unclear. Here, we determine the relative contributions of local molecular clocks and daily feeding cycles on liver and muscle proteomes during the active phase in mice. LC-MS/MS was performed on liver and gastrocnemius muscle harvested 4 h into the dark phase from WT, Bmal1 KO, and dual liver- and muscle-Bmal1-rescued mice under either ad libitum feeding or time-restricted feeding during the dark phase. Feeding-fasting cycles had only minimal effects on levels of liver proteins and few, if any, on the muscle proteome. In contrast, Bmal1 KO altered the abundance of 674 proteins in liver and 80 proteins in muscle. Local rescue of liver and muscle Bmal1 restored ∼50% of proteins in liver and ∼25% in muscle. These included proteins involved in fatty acid oxidation in liver and carbohydrate metabolism in muscle. For liver, proteins involved in de novo lipogenesis were largely dependent on Bmal1 function in other tissues (i.e., the wider clock system). Proteins regulated by BMAL1 in liver and muscle were enriched for secreted proteins. We found that the abundance of fibroblast growth factor 1, a liver secreted protein, requires BMAL1 and that autocrine fibroblast growth factor 1 signaling modulates mitochondrial respiration in hepatocytes. In liver and muscle, BMAL1 is a more potent regulator of dark phase proteomes than daily feeding cycles, highlighting the need to assess protein levels in addition to mRNA when investigating clock mechanisms. The proteome is more extensively regulated by BMAL1 in liver than in muscle, and many metabolic pathways in peripheral tissues are reliant on the function of the clock system as a whole.
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Affiliation(s)
- Jacob G Smith
- Department of Medical and Life Sciences (MELIS), Pompeu Fabra University (UPF), Parc de Recerca Biomèdica de Barcelona (PRBB), Barcelona, Spain
| | - Jeffrey Molendijk
- Department of Anatomy and Physiology, Centre for Muscle Research, The University of Melbourne, Melbourne, Victoria, Australia
| | - Ronnie Blazev
- Department of Anatomy and Physiology, Centre for Muscle Research, The University of Melbourne, Melbourne, Victoria, Australia
| | - Wan Hsi Chen
- Department of Radiation Oncology, Mays Cancer Center at UT Health San Antonio MD Anderson, Joe R. and Teresa Lozano Long School of Medicine, San Antonio, Texas, USA; Barshop Institute for Longevity and Aging Studies at UT Health San Antonio, San Antonio, Texas, USA
| | - Qing Zhang
- Department of Biochemistry & Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, USA
| | - Christopher Litwin
- Department of Biochemistry & Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, USA
| | - Valentina M Zinna
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Patrick-Simon Welz
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; Hospital del Mar Research Institute Barcelona, Cancer Research Program, Barcelona Biomedical Research Park (PRBB), Barcelona, Spain
| | - Salvador Aznar Benitah
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Carolina M Greco
- Department of Biomedical Sciences, Humanitas University, Milan, Italy; IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy
| | - Paolo Sassone-Corsi
- Department of Biological Chemistry, Center for Epigenetics and Metabolism, U1233 INSERM, University of California, Irvine, California, USA
| | - Pura Muñoz-Cánoves
- Department of Medical and Life Sciences (MELIS), Pompeu Fabra University (UPF), Parc de Recerca Biomèdica de Barcelona (PRBB), Barcelona, Spain; Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain; Altos Labs, Inc, San Diego Institute of Science, San Diego, California, USA
| | - Benjamin L Parker
- Department of Anatomy and Physiology, Centre for Muscle Research, The University of Melbourne, Melbourne, Victoria, Australia.
| | - Kevin B Koronowski
- Barshop Institute for Longevity and Aging Studies at UT Health San Antonio, San Antonio, Texas, USA; Department of Biochemistry & Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, USA.
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13
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Millius A, Yamada RG, Fujishima H, Maeda K, Standley DM, Sumiyama K, Perrin D, Ueda HR. Circadian ribosome profiling reveals a role for the Period2 upstream open reading frame in sleep. Proc Natl Acad Sci U S A 2023; 120:e2214636120. [PMID: 37769257 PMCID: PMC10556633 DOI: 10.1073/pnas.2214636120] [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: 08/30/2022] [Accepted: 08/29/2023] [Indexed: 09/30/2023] Open
Abstract
Many mammalian proteins have circadian cycles of production and degradation, and many of these rhythms are altered posttranscriptionally. We used ribosome profiling to examine posttranscriptional control of circadian rhythms by quantifying RNA translation in the liver over a 24-h period from circadian-entrained mice transferred to constant darkness conditions and by comparing ribosome binding levels to protein levels for 16 circadian proteins. We observed large differences in ribosome binding levels compared to protein levels, and we observed delays between peak ribosome binding and peak protein abundance. We found extensive binding of ribosomes to upstream open reading frames (uORFs) in circadian mRNAs, including the core clock gene Period2 (Per2). An increase in the number of uORFs in the 5'UTR was associated with a decrease in ribosome binding in the main coding sequence and a reduction in expression of synthetic reporter constructs. Mutation of the Per2 uORF increased luciferase and fluorescence reporter expression in 3T3 cells and increased luciferase expression in PER2:LUC MEF cells. Mutation of the Per2 uORF in mice increased Per2 mRNA expression, enhanced ribosome binding on Per2, and reduced total sleep time compared to that in wild-type mice. These results suggest that uORFs affect mRNA posttranscriptionally, which can impact physiological rhythms and sleep.
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Affiliation(s)
- Arthur Millius
- Laboratory for Synthetic Biology, RIKEN Quantitative Biology Center, Suita, Osaka565-0871, Japan
- Laboratory for Host Defense, Immunology Frontier Research Center, Suita, Osaka565-0871, Japan
- Laboratory for Systems Immunology, Immunology Frontier Research Center, Suita, Osaka565-0871, Japan
| | - Rikuhiro G. Yamada
- Laboratory for Synthetic Biology, RIKEN Quantitative Biology Center, Suita, Osaka565-0871, Japan
| | - Hiroshi Fujishima
- Laboratory for Synthetic Biology, RIKEN Quantitative Biology Center, Suita, Osaka565-0871, Japan
| | - Kazuhiko Maeda
- Laboratory for Host Defense, Immunology Frontier Research Center, Suita, Osaka565-0871, Japan
| | - Daron M. Standley
- Laboratory for Systems Immunology, Immunology Frontier Research Center, Suita, Osaka565-0871, Japan
| | - Kenta Sumiyama
- Laboratory of Animal Genetics and Breeding, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya464-8601, Japan
| | - Dimitri Perrin
- School of Computer Science, Queensland University of Technology, BrisbaneQLD 4000, Australia
- Centre for Data Science, Queensland University of Technology, BrisbaneQLD 4000, Australia
| | - Hiroki R. Ueda
- Laboratory for Synthetic Biology, RIKEN Quantitative Biology Center, Suita, Osaka565-0871, Japan
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Tokyo113-0033, Japan
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14
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Xu W, Li X. Regulation of Pol II Pausing during Daily Gene Transcription in Mouse Liver. BIOLOGY 2023; 12:1107. [PMID: 37626993 PMCID: PMC10452108 DOI: 10.3390/biology12081107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 07/20/2023] [Accepted: 08/03/2023] [Indexed: 08/27/2023]
Abstract
Cell autonomous circadian oscillation is present in central and various peripheral tissues. The intrinsic tissue clock and various extrinsic cues drive gene expression rhythms. Transcription regulation is thought to be the main driving force for gene rhythms. However, how transcription rhythms arise remains to be fully characterized due to the fact that transcription is regulated at multiple steps. In particular, Pol II recruitment, pause release, and premature transcription termination are critical regulatory steps that determine the status of Pol II pausing and transcription output near the transcription start site (TSS) of the promoter. Recently, we showed that Pol II pausing exhibits genome-wide changes during daily transcription in mouse liver. In this article, we review historical as well as recent findings on the regulation of transcription rhythms by the circadian clock and other transcription factors, and the potential limitations of those results in explaining rhythmic transcription at the TSS. We then discuss our results on the genome-wide characteristics of daily changes in Pol II pausing, the possible regulatory mechanisms involved, and their relevance to future research on circadian transcription regulation.
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Affiliation(s)
| | - Xiaodong Li
- College of Life Sciences, Wuhan University, Wuhan 430072, China;
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15
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Unruh BA, Weidemann DE, Kojima S. Coordination of rhythmic RNA synthesis and degradation orchestrates 24-hour and 12-hour RNA expression patterns in mouse fibroblasts. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.26.550672. [PMID: 37546997 PMCID: PMC10402069 DOI: 10.1101/2023.07.26.550672] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Circadian RNA expression is essential to ultimately regulate a plethora of downstream rhythmic biochemical, physiological, and behavioral processes. Both transcriptional and post-transcriptional mechanisms are considered important to drive rhythmic RNA expression, however, the extent to which each regulatory process contributes to the rhythmic RNA expression remains controversial. To systematically address this, we monitored RNA dynamics using metabolic RNA labeling technology during a circadian cycle in mouse fibroblasts. We find that rhythmic RNA synthesis is the primary contributor of 24 hr RNA rhythms, while rhythmic degradation is more important for 12 hr RNA rhythms. These rhythms were predominantly regulated by Bmal1 and/or the core clock mechanism, and interplay between rhythmic synthesis and degradation has a significant impact in shaping rhythmic RNA expression patterns. Interestingly, core clock RNAs are regulated by multiple rhythmic processes and have the highest amplitude of synthesis and degradation, presumably critical to sustain robust rhythmicity of cell-autonomous circadian rhythms. Our study yields invaluable insights into the temporal dynamics of both 24 hr and 12 hr RNA rhythms in mouse fibroblasts.
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Affiliation(s)
- Benjamin A Unruh
- Department of Biological Sciences, Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA USA
| | - Douglas E Weidemann
- Department of Biological Sciences, Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA USA
| | - Shihoko Kojima
- Department of Biological Sciences, Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA USA
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16
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Weger M, Weger BD, Gachon F. Understanding circadian dynamics: current progress and future directions for chronobiology in drug discovery. Expert Opin Drug Discov 2023. [PMID: 37300813 DOI: 10.1080/17460441.2023.2224554] [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: 04/14/2023] [Accepted: 06/08/2023] [Indexed: 06/12/2023]
Abstract
INTRODUCTION Most mammalian physiology is orchestrated by the circadian clock, including drug transport and metabolism. As a result, efficacy and toxicity of many drugs are influenced by the timing of their administration, which has led to the establishment of the field of chronopharmacology. AREAS COVERED In this review, the authors provide an overview of the current knowledge about the time-of-day dependent aspects of drug metabolism and the importance of chronopharmacological strategies for drug development. They also discuss the factors influencing rhythmic drug pharmacokinetic including sex, metabolic diseases, feeding rhythms, and microbiota, that are often overlooked in the context of chronopharmacology. This article summarizes the involved molecular mechanisms and functions and explains why these parameters should be considered in the process of drug discovery. EXPERT OPINION Although chronomodulated treatments have shown promising results, particularly for cancer, the practice is still underdeveloped due to the associated high cost and time investments. However, implementing this strategy at the preclinical stage could offer a new opportunity to translate preclinical discoveries into successful clinical treatments.
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Affiliation(s)
- Meltem Weger
- Institute for Molecular Bioscience, The University of Queensland, QLD, Australia
| | - Benjamin D Weger
- Institute for Molecular Bioscience, The University of Queensland, QLD, Australia
| | - Frédéric Gachon
- Institute for Molecular Bioscience, The University of Queensland, QLD, Australia
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17
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Yanaizu M, Adachi H, Araki M, Kontani K, Kino Y. Translational regulation and protein-coding capacity of the 5' untranslated region of human TREM2. Commun Biol 2023; 6:616. [PMID: 37291187 PMCID: PMC10250343 DOI: 10.1038/s42003-023-04998-6] [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: 09/08/2022] [Accepted: 05/30/2023] [Indexed: 06/10/2023] Open
Abstract
TREM2 is a transmembrane receptor expressed in microglia and macrophages. Elevated TREM2 levels in these cells are associated with age-related pathological conditions, including Alzheimer's disease. However, the regulatory mechanism underlying the protein expression of TREM2 remains unclear. In this study, we uncover the role of the 5' untranslated region (5'-UTR) of human TREM2 in translation. An upstream start codon (uAUG) in the 5'-UTR of TREM2 is specific to some primates, including humans. The expression of the conventional TREM2 protein, starting from the downstream AUG (dTREM2), is repressed by the 5'-UTR in a uAUG-mediated manner. We also detect a TREM2 protein isoform starting from uAUG (uTREM2) that is largely degraded by proteasomes. Finally, the 5'-UTR is essential for the downregulation of dTREM2 expression in response to amino acid starvation. Collectively, our study identifies a species-specific regulatory role of the 5'-UTR in TREM2 translation.
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Affiliation(s)
- Motoaki Yanaizu
- Department of Bioinformatics and Molecular Neuropathology, Meiji Pharmaceutical University, 2-522-1, Noshio, Kiyose-shi, Tokyo, 204-8588, Japan
- Department of RNA Pathobiology and Therapeutics, Meiji Pharmaceutical University, 2-522-1, Noshio, Kiyose-shi, Tokyo, 204-8588, Japan
| | - Haruka Adachi
- Department of Bioinformatics and Molecular Neuropathology, Meiji Pharmaceutical University, 2-522-1, Noshio, Kiyose-shi, Tokyo, 204-8588, Japan
| | - Makoto Araki
- Department of Biochemistry, Meiji Pharmaceutical University, 2-522-1, Noshio, Kiyose-shi, Tokyo, 204-8588, Japan
| | - Kenji Kontani
- Department of Biochemistry, Meiji Pharmaceutical University, 2-522-1, Noshio, Kiyose-shi, Tokyo, 204-8588, Japan
| | - Yoshihiro Kino
- Department of Bioinformatics and Molecular Neuropathology, Meiji Pharmaceutical University, 2-522-1, Noshio, Kiyose-shi, Tokyo, 204-8588, Japan.
- Department of RNA Pathobiology and Therapeutics, Meiji Pharmaceutical University, 2-522-1, Noshio, Kiyose-shi, Tokyo, 204-8588, Japan.
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18
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Bowazolo C, Morse D. Insights into daily metabolic changes of the dinoflagellate Lingulodinium from ribosome profiling. Cell Cycle 2023; 22:1343-1352. [PMID: 37125841 PMCID: PMC10228409 DOI: 10.1080/15384101.2023.2206771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/15/2023] [Accepted: 02/16/2023] [Indexed: 05/02/2023] Open
Abstract
The dinoflagellate Lingulodinium specializes its metabolism to perform different tasks better at specific times of day. For example, cells are specialized for photosynthesis during the day and bioluminescence and cell division at night. These rhythms are circadian as they are controlled by an endogenous circadian clock whose mechanism is currently unknown. Despite this, the metabolic rhythms follow coordinated changes in gene expression that occur at a translational level. These changes are revealed by ribosome profiling, a surrogate measure of protein synthesis rates in vivo. Lingulodinium regulates the synthesis rate of over three thousand transcripts. Peak synthesis rates for the different transcripts are clustered around three different times over a light/dark cycle. Furthermore, transcripts involved in the same metabolic process are coordinately regulated. We review the basic principles underlying the correlation of coordinated translation of cell metabolic pathway enzymes with known circadian rhythms, and offer examples where previously unsuspected rhythms are suggested by synchronized changes in gene expression.
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Affiliation(s)
- Carl Bowazolo
- Institut de Recherche en biologie Végétale, Département de Sciences Biologiques, Université de Montréal, Montréal, Québec, Canada
| | - David Morse
- Institut de Recherche en biologie Végétale, Département de Sciences Biologiques, Université de Montréal, Montréal, Québec, Canada
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19
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Ji S, Xiong M, Chen H, Liu Y, Zhou L, Hong Y, Wang M, Wang C, Fu X, Sun X. Cellular rejuvenation: molecular mechanisms and potential therapeutic interventions for diseases. Signal Transduct Target Ther 2023; 8:116. [PMID: 36918530 PMCID: PMC10015098 DOI: 10.1038/s41392-023-01343-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 12/16/2022] [Accepted: 01/19/2023] [Indexed: 03/16/2023] Open
Abstract
The ageing process is a systemic decline from cellular dysfunction to organ degeneration, with more predisposition to deteriorated disorders. Rejuvenation refers to giving aged cells or organisms more youthful characteristics through various techniques, such as cellular reprogramming and epigenetic regulation. The great leaps in cellular rejuvenation prove that ageing is not a one-way street, and many rejuvenative interventions have emerged to delay and even reverse the ageing process. Defining the mechanism by which roadblocks and signaling inputs influence complex ageing programs is essential for understanding and developing rejuvenative strategies. Here, we discuss the intrinsic and extrinsic factors that counteract cell rejuvenation, and the targeted cells and core mechanisms involved in this process. Then, we critically summarize the latest advances in state-of-art strategies of cellular rejuvenation. Various rejuvenation methods also provide insights for treating specific ageing-related diseases, including cellular reprogramming, the removal of senescence cells (SCs) and suppression of senescence-associated secretory phenotype (SASP), metabolic manipulation, stem cells-associated therapy, dietary restriction, immune rejuvenation and heterochronic transplantation, etc. The potential applications of rejuvenation therapy also extend to cancer treatment. Finally, we analyze in detail the therapeutic opportunities and challenges of rejuvenation technology. Deciphering rejuvenation interventions will provide further insights into anti-ageing and ageing-related disease treatment in clinical settings.
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Affiliation(s)
- Shuaifei Ji
- Research Center for Tissue Repair and Regeneration Affiliated to Medical Innovation Research Department and 4th Medical Center, PLA General Hospital and PLA Medical College; PLA Key Laboratory of Tissue Repair and Regenerative Medicine and Beijing Key Research Laboratory of Skin Injury, Repair and Regeneration; Research Unit of Trauma Care, Tissue Repair and Regeneration, Chinese Academy of Medical Sciences, 2019RU051, Beijing, 100048, P. R. China
| | - Mingchen Xiong
- Research Center for Tissue Repair and Regeneration Affiliated to Medical Innovation Research Department and 4th Medical Center, PLA General Hospital and PLA Medical College; PLA Key Laboratory of Tissue Repair and Regenerative Medicine and Beijing Key Research Laboratory of Skin Injury, Repair and Regeneration; Research Unit of Trauma Care, Tissue Repair and Regeneration, Chinese Academy of Medical Sciences, 2019RU051, Beijing, 100048, P. R. China
| | - Huating Chen
- Research Center for Tissue Repair and Regeneration Affiliated to Medical Innovation Research Department and 4th Medical Center, PLA General Hospital and PLA Medical College; PLA Key Laboratory of Tissue Repair and Regenerative Medicine and Beijing Key Research Laboratory of Skin Injury, Repair and Regeneration; Research Unit of Trauma Care, Tissue Repair and Regeneration, Chinese Academy of Medical Sciences, 2019RU051, Beijing, 100048, P. R. China
| | - Yiqiong Liu
- Research Center for Tissue Repair and Regeneration Affiliated to Medical Innovation Research Department and 4th Medical Center, PLA General Hospital and PLA Medical College; PLA Key Laboratory of Tissue Repair and Regenerative Medicine and Beijing Key Research Laboratory of Skin Injury, Repair and Regeneration; Research Unit of Trauma Care, Tissue Repair and Regeneration, Chinese Academy of Medical Sciences, 2019RU051, Beijing, 100048, P. R. China
| | - Laixian Zhou
- Research Center for Tissue Repair and Regeneration Affiliated to Medical Innovation Research Department and 4th Medical Center, PLA General Hospital and PLA Medical College; PLA Key Laboratory of Tissue Repair and Regenerative Medicine and Beijing Key Research Laboratory of Skin Injury, Repair and Regeneration; Research Unit of Trauma Care, Tissue Repair and Regeneration, Chinese Academy of Medical Sciences, 2019RU051, Beijing, 100048, P. R. China
| | - Yiyue Hong
- Research Center for Tissue Repair and Regeneration Affiliated to Medical Innovation Research Department and 4th Medical Center, PLA General Hospital and PLA Medical College; PLA Key Laboratory of Tissue Repair and Regenerative Medicine and Beijing Key Research Laboratory of Skin Injury, Repair and Regeneration; Research Unit of Trauma Care, Tissue Repair and Regeneration, Chinese Academy of Medical Sciences, 2019RU051, Beijing, 100048, P. R. China
| | - Mengyang Wang
- Research Center for Tissue Repair and Regeneration Affiliated to Medical Innovation Research Department and 4th Medical Center, PLA General Hospital and PLA Medical College; PLA Key Laboratory of Tissue Repair and Regenerative Medicine and Beijing Key Research Laboratory of Skin Injury, Repair and Regeneration; Research Unit of Trauma Care, Tissue Repair and Regeneration, Chinese Academy of Medical Sciences, 2019RU051, Beijing, 100048, P. R. China
| | - Chunming Wang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, 999078, Macau SAR, China.
| | - Xiaobing Fu
- Research Center for Tissue Repair and Regeneration Affiliated to Medical Innovation Research Department and 4th Medical Center, PLA General Hospital and PLA Medical College; PLA Key Laboratory of Tissue Repair and Regenerative Medicine and Beijing Key Research Laboratory of Skin Injury, Repair and Regeneration; Research Unit of Trauma Care, Tissue Repair and Regeneration, Chinese Academy of Medical Sciences, 2019RU051, Beijing, 100048, P. R. China.
| | - Xiaoyan Sun
- Research Center for Tissue Repair and Regeneration Affiliated to Medical Innovation Research Department and 4th Medical Center, PLA General Hospital and PLA Medical College; PLA Key Laboratory of Tissue Repair and Regenerative Medicine and Beijing Key Research Laboratory of Skin Injury, Repair and Regeneration; Research Unit of Trauma Care, Tissue Repair and Regeneration, Chinese Academy of Medical Sciences, 2019RU051, Beijing, 100048, P. R. China.
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20
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Translational Control of Metabolism and Cell Cycle Progression in Hepatocellular Carcinoma. Int J Mol Sci 2023; 24:ijms24054885. [PMID: 36902316 PMCID: PMC10002961 DOI: 10.3390/ijms24054885] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 02/27/2023] [Accepted: 03/01/2023] [Indexed: 03/06/2023] Open
Abstract
The liver is a metabolic hub characterized by high levels of protein synthesis. Eukaryotic initiation factors, eIFs, control the first phase of translation, initiation. Initiation factors are essential for tumor progression and, since they regulate the translation of specific mRNAs downstream of oncogenic signaling cascades, may be druggable. In this review, we address the issue of whether the massive translational machinery of liver cells contributes to liver pathology and to the progression of hepatocellular carcinoma (HCC); it represents a valuable biomarker and druggable target. First, we observe that the common markers of HCC cells, such as phosphorylated ribosomal protein S6, belong to the ribosomal and translational apparatus. This fact is in agreement with observations that demonstrate a huge amplification of the ribosomal machinery during the progression to HCC. Some translation factors, such as eIF4E and eIF6, are then harnessed by oncogenic signaling. In particular, the action of eIF4E and eIF6 is particularly important in HCC when driven by fatty liver pathologies. Indeed, both eIF4E and eIF6 amplify at the translational level the production and accumulation of fatty acids. As it is evident that abnormal levels of these factors drive cancer, we discuss their therapeutic value.
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21
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Talamanca L, Gobet C, Naef F. Sex-dimorphic and age-dependent organization of 24-hour gene expression rhythms in humans. Science 2023; 379:478-483. [PMID: 36730411 DOI: 10.1126/science.add0846] [Citation(s) in RCA: 48] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The circadian clock modulates human physiology. However, the organization of tissue-specific gene expression rhythms and how these depend on age and sex is not defined in humans. We combined data from the Genotype-Tissue Expression (GTEx) project with an algorithm that assigns circadian phases to 914 donors, by integrating temporal information from multiple tissues in each individual, to identify messenger RNA (mRNA) rhythms in 46 tissues. Clock transcripts showed conserved timing relationships and tight synchrony across the body. mRNA rhythms varied in breadth, covering global and tissue-specific functions, including metabolic pathways and systemic responses. The clock structure was conserved across sexes and age groups. However, overall gene expression rhythms were highly sex-dimorphic and more sustained in females. Rhythmic programs generally dampened with age across the body.
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Affiliation(s)
- Lorenzo Talamanca
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Cédric Gobet
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Felix Naef
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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22
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Obodo D, Outland EH, Hughey JJ. Sex Inclusion in Transcriptome Studies of Daily Rhythms. J Biol Rhythms 2023; 38:3-14. [PMID: 36419398 PMCID: PMC9903005 DOI: 10.1177/07487304221134160] [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] [Indexed: 11/26/2022]
Abstract
Biomedical research on mammals has traditionally neglected females, raising the concern that some scientific findings may generalize poorly to half the population. Although this lack of sex inclusion has been broadly documented, its extent within circadian genomics remains undescribed. To address this gap, we examined sex inclusion practices in a comprehensive collection of publicly available transcriptome studies on daily rhythms. Among 148 studies having samples from mammals in vivo, we found strong underrepresentation of females across organisms and tissues. Overall, only 23 of 123 studies in mice, 0 of 10 studies in rats, and 9 of 15 studies in humans included samples from females. In addition, studies having samples from both sexes tended to have more samples from males than from females. These trends appear to have changed little over time, including since 2016, when the US National Institutes of Health began requiring investigators to consider sex as a biological variable. Our findings highlight an opportunity to dramatically improve representation of females in circadian research and to explore sex differences in daily rhythms at the genome level.
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Affiliation(s)
- Dora Obodo
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee,Program in Chemical and Physical Biology, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Elliot H. Outland
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Jacob J. Hughey
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee,Program in Chemical and Physical Biology, Vanderbilt University School of Medicine, Nashville, Tennessee,Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee,Jacob J. Hughey, Department of Biomedical Informatics, Vanderbilt University Medical Center, 2525 West End Ave., Suite 1475, Nashville, TN 37232, USA; e-mail:
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23
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Martini T, Naef F, Tchorz JS. Spatiotemporal Metabolic Liver Zonation and Consequences on Pathophysiology. ANNUAL REVIEW OF PATHOLOGY 2023; 18:439-466. [PMID: 36693201 DOI: 10.1146/annurev-pathmechdis-031521-024831] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Hepatocytes are the main workers in the hepatic factory, managing metabolism of nutrients and xenobiotics, production and recycling of proteins, and glucose and lipid homeostasis. Division of labor between hepatocytes is critical to coordinate complex complementary or opposing multistep processes, similar to distributed tasks at an assembly line. This so-called metabolic zonation has both spatial and temporal components. Spatial distribution of metabolic function in hepatocytes of different lobular zones is necessary to perform complex sequential multistep metabolic processes and to assign metabolic tasks to the right environment. Moreover, temporal control of metabolic processes is critical to align required metabolic processes to the feeding and fasting cycles. Disruption of this complex spatiotemporal hepatic organization impairs key metabolic processes with both local and systemic consequences. Many metabolic diseases, such as nonalcoholic steatohepatitis and diabetes, are associated with impaired metabolic liver zonation. Recent technological advances shed new light on the spatiotemporal gene expression networks controlling liver function and how their deregulation may be involved in a large variety of diseases. We summarize the current knowledge about spatiotemporal metabolic liver zonation and consequences on liver pathobiology.
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Affiliation(s)
- Tomaz Martini
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland;
| | - Felix Naef
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland;
| | - Jan S Tchorz
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland;
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24
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Castillo KD, Wu C, Ding Z, Lopez-Garcia OK, Rowlinson E, Sachs MS, Bell-Pedersen D. A circadian clock translational control mechanism targets specific mRNAs to cytoplasmic messenger ribonucleoprotein granules. Cell Rep 2022; 41:111879. [PMID: 36577368 PMCID: PMC10241597 DOI: 10.1016/j.celrep.2022.111879] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 09/13/2022] [Accepted: 12/04/2022] [Indexed: 12/29/2022] Open
Abstract
Phosphorylation of Neurospora crassa eukaryotic initiation factor 2 α (eIF2α), a conserved translation initiation factor, is clock controlled. To determine the impact of rhythmic eIF2α phosphorylation on translation, we performed temporal ribosome profiling and RNA sequencing (RNA-seq) in wild-type (WT), clock mutant Δfrq, eIF2α kinase mutant Δcpc-3, and constitutively active cpc-3c cells. About 14% of mRNAs are rhythmically translated in WT cells, and translation rhythms for ∼30% of these mRNAs, which we named circadian translation-initiation-controlled genes (cTICs), are dependent on the clock and CPC-3. Most cTICs are expressed from arrhythmic mRNAs and contain a P-body (PB) localization motif in their 5' leader sequence. Deletion of SNR-1, a component of cytoplasmic messenger ribonucleoprotein granules (cmRNPgs) that include PBs and stress granules (SGs), and the PB motif on one of the cTIC mRNAs, zip-1, significantly alters zip-1 rhythmic translation. These results reveal that the clock regulates rhythmic translation of specific mRNAs through rhythmic eIF2α activity and cmRNPg metabolism.
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Affiliation(s)
- Kathrina D Castillo
- Center for Biological Clocks Research, Texas A&M University, College Station, TX 77843, USA; Department of Biology, Texas A&M University, College Station, TX 77843, USA
| | - Cheng Wu
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
| | - Zhaolan Ding
- Center for Biological Clocks Research, Texas A&M University, College Station, TX 77843, USA; Department of Biology, Texas A&M University, College Station, TX 77843, USA
| | | | - Emma Rowlinson
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
| | - Matthew S Sachs
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
| | - Deborah Bell-Pedersen
- Center for Biological Clocks Research, Texas A&M University, College Station, TX 77843, USA; Department of Biology, Texas A&M University, College Station, TX 77843, USA.
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25
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Chu CMJ, Modi H, Ellis C, Krentz NAJ, Skovsø S, Zhao YB, Cen H, Noursadeghi N, Panzhinskiy E, Hu X, Dionne DA, Xia YH, Xuan S, Huising MO, Kieffer TJ, Lynn FC, Johnson JD. Dynamic Ins2 Gene Activity Defines β-Cell Maturity States. Diabetes 2022; 71:2612-2631. [PMID: 36170671 DOI: 10.2337/db21-1065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 09/20/2022] [Indexed: 01/11/2023]
Abstract
Transcriptional and functional cellular specialization has been described for insulin-secreting β-cells of the endocrine pancreas. However, it is not clear whether β-cell heterogeneity is stable or reflects dynamic cellular states. We investigated the temporal kinetics of endogenous insulin gene activity using live cell imaging, with complementary experiments using FACS and single-cell RNA sequencing, in β-cells from Ins2GFP knockin mice. In vivo staining and FACS analysis of islets from Ins2GFP mice confirmed that at a given moment, ∼25% of β-cells exhibited significantly higher activity at the evolutionarily conserved insulin gene, Ins2. Live cell imaging over days captured Ins2 gene activity dynamics in single β-cells. Autocorrelation analysis revealed a subset of oscillating cells, with mean oscillation periods of 17 h. Increased glucose concentrations stimulated more cells to oscillate and resulted in higher average Ins2 gene activity per cell. Single-cell RNA sequencing showed that Ins2(GFP)HIGH β-cells were enriched for markers of β-cell maturity. Ins2(GFP)HIGH β-cells were also significantly less viable at all glucose concentrations and in the context of endoplasmic reticulum stress. Collectively, our results demonstrate that the heterogeneity of insulin production, observed in mouse and human β-cells, can be accounted for by dynamic states of insulin gene activity.
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Affiliation(s)
- Chieh Min Jamie Chu
- Diabetes Focus Team, Life Sciences Institute, Departments of Cellular and Physiological Sciences and Surgery, University of British Columbia, Vancouver, Canada
| | - Honey Modi
- Diabetes Focus Team, Life Sciences Institute, Departments of Cellular and Physiological Sciences and Surgery, University of British Columbia, Vancouver, Canada
| | - Cara Ellis
- Diabetes Focus Team, Life Sciences Institute, Departments of Cellular and Physiological Sciences and Surgery, University of British Columbia, Vancouver, Canada
| | - Nicole A J Krentz
- BC Children's Hospital Research Institute, Department of Surgery, University of British Columbia, Vancouver, Canada
| | - Søs Skovsø
- Diabetes Focus Team, Life Sciences Institute, Departments of Cellular and Physiological Sciences and Surgery, University of British Columbia, Vancouver, Canada
| | - Yiwei Bernie Zhao
- Biomedical Research Centre, Departments of Cellular and Physiological Sciences and Surgery, University of British Columbia, Vancouver, Canada
| | - Haoning Cen
- Diabetes Focus Team, Life Sciences Institute, Departments of Cellular and Physiological Sciences and Surgery, University of British Columbia, Vancouver, Canada
| | - Nilou Noursadeghi
- Diabetes Focus Team, Life Sciences Institute, Departments of Cellular and Physiological Sciences and Surgery, University of British Columbia, Vancouver, Canada
| | - Evgeniy Panzhinskiy
- Diabetes Focus Team, Life Sciences Institute, Departments of Cellular and Physiological Sciences and Surgery, University of British Columbia, Vancouver, Canada
| | - Xiaoke Hu
- Diabetes Focus Team, Life Sciences Institute, Departments of Cellular and Physiological Sciences and Surgery, University of British Columbia, Vancouver, Canada
| | - Derek A Dionne
- Diabetes Focus Team, Life Sciences Institute, Departments of Cellular and Physiological Sciences and Surgery, University of British Columbia, Vancouver, Canada
| | - Yi Han Xia
- Diabetes Focus Team, Life Sciences Institute, Departments of Cellular and Physiological Sciences and Surgery, University of British Columbia, Vancouver, Canada
| | - Shouhong Xuan
- Division of Hematology/Oncology, Department of Medicine, Columbia University Medical Center, New York, NY
| | - Mark O Huising
- Department of Neurobiology, Physiology and Behavior, University of California, Davis, Davis, CA
- Department of Physiology and Membrane Biology, University of California, Davis, Davis, CA
| | - Timothy J Kieffer
- Diabetes Focus Team, Life Sciences Institute, Departments of Cellular and Physiological Sciences and Surgery, University of British Columbia, Vancouver, Canada
| | - Francis C Lynn
- BC Children's Hospital Research Institute, Department of Surgery, University of British Columbia, Vancouver, Canada
| | - James D Johnson
- Diabetes Focus Team, Life Sciences Institute, Departments of Cellular and Physiological Sciences and Surgery, University of British Columbia, Vancouver, Canada
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26
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Liu X, Chiu JC. Nutrient-sensitive protein O-GlcNAcylation shapes daily biological rhythms. Open Biol 2022; 12:220215. [PMID: 36099933 PMCID: PMC9470261 DOI: 10.1098/rsob.220215] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 08/17/2022] [Indexed: 11/12/2022] Open
Abstract
O-linked-N-acetylglucosaminylation (O-GlcNAcylation) is a nutrient-sensitive protein modification that alters the structure and function of a wide range of proteins involved in diverse cellular processes. Similar to phosphorylation, another protein modification that targets serine and threonine residues, O-GlcNAcylation occupancy on cellular proteins exhibits daily rhythmicity and has been shown to play critical roles in regulating daily rhythms in biology by modifying circadian clock proteins and downstream effectors. We recently reported that daily rhythm in global O-GlcNAcylation observed in Drosophila tissues is regulated via the integration of circadian and metabolic signals. Significantly, mistimed feeding, which disrupts coordination of these signals, is sufficient to dampen daily O-GlcNAcylation rhythm and is predicted to negatively impact animal biological rhythms and health span. In this review, we provide an overview of published and potential mechanisms by which metabolic and circadian signals regulate hexosamine biosynthetic pathway metabolites and enzymes, as well as O-GlcNAc processing enzymes to shape daily O-GlcNAcylation rhythms. We also discuss the significance of functional interactions between O-GlcNAcylation and other post-translational modifications in regulating biological rhythms. Finally, we highlight organ/tissue-specific cellular processes and molecular pathways that could be modulated by rhythmic O-GlcNAcylation to regulate time-of-day-specific biology.
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Affiliation(s)
- Xianhui Liu
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, Davis, CA, USA
- Department of Pharmacology, School of Medicine, University of California Davis, Davis, CA, USA
| | - Joanna C. Chiu
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, Davis, CA, USA
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27
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Comprehensive analysis of the circadian nuclear and cytoplasmic transcriptome in mouse liver. PLoS Genet 2022; 18:e1009903. [PMID: 35921362 PMCID: PMC9377612 DOI: 10.1371/journal.pgen.1009903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 08/15/2022] [Accepted: 07/06/2022] [Indexed: 11/19/2022] Open
Abstract
In eukaryotes, RNA is synthesised in the nucleus, spliced, and exported to the cytoplasm where it is translated and finally degraded. Any of these steps could be subject to temporal regulation during the circadian cycle, resulting in daily fluctuations of RNA accumulation and affecting the distribution of transcripts in different subcellular compartments. Our study analysed the nuclear and cytoplasmic, poly(A) and total transcriptomes of mouse livers collected over the course of a day. These data provide a genome-wide temporal inventory of enrichment in subcellular RNA, and revealed specific signatures of splicing, nuclear export and cytoplasmic mRNA stability related to transcript and gene lengths. Combined with a mathematical model describing rhythmic RNA profiles, we could test the rhythmicity of export rates and cytoplasmic degradation rates of approximately 1400 genes. With nuclear export times usually much shorter than cytoplasmic half-lives, we found that nuclear export contributes to the modulation and generation of rhythmic profiles of 10% of the cycling nuclear mRNAs. This study contributes to a better understanding of the dynamic regulation of the transcriptome during the day-night cycle.
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28
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Taleb Z, Karpowicz P. Circadian regulation of digestive and metabolic tissues. Am J Physiol Cell Physiol 2022; 323:C306-C321. [PMID: 35675638 DOI: 10.1152/ajpcell.00166.2022] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The circadian clock is a self-sustained molecular timekeeper that drives 24-h (circadian) rhythms in animals. The clock governs important aspects of behavior and physiology including wake/sleep activity cycles that regulate the activity of metabolic and digestive systems. Light/dark cycles (photoperiod) and cycles in the time of feeding synchronize the circadian clock to the surrounding environment, providing an anticipatory benefit that promotes digestive health. The availability of animal models targeting the genetic components of the circadian clock has made it possible to investigate the circadian clock's role in cellular functions. Circadian clock genes have been shown to regulate the physiological function of hepatocytes, gastrointestinal cells, and adipocytes; disruption of the circadian clock leads to the exacerbation of liver diseases and liver cancer, inflammatory bowel disease and colorectal cancer, and obesity. Previous findings provide strong evidence that the circadian clock plays an integral role in digestive/metabolic disease pathogenesis, hence, the circadian clock is a necessary component in metabolic and digestive health and homeostasis. Circadian rhythms and circadian clock function provide an opportunity to improve the prevention and treatment of digestive and metabolic diseases by aligning digestive system tissue with the 24-h day.
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Affiliation(s)
- Zainab Taleb
- Department of Biomedical Sciences, University of Windsor, Windsor, Ontario, Canada
| | - Phillip Karpowicz
- Department of Biomedical Sciences, University of Windsor, Windsor, Ontario, Canada
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29
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The Circadian Regulation of Nutrient Metabolism in Diet-Induced Obesity and Metabolic Disease. Nutrients 2022; 14:nu14153136. [PMID: 35956312 PMCID: PMC9370226 DOI: 10.3390/nu14153136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/18/2022] [Accepted: 07/26/2022] [Indexed: 02/04/2023] Open
Abstract
Obesity and other metabolic diseases are major public health issues that are particularly prevalent in industrialized societies where circadian rhythmicity is disturbed by shift work, jet lag, and/or social obligations. In mammals, daylight entrains the hypothalamic suprachiasmatic nucleus (SCN) to a ≈24 h cycle by initiating a transcription/translation feedback loop (TTFL) of molecular clock genes. The downstream impacts of the TTFL on clock-controlled genes allow the SCN to set the rhythm for the majority of physiological, metabolic, and behavioral processes. The TTFL, however, is ubiquitous and oscillates in tissues throughout the body. Tissues outside of the SCN are entrained to other signals, such as fed/fasting state, rather than light input. This system requires a considerable amount of biological flexibility as it functions to maintain homeostasis across varying conditions contained within a 24 h day. In the face of either circadian disruption (e.g., jet lag and shift work) or an obesity-induced decrease in metabolic flexibility, this finely tuned mechanism breaks down. Indeed, both human and rodent studies have found that obesity and metabolic disease develop when endogenous circadian pacing is at odds with the external cues. In the following review, we will delve into what is known on the circadian rhythmicity of nutrient metabolism and discuss obesity as a circadian disease.
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30
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Orchestrated translation specializes dinoflagellate metabolism three times per day. Proc Natl Acad Sci U S A 2022; 119:e2122335119. [PMID: 35858433 PMCID: PMC9335273 DOI: 10.1073/pnas.2122335119] [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] [Indexed: 01/21/2023] Open
Abstract
Many cells specialize for different metabolic tasks at different times over their normal ZT cycle by changes in gene expression. However, in most cases, circadian gene expression has been assessed at the mRNA accumulation level, which may not faithfully reflect protein synthesis rates. Here, we use ribosome profiling in the dinoflagellate Lingulodinium polyedra to identify thousands of transcripts showing coordinated translation. All of the components in carbon fixation are concurrently regulated at ZT0, predicting the known rhythm of carbon fixation, and many enzymes involved in DNA replication are concurrently regulated at ZT12, also predicting the known rhythm in this process. Most of the enzymes in glycolysis and the TCA cycle are also regulated together, suggesting rhythms in these processes as well. Surprisingly, a third cluster of transcripts show peak translation at approximately ZT16, and these transcripts encode enzymes involved in transcription, translation, and amino acid biosynthesis. The latter has physiological consequences, as measured free amino acid levels increase at night and thus represent a previously undocumented rhythm in this model. Our results suggest that ribosome profiling may be a more accurate predictor of changed metabolic state than transcriptomics.
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31
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Li S, Xiao J, Sun T, Yu F, Zhang K, Feng Y, Xu C, Wang B, Cheng L. Synthetic microbial consortia with programmable ecological interactions. Methods Ecol Evol 2022. [DOI: 10.1111/2041-210x.13894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Shuyao Li
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences Zhejiang University Hangzhou 310058 China
| | - Jing Xiao
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences Zhejiang University Hangzhou 310058 China
| | - Tianzheng Sun
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences Zhejiang University Hangzhou 310058 China
| | - Fangjian Yu
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences Zhejiang University Hangzhou 310058 China
| | - Kaihang Zhang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences Zhejiang University Hangzhou 310058 China
| | - Yuantao Feng
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences Zhejiang University Hangzhou 310058 China
| | - Chenchao Xu
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences Zhejiang University Hangzhou 310058 China
| | - Baojun Wang
- Hangzhou Innovation Center & College of Chemical and Biological Engineering Zhejiang University Hangzhou 311200 China
- Research Centre for Biological Computation, Zhejiang Laboratory Hangzhou 311100 China
| | - Lei Cheng
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences Zhejiang University Hangzhou 310058 China
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32
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Fougeray T, Polizzi A, Régnier M, Fougerat A, Ellero-Simatos S, Lippi Y, Smati S, Lasserre F, Tramunt B, Huillet M, Dopavogui L, Salvi J, Nédélec E, Gigot V, Smith L, Naylies C, Sommer C, Haas JT, Wahli W, Duez H, Gourdy P, Gamet-Payrastre L, Benani A, Burnol AF, Loiseau N, Postic C, Montagner A, Guillou H. The hepatocyte insulin receptor is required to program the liver clock and rhythmic gene expression. Cell Rep 2022; 39:110674. [PMID: 35417722 DOI: 10.1016/j.celrep.2022.110674] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 02/03/2022] [Accepted: 03/23/2022] [Indexed: 12/30/2022] Open
Abstract
Liver physiology is circadian and sensitive to feeding and insulin. Food intake regulates insulin secretion and is a dominant signal for the liver clock. However, how much insulin contributes to the effect of feeding on the liver clock and rhythmic gene expression remains to be investigated. Insulin action partly depends on changes in insulin receptor (IR)-dependent gene expression. Here, we use hepatocyte-restricted gene deletion of IR to evaluate its role in the regulation and oscillation of gene expression as well as in the programming of the circadian clock in the adult mouse liver. We find that, in the absence of IR, the rhythmicity of core-clock gene expression is altered in response to day-restricted feeding. This change in core-clock gene expression is associated with defective reprogramming of liver gene expression. Our data show that an intact hepatocyte insulin receptor is required to program the liver clock and associated rhythmic gene expression.
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Affiliation(s)
- Tiffany Fougeray
- Toxalim (Research Center in Food Toxicology), INRAE, ENVT, INP- PURPAN, UMR 1331, UPS, Université de Toulouse, 180 Chemin de Tournefeuille, 31027 Toulouse, France; Institut des Maladies Métaboliques et Cardiovasculaires (I2MC), UMR1297, INSERM/UPS, Université de Toulouse, 1 Avenue Jean Poulhès, BP 84225, 31432 Toulouse, France
| | - Arnaud Polizzi
- Toxalim (Research Center in Food Toxicology), INRAE, ENVT, INP- PURPAN, UMR 1331, UPS, Université de Toulouse, 180 Chemin de Tournefeuille, 31027 Toulouse, France
| | - Marion Régnier
- Toxalim (Research Center in Food Toxicology), INRAE, ENVT, INP- PURPAN, UMR 1331, UPS, Université de Toulouse, 180 Chemin de Tournefeuille, 31027 Toulouse, France
| | - Anne Fougerat
- Toxalim (Research Center in Food Toxicology), INRAE, ENVT, INP- PURPAN, UMR 1331, UPS, Université de Toulouse, 180 Chemin de Tournefeuille, 31027 Toulouse, France
| | - Sandrine Ellero-Simatos
- Toxalim (Research Center in Food Toxicology), INRAE, ENVT, INP- PURPAN, UMR 1331, UPS, Université de Toulouse, 180 Chemin de Tournefeuille, 31027 Toulouse, France
| | - Yannick Lippi
- Toxalim (Research Center in Food Toxicology), INRAE, ENVT, INP- PURPAN, UMR 1331, UPS, Université de Toulouse, 180 Chemin de Tournefeuille, 31027 Toulouse, France
| | - Sarra Smati
- Toxalim (Research Center in Food Toxicology), INRAE, ENVT, INP- PURPAN, UMR 1331, UPS, Université de Toulouse, 180 Chemin de Tournefeuille, 31027 Toulouse, France; Institut des Maladies Métaboliques et Cardiovasculaires (I2MC), UMR1297, INSERM/UPS, Université de Toulouse, 1 Avenue Jean Poulhès, BP 84225, 31432 Toulouse, France; Université de Nantes, INSERM, CNRS, CHU Nantes, Institut du Thorax, 44000 Nantes, France
| | - Frédéric Lasserre
- Toxalim (Research Center in Food Toxicology), INRAE, ENVT, INP- PURPAN, UMR 1331, UPS, Université de Toulouse, 180 Chemin de Tournefeuille, 31027 Toulouse, France
| | - Blandine Tramunt
- Institut des Maladies Métaboliques et Cardiovasculaires (I2MC), UMR1297, INSERM/UPS, Université de Toulouse, 1 Avenue Jean Poulhès, BP 84225, 31432 Toulouse, France; Service de Diabétologie, Maladies Métaboliques et Nutrition, CHU de Toulouse, Université de Toulouse, Toulouse, France
| | - Marine Huillet
- Toxalim (Research Center in Food Toxicology), INRAE, ENVT, INP- PURPAN, UMR 1331, UPS, Université de Toulouse, 180 Chemin de Tournefeuille, 31027 Toulouse, France
| | - Léonie Dopavogui
- Toxalim (Research Center in Food Toxicology), INRAE, ENVT, INP- PURPAN, UMR 1331, UPS, Université de Toulouse, 180 Chemin de Tournefeuille, 31027 Toulouse, France
| | - Juliette Salvi
- Centre des Sciences du Goût et de l'Alimentation, CNRS, INRAE, Université Bourgogne Franche-Comté, Institut Agro Dijon, 21000 Dijon, France
| | - Emmanuelle Nédélec
- Centre des Sciences du Goût et de l'Alimentation, CNRS, INRAE, Université Bourgogne Franche-Comté, Institut Agro Dijon, 21000 Dijon, France
| | - Vincent Gigot
- Centre des Sciences du Goût et de l'Alimentation, CNRS, INRAE, Université Bourgogne Franche-Comté, Institut Agro Dijon, 21000 Dijon, France
| | - Lorraine Smith
- Toxalim (Research Center in Food Toxicology), INRAE, ENVT, INP- PURPAN, UMR 1331, UPS, Université de Toulouse, 180 Chemin de Tournefeuille, 31027 Toulouse, France
| | - Claire Naylies
- Toxalim (Research Center in Food Toxicology), INRAE, ENVT, INP- PURPAN, UMR 1331, UPS, Université de Toulouse, 180 Chemin de Tournefeuille, 31027 Toulouse, France
| | - Caroline Sommer
- Toxalim (Research Center in Food Toxicology), INRAE, ENVT, INP- PURPAN, UMR 1331, UPS, Université de Toulouse, 180 Chemin de Tournefeuille, 31027 Toulouse, France
| | - Joel T Haas
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011-EGID, F-59000 Lille, France
| | - Walter Wahli
- Toxalim (Research Center in Food Toxicology), INRAE, ENVT, INP- PURPAN, UMR 1331, UPS, Université de Toulouse, 180 Chemin de Tournefeuille, 31027 Toulouse, France; Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, Singapore 308232, Singapore; Center for Integrative Genomics, University of Lausanne, Le Génopode, 1015 Lausanne, Switzerland
| | - Hélène Duez
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011-EGID, F-59000 Lille, France
| | - Pierre Gourdy
- Institut des Maladies Métaboliques et Cardiovasculaires (I2MC), UMR1297, INSERM/UPS, Université de Toulouse, 1 Avenue Jean Poulhès, BP 84225, 31432 Toulouse, France; Service de Diabétologie, Maladies Métaboliques et Nutrition, CHU de Toulouse, Université de Toulouse, Toulouse, France
| | - Laurence Gamet-Payrastre
- Toxalim (Research Center in Food Toxicology), INRAE, ENVT, INP- PURPAN, UMR 1331, UPS, Université de Toulouse, 180 Chemin de Tournefeuille, 31027 Toulouse, France
| | - Alexandre Benani
- Centre des Sciences du Goût et de l'Alimentation, CNRS, INRAE, Université Bourgogne Franche-Comté, Institut Agro Dijon, 21000 Dijon, France
| | | | - Nicolas Loiseau
- Toxalim (Research Center in Food Toxicology), INRAE, ENVT, INP- PURPAN, UMR 1331, UPS, Université de Toulouse, 180 Chemin de Tournefeuille, 31027 Toulouse, France
| | - Catherine Postic
- Université de Paris, Institut Cochin, CNRS, INSERM, 75014 Paris, France
| | - Alexandra Montagner
- Institut des Maladies Métaboliques et Cardiovasculaires (I2MC), UMR1297, INSERM/UPS, Université de Toulouse, 1 Avenue Jean Poulhès, BP 84225, 31432 Toulouse, France.
| | - Hervé Guillou
- Toxalim (Research Center in Food Toxicology), INRAE, ENVT, INP- PURPAN, UMR 1331, UPS, Université de Toulouse, 180 Chemin de Tournefeuille, 31027 Toulouse, France.
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Summers KM, Bush SJ, Wu C, Hume DA. Generation and network analysis of an RNA-seq transcriptional atlas for the rat. NAR Genom Bioinform 2022; 4:lqac017. [PMID: 35265836 PMCID: PMC8900154 DOI: 10.1093/nargab/lqac017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 01/13/2022] [Accepted: 02/15/2022] [Indexed: 12/19/2022] Open
Abstract
Abstract
The laboratory rat is an important model for biomedical research. To generate a comprehensive rat transcriptomic atlas, we curated and downloaded 7700 rat RNA-seq datasets from public repositories, downsampled them to a common depth and quantified expression. Data from 585 rat tissues and cells, averaged from each BioProject, can be visualized and queried at http://biogps.org/ratatlas. Gene co-expression network (GCN) analysis revealed clusters of transcripts that were tissue or cell type restricted and contained transcription factors implicated in lineage determination. Other clusters were enriched for transcripts associated with biological processes. Many of these clusters overlap with previous data from analysis of other species, while some (e.g. expressed specifically in immune cells, retina/pineal gland, pituitary and germ cells) are unique to these data. GCN analysis on large subsets of the data related specifically to liver, nervous system, kidney, musculoskeletal system and cardiovascular system enabled deconvolution of cell type-specific signatures. The approach is extensible and the dataset can be used as a point of reference from which to analyse the transcriptomes of cell types and tissues that have not yet been sampled. Sets of strictly co-expressed transcripts provide a resource for critical interpretation of single-cell RNA-seq data.
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Affiliation(s)
- Kim M Summers
- Mater Research Institute—University of Queensland, Translational Research Institute, 37 Kent St, Woolloongabba, QLD 4102, Australia
| | - Stephen J Bush
- Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Chunlei Wu
- Department of Integrative and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - David A Hume
- Mater Research Institute—University of Queensland, Translational Research Institute, 37 Kent St, Woolloongabba, QLD 4102, Australia
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Trott AJ, Greenwell BJ, Karhadkar TR, Guerrero-Vargas NN, Escobar C, Buijs RM, Menet JS. Lack of food intake during shift work alters the heart transcriptome and leads to cardiac tissue fibrosis and inflammation in rats. BMC Biol 2022; 20:58. [PMID: 35236346 PMCID: PMC8892784 DOI: 10.1186/s12915-022-01256-9] [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: 06/18/2021] [Accepted: 02/16/2022] [Indexed: 12/14/2022] Open
Abstract
Background Many epidemiological studies revealed that shift work is associated with an increased risk of a number of pathologies, including cardiovascular diseases. An experimental model of shift work in rats has additionally been shown to recapitulate aspects of metabolic disorders observed in human shift workers, including increased fat content and impaired glucose tolerance, and used to demonstrate that restricting food consumption outside working hours prevents shift work-associated obesity and metabolic disturbance. However, the way distinct shift work parameters, such as type of work, quantity, and duration, affect cardiovascular function and the underlying mechanisms, remains poorly understood. Here, we used the rat as a model to characterize the effects of shift work in the heart and determine whether they can be modulated by restricting food intake during the normal active phase. Results We show that experimental shift work reprograms the heart cycling transcriptome independently of food consumption. While phases of rhythmic gene expression are distributed across the 24-h day in control rats, they are clustered towards discrete times in shift workers. Additionally, preventing food intake during shift work affects the expression level of hundreds of genes in the heart, including genes encoding components of the extracellular matrix and inflammatory markers found in transcriptional signatures associated with pressure overload and cardiac hypertrophy. Consistent with this, the heart of shift worker rats not eating during work hours, but having access to food outside of shift work, exhibits increased collagen 1 deposition and displays increased infiltration by immune cells. While maintaining food access during shift work has less effects on gene expression, genes found in transcriptional signatures of cardiac hypertrophy remain affected, and the heart of shift worker rats exhibits fibrosis without inflammation. Conclusions Together, our findings unraveled differential effects of food consumption on remodeled transcriptional profiles of the heart in shift worker rats. They also provide insights into how shift work affects cardiac function and suggest that some interventions aiming at mitigating metabolic disorders in shift workers may have adverse effects on cardiovascular diseases. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01256-9.
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Affiliation(s)
- Alexandra J Trott
- Department of Biology, Texas A&M University, College Station, TX, 77843, USA.,Program of Genetics, Texas A&M University, College Station, TX, 77843, USA.,Center for Biological Clock Research, Texas A&M University, College Station, TX, 77843, USA
| | - Ben J Greenwell
- Department of Biology, Texas A&M University, College Station, TX, 77843, USA.,Program of Genetics, Texas A&M University, College Station, TX, 77843, USA.,Center for Biological Clock Research, Texas A&M University, College Station, TX, 77843, USA
| | - Tejas R Karhadkar
- Department of Biology, Texas A&M University, College Station, TX, 77843, USA.,Program of Genetics, Texas A&M University, College Station, TX, 77843, USA
| | - Natali N Guerrero-Vargas
- Departamento de Anatomía, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad Universitaria, Mexico City, Mexico
| | - Carolina Escobar
- Departamento de Anatomía, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad Universitaria, Mexico City, Mexico
| | - Ruud M Buijs
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Mexico City, Mexico
| | - Jerome S Menet
- Department of Biology, Texas A&M University, College Station, TX, 77843, USA. .,Program of Genetics, Texas A&M University, College Station, TX, 77843, USA. .,Center for Biological Clock Research, Texas A&M University, College Station, TX, 77843, USA.
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35
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Wu Y, Xue L, Huang W, Deng M, Lin Y. Profiling transcription factor activity dynamics using intronic reads in time-series transcriptome data. PLoS Comput Biol 2022; 18:e1009762. [PMID: 35007289 PMCID: PMC8782462 DOI: 10.1371/journal.pcbi.1009762] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 01/21/2022] [Accepted: 12/15/2021] [Indexed: 11/19/2022] Open
Abstract
Activities of transcription factors (TFs) are temporally modulated to regulate dynamic cellular processes, including development, homeostasis, and disease. Recent developments of bioinformatic tools have enabled the analysis of TF activities using transcriptome data. However, because these methods typically use exon-based target expression levels, the estimated TF activities have limited temporal accuracy. To address this, we proposed a TF activity measure based on intron-level information in time-series RNA-seq data, and implemented it to decode the temporal control of TF activities during dynamic processes. We showed that TF activities inferred from intronic reads can better recapitulate instantaneous TF activities compared to the exon-based measure. By analyzing public and our own time-series transcriptome data, we found that intron-based TF activities improve the characterization of temporal phasing of cycling TFs during circadian rhythm, and facilitate the discovery of two temporally opposing TF modules during T cell activation. Collectively, we anticipate that the proposed approach would be broadly applicable for decoding global transcriptional architecture during dynamic processes.
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Affiliation(s)
- Yan Wu
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- School of Mathematical Sciences and Center for Statistical Science, Peking University, Beijing, China
| | - Lingfeng Xue
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Wen Huang
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Minghua Deng
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- School of Mathematical Sciences and Center for Statistical Science, Peking University, Beijing, China
| | - Yihan Lin
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- * E-mail:
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36
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Tuning up an aged clock: Circadian clock regulation in metabolism and aging. TRANSLATIONAL MEDICINE OF AGING 2022. [DOI: 10.1016/j.tma.2021.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
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37
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Shirokikh NE. Translation complex stabilization on messenger RNA and footprint profiling to study the RNA responses and dynamics of protein biosynthesis in the cells. Crit Rev Biochem Mol Biol 2021; 57:261-304. [PMID: 34852690 DOI: 10.1080/10409238.2021.2006599] [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] [Indexed: 01/28/2023]
Abstract
During protein biosynthesis, ribosomes bind to messenger (m)RNA, locate its protein-coding information, and translate the nucleotide triplets sequentially as codons into the corresponding sequence of amino acids, forming proteins. Non-coding mRNA features, such as 5' and 3' untranslated regions (UTRs), start sites or stop codons of different efficiency, stretches of slower or faster code and nascent polypeptide interactions can alter the translation rates transcript-wise. Most of the homeostatic and signal response pathways of the cells converge on individual mRNA control, as well as alter the global translation output. Among the multitude of approaches to study translational control, one of the most powerful is to infer the locations of translational complexes on mRNA based on the mRNA fragments protected by these complexes from endonucleolytic hydrolysis, or footprints. Translation complex profiling by high-throughput sequencing of the footprints allows to quantify the transcript-wise, as well as global, alterations of translation, and uncover the underlying control mechanisms by attributing footprint locations and sizes to different configurations of the translational complexes. The accuracy of all footprint profiling approaches critically depends on the fidelity of footprint generation and many methods have emerged to preserve certain or multiple configurations of the translational complexes, often in challenging biological material. In this review, a systematic summary of approaches to stabilize translational complexes on mRNA for footprinting is presented and major findings are discussed. Future directions of translation footprint profiling are outlined, focusing on the fidelity and accuracy of inference of the native in vivo translation complex distribution on mRNA.
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Affiliation(s)
- Nikolay E Shirokikh
- Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, The Australian National University, Canberra, Australia
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38
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Stangherlin A, Seinkmane E, O'Neill JS. Understanding circadian regulation of mammalian cell function, protein homeostasis, and metabolism. CURRENT OPINION IN SYSTEMS BIOLOGY 2021; 28:None. [PMID: 34950808 PMCID: PMC8660647 DOI: 10.1016/j.coisb.2021.100391] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Circadian rhythms are ∼24 h cycles of organismal and cellular activity ubiquitous to mammalian physiology. A prevailing paradigm suggests that timing information flows linearly from rhythmic transcription via protein abundance changes to drive circadian regulation of cellular function. Challenging this view, recent evidence indicates daily variation in many cellular functions arises through rhythmic post-translational regulation of protein activity. We suggest cellular circadian timing primarily functions to maintain proteome homeostasis rather than perturb it. Indeed, although relevant to timekeeping mechanism, daily rhythms of clock protein abundance may be the exception, not the rule. Informed by insights from yeast and mammalian models, we propose that optimal bioenergetic efficiency results from coupled rhythms in mammalian target of rapamycin complex activity, protein synthesis/turnover, ion transport and protein sequestration, which drive facilitatory rhythms in metabolic flux and substrate utilisation. Such daily consolidation of proteome renewal would account for many aspects of circadian cell biology whilst maintaining osmotic homeostasis.
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39
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Wei S, Zheng Q, Pan Y, Xu Y, Tang J, Cai X. Interplay between liver circadian rhythm and regeneration after PHx. Genomics 2021; 114:1-8. [PMID: 34822968 DOI: 10.1016/j.ygeno.2021.11.023] [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: 07/15/2021] [Revised: 11/04/2021] [Accepted: 11/16/2021] [Indexed: 11/04/2022]
Abstract
Diurnal oscillations in gene expression are a hallmark of the liver internal clock and can be regulated by a variety of environmental stimuli. The circadian rhythm and liver regeneration (LR) are intimately linked. However, how they affect each other at the transcriptomic level is mainly unknown. Here, we revealed that partial hepatectomy (PHx)-induced LR led to reprogramming of rhythmic gene expression profiles as a consequence of disrupted BMAL1 occupation on the chromatin, while the rhythm of core clock genes remained robust. Furthermore, we demonstrated retarded LR when PHx was carried out in the evening, possibly due to the accumulation of DEC1. In summary, our data offer a broad perspective of the relationship between circadian rhythm and LR and suggest that the timing of PHx should be considered in the clinic application.
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Affiliation(s)
- Saisai Wei
- Key Laboratory of Laparoscopic Technology of Zhejiang Province, Department of General Surgery, Sir Run-Run Shaw Hospital, Zhejiang University School of Medicine, 310016 Hangzhou, China; Zhejiang Minimal Invasive Diagnosis and Treatment Technology Research Center of Severe Hepatobiliary Disease, Zhejiang Research and Development Engineering Laboratory of Minimally Invasive Technology and Equipment, 310016 Hangzhou, China; Zhejiang University Cancer Center, 310058 Hangzhou, China
| | - Qiang Zheng
- Key Laboratory of Laparoscopic Technology of Zhejiang Province, Department of General Surgery, Sir Run-Run Shaw Hospital, Zhejiang University School of Medicine, 310016 Hangzhou, China; Zhejiang Minimal Invasive Diagnosis and Treatment Technology Research Center of Severe Hepatobiliary Disease, Zhejiang Research and Development Engineering Laboratory of Minimally Invasive Technology and Equipment, 310016 Hangzhou, China; Zhejiang University Cancer Center, 310058 Hangzhou, China
| | - Yu Pan
- Key Laboratory of Laparoscopic Technology of Zhejiang Province, Department of General Surgery, Sir Run-Run Shaw Hospital, Zhejiang University School of Medicine, 310016 Hangzhou, China; Zhejiang Minimal Invasive Diagnosis and Treatment Technology Research Center of Severe Hepatobiliary Disease, Zhejiang Research and Development Engineering Laboratory of Minimally Invasive Technology and Equipment, 310016 Hangzhou, China; Zhejiang University Cancer Center, 310058 Hangzhou, China
| | - Yunwan Xu
- Shenzhen NeoCura Biotechnology corporation, Shenzhen 518055, China
| | - Jiacheng Tang
- Key Laboratory of Laparoscopic Technology of Zhejiang Province, Department of General Surgery, Sir Run-Run Shaw Hospital, Zhejiang University School of Medicine, 310016 Hangzhou, China; Zhejiang Minimal Invasive Diagnosis and Treatment Technology Research Center of Severe Hepatobiliary Disease, Zhejiang Research and Development Engineering Laboratory of Minimally Invasive Technology and Equipment, 310016 Hangzhou, China; Zhejiang University Cancer Center, 310058 Hangzhou, China
| | - Xiujun Cai
- Key Laboratory of Laparoscopic Technology of Zhejiang Province, Department of General Surgery, Sir Run-Run Shaw Hospital, Zhejiang University School of Medicine, 310016 Hangzhou, China; Zhejiang Minimal Invasive Diagnosis and Treatment Technology Research Center of Severe Hepatobiliary Disease, Zhejiang Research and Development Engineering Laboratory of Minimally Invasive Technology and Equipment, 310016 Hangzhou, China; Zhejiang University Cancer Center, 310058 Hangzhou, China; Liangzhu Laboratory, Zhejiang University Medical Center, 311121 Hangzhou,China.
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40
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Præstholm SM, Correia CM, Goitea VE, Siersbæk MS, Jørgensen M, Havelund JF, Pedersen TÅ, Færgeman NJ, Grøntved L. Impaired glucocorticoid receptor expression in liver disrupts feeding-induced gene expression, glucose uptake, and glycogen storage. Cell Rep 2021; 37:109938. [PMID: 34731602 DOI: 10.1016/j.celrep.2021.109938] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 09/08/2021] [Accepted: 10/13/2021] [Indexed: 10/19/2022] Open
Abstract
The transition from a fasted to a fed state is associated with extensive transcriptional remodeling in hepatocytes facilitated by hormonal- and nutritional-regulated transcription factors. Here, we use a liver-specific glucocorticoid receptor (GR) knockout (L-GRKO) model to investigate the temporal hepatic expression of GR target genes in response to feeding. Interestingly, in addition to the well-described fasting-regulated genes, we identify a subset of hepatic feeding-induced genes that requires GR for full expression. This includes Gck, which is important for hepatic glucose uptake, utilization, and storage. We show that insulin and glucocorticoids cooperatively regulate hepatic Gck expression in a direct GR-dependent manner by a 4.6 kb upstream GR binding site operating as a Gck enhancer. L-GRKO blunts preprandial and early postprandial Gck expression, which ultimately affects early postprandial hepatic glucose uptake, phosphorylation, and glycogen storage. Thus, GR is positively involved in feeding-induced gene expression and important for postprandial glucose metabolism in the liver.
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Affiliation(s)
- Stine M Præstholm
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
| | - Catarina M Correia
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
| | - Victor E Goitea
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
| | - Majken S Siersbæk
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
| | - Mathilde Jørgensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
| | - Jesper F Havelund
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
| | | | - Nils J Færgeman
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
| | - Lars Grøntved
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark.
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41
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Compensatory ion transport buffers daily protein rhythms to regulate osmotic balance and cellular physiology. Nat Commun 2021; 12:6035. [PMID: 34654800 PMCID: PMC8520019 DOI: 10.1038/s41467-021-25942-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 08/04/2021] [Indexed: 01/15/2023] Open
Abstract
Between 6-20% of the cellular proteome is under circadian control and tunes mammalian cell function with daily environmental cycles. For cell viability, and to maintain volume within narrow limits, the daily variation in osmotic potential exerted by changes in the soluble proteome must be counterbalanced. The mechanisms and consequences of this osmotic compensation have not been investigated before. In cultured cells and in tissue we find that compensation involves electroneutral active transport of Na+, K+, and Cl- through differential activity of SLC12A family cotransporters. In cardiomyocytes ex vivo and in vivo, compensatory ion fluxes confer daily variation in electrical activity. Perturbation of soluble protein abundance has commensurate effects on ion composition and cellular function across the circadian cycle. Thus, circadian regulation of the proteome impacts ion homeostasis with substantial consequences for the physiology of electrically active cells such as cardiomyocytes.
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42
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Kay H, Grünewald E, Feord HK, Gil S, Peak-Chew SY, Stangherlin A, O'Neill JS, van Ooijen G. Deep-coverage spatiotemporal proteome of the picoeukaryote Ostreococcus tauri reveals differential effects of environmental and endogenous 24-hour rhythms. Commun Biol 2021; 4:1147. [PMID: 34593975 PMCID: PMC8484446 DOI: 10.1038/s42003-021-02680-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 09/07/2021] [Indexed: 11/18/2022] Open
Abstract
The cellular landscape changes dramatically over the course of a 24 h day. The proteome responds directly to daily environmental cycles and is additionally regulated by the circadian clock. To quantify the relative contribution of diurnal versus circadian regulation, we mapped proteome dynamics under light:dark cycles compared with constant light. Using Ostreococcus tauri, a prototypical eukaryotic cell, we achieved 85% coverage, which allowed an unprecedented insight into the identity of proteins that facilitate rhythmic cellular functions. The overlap between diurnally- and circadian-regulated proteins was modest and these proteins exhibited different phases of oscillation between the two conditions. Transcript oscillations were generally poorly predictive of protein oscillations, in which a far lower relative amplitude was observed. We observed coordination between the rhythmic regulation of organelle-encoded proteins with the nuclear-encoded proteins that are targeted to organelles. Rhythmic transmembrane proteins showed a different phase distribution compared with rhythmic soluble proteins, indicating the existence of a circadian regulatory process specific to the biogenesis and/or degradation of membrane proteins. Our observations argue that the cellular spatiotemporal proteome is shaped by a complex interaction between intrinsic and extrinsic regulatory factors through rhythmic regulation at the transcriptional as well as post-transcriptional, translational, and post-translational levels. Holly Kay, Ellen Grünewald, et al. provide an in-depth examination of the proteome in the eukaryotic green alga, Ostreococcus tauri, under circadian constant light or cycling diurnal light-dark conditions. They observe that there is little overlap between mRNA and protein expression rhythms, or the diurnal and circadian proteome, suggesting that the cellular spatiotemporal proteome is shaped through rhythmic regulation at multiple stages of transcription and translation.
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Affiliation(s)
- Holly Kay
- School of Biological Sciences, University of Edinburgh, Max Born Crescent, Edinburgh, EH9 3BF, UK
| | - Ellen Grünewald
- School of Biological Sciences, University of Edinburgh, Max Born Crescent, Edinburgh, EH9 3BF, UK
| | - Helen K Feord
- School of Biological Sciences, University of Edinburgh, Max Born Crescent, Edinburgh, EH9 3BF, UK
| | - Sergio Gil
- School of Biological Sciences, University of Edinburgh, Max Born Crescent, Edinburgh, EH9 3BF, UK
| | - Sew Y Peak-Chew
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | | | - John S O'Neill
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Gerben van Ooijen
- School of Biological Sciences, University of Edinburgh, Max Born Crescent, Edinburgh, EH9 3BF, UK.
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43
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Cunningham RP, Porat-Shliom N. Liver Zonation - Revisiting Old Questions With New Technologies. Front Physiol 2021; 12:732929. [PMID: 34566696 PMCID: PMC8458816 DOI: 10.3389/fphys.2021.732929] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 08/10/2021] [Indexed: 12/12/2022] Open
Abstract
Despite the ever-increasing prevalence of non-alcoholic fatty liver disease (NAFLD), the etiology and pathogenesis remain poorly understood. This is due, in part, to the liver's complex physiology and architecture. The liver maintains glucose and lipid homeostasis by coordinating numerous metabolic processes with great efficiency. This is made possible by the spatial compartmentalization of metabolic pathways a phenomenon known as liver zonation. Despite the importance of zonation to normal liver function, it is unresolved if and how perturbations to liver zonation can drive hepatic pathophysiology and NAFLD development. While hepatocyte heterogeneity has been identified over a century ago, its examination had been severely hindered due to technological limitations. Recent advances in single cell analysis and imaging technologies now permit further characterization of cells across the liver lobule. This review summarizes the advances in examining liver zonation and elucidating its regulatory role in liver physiology and pathology. Understanding the spatial organization of metabolism is vital to further our knowledge of liver disease and to provide targeted therapeutic avenues.
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Affiliation(s)
- Rory P Cunningham
- Thoracic and GI Malignancies Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, United States
| | - Natalie Porat-Shliom
- Thoracic and GI Malignancies Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, United States
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44
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Greco CM, Koronowski KB, Smith JG, Shi J, Kunderfranco P, Carriero R, Chen S, Samad M, Welz PS, Zinna VM, Mortimer T, Chun SK, Shimaji K, Sato T, Petrus P, Kumar A, Vaca-Dempere M, Deryagian O, Van C, Kuhn JMM, Lutter D, Seldin MM, Masri S, Li W, Baldi P, Dyar KA, Muñoz-Cánoves P, Benitah SA, Sassone-Corsi P. Integration of feeding behavior by the liver circadian clock reveals network dependency of metabolic rhythms. SCIENCE ADVANCES 2021; 7:eabi7828. [PMID: 34550736 PMCID: PMC8457671 DOI: 10.1126/sciadv.abi7828] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 07/29/2021] [Indexed: 05/28/2023]
Abstract
The mammalian circadian clock, expressed throughout the brain and body, controls daily metabolic homeostasis. Clock function in peripheral tissues is required, but not sufficient, for this task. Because of the lack of specialized animal models, it is unclear how tissue clocks interact with extrinsic signals to drive molecular oscillations. Here, we isolated the interaction between feeding and the liver clock by reconstituting Bmal1 exclusively in hepatocytes (Liver-RE), in otherwise clock-less mice, and controlling timing of food intake. We found that the cooperative action of BMAL1 and the transcription factor CEBPB regulates daily liver metabolic transcriptional programs. Functionally, the liver clock and feeding rhythm are sufficient to drive temporal carbohydrate homeostasis. By contrast, liver rhythms tied to redox and lipid metabolism required communication with the skeletal muscle clock, demonstrating peripheral clock cross-talk. Our results highlight how the inner workings of the clock system rely on communicating signals to maintain daily metabolism.
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Affiliation(s)
- Carolina M. Greco
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Kevin B. Koronowski
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Jacob G. Smith
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Jiejun Shi
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Paolo Kunderfranco
- Bioinformatics Unit, Humanitas Clinical and Research Center–IRCCS, Rozzano 20089, Italy
| | - Roberta Carriero
- Bioinformatics Unit, Humanitas Clinical and Research Center–IRCCS, Rozzano 20089, Italy
| | - Siwei Chen
- Institute for Genomics and Bioinformatics, Department of Computer Science, UCI, Irvine, CA 92697, USA
| | - Muntaha Samad
- Institute for Genomics and Bioinformatics, Department of Computer Science, UCI, Irvine, CA 92697, USA
| | - Patrick-Simon Welz
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona 08028, Spain
- Program in Cancer Research, Hospital del Mar Medical Research Institute (IMIM), Dr. Aiguader 88, Barcelona 08003, Spain
| | - Valentina M. Zinna
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona 08028, Spain
| | - Thomas Mortimer
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona 08028, Spain
| | - Sung Kook Chun
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Kohei Shimaji
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Tomoki Sato
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Paul Petrus
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Arun Kumar
- Department of Experimental and Health Sciences, Pompeu Fabra University (UPF), CIBER on Neurodegenerative Diseases (CIBERNED), Barcelona 08003, Spain
| | - Mireia Vaca-Dempere
- Department of Experimental and Health Sciences, Pompeu Fabra University (UPF), CIBER on Neurodegenerative Diseases (CIBERNED), Barcelona 08003, Spain
| | - Oleg Deryagian
- Department of Experimental and Health Sciences, Pompeu Fabra University (UPF), CIBER on Neurodegenerative Diseases (CIBERNED), Barcelona 08003, Spain
| | - Cassandra Van
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - José Manuel Monroy Kuhn
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Computational Discovery Research, Institute for Diabetes and Obesity (IDO), Helmholtz Diabetes Center (HDC), Helmholtz Zentrum München, Neuherberg, Germany
| | - Dominik Lutter
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Computational Discovery Research, Institute for Diabetes and Obesity (IDO), Helmholtz Diabetes Center (HDC), Helmholtz Zentrum München, Neuherberg, Germany
| | - Marcus M. Seldin
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Selma Masri
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Wei Li
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Pierre Baldi
- Institute for Genomics and Bioinformatics, Department of Computer Science, UCI, Irvine, CA 92697, USA
| | - Kenneth A. Dyar
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Metabolic Physiology, Institute for Diabetes and Cancer (IDC), Helmholtz Diabetes Center, Helmholtz Zentrum München, Neuherberg, Germany
| | - Pura Muñoz-Cánoves
- Department of Experimental and Health Sciences, Pompeu Fabra University (UPF), CIBER on Neurodegenerative Diseases (CIBERNED), Barcelona 08003, Spain
- Spanish National Center on Cardiovascular Research (CNIC), Madrid 28029, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona 08010, Spain
| | - Salvador Aznar Benitah
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona 08028, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona 08010, Spain
| | - Paolo Sassone-Corsi
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
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45
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Aviram R, Adamovich Y, Asher G. Circadian Organelles: Rhythms at All Scales. Cells 2021; 10:2447. [PMID: 34572096 PMCID: PMC8469338 DOI: 10.3390/cells10092447] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Revised: 09/14/2021] [Accepted: 09/14/2021] [Indexed: 12/12/2022] Open
Abstract
Circadian clocks have evolved in most light-sensitive organisms, from unicellular organisms to mammals. Consequently, a myriad of biological functions exhibits circadian rhythmicity, from behavior to physiology, through tissue and cellular functions to subcellular processes. Circadian rhythms in intracellular organelles are an emerging and exciting research arena. We summarize herein the current literature for rhythmicity in major intracellular organelles in mammals. These include changes in the morphology, content, and functions of different intracellular organelles. While these data highlight the presence of rhythmicity in these organelles, a gap remains in our knowledge regarding the underlying molecular mechanisms and their functional significance. Finally, we discuss the importance and challenges faced by spatio-temporal studies on these organelles and speculate on the presence of oscillators in organelles and their potential mode of communication. As circadian biology has been and continues to be studied throughout temporal and spatial axes, circadian organelles appear to be the next frontier.
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Affiliation(s)
| | | | - Gad Asher
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel; (R.A.); (Y.A.)
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46
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Elowe C, Tomanek L. Circadian and circatidal rhythms of protein abundance in the California mussel (Mytilus californianus). Mol Ecol 2021; 30:5151-5163. [PMID: 34390513 DOI: 10.1111/mec.16122] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 08/04/2021] [Accepted: 08/11/2021] [Indexed: 11/26/2022]
Abstract
Coastal habitats fluctuate with the 12.4 h tidal and 24 h light/dark cycle to predictably alter conditions such as air exposure, temperature, and food availability. Intertidal sessile bivalves exhibit behavioral and physiological adjustments to minimize the challenges of this environment. We investigated a high-resolution time course of the changes in protein abundance in the gill tissue of the intertidal mussel Mytilus californianus in a simulated tidal environment of 12:12 h light:dark cycles and a matching 6:6 h high:low tide cycle within each 12 h period. Approximately 38% of detected proteins showed significant rhythms in their abundances, with diversity in the phases of rhythmic isoforms. The circadian rhythm was dominant in protein abundance changes, particularly with oxidative metabolism. A tidal cycle elicited changes within functional groups, including in cytoskeletal proteins, chaperones, and oxidative stress proteins. In addition to protein abundance changes, we found the possibility for post-translational modifications driving rhythms, including methylation, mitochondrial peptide processing (proteolysis), and acylation. Dynamic changes in the proteome across functional categories demonstrate the importance of the tidal environment in entraining cellular processes, confirming that differential expression studies should not assume a static baseline of cellular conditions in intertidal organisms.
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Affiliation(s)
- Cory Elowe
- California Polytechnic State University, Department of Biological Sciences Environmental Proteomics Laboratory, Grand Avenue San Luis Obispo, CA, USA
| | - Lars Tomanek
- California Polytechnic State University, Department of Biological Sciences Environmental Proteomics Laboratory, Grand Avenue San Luis Obispo, CA, USA
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47
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Levine DC, Ramsey KM, Bass J. Circadian NAD(P)(H) cycles in cell metabolism. Semin Cell Dev Biol 2021; 126:15-26. [PMID: 34281771 DOI: 10.1016/j.semcdb.2021.07.008] [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: 03/31/2021] [Revised: 07/02/2021] [Accepted: 07/08/2021] [Indexed: 10/20/2022]
Abstract
Intrinsic circadian clocks are present in all forms of photosensitive life, enabling daily anticipation of the light/dark cycle and separation of energy storage and utilization cycles on a 24-h timescale. The core mechanism underlying circadian rhythmicity involves a cell-autonomous transcription/translation feedback loop that in turn drives rhythmic organismal physiology. In mammals, genetic studies have established that the core clock plays an essential role in maintaining metabolic health through actions within both brain pacemaker neurons and peripheral tissues and that disruption of the clock contributes to disease. Peripheral clocks, in turn, can be entrained by metabolic cues. In this review, we focus on the role of the nucleotide NAD(P)(H) and NAD+-dependent sirtuin deacetylases as integrators of circadian and metabolic cycles, as well as the implications for this interrelationship in healthful aging.
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Affiliation(s)
- Daniel C Levine
- Department of Medicine, Division of Endocrinology, Metabolism, and Molecular Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Kathryn M Ramsey
- Department of Medicine, Division of Endocrinology, Metabolism, and Molecular Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Joseph Bass
- Department of Medicine, Division of Endocrinology, Metabolism, and Molecular Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.
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48
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Galloway A, Kaskar A, Ditsova D, Atrih A, Yoshikawa H, Gomez-Moreira C, Suska O, Warminski M, Grzela R, Lamond AI, Darzynkiewicz E, Jemielity J, Cowling V. Upregulation of RNA cap methyltransferase RNMT drives ribosome biogenesis during T cell activation. Nucleic Acids Res 2021; 49:6722-6738. [PMID: 34125914 PMCID: PMC8266598 DOI: 10.1093/nar/gkab465] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 05/09/2021] [Accepted: 05/17/2021] [Indexed: 01/07/2023] Open
Abstract
The m7G cap is ubiquitous on RNAPII-transcribed RNA and has fundamental roles in eukaryotic gene expression, however its in vivo role in mammals has remained unknown. Here, we identified the m7G cap methyltransferase, RNMT, as a key mediator of T cell activation, which specifically regulates ribosome production. During T cell activation, induction of mRNA expression and ribosome biogenesis drives metabolic reprogramming, rapid proliferation and differentiation generating effector populations. We report that RNMT is induced by T cell receptor (TCR) stimulation and co-ordinates the mRNA, snoRNA and rRNA production required for ribosome biogenesis. Using transcriptomic and proteomic analyses, we demonstrate that RNMT selectively regulates the expression of terminal polypyrimidine tract (TOP) mRNAs, targets of the m7G-cap binding protein LARP1. The expression of LARP1 targets and snoRNAs involved in ribosome biogenesis is selectively compromised in Rnmt cKO CD4 T cells resulting in decreased ribosome synthesis, reduced translation rates and proliferation failure. By enhancing ribosome abundance, upregulation of RNMT co-ordinates mRNA capping and processing with increased translational capacity during T cell activation.
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Affiliation(s)
- Alison Galloway
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Aneesa Kaskar
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Dimitrinka Ditsova
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Abdelmadjid Atrih
- FingerPrints Proteomics Facility, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Harunori Yoshikawa
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Carolina Gomez-Moreira
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Olga Suska
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Marcin Warminski
- Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland
| | - Renata Grzela
- Centre of New Technologies, University of Warsaw, 02-097 Warsaw, and Division of Physics, 02-093 Warsaw, Poland
| | - Angus I Lamond
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Edward Darzynkiewicz
- Centre of New Technologies, University of Warsaw, 02-097 Warsaw, and Division of Physics, 02-093 Warsaw, Poland
| | - Jacek Jemielity
- Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland
| | - Victoria H Cowling
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
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Pelikan A, Herzel H, Kramer A, Ananthasubramaniam B. Venn diagram analysis overestimates the extent of circadian rhythm reprogramming. FEBS J 2021; 289:6605-6621. [PMID: 34189845 DOI: 10.1111/febs.16095] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 05/18/2021] [Accepted: 06/28/2021] [Indexed: 12/13/2022]
Abstract
The circadian clock modulates key physiological processes in many organisms. This widespread role of circadian rhythms is typically characterized at the molecular level by profiling the transcriptome at multiple time points. Subsequent analysis identifies transcripts with altered rhythms between control and perturbed conditions, that is, are differentially rhythmic (DiffR). Commonly, Venn diagram analysis (VDA) compares lists of rhythmic transcripts to catalog transcripts with rhythms in both conditions, or that have gained or lost rhythms. However, unavoidable errors in rhythmicity detection propagate to the final DiffR classification resulting in overestimated DiffR. We show using artificial experiments on biological data that VDA indeed produces excessive false DiffR hits both in the presence and absence of true DiffR transcripts. We review and benchmark hypothesis testing and model selection approaches that instead compare circadian amplitude and phase of transcripts between the two conditions. These methods identify transcripts that 'gain', 'lose', 'change', or have the 'same' rhythms; the third category is missed by VDA. We reanalyzed three studies on the interplay between metabolism and the clock in the mouse liver that used VDA. We found not only fewer DiffR transcripts than originally reported, but VDA overlooked many relevant DiffR transcripts. Our analyses confirmed some and contradicted other conclusions in the original studies and also generated novel insights. Our conclusions equally apply to circadian studies using other omics technologies. We believe that avoiding Venn diagrams and using our convenient r-package comparerhythms will improve the reliability of analyses in chronobiology.
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Affiliation(s)
- Anne Pelikan
- Institute for Theoretical Biology, Humboldt Universität zu Berlin, Germany
| | - Hanspeter Herzel
- Institute for Theoretical Biology, Charité Universitätsmedizin Berlin, Germany
| | - Achim Kramer
- Institute for Medical Immunology, Charité Universitätsmedizin Berlin, Germany
| | - Bharath Ananthasubramaniam
- Institute for Theoretical Biology, Humboldt Universität zu Berlin, Germany.,Institute for Theoretical Biology, Charité Universitätsmedizin Berlin, Germany
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50
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Kinouchi K, Mikami Y, Kanai T, Itoh H. Circadian rhythms in the tissue-specificity from metabolism to immunity; insights from omics studies. Mol Aspects Med 2021; 80:100984. [PMID: 34158177 DOI: 10.1016/j.mam.2021.100984] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 05/04/2021] [Accepted: 06/07/2021] [Indexed: 12/31/2022]
Abstract
Creatures on earth have the capacity to preserve homeostasis in response to changing environments. The circadian clock enables organisms to adapt to daily predictable rhythms in surrounding conditions. In mammals, circadian clocks constitute hierarchical network, where the central pacemaker in hypothalamic suprachiasmatic nucleus (SCN) serves as a time-keeping machinery and governs peripheral clocks in every other organ through descending neural and humoral factors. The central clock in SCN is reset by light, whilst peripheral clocks are entrained by feeding-fasting rhythms, emphasizing the point that temporal patterns of nutrient availability specifies peripheral clock functions. Indeed, emerging evidence revealed various types of diets or timing of food intake reprogram circadian rhythms in a tissue specific manner. This advancement in understanding of mechanisms underlying tissue specific responsiveness of circadian oscillators to nutrients at the genomic and epigenomic levels is largely owing to employment of state-of-the-art technologies. Specifically, high-throughput transcriptome, proteome, and metabolome have provided insights into how genes, proteins, and metabolites behave over circadian cycles in a given tissue under a certain dietary condition in an unbiased fashion. Additionally, combinations with specialized types of sequencing such as nascent-seq and ribosomal profiling allow us to dissect how circadian rhythms are generated or obliterated at each step of gene regulation. Importantly, chromatin immunoprecipitation followed by deep sequencing methods provide chromatin landscape in terms of regulatory mechanisms of circadian gene expression. In this review, we outline recent discoveries on temporal genomic and epigenomic regulation of circadian rhythms, discussing entrainment of the circadian rhythms by feeding as a fundamental new comprehension of metabolism and immune response, and as a potential therapeutic strategy of metabolic and inflammatory diseases.
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Affiliation(s)
- Kenichiro Kinouchi
- Division of Endocrinology, Metabolism, and Nephrology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, 160-8582, Japan.
| | - Yohei Mikami
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan.
| | - Takanori Kanai
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Hiroshi Itoh
- Division of Endocrinology, Metabolism, and Nephrology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, 160-8582, Japan
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