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Xie X, Zhang M, Luo H. Regulation of metabolism by circadian rhythms: Support from time-restricted eating, intestinal microbiota & omics analysis. Life Sci 2024; 351:122814. [PMID: 38857654 DOI: 10.1016/j.lfs.2024.122814] [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: 02/18/2024] [Revised: 05/05/2024] [Accepted: 06/04/2024] [Indexed: 06/12/2024]
Abstract
Circadian oscillatory system plays a key role in coordinating the metabolism of most organisms. Perturbation of genetic effects and misalignment of circadian rhythms result in circadian dysfunction and signs of metabolic disorders. The eating-fasting cycle can act on the peripheral circadian clocks, bypassing the photoperiod. Therefore, time-restricted eating (TRE) can improve metabolic health by adjusting eating rhythms, a process achieved through reprogramming of circadian genomes and metabolic programs at different tissue levels or remodeling of the intestinal microbiota, with omics technology allowing visualization of the regulatory processes. Here, we review recent advances in circadian regulation of metabolism, focus on the potential application of TRE for rescuing circadian dysfunction and metabolic disorders with the contribution of intestinal microbiota in between, and summarize the significance of omics technology.
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Affiliation(s)
- Ximei Xie
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, PR China
| | - Mengjie Zhang
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, PR China
| | - Hailing Luo
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, PR China.
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2
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Inoue SI, Emmett MJ, Lim HW, Midha M, Richter HJ, Celwyn IJ, Mehmood R, Chondronikola M, Klein S, Hauck AK, Lazar MA. Short-term cold exposure induces persistent epigenomic memory in brown fat. Cell Metab 2024; 36:1764-1778.e9. [PMID: 38889724 PMCID: PMC11305953 DOI: 10.1016/j.cmet.2024.05.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 04/01/2024] [Accepted: 05/21/2024] [Indexed: 06/20/2024]
Abstract
Deficiency of the epigenome modulator histone deacetylase 3 (HDAC3) in brown adipose tissue (BAT) impairs the ability of mice to survive in near-freezing temperatures. Here, we report that short-term exposure to mild cold temperature (STEMCT: 15°C for 24 h) averted lethal hypothermia of mice lacking HDAC3 in BAT (HDAC3 BAT KO) exposed to 4°C. STEMCT restored the induction of the thermogenic coactivator PGC-1α along with UCP1 at 22°C, which is greatly impaired in HDAC3-deficient BAT, and deletion of either UCP1 or PGC-1α prevented the protective effect of STEMCT. Remarkably, this protection lasted for up to 7 days. Transcriptional activator C/EBPβ was induced by short-term cold exposure in mouse and human BAT and, uniquely, remained high for 7 days following STEMCT. Adeno-associated virus-mediated knockdown of BAT C/EBPβ in HDAC3 BAT KO mice erased the persistent memory of STEMCT, revealing the existence of a C/EBPβ-dependent and HDAC3-independent cold-adaptive epigenomic memory.
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Affiliation(s)
- Shin-Ichi Inoue
- Institute for Diabetes, Obesity, and Metabolism, and Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Matthew J Emmett
- Institute for Diabetes, Obesity, and Metabolism, and Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Medical Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Hee-Woong Lim
- Institute for Diabetes, Obesity, and Metabolism, and Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Mohit Midha
- Institute for Diabetes, Obesity, and Metabolism, and Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Hannah J Richter
- Institute for Diabetes, Obesity, and Metabolism, and Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Isaac J Celwyn
- Institute for Diabetes, Obesity, and Metabolism, and Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Rashid Mehmood
- Institute for Diabetes, Obesity, and Metabolism, and Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Maria Chondronikola
- Institute of Metabolic Science-Metabolic Research Laboratories and Medical Research Council Metabolic Diseases Unit, University of Cambridge, Cambridge, UK; Department of Nutrition and Dietetics, Harokopio University of Athens, Athens, Greece
| | - Samuel Klein
- Division of Geriatrics and Nutritional Science, Washington University School of Medicine, St. Louis, MO, USA
| | - Amy K Hauck
- Institute for Diabetes, Obesity, and Metabolism, and Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Mitchell A Lazar
- Institute for Diabetes, Obesity, and Metabolism, and Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA.
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Guan D, Chen Y, Liu P, Sabo A. Human genetic variation determines 24-hour rhythmic gene expression and disease risk. RESEARCH SQUARE 2024:rs.3.rs-4790200. [PMID: 39149455 PMCID: PMC11326361 DOI: 10.21203/rs.3.rs-4790200/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
24-hour biological rhythms are essential to maintain physiological homeostasis. Disruption of these rhythms increases the risks of multiple diseases. The biological rhythms are known to have a genetic basis formed by core clock genes, but how individual genetic variation shapes the oscillating transcriptome and contributes to human chronophysiology and disease risk is largely unknown. Here, we mapped interactions between temporal gene expression and genotype to identify quantitative trait loci (QTLs) contributing to rhythmic gene expression. These newly identified QTLs were termed as rhythmic QTLs (rhyQTLs), which determine previously unappreciated rhythmic genes in human subpopulations with specific genotypes. Functionally, rhyQTLs and their associated rhythmic genes contribute extensively to essential chronophysiological processes, including bile acid and lipid metabolism. The identification of rhyQTLs sheds light on the genetic mechanisms of gene rhythmicity, offers mechanistic insights into variations in human disease risk, and enables precision chronotherapeutic approaches for patients.
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Pacheco-Bernal I, Becerril-Pérez F, Bustamante-Zepeda M, González-Suárez M, Olmedo-Suárez MA, Hernández-Barrientos LR, Alarcón-Del-Carmen A, Escalante-Covarrubias Q, Mendoza-Viveros L, Hernández-Lemus E, León-Del-Río A, de la Rosa-Velázquez IA, Orozco-Solis R, Aguilar-Arnal L. Transitions in chromatin conformation shaped by fatty acids and the circadian clock underlie hepatic transcriptional reorganization in obese mice. Cell Mol Life Sci 2024; 81:309. [PMID: 39060446 PMCID: PMC11335233 DOI: 10.1007/s00018-024-05364-3] [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: 02/15/2024] [Revised: 06/25/2024] [Accepted: 07/12/2024] [Indexed: 07/28/2024]
Abstract
The circadian clock system coordinates metabolic, physiological, and behavioral functions across a 24-h cycle, crucial for adapting to environmental changes. Disruptions in circadian rhythms contribute to major metabolic pathologies like obesity and Type 2 diabetes. Understanding the regulatory mechanisms governing circadian control is vital for identifying therapeutic targets. It is well characterized that chromatin remodeling and 3D structure at genome regulatory elements contributes to circadian transcriptional cycles; yet the impact of rhythmic chromatin topology in metabolic disease is largely unexplored. In this study, we explore how the spatial configuration of the genome adapts to diet, rewiring circadian transcription and contributing to dysfunctional metabolism. We describe daily fluctuations in chromatin contacts between distal regulatory elements of metabolic control genes in livers from lean and obese mice and identify specific lipid-responsive regions recruiting the clock molecular machinery. Interestingly, under high-fat feeding, a distinct interactome for the clock-controlled gene Dbp strategically promotes the expression of distal metabolic genes including Fgf21. Alongside, new chromatin loops between regulatory elements from genes involved in lipid metabolism control contribute to their transcriptional activation. These enhancers are responsive to lipids through CEBPβ, counteracting the circadian repressor REVERBa. Our findings highlight the intricate coupling of circadian gene expression to a dynamic nuclear environment under high-fat feeding, supporting a temporally regulated program of gene expression and transcriptional adaptation to diet.
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Affiliation(s)
- Ignacio Pacheco-Bernal
- Departamento de Biología Celular y Fisiología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Fernando Becerril-Pérez
- Departamento de Biología Celular y Fisiología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Marcia Bustamante-Zepeda
- Departamento de Biología Celular y Fisiología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Mirna González-Suárez
- Departamento de Biología Celular y Fisiología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Miguel A Olmedo-Suárez
- Departamento de Biología Celular y Fisiología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Luis Ricardo Hernández-Barrientos
- Departamento de Biología Celular y Fisiología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Alejandro Alarcón-Del-Carmen
- Departamento de Biología Celular y Fisiología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Quetzalcoatl Escalante-Covarrubias
- Departamento de Biología Celular y Fisiología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Lucía Mendoza-Viveros
- Departamento de Biología Celular y Fisiología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
- Laboratorio de Cronobiología, Metabolismo y Envejecimiento, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico
- Centro de Investigacíon sobre el Envejecimiento, Centro de Investigación y de Estudios Avanzados (CIE-CINVESTAV), Mexico City, México
- Instituto Potosino de Investigación Científica y Tecnológica, San Luis Potosí, Mexico
| | - Enrique Hernández-Lemus
- Department of Computational Genomics, Centro de Ciencias de La Complejidad (C3), Instituto Nacional de Medicina Genómica (INMEGEN), Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Alfonso León-Del-Río
- Departamento de Medicina Genómica y Toxicología Ambiental, Programa Institucional de Cáncer de Mama, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Inti A de la Rosa-Velázquez
- Genomics Laboratory, Red de Apoyo a la Investigación-CIC, Universidad Nacional Autónoma de México, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, 14080, Mexico City, Mexico
- Next Generation Sequencing Core Facility, Helmholtz Zentrum Muenchen, Ingolstaedter Landstr 1, 85754, Neuherberg, Germany
| | - Ricardo Orozco-Solis
- Laboratorio de Cronobiología, Metabolismo y Envejecimiento, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico
- Centro de Investigacíon sobre el Envejecimiento, Centro de Investigación y de Estudios Avanzados (CIE-CINVESTAV), Mexico City, México
| | - Lorena Aguilar-Arnal
- Departamento de Biología Celular y Fisiología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico.
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Lee K, Hong KS, Park J, Park W. Readjustment of circadian clocks by exercise intervention is a potential therapeutic target for sleep disorders: a narrative review. Phys Act Nutr 2024; 28:35-42. [PMID: 39097996 PMCID: PMC11298283 DOI: 10.20463/pan.2024.0014] [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: 03/21/2024] [Revised: 04/25/2024] [Accepted: 05/17/2024] [Indexed: 08/06/2024] Open
Abstract
PURPOSE Circadian clocks are evolved endogenous biological systems that communicate with environmental cues to optimize physiological processes, such as the sleep-wake cycle, which is nearly related to quality of life. Sleep disorders can be treated using pharmacological strategies targeting melatonin, orexin, or core clock genes. Exercise has been widely explored as a behavioral treatment because it challenges homeostasis in the human body and affects the regulation of core clock genes. Exercise intervention at the appropriate time of the day can induce a phase shift in internal clocks. Although exercise is a strong external time cue for resetting the circadian clock, exercise therapy for sleep disorders remains poorly understood. METHODS This review focused on exercise as a potential treatment for sleep disorders by tuning the internal circadian clock. We used scientific paper depositories, including Google Scholar, PubMed, and the Cochrane Library, to identify previous studies that investigated the effects of exercise on circadian clocks and sleep disorders. RESULTS The exercise-induced adjustment of the circadian clock phase depended on exercise timing and individual chronotypes. Adjustment of circadian clocks through scheduled morning exercises can be appropriately prescribed for individuals with delayed sleep phase disorders. Individuals with advanced sleep phase disorders can synchronize their internal clocks with their living environment by performing evening exercises. Exercise-induced physiological responses are affected by age, sex, and current fitness conditions. CONCLUSION Personalized approaches are necessary when implementing exercise interventions for sleep disorders.
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Affiliation(s)
- Kwangjun Lee
- Department of Neurology, Rosamund Stone Zander Translational Neuroscience Center, Boston Children’s Hospital, Boston, Massachusetts, USA
| | - Kwang-Seok Hong
- Department of Physical Education, College of Education, Chung-Ang University, Seoul, Republic of Korea
| | - Jonghoon Park
- Department of Physical Education, Korea University, Seoul, Republic of Korea
| | - Wonil Park
- Department of Physical Education, College of Education, Chung-Ang University, Seoul, Republic of Korea
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Tikhomirov R, Oakley RH, Anderson C, Xiang Y, Al-Othman S, Smith M, Yaar S, Torre E, Li J, Wilson LR, Goulding DR, Donaldson I, Harno E, Soattin L, Shiels HA, Morris GM, Zhang H, Boyett MR, Cidlowski JA, Mesirca P, Mangoni ME, D'Souza A. Cardiac GR Mediates the Diurnal Rhythm in Ventricular Arrhythmia Susceptibility. Circ Res 2024; 134:1306-1326. [PMID: 38533639 PMCID: PMC11081863 DOI: 10.1161/circresaha.123.323464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 02/15/2024] [Accepted: 03/13/2024] [Indexed: 03/28/2024]
Abstract
BACKGROUND Ventricular arrhythmias (VAs) demonstrate a prominent day-night rhythm, commonly presenting in the morning. Transcriptional rhythms in cardiac ion channels accompany this phenomenon, but their role in the morning vulnerability to VAs and the underlying mechanisms are not understood. We investigated the recruitment of transcription factors that underpins transcriptional rhythms in ion channels and assessed whether this mechanism was pertinent to the heart's intrinsic diurnal susceptibility to VA. METHODS AND RESULTS Assay for transposase-accessible chromatin with sequencing performed in mouse ventricular myocyte nuclei at the beginning of the animals' inactive (ZT0) and active (ZT12) periods revealed differentially accessible chromatin sites annotating to rhythmically transcribed ion channels and distinct transcription factor binding motifs in these regions. Notably, motif enrichment for the glucocorticoid receptor (GR; transcriptional effector of corticosteroid signaling) in open chromatin profiles at ZT12 was observed, in line with the well-recognized ZT12 peak in circulating corticosteroids. Molecular, electrophysiological, and in silico biophysically-detailed modeling approaches demonstrated GR-mediated transcriptional control of ion channels (including Scn5a underlying the cardiac Na+ current, Kcnh2 underlying the rapid delayed rectifier K+ current, and Gja1 responsible for electrical coupling) and their contribution to the day-night rhythm in the vulnerability to VA. Strikingly, both pharmacological block of GR and cardiomyocyte-specific genetic knockout of GR blunted or abolished ion channel expression rhythms and abolished the ZT12 susceptibility to pacing-induced VA in isolated hearts. CONCLUSIONS Our study registers a day-night rhythm in chromatin accessibility that accompanies diurnal cycles in ventricular myocytes. Our approaches directly implicate the cardiac GR in the myocyte excitability rhythm and mechanistically link the ZT12 surge in glucocorticoids to intrinsic VA propensity at this time.
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Affiliation(s)
- Roman Tikhomirov
- Division of Cardiovascular Sciences (R.T., C.A., S.A.O., M.S., S.Y., L.S., H.A.S., G.M.M., A.D.), The University of Manchester, United Kingdom
- Myocardial Function Section, National Heart and Lung Institute, Imperial College London, United Kingdom (R.T., M.S., A.D.)
| | - Robert H Oakley
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health (R.H.O., J.L., L.R.W., D.R.G., J.A.C.)
| | - Cali Anderson
- Division of Cardiovascular Sciences (R.T., C.A., S.A.O., M.S., S.Y., L.S., H.A.S., G.M.M., A.D.), The University of Manchester, United Kingdom
| | - Yirong Xiang
- Department of Physics and Astronomy (Y.X., H.Z.), The University of Manchester, United Kingdom
| | - Sami Al-Othman
- Division of Cardiovascular Sciences (R.T., C.A., S.A.O., M.S., S.Y., L.S., H.A.S., G.M.M., A.D.), The University of Manchester, United Kingdom
| | - Matthew Smith
- Division of Cardiovascular Sciences (R.T., C.A., S.A.O., M.S., S.Y., L.S., H.A.S., G.M.M., A.D.), The University of Manchester, United Kingdom
- Myocardial Function Section, National Heart and Lung Institute, Imperial College London, United Kingdom (R.T., M.S., A.D.)
| | - Sana Yaar
- Division of Cardiovascular Sciences (R.T., C.A., S.A.O., M.S., S.Y., L.S., H.A.S., G.M.M., A.D.), The University of Manchester, United Kingdom
| | - Eleonora Torre
- Institut de Génomique Fonctionnelle, Université de Montpellier, Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), F-34094 Montpellier France (E.T., P.M., M.E.M.)
| | - Jianying Li
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health (R.H.O., J.L., L.R.W., D.R.G., J.A.C.)
| | - Leslie R Wilson
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health (R.H.O., J.L., L.R.W., D.R.G., J.A.C.)
| | - David R Goulding
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health (R.H.O., J.L., L.R.W., D.R.G., J.A.C.)
| | - Ian Donaldson
- Bioinformatics Core Facility (I.D.), The University of Manchester, United Kingdom
| | - Erika Harno
- Division of Diabetes, Endocrinology and Gastroenterology (E.H.), The University of Manchester, United Kingdom
| | - Luca Soattin
- Division of Cardiovascular Sciences (R.T., C.A., S.A.O., M.S., S.Y., L.S., H.A.S., G.M.M., A.D.), The University of Manchester, United Kingdom
| | - Holly A Shiels
- Division of Cardiovascular Sciences (R.T., C.A., S.A.O., M.S., S.Y., L.S., H.A.S., G.M.M., A.D.), The University of Manchester, United Kingdom
| | - Gwilym M Morris
- Division of Cardiovascular Sciences (R.T., C.A., S.A.O., M.S., S.Y., L.S., H.A.S., G.M.M., A.D.), The University of Manchester, United Kingdom
- Department of Cardiology, John Hunter Hospital, Newcastle, NSW, Australia (G.M.M.)
| | - Henggui Zhang
- Department of Physics and Astronomy (Y.X., H.Z.), The University of Manchester, United Kingdom
| | - Mark R Boyett
- Faculty of Life Sciences, University of Bradford, United Kingdom (M.R.B.)
| | - John A Cidlowski
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health (R.H.O., J.L., L.R.W., D.R.G., J.A.C.)
| | - Pietro Mesirca
- Institut de Génomique Fonctionnelle, Université de Montpellier, Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), F-34094 Montpellier France (E.T., P.M., M.E.M.)
| | - Matteo E Mangoni
- Institut de Génomique Fonctionnelle, Université de Montpellier, Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), F-34094 Montpellier France (E.T., P.M., M.E.M.)
| | - Alicia D'Souza
- Division of Cardiovascular Sciences (R.T., C.A., S.A.O., M.S., S.Y., L.S., H.A.S., G.M.M., A.D.), The University of Manchester, United Kingdom
- Myocardial Function Section, National Heart and Lung Institute, Imperial College London, United Kingdom (R.T., M.S., A.D.)
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Chen J, Wang R, Xiong F, Sun H, Kemper B, Li W, Kemper J. Hammerhead-type FXR agonists induce an enhancer RNA Fincor that ameliorates nonalcoholic steatohepatitis in mice. eLife 2024; 13:RP91438. [PMID: 38619504 PMCID: PMC11018349 DOI: 10.7554/elife.91438] [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] [Indexed: 04/16/2024] Open
Abstract
The nuclear receptor, farnesoid X receptor (FXR/NR1H4), is increasingly recognized as a promising drug target for metabolic diseases, including nonalcoholic steatohepatitis (NASH). Protein-coding genes regulated by FXR are well known, but whether FXR also acts through regulation of long non-coding RNAs (lncRNAs), which vastly outnumber protein-coding genes, remains unknown. Utilizing RNA-seq and global run-on sequencing (GRO-seq) analyses in mouse liver, we found that FXR activation affects the expression of many RNA transcripts from chromatin regions bearing enhancer features. Among these we discovered a previously unannotated liver-enriched enhancer-derived lncRNA (eRNA), termed FXR-induced non-coding RNA (Fincor). We show that Fincor is specifically induced by the hammerhead-type FXR agonists, including GW4064 and tropifexor. CRISPR/Cas9-mediated liver-specific knockdown of Fincor in dietary NASH mice reduced the beneficial effects of tropifexor, an FXR agonist currently in clinical trials for NASH and primary biliary cholangitis (PBC), indicating that amelioration of liver fibrosis and inflammation in NASH treatment by tropifexor is mediated in part by Fincor. Overall, our findings highlight that pharmacological activation of FXR by hammerhead-type agonists induces a novel eRNA, Fincor, contributing to the amelioration of NASH in mice. Fincor may represent a new drug target for addressing metabolic disorders, including NASH.
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Affiliation(s)
- Jinjing Chen
- Department of Molecular and Integrative Physiology, University of Illinois at Urbana-ChampaignUrbanaUnited States
| | - Ruoyu Wang
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science CenterHoustonUnited States
| | - Feng Xiong
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science CenterHoustonUnited States
| | - Hao Sun
- Department of Molecular and Integrative Physiology, University of Illinois at Urbana-ChampaignUrbanaUnited States
| | - Byron Kemper
- Department of Molecular and Integrative Physiology, University of Illinois at Urbana-ChampaignUrbanaUnited States
| | - Wenbo Li
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science CenterHoustonUnited States
| | - Jongsook Kemper
- Department of Molecular and Integrative Physiology, University of Illinois at Urbana-ChampaignUrbanaUnited States
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8
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Bass J. Interorgan rhythmicity as a feature of healthful metabolism. Cell Metab 2024; 36:655-669. [PMID: 38335957 PMCID: PMC10990795 DOI: 10.1016/j.cmet.2024.01.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 01/10/2024] [Accepted: 01/17/2024] [Indexed: 02/12/2024]
Abstract
The finding that animals with circadian gene mutations exhibit diet-induced obesity and metabolic syndrome with hypoinsulinemia revealed a distinct role for the clock in the brain and peripheral tissues. Obesogenic diets disrupt rhythmic sleep/wake patterns, feeding behavior, and transcriptional networks, showing that metabolic signals reciprocally control the clock. Providing access to high-fat diet only during the sleep phase (light period) in mice accelerates weight gain, whereas isocaloric time-restricted feeding during the active period enhances energy expenditure due to circadian induction of adipose thermogenesis. This perspective focuses on advances and unanswered questions in understanding the interorgan circadian control of healthful metabolism.
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Affiliation(s)
- 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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9
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Liao Z, Tang S, Nozawa K, Shimada K, Ikawa M, Monsivais D, Matzuk M. Affinity-tagged SMAD1 and SMAD5 mouse lines reveal transcriptional reprogramming mechanisms during early pregnancy. eLife 2024; 12:RP91434. [PMID: 38536963 PMCID: PMC10972565 DOI: 10.7554/elife.91434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024] Open
Abstract
Endometrial decidualization, a prerequisite for successful pregnancies, relies on transcriptional reprogramming driven by progesterone receptor (PR) and bone morphogenetic protein (BMP)-SMAD1/SMAD5 signaling pathways. Despite their critical roles in early pregnancy, how these pathways intersect in reprogramming the endometrium into a receptive state remains unclear. To define how SMAD1 and/or SMAD5 integrate BMP signaling in the uterus during early pregnancy, we generated two novel transgenic mouse lines with affinity tags inserted into the endogenous SMAD1 and SMAD5 loci (Smad1HA/HA and Smad5PA/PA). By profiling the genome-wide distribution of SMAD1, SMAD5, and PR in the mouse uterus, we demonstrated the unique and shared roles of SMAD1 and SMAD5 during the window of implantation. We also showed the presence of a conserved SMAD1, SMAD5, and PR genomic binding signature in the uterus during early pregnancy. To functionally characterize the translational aspects of our findings, we demonstrated that SMAD1/5 knockdown in human endometrial stromal cells suppressed expressions of canonical decidual markers (IGFBP1, PRL, FOXO1) and PR-responsive genes (RORB, KLF15). Here, our studies provide novel tools to study BMP signaling pathways and highlight the fundamental roles of SMAD1/5 in mediating both BMP signaling pathways and the transcriptional response to progesterone (P4) during early pregnancy.
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Affiliation(s)
- Zian Liao
- Department of Pathology & Immunology, Baylor College of MedicineHoustonUnited States
- Graduate Program of Genetics and Genomics, Baylor College of MedicineHoustonUnited States
- Department of Molecular and Human Genetics, Baylor College of MedicineHoustonUnited States
- Center for Drug Discovery, Baylor College of MedicineHoustonUnited States
| | - Suni Tang
- Department of Pathology & Immunology, Baylor College of MedicineHoustonUnited States
- Department of Molecular and Human Genetics, Baylor College of MedicineHoustonUnited States
| | - Kaori Nozawa
- Department of Pathology & Immunology, Baylor College of MedicineHoustonUnited States
- Center for Drug Discovery, Baylor College of MedicineHoustonUnited States
| | - Keisuke Shimada
- Research Institute for Microbial Diseases, Osaka UniversityOsakaJapan
| | - Masahito Ikawa
- Research Institute for Microbial Diseases, Osaka UniversityOsakaJapan
| | - Diana Monsivais
- Department of Pathology & Immunology, Baylor College of MedicineHoustonUnited States
- Center for Drug Discovery, Baylor College of MedicineHoustonUnited States
| | - Martin Matzuk
- Department of Pathology & Immunology, Baylor College of MedicineHoustonUnited States
- Graduate Program of Genetics and Genomics, Baylor College of MedicineHoustonUnited States
- Department of Molecular and Human Genetics, Baylor College of MedicineHoustonUnited States
- Center for Drug Discovery, Baylor College of MedicineHoustonUnited States
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10
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Scoyni F, Sitnikova V, Giudice L, Korhonen P, Trevisan DM, Hernandez de Sande A, Gomez-Budia M, Giniatullina R, Ugidos IF, Dhungana H, Pistono C, Korvenlaita N, Välimäki NN, Kangas SM, Hiltunen AE, Gribchenko E, Kaikkonen-Määttä MU, Koistinaho J, Ylä-Herttuala S, Hinttala R, Venø MT, Su J, Stoffel M, Schaefer A, Rajewsky N, Kjems J, LaPierre MP, Piwecka M, Jolkkonen J, Giniatullin R, Hansen TB, Malm T. ciRS-7 and miR-7 regulate ischemia-induced neuronal death via glutamatergic signaling. Cell Rep 2024; 43:113862. [PMID: 38446664 DOI: 10.1016/j.celrep.2024.113862] [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: 06/02/2023] [Revised: 11/30/2023] [Accepted: 02/08/2024] [Indexed: 03/08/2024] Open
Abstract
Brain functionality relies on finely tuned regulation of gene expression by networks of non-coding RNAs (ncRNAs) such as the one composed by the circular RNA ciRS-7 (also known as CDR1as), the microRNA miR-7, and the long ncRNA Cyrano. We describe ischemia-induced alterations in the ncRNA network both in vitro and in vivo and in transgenic mice lacking ciRS-7 or miR-7. Our data show that cortical neurons downregulate ciRS-7 and Cyrano and upregulate miR-7 expression during ischemia. Mice lacking ciRS-7 exhibit reduced lesion size and motor impairment, while the absence of miR-7 alone results in increased ischemia-induced neuronal death. Moreover, miR-7 levels in pyramidal excitatory neurons regulate neurite morphology and glutamatergic signaling, suggesting a potential molecular link to the in vivo phenotype. Our data reveal the role of ciRS-7 and miR-7 in modulating ischemic stroke outcome, shedding light on the pathophysiological function of intracellular ncRNA networks in the brain.
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Affiliation(s)
- Flavia Scoyni
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70221 Kuopio, Finland.
| | - Valeriia Sitnikova
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70221 Kuopio, Finland
| | - Luca Giudice
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70221 Kuopio, Finland
| | - Paula Korhonen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70221 Kuopio, Finland
| | - Davide M Trevisan
- Department of Biosciences and Nutrition, Karolinska Institute, 17177 Stockholm, Sweden
| | | | - Mireia Gomez-Budia
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70221 Kuopio, Finland
| | - Raisa Giniatullina
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70221 Kuopio, Finland
| | - Irene F Ugidos
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70221 Kuopio, Finland
| | - Hiramani Dhungana
- Neuroscience Center, University of Helsinki, 00290 Helsinki, Finland
| | - Cristiana Pistono
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70221 Kuopio, Finland
| | - Nea Korvenlaita
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70221 Kuopio, Finland
| | - Nelli-Noora Välimäki
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70221 Kuopio, Finland
| | | | - Anniina E Hiltunen
- Medical Research Center Oulu and Research Unit of Clinical Medicine, University of Oulu and Oulu University Hospital, 90014 Oulu, Finland
| | - Emma Gribchenko
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70221 Kuopio, Finland
| | - Minna U Kaikkonen-Määttä
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70221 Kuopio, Finland
| | - Jari Koistinaho
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70221 Kuopio, Finland; Neuroscience Center, University of Helsinki, 00290 Helsinki, Finland
| | - Seppo Ylä-Herttuala
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70221 Kuopio, Finland
| | - Reetta Hinttala
- Biocenter Oulu, University of Oulu, 90014 Oulu, Finland; Medical Research Center Oulu and Research Unit of Clinical Medicine, University of Oulu and Oulu University Hospital, 90014 Oulu, Finland
| | - Morten T Venø
- Omiics ApS, 8200 Aarhus, Denmark; Interdisciplinary Nanoscience Center, Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark
| | - Junyi Su
- Interdisciplinary Nanoscience Center, Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark
| | - Markus Stoffel
- Institute of Molecular Health Sciences, ETH Zurich, 8093 Zürich, Switzerland
| | - Anne Schaefer
- Departments of Neuroscience and Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6504, USA; Max Planck Institute, Biology of Ageing, 50931 Cologne, Germany
| | - Nikolaus Rajewsky
- Systems Biology of Gene Regulatory Elements, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), 10115 Berlin, Germany
| | - Jørgen Kjems
- Interdisciplinary Nanoscience Center, Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark
| | - Mary P LaPierre
- Institute of Molecular Health Sciences, ETH Zurich, 8093 Zürich, Switzerland
| | - Monika Piwecka
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Jukka Jolkkonen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70221 Kuopio, Finland
| | - Rashid Giniatullin
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70221 Kuopio, Finland
| | - Thomas B Hansen
- Interdisciplinary Nanoscience Center, Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark
| | - Tarja Malm
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70221 Kuopio, Finland.
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11
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Li X, Zeng S, Chen L, Zhang Y, Li X, Zhang B, Su D, Du Q, Zhang J, Wang H, Zhong Z, Zhang J, Li P, Jiang A, Long K, Li M, Ge L. An intronic enhancer of Cebpa regulates adipocyte differentiation and adipose tissue development via long-range loop formation. Cell Prolif 2024; 57:e13552. [PMID: 37905345 PMCID: PMC10905358 DOI: 10.1111/cpr.13552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 08/29/2023] [Accepted: 09/11/2023] [Indexed: 11/02/2023] Open
Abstract
Cebpa is a master transcription factor gene for adipogenesis. However, the mechanisms of enhancer-promoter chromatin interactions controlling Cebpa transcriptional regulation during adipogenic differentiation remain largely unknown. To reveal how the three-dimensional structure of Cebpa changes during adipogenesis, we generated high-resolution chromatin interactions of Cebpa in 3T3-L1 preadipocytes and 3T3-L1 adipocytes using circularized chromosome conformation capture sequencing (4C-seq). We revealed dramatic changes in chromatin interactions and chromatin status at interaction sites during adipogenic differentiation. Based on this, we identified five active enhancers of Cebpa in 3T3-L1 adipocytes through epigenomic data and luciferase reporter assays. Next, epigenetic repression of Cebpa-L1-AD-En2 or -En3 by the dCas9-KRAB system significantly down-regulated Cebpa expression and inhibited adipocyte differentiation. Furthermore, experimental depletion of cohesin decreased the interaction intensity between Cebpa-L1-AD-En2 and the Cebpa promoter and down-regulated Cebpa expression, indicating that long-range chromatin loop formation was mediated by cohesin. Two transcription factors, RXRA and PPARG, synergistically regulate the activity of Cebpa-L1-AD-En2. To test whether Cebpa-L1-AD-En2 plays a role in adipose tissue development, we injected dCas9-KRAB-En2 lentivirus into the inguinal white adipose tissue (iWAT) of mice to suppress the activity of Cebpa-L1-AD-En2. Repression of Cebpa-L1-AD-En2 significantly decreased Cebpa expression and adipocyte size, altered iWAT transcriptome, and affected iWAT development. We identified functional enhancers regulating Cebpa expression and clarified the crucial roles of Cebpa-L1-AD-En2 and Cebpa promoter interaction in adipocyte differentiation and adipose tissue development.
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Affiliation(s)
- Xiaokai Li
- State Key Laboratory of Swine and Poultry Breeding IndustrySichuan Agricultural UniversityChengduChina
- Livestock and Poultry Multi‐omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Sha Zeng
- State Key Laboratory of Swine and Poultry Breeding IndustrySichuan Agricultural UniversityChengduChina
- Livestock and Poultry Multi‐omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Li Chen
- Chongqing Academy of Animal SciencesChongqingChina
- National Center of Technology Innovation for PigsChongqingChina
- Key Laboratory of Pig Industry ScienceMinistry of AgricultureChongqingChina
| | - Yu Zhang
- State Key Laboratory of Swine and Poultry Breeding IndustrySichuan Agricultural UniversityChengduChina
- Livestock and Poultry Multi‐omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Xuemin Li
- State Key Laboratory of Swine and Poultry Breeding IndustrySichuan Agricultural UniversityChengduChina
- Livestock and Poultry Multi‐omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Biwei Zhang
- State Key Laboratory of Swine and Poultry Breeding IndustrySichuan Agricultural UniversityChengduChina
- Livestock and Poultry Multi‐omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Duo Su
- State Key Laboratory of Swine and Poultry Breeding IndustrySichuan Agricultural UniversityChengduChina
- Livestock and Poultry Multi‐omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Qinjiao Du
- State Key Laboratory of Swine and Poultry Breeding IndustrySichuan Agricultural UniversityChengduChina
- Livestock and Poultry Multi‐omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Jiaman Zhang
- State Key Laboratory of Swine and Poultry Breeding IndustrySichuan Agricultural UniversityChengduChina
- Livestock and Poultry Multi‐omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Haoming Wang
- State Key Laboratory of Swine and Poultry Breeding IndustrySichuan Agricultural UniversityChengduChina
- Livestock and Poultry Multi‐omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Zhining Zhong
- State Key Laboratory of Swine and Poultry Breeding IndustrySichuan Agricultural UniversityChengduChina
- Livestock and Poultry Multi‐omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Jinwei Zhang
- Chongqing Academy of Animal SciencesChongqingChina
- National Center of Technology Innovation for PigsChongqingChina
- Key Laboratory of Pig Industry ScienceMinistry of AgricultureChongqingChina
| | - Penghao Li
- Jinxin Research Institute for Reproductive Medicine and GeneticsSichuan Jinxin Xi'nan Women's and Children's HospitalChengduChina
| | - Anan Jiang
- State Key Laboratory of Swine and Poultry Breeding IndustrySichuan Agricultural UniversityChengduChina
- Livestock and Poultry Multi‐omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Keren Long
- State Key Laboratory of Swine and Poultry Breeding IndustrySichuan Agricultural UniversityChengduChina
- Livestock and Poultry Multi‐omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and TechnologySichuan Agricultural UniversityChengduChina
- Chongqing Academy of Animal SciencesChongqingChina
| | - Mingzhou Li
- State Key Laboratory of Swine and Poultry Breeding IndustrySichuan Agricultural UniversityChengduChina
- Livestock and Poultry Multi‐omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Liangpeng Ge
- Chongqing Academy of Animal SciencesChongqingChina
- National Center of Technology Innovation for PigsChongqingChina
- Key Laboratory of Pig Industry ScienceMinistry of AgricultureChongqingChina
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12
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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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13
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Chen J, Wang R, Xiong F, Sun H, Kemper B, Li W, Kemper JK. Hammerhead-type FXR agonists induce an eRNA FincoR that ameliorates nonalcoholic steatohepatitis in mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.20.567833. [PMID: 38045226 PMCID: PMC10690184 DOI: 10.1101/2023.11.20.567833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
The nuclear receptor, Farnesoid X Receptor (FXR/NR1H4), is increasingly recognized as a promising drug target for metabolic diseases, including nonalcoholic steatohepatitis (NASH). Protein coding genes regulated by FXR are well known, but whether FXR also acts through regulation of long non-coding RNAs (lncRNAs), which vastly outnumber protein-coding genes, remains unknown. Utilizing RNA-seq and GRO-seq analyses in mouse liver, we found that FXR activation affects the expression of many RNA transcripts from chromatin regions bearing enhancer features. Among these we discovered a previously unannotated liver-enriched enhancer-derived lncRNA (eRNA), termed FincoR. We show that FincoR is specifically induced by the hammerhead-type FXR agonists, including GW4064 and tropifexor. CRISPR/Cas9-mediated liver-specific knockdown of FincoR in dietary NASH mice reduced the beneficial effects of tropifexor, an FXR agonist currently in clinical trials for NASH and primary biliary cholangitis (PBC), indicating that that amelioration of liver fibrosis and inflammation in NASH treatment by tropifexor is mediated in part by FincoR. Overall, our findings highlight that pharmacological activation of FXR by hammerhead-type agonists induces a novel eRNA, FincoR, contributing to the amelioration of NASH in mice. FincoR may represent a new drug target for addressing metabolic disorders, including NASH.
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Affiliation(s)
- Jinjing Chen
- Department of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Ruoyu Wang
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center, Houston, TX, USA
| | - Feng Xiong
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center, Houston, TX, USA
| | - Hao Sun
- Department of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Byron Kemper
- Department of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Wenbo Li
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center, Houston, TX, USA
| | - Jongsook Kim Kemper
- Department of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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14
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Liao Z, Tang S, Nozawa K, Shimada K, Ikawa M, Monsivais D, Matzuk MM. Affinity-tagged SMAD1 and SMAD5 mouse lines reveal transcriptional reprogramming mechanisms during early pregnancy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.25.559321. [PMID: 38106095 PMCID: PMC10723262 DOI: 10.1101/2023.09.25.559321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Endometrial decidualization, a prerequisite for successful pregnancies, relies on transcriptional reprogramming driven by progesterone receptor (PR) and bone morphogenetic protein (BMP)-SMAD1/SMAD5 signaling pathways. Despite their critical roles in early pregnancy, how these pathways intersect in reprogramming the endometrium into a receptive state remains unclear. To define how SMAD1 and/or SMAD5 integrate BMP signaling in the uterus during early pregnancy, we generated two novel transgenic mouse lines with affinity tags inserted into the endogenous SMAD1 and SMAD5 loci (Smad1HA/HA and Smad5PA/PA). By profiling the genome-wide distribution of SMAD1, SMAD5, and PR in the mouse uterus, we demonstrated the unique and shared roles of SMAD1 and SMAD5 during the window of implantation. We also showed the presence of a conserved SMAD1, SMAD5, and PR genomic binding signature in the uterus during early pregnancy. To functionally characterize the translational aspects of our findings, we demonstrated that SMAD1/5 knockdown in human endometrial stromal cells suppressed expressions of canonical decidual markers (IGFBP1, PRL, FOXO1) and PR-responsive genes (RORB, KLF15). Here, our studies provide novel tools to study BMP signaling pathways and highlight the fundamental roles of SMAD1/5 in mediating both BMP signaling pathways and the transcriptional response to progesterone (P4) during early pregnancy.
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Affiliation(s)
- Zian Liao
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Graduate Program of Genetics and Genomics, Baylor College of Medicine, Houston, TX, 77030, USA
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Suni Tang
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Kaori Nozawa
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Keisuke Shimada
- Research Institute for Microbial Diseases, Osaka University, Osaka, 565-0871, Japan
| | - Masahito Ikawa
- Research Institute for Microbial Diseases, Osaka University, Osaka, 565-0871, Japan
| | - Diana Monsivais
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Martin M. Matzuk
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Graduate Program of Genetics and Genomics, Baylor College of Medicine, Houston, TX, 77030, USA
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX, 77030, USA
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15
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Vlachou D, Veretennikova M, Usselmann L, Vasilyev V, Ott S, Bjarnason GA, Dallmann R, Levi F, Rand DA. TimeTeller: A tool to probe the circadian clock as a multigene dynamical system. PLoS Comput Biol 2024; 20:e1011779. [PMID: 38422117 DOI: 10.1371/journal.pcbi.1011779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 03/12/2024] [Accepted: 12/21/2023] [Indexed: 03/02/2024] Open
Abstract
Recent studies have established that the circadian clock influences onset, progression and therapeutic outcomes in a number of diseases including cancer and heart diseases. Therefore, there is a need for tools to measure the functional state of the molecular circadian clock and its downstream targets in patients. Moreover, the clock is a multi-dimensional stochastic oscillator and there are few tools for analysing it as a noisy multigene dynamical system. In this paper we consider the methodology behind TimeTeller, a machine learning tool that analyses the clock as a noisy multigene dynamical system and aims to estimate circadian clock function from a single transcriptome by modelling the multi-dimensional state of the clock. We demonstrate its potential for clock systems assessment by applying it to mouse, baboon and human microarray and RNA-seq data and show how to visualise and quantify the global structure of the clock, quantitatively stratify individual transcriptomic samples by clock dysfunction and globally compare clocks across individuals, conditions and tissues thus highlighting its potential relevance for advancing circadian medicine.
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Affiliation(s)
- Denise Vlachou
- Mathematics Institute & Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research, University of Warwick, Coventry, United Kingdom
| | - Maria Veretennikova
- Mathematics Institute & Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research, University of Warwick, Coventry, United Kingdom
| | - Laura Usselmann
- Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, United Kingdom
| | - Vadim Vasilyev
- Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, United Kingdom
| | - Sascha Ott
- Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, United Kingdom
| | - Georg A Bjarnason
- Odette Cancer Centre, Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada
| | - Robert Dallmann
- Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, United Kingdom
| | - Francis Levi
- Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, United Kingdom
- Department of Statistics, University of Warwick, Coventry, United Kingdom
- UPR "Chronotherapy, Cancer and Transplantation", Medical School, Paris-Saclay University, Medical Oncology Department, Paul Brousse Hospital, Villejuif, France
| | - David A Rand
- Mathematics Institute & Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research, University of Warwick, Coventry, United Kingdom
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16
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Weidemann BJ, Marcheva B, Kobayashi M, Omura C, Newman MV, Kobayashi Y, Waldeck NJ, Perelis M, Lantier L, McGuinness OP, Ramsey KM, Stein RW, Bass J. Repression of latent NF-κB enhancers by PDX1 regulates β cell functional heterogeneity. Cell Metab 2024; 36:90-102.e7. [PMID: 38171340 PMCID: PMC10793877 DOI: 10.1016/j.cmet.2023.11.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 07/17/2023] [Accepted: 11/30/2023] [Indexed: 01/05/2024]
Abstract
Interactions between lineage-determining and activity-dependent transcription factors determine single-cell identity and function within multicellular tissues through incompletely known mechanisms. By assembling a single-cell atlas of chromatin state within human islets, we identified β cell subtypes governed by either high or low activity of the lineage-determining factor pancreatic duodenal homeobox-1 (PDX1). β cells with reduced PDX1 activity displayed increased chromatin accessibility at latent nuclear factor κB (NF-κB) enhancers. Pdx1 hypomorphic mice exhibited de-repression of NF-κB and impaired glucose tolerance at night. Three-dimensional analyses in tandem with chromatin immunoprecipitation (ChIP) sequencing revealed that PDX1 silences NF-κB at circadian and inflammatory enhancers through long-range chromatin contacts involving SIN3A. Conversely, Bmal1 ablation in β cells disrupted genome-wide PDX1 and NF-κB DNA binding. Finally, antagonizing the interleukin (IL)-1β receptor, an NF-κB target, improved insulin secretion in Pdx1 hypomorphic islets. Our studies reveal functional subtypes of single β cells defined by a gradient in PDX1 activity and identify NF-κB as a target for insulinotropic therapy.
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Affiliation(s)
- Benjamin J Weidemann
- Department of Medicine, Division of Endocrinology, Metabolism and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Biliana Marcheva
- Department of Medicine, Division of Endocrinology, Metabolism and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Mikoto Kobayashi
- Department of Medicine, Division of Endocrinology, Metabolism and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Chiaki Omura
- Department of Medicine, Division of Endocrinology, Metabolism and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Marsha V Newman
- Department of Medicine, Division of Endocrinology, Metabolism and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Yumiko Kobayashi
- Department of Medicine, Division of Endocrinology, Metabolism and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Nathan J Waldeck
- Department of Medicine, Division of Endocrinology, Metabolism and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Mark Perelis
- Department of Medicine, Division of Endocrinology, Metabolism and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Ionis Pharmaceuticals, Carlsbad, CA 92010, USA
| | - Louise Lantier
- Vanderbilt-NIH Mouse Metabolic Phenotyping Center, Nashville, TN 37232, USA; Department of Molecular Physiology and Biophysics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Owen P McGuinness
- Vanderbilt-NIH Mouse Metabolic Phenotyping Center, Nashville, TN 37232, USA; Department of Molecular Physiology and Biophysics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Kathryn Moynihan Ramsey
- Department of Medicine, Division of Endocrinology, Metabolism and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Roland W Stein
- Department of Molecular Physiology and Biophysics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Joseph Bass
- Department of Medicine, Division of Endocrinology, Metabolism and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA.
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Woodie LN, Melink LC, Alberto AJ, Burrows M, Fortin SM, Chan CC, Hayes MR, Lazar MA. Hindbrain REV-ERB nuclear receptors regulate sensitivity to diet-induced obesity and brown adipose tissue pathophysiology. Mol Metab 2024; 79:101861. [PMID: 38142970 PMCID: PMC10792761 DOI: 10.1016/j.molmet.2023.101861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 12/08/2023] [Accepted: 12/20/2023] [Indexed: 12/26/2023] Open
Abstract
OBJECTIVE The dorsal vagal complex (DVC) of the hindbrain is a major point of integration for central and peripheral signals that regulate a wide variety of metabolic functions to maintain energy balance. The REV-ERB nuclear receptors are important modulators of molecular metabolism, but their role in the DVC has yet to be established. METHODS Male REV-ERBα/β floxed mice received stereotaxic injections of a Cre expressing virus to the DVC to create the DVC REV-ERBα/β double knockout (DVC RDKO). Control littermates received stereotaxic injections to the DVC of a green fluorescent protein expressing virus. Animals were maintained on a normal chow diet or a 60% high-fat diet to observe the metabolic phenotype arising from DVC RDKO under healthy and metabolically stressed conditions. RESULTS DVC RDKO animals on high-fat diet exhibited increased weight gain compared to control animals maintained on the same diet. Increased weight gain in DVC RDKO animals was associated with decreased basal metabolic rate and dampened signature of brown adipose tissue activity. RDKO decreased gene expression of calcitonin receptor in the DVC and tyrosine hydroxylase in the brown adipose tissue. CONCLUSIONS These results suggest a previously unappreciated role of REV-ERB nuclear receptors in the DVC for maintaining energy balance and metabolic rate potentially through indirect sympathetic outflow to the brown adipose tissue.
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Affiliation(s)
- Lauren N Woodie
- Institute for Diabetes, Obesity, and Metabolism, and Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Lily C Melink
- Institute for Diabetes, Obesity, and Metabolism, and Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ahren J Alberto
- Institute for Diabetes, Obesity, and Metabolism, and Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Michelle Burrows
- Institute for Diabetes, Obesity, and Metabolism, and Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Samantha M Fortin
- Department of Psychiatry, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Calvin C Chan
- Institute for Diabetes, Obesity, and Metabolism, and Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Psychiatry, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Matthew R Hayes
- Institute for Diabetes, Obesity, and Metabolism, and Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Psychiatry, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Mitchell A Lazar
- Institute for Diabetes, Obesity, and Metabolism, and Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA.
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18
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Zhu K, Celwyn IJ, Guan D, Xiao Y, Wang X, Hu W, Jiang C, Cheng L, Casellas R, Lazar MA. An intrinsically disordered region controlling condensation of a circadian clock component and rhythmic transcription in the liver. Mol Cell 2023; 83:3457-3469.e7. [PMID: 37802023 PMCID: PMC10575687 DOI: 10.1016/j.molcel.2023.09.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 08/09/2023] [Accepted: 09/08/2023] [Indexed: 10/08/2023]
Abstract
Circadian gene transcription is fundamental to metabolic physiology. Here we report that the nuclear receptor REV-ERBα, a repressive component of the molecular clock, forms circadian condensates in the nuclei of mouse liver. These condensates are dictated by an intrinsically disordered region (IDR) located in the protein's hinge region which specifically concentrates nuclear receptor corepressor 1 (NCOR1) at the genome. IDR deletion diminishes the recruitment of NCOR1 and disrupts rhythmic gene transcription in vivo. REV-ERBα condensates are located at high-order transcriptional repressive hubs in the liver genome that are highly correlated with circadian gene repression. Deletion of the IDR disrupts transcriptional repressive hubs and diminishes silencing of target genes by REV-ERBα. This work demonstrates physiological circadian protein condensates containing REV-ERBα whose IDR is required for hub formation and the control of rhythmic gene expression.
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Affiliation(s)
- Kun Zhu
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Isaac J Celwyn
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Dongyin Guan
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Medicine, Division of Diabetes, Endocrinology and Metabolism, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yang Xiao
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Xiang Wang
- Laboratory of Lymphocyte Nuclear Biology, NIAMS, NIH, Bethesda, MD 20892, USA
| | - Wenxiang Hu
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Basic Research, Guangzhou Laboratory, Guangdong 510005, China
| | - Chunjie Jiang
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Lan Cheng
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Rafael Casellas
- Laboratory of Lymphocyte Nuclear Biology, NIAMS, NIH, Bethesda, MD 20892, USA
| | - Mitchell A Lazar
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA.
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19
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Zhang Y, Chen G, Deng L, Gao B, Yang J, Ding C, Zhang Q, Ouyang W, Guo M, Wang W, Liu B, Zhang Q, Sung WK, Yan J, Li G, Li X. Integrated 3D genome, epigenome and transcriptome analyses reveal transcriptional coordination of circadian rhythm in rice. Nucleic Acids Res 2023; 51:9001-9018. [PMID: 37572350 PMCID: PMC10516653 DOI: 10.1093/nar/gkad658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 07/11/2023] [Accepted: 08/01/2023] [Indexed: 08/14/2023] Open
Abstract
Photoperiods integrate with the circadian clock to coordinate gene expression rhythms and thus ensure plant fitness to the environment. Genome-wide characterization and comparison of rhythmic genes under different light conditions revealed delayed phase under constant darkness (DD) and reduced amplitude under constant light (LL) in rice. Interestingly, ChIP-seq and RNA-seq profiling of rhythmic genes exhibit synchronous circadian oscillation in H3K9ac modifications at their loci and long non-coding RNAs (lncRNAs) expression at proximal loci. To investigate how gene expression rhythm is regulated in rice, we profiled the open chromatin regions and transcription factor (TF) footprints by time-series ATAC-seq. Although open chromatin regions did not show circadian change, a significant number of TFs were identified to rhythmically associate with chromatin and drive gene expression in a time-dependent manner. Further transcriptional regulatory networks mapping uncovered significant correlation between core clock genes and transcription factors involved in light/temperature signaling. In situ Hi-C of ZT8-specific expressed genes displayed highly connected chromatin association at the same time, whereas this ZT8 chromatin connection network dissociates at ZT20, suggesting the circadian control of gene expression by dynamic spatial chromatin conformation. These findings together implicate the existence of a synchronization mechanism between circadian H3K9ac modifications, chromatin association of TF and gene expression, and provides insights into circadian dynamics of spatial chromatin conformation that associate with gene expression rhythms.
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Affiliation(s)
- Ying Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Guoting Chen
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
- Laboratory of Agricultural Bioinformatics, Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Li Deng
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Baibai Gao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Jing Yang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Cheng Ding
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Qing Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Weizhi Ouyang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Minrong Guo
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Wenxia Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Beibei Liu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Qinghua Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Wing-Kin Sung
- Department of Chemical Pathology, Chinese University of Hong Kong, Hong Kong, China
| | - Jiapei Yan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Guoliang Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Laboratory of Agricultural Bioinformatics, Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Xingwang Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
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20
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Inoue Y, Suzuki Y, Kunishima Y, Washio T, Morishita S, Takeda H. High-fat diet in early life triggers both reversible and persistent epigenetic changes in the medaka fish (Oryzias latipes). BMC Genomics 2023; 24:472. [PMID: 37605229 PMCID: PMC10441761 DOI: 10.1186/s12864-023-09557-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 08/04/2023] [Indexed: 08/23/2023] Open
Abstract
BACKGROUND The nutritional status during early life can have enduring effects on an animal's metabolism, although the mechanisms underlying these long-term effects are still unclear. Epigenetic modifications are considered a prime candidate mechanism for encoding early-life nutritional memories during this critical developmental period. However, the extent to which these epigenetic changes occur and persist over time remains uncertain, in part due to challenges associated with directly stimulating the fetus with specific nutrients in viviparous mammalian systems. RESULTS In this study, we used medaka as an oviparous vertebrate model to establish an early-life high-fat diet (HFD) model. Larvae were fed with HFD from the hatching stages (one week after fertilization) for six weeks, followed by normal chow (NC) for eight weeks until the adult stage. We examined the changes in the transcriptomic and epigenetic state of the liver over this period. We found that HFD induces simple liver steatosis, accompanied by drastic changes in the hepatic transcriptome, chromatin accessibility, and histone modifications, especially in metabolic genes. These changes were largely reversed after the long-term NC, demonstrating the high plasticity of the epigenetic state in hepatocytes. However, we found a certain number of genomic loci showing non-reversible epigenetic changes, especially around genes related to cell signaling, liver fibrosis, and hepatocellular carcinoma, implying persistent changes in the cellular state of the liver triggered by early-life HFD feeding. CONCLUSION In summary, our data show that early-life HFD feeding triggers both reversible and persistent epigenetic changes in medaka hepatocytes. Our data provide novel insights into the epigenetic mechanism of nutritional programming and a comprehensive atlas of the long-term epigenetic state in an early-life HFD model of non-mammalian vertebrates.
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Affiliation(s)
- Yusuke Inoue
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-0033, Japan.
| | - Yuta Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan
| | - Yoshimi Kunishima
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-0033, Japan
| | - Terumi Washio
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-0033, Japan
| | - Shinichi Morishita
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan.
| | - Hiroyuki Takeda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-0033, Japan.
- Faculty of Life Sciences, Kyoto Sangyo University, Motoyama, Kamigamo, Kita-ku, Kyoto, 603-8555, Japan.
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21
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Evangelou K, Belogiannis K, Papaspyropoulos A, Petty R, Gorgoulis VG. Escape from senescence: molecular basis and therapeutic ramifications. J Pathol 2023; 260:649-665. [PMID: 37550877 DOI: 10.1002/path.6164] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 06/16/2023] [Accepted: 06/19/2023] [Indexed: 08/09/2023]
Abstract
Cellular senescence constitutes a stress response mechanism in reaction to a plethora of stimuli. Senescent cells exhibit cell-cycle arrest and altered function. While cell-cycle withdrawal has been perceived as permanent, recent evidence in cancer research introduced the so-called escape-from-senescence concept. In particular, under certain conditions, senescent cells may resume proliferation, acquiring highly aggressive features. As such, they have been associated with tumour relapse, rendering senescence less effective in inhibiting cancer progression. Thus, conventional cancer treatments, incapable of eliminating senescence, may benefit if revisited to include senolytic agents. To this end, it is anticipated that the assessment of the senescence burden in everyday clinical material by pathologists will play a crucial role in the near future, laying the foundation for more personalised approaches. Here, we provide an overview of the investigations that introduced the escape-from-senescence phenomenon, the identified mechanisms, as well as the major implications for pathology and therapy. © 2023 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Konstantinos Evangelou
- Molecular Carcinogenesis Group, Department of Histology and Embryology, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Konstantinos Belogiannis
- Molecular Carcinogenesis Group, Department of Histology and Embryology, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Angelos Papaspyropoulos
- Molecular Carcinogenesis Group, Department of Histology and Embryology, Medical School, National and Kapodistrian University of Athens, Athens, Greece
- Biomedical Research Foundation, Academy of Athens, Athens, Greece
| | - Russell Petty
- Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | - Vassilis G Gorgoulis
- Molecular Carcinogenesis Group, Department of Histology and Embryology, Medical School, National and Kapodistrian University of Athens, Athens, Greece
- Biomedical Research Foundation, Academy of Athens, Athens, Greece
- Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
- Faculty Institute for Cancer Sciences, Manchester Academic Health Sciences Centre, University of Manchester, Manchester, UK
- Center for New Biotechnologies and Precision Medicine, Medical School, National and Kapodistrian University of Athens, Athens, Greece
- Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
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22
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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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23
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Niu Y, Wang Y, Chen H, Liu X, Liu J. Overview of the Circadian Clock in the Hair Follicle Cycle. Biomolecules 2023; 13:1068. [PMID: 37509104 PMCID: PMC10377266 DOI: 10.3390/biom13071068] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/27/2023] [Accepted: 06/28/2023] [Indexed: 07/30/2023] Open
Abstract
The circadian clock adapts to the light-dark cycle and autonomously generates physiological and metabolic rhythmicity. Its activity depends on the central suprachiasmatic pacemaker. However, it also has an independent function in peripheral tissues such as the liver, adipose tissue, and skin, which integrate environmental signals and energy homeostasis. Hair follicles (HFs) maintain homeostasis through the HF cycle, which depends heavily on HF stem cell self-renewal and the related metabolic reprogramming. Studies have shown that circadian clock dysregulation in HFs perturbs cell cycle progression. Moreover, there is increasing evidence that the circadian clock exerts a significant influence on glucose metabolism, feeding/fasting, stem cell differentiation, and senescence. This suggests that circadian metabolic crosstalk plays an essential role in regulating HF regeneration. An improved understanding of the role of the circadian clock in HFs may facilitate the discovery of new drug targets for hair loss. Therefore, the present review provides a discussion of the relationship between the circadian clock and HF regeneration, mainly from the perspective of HF metabolism, and summarizes the current understanding of the mechanisms by which HFs function.
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Affiliation(s)
- Ye Niu
- Department of Toxicology, School of Public Health, Jilin University, Changchun 130021, China
| | - Yujie Wang
- Department of Toxicology, School of Public Health, Jilin University, Changchun 130021, China
| | - Hao Chen
- Department of Toxicology, School of Public Health, Jilin University, Changchun 130021, China
| | - Xiaomei Liu
- Department of Toxicology, School of Public Health, Jilin University, Changchun 130021, China
| | - Jinyu Liu
- Department of Toxicology, School of Public Health, Jilin University, Changchun 130021, China
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24
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Bafna A, Banks G, Hastings MH, Nolan PM. Dynamic modulation of genomic enhancer elements in the suprachiasmatic nucleus, the site of the mammalian circadian clock. Genome Res 2023; 33:673-688. [PMID: 37156620 PMCID: PMC10317116 DOI: 10.1101/gr.277581.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 05/03/2023] [Indexed: 05/10/2023]
Abstract
The mammalian suprachiasmatic nucleus (SCN), located in the ventral hypothalamus, synchronizes and maintains daily cellular and physiological rhythms across the body, in accordance with environmental and visceral cues. Consequently, the systematic regulation of spatiotemporal gene transcription in the SCN is vital for daily timekeeping. So far, the regulatory elements assisting circadian gene transcription have only been studied in peripheral tissues, lacking the critical neuronal dimension intrinsic to the role of the SCN as central brain pacemaker. By using histone-ChIP-seq, we identified SCN-enriched gene regulatory elements that associated with temporal gene expression. Based on tissue-specific H3K27ac and H3K4me3 marks, we successfully produced the first-ever SCN gene-regulatory map. We found that a large majority of SCN enhancers not only show robust 24-h rhythmic modulation in H3K27ac occupancy, peaking at distinct times of day, but also possess canonical E-box (CACGTG) motifs potentially influencing downstream cycling gene expression. To establish enhancer-gene relationships in the SCN, we conducted directional RNA-seq at six distinct times across the day and night, and studied the association between dynamically changing histone acetylation and gene transcript levels. About 35% of the cycling H3K27ac sites were found adjacent to rhythmic gene transcripts, often preceding the rise in mRNA levels. We also noted that enhancers encompass noncoding, actively transcribing enhancer RNAs (eRNAs) in the SCN, which in turn oscillate, along with cyclic histone acetylation, and correlate with rhythmic gene transcription. Taken together, these findings shed light on genome-wide pretranscriptional regulation operative in the central clock that confers its precise and robust oscillation necessary to orchestrate daily timekeeping in mammals.
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Affiliation(s)
- Akanksha Bafna
- Medical Research Council, Harwell Science Campus, Oxfordshire OX11 0RD, United Kingdom;
| | - Gareth Banks
- Medical Research Council, Harwell Science Campus, Oxfordshire OX11 0RD, United Kingdom
| | - Michael H Hastings
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom
| | - Patrick M Nolan
- Medical Research Council, Harwell Science Campus, Oxfordshire OX11 0RD, United Kingdom;
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25
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Escalante-Covarrubias Q, Mendoza-Viveros L, González-Suárez M, Sitten-Olea R, Velázquez-Villegas LA, Becerril-Pérez F, Pacheco-Bernal I, Carreño-Vázquez E, Mass-Sánchez P, Bustamante-Zepeda M, Orozco-Solís R, Aguilar-Arnal L. Time-of-day defines NAD + efficacy to treat diet-induced metabolic disease by synchronizing the hepatic clock in mice. Nat Commun 2023; 14:1685. [PMID: 36973248 PMCID: PMC10043291 DOI: 10.1038/s41467-023-37286-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 03/07/2023] [Indexed: 03/29/2023] Open
Abstract
The circadian clock is an endogenous time-tracking system that anticipates daily environmental changes. Misalignment of the clock can cause obesity, which is accompanied by reduced levels of the clock-controlled, rhythmic metabolite NAD+. Increasing NAD+ is becoming a therapy for metabolic dysfunction; however, the impact of daily NAD+ fluctuations remains unknown. Here, we demonstrate that time-of-day determines the efficacy of NAD+ treatment for diet-induced metabolic disease in mice. Increasing NAD+ prior to the active phase in obese male mice ameliorated metabolic markers including body weight, glucose and insulin tolerance, hepatic inflammation and nutrient sensing pathways. However, raising NAD+ immediately before the rest phase selectively compromised these responses. Remarkably, timed NAD+ adjusted circadian oscillations of the liver clock until completely inverting its oscillatory phase when increased just before the rest period, resulting in misaligned molecular and behavioral rhythms in male and female mice. Our findings unveil the time-of-day dependence of NAD+-based therapies and support a chronobiology-based approach.
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Affiliation(s)
- Quetzalcoatl Escalante-Covarrubias
- Departamento de Biología Celular y Fisiología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Lucía Mendoza-Viveros
- Departamento de Biología Celular y Fisiología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
- Laboratorio de Cronobiología y Metabolismo, Instituto Nacional de Medicina Genómica, 14610, Mexico City, Mexico
| | - Mirna González-Suárez
- Departamento de Biología Celular y Fisiología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Román Sitten-Olea
- Departamento de Biología Celular y Fisiología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Laura A Velázquez-Villegas
- Departamento de Fisiología de la Nutrición, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, 14080, Mexico City, Mexico
| | - Fernando Becerril-Pérez
- Departamento de Biología Celular y Fisiología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Ignacio Pacheco-Bernal
- Departamento de Biología Celular y Fisiología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Erick Carreño-Vázquez
- Laboratorio de Cronobiología y Metabolismo, Instituto Nacional de Medicina Genómica, 14610, Mexico City, Mexico
| | - Paola Mass-Sánchez
- Departamento de Biología Celular y Fisiología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Marcia Bustamante-Zepeda
- Departamento de Biología Celular y Fisiología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Ricardo Orozco-Solís
- Laboratorio de Cronobiología y Metabolismo, Instituto Nacional de Medicina Genómica, 14610, Mexico City, Mexico
- Centro de Investigación sobre el Envejecimiento, Centro de Investigación y de Estudios Avanzados, 14330, Mexico City, Mexico
| | - Lorena Aguilar-Arnal
- Departamento de Biología Celular y Fisiología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico.
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The circadian demethylation of a unique intronic deoxymethylCpG-rich island boosts the transcription of its cognate circadian clock output gene. Proc Natl Acad Sci U S A 2023; 120:e2214062120. [PMID: 36791105 PMCID: PMC9974474 DOI: 10.1073/pnas.2214062120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023] Open
Abstract
We demonstrate that there is a tight functional relationship between two highly evolutionary conserved cell processes, i.e., the circadian clock (CC) and the circadian DNA demethylation-methylation of cognate deoxyCpG-rich islands. We have discovered that every circadian clock-controlled output gene (CCG), but not the core clock nor its immediate-output genes, contains a single cognate intronic deoxyCpG-rich island, the demethylation-methylation of which is controlled by the CC. During the transcriptional activation period, these intronic islands are demethylated and, upon dimerization of two YY1 protein binding sites located upstream to the transcriptional enhancer and downstream from the deoxyCpG-rich island, store activating components initially assembled on a cognate active enhancer (a RORE, a D-box or an E-box), in keeping with the generation of a transcriptionally active condensate that boosts the initiation of transcription of their cognate pre-mRNAs. We report how these single intronic deoxyCpG-rich islands are instrumental in such a circadian activation/repression transcriptional process.
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Meléndez-Fernández OH, Liu JA, Nelson RJ. Circadian Rhythms Disrupted by Light at Night and Mistimed Food Intake Alter Hormonal Rhythms and Metabolism. Int J Mol Sci 2023; 24:3392. [PMID: 36834801 PMCID: PMC9963929 DOI: 10.3390/ijms24043392] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 02/04/2023] [Accepted: 02/07/2023] [Indexed: 02/10/2023] Open
Abstract
Availability of artificial light and light-emitting devices have altered human temporal life, allowing 24-hour healthcare, commerce and production, and expanding social life around the clock. However, physiology and behavior that evolved in the context of 24 h solar days are frequently perturbed by exposure to artificial light at night. This is particularly salient in the context of circadian rhythms, the result of endogenous biological clocks with a rhythm of ~24 h. Circadian rhythms govern the temporal features of physiology and behavior, and are set to precisely 24 h primarily by exposure to light during the solar day, though other factors, such as the timing of meals, can also affect circadian rhythms. Circadian rhythms are significantly affected by night shift work because of exposure to nocturnal light, electronic devices, and shifts in the timing of meals. Night shift workers are at increased risk for metabolic disorder, as well as several types of cancer. Others who are exposed to artificial light at night or late mealtimes also show disrupted circadian rhythms and increased metabolic and cardiac disorders. It is imperative to understand how disrupted circadian rhythms alter metabolic function to develop strategies to mitigate their negative effects. In this review, we provide an introduction to circadian rhythms, physiological regulation of homeostasis by the suprachiasmatic nucleus (SCN), and SCN-mediated hormones that display circadian rhythms, including melatonin and glucocorticoids. Next, we discuss circadian-gated physiological processes including sleep and food intake, followed by types of disrupted circadian rhythms and how modern lighting disrupts molecular clock rhythms. Lastly, we identify how disruptions to hormones and metabolism can increase susceptibility to metabolic syndrome and risk for cardiovascular diseases, and discuss various strategies to mitigate the harmful consequences associated with disrupted circadian rhythms on human health.
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28
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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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29
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Kong T, Laranjeira ABA, Yang K, Fisher DAC, Yu L, Poittevin De La Frégonnière L, Wang AZ, Ruzinova MB, Fowles JS, Fulbright MC, Cox MJ, Celik H, Challen GA, Huang S, Oh ST. DUSP6 mediates resistance to JAK2 inhibition and drives leukemic progression. NATURE CANCER 2023; 4:108-127. [PMID: 36581736 PMCID: PMC11288645 DOI: 10.1038/s43018-022-00486-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 11/08/2022] [Indexed: 12/31/2022]
Abstract
Myeloproliferative neoplasms (MPNs) exhibit a propensity for transformation to secondary acute myeloid leukemia (sAML), for which the underlying mechanisms remain poorly understood, resulting in limited treatment options and dismal clinical outcomes. Here, we performed single-cell RNA sequencing on serial MPN and sAML patient stem and progenitor cells, identifying aberrantly increased expression of DUSP6 underlying disease transformation. Pharmacologic dual-specificity phosphatase (DUSP)6 targeting led to inhibition of S6 and Janus kinase (JAK)-signal transducer and activator of transcription (STAT) signaling while also reducing inflammatory cytokine production. DUSP6 perturbation further inhibited ribosomal S6 kinase (RSK)1, which we identified as a second indispensable candidate associated with poor clinical outcome. Ectopic expression of DUSP6 mediated JAK2-inhibitor resistance and exacerbated disease severity in patient-derived xenograft (PDX) models. Contrastingly, DUSP6 inhibition potently suppressed disease development across Jak2V617F and MPLW515L MPN mouse models and sAML PDXs without inducing toxicity in healthy controls. These findings underscore DUSP6 in driving disease transformation and highlight the DUSP6-RSK1 axis as a vulnerable, druggable pathway in myeloid malignancies.
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Affiliation(s)
- Tim Kong
- Division of Hematology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Angelo B A Laranjeira
- Division of Hematology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Kangning Yang
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
- Goodman Cancer Research Centre, McGill University, Montreal, Quebec, Canada
| | - Daniel A C Fisher
- Division of Hematology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - LaYow Yu
- Division of Hematology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Laure Poittevin De La Frégonnière
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
- Goodman Cancer Research Centre, McGill University, Montreal, Quebec, Canada
| | - Anthony Z Wang
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Marianna B Ruzinova
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Jared S Fowles
- Division of Hematology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Mary C Fulbright
- Division of Hematology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Maggie J Cox
- Division of Hematology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Hamza Celik
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Grant A Challen
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Sidong Huang
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
- Goodman Cancer Research Centre, McGill University, Montreal, Quebec, Canada
| | - Stephen T Oh
- Division of Hematology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA.
- Immunomonitoring Laboratory, Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO, USA.
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Meriin AB, Zaarur N, Roy D, Kandror KV. Egr1 plays a major role in the transcriptional response of white adipocytes to insulin and environmental cues. Front Cell Dev Biol 2022; 10:1003030. [PMID: 36246998 PMCID: PMC9554007 DOI: 10.3389/fcell.2022.1003030] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 09/08/2022] [Indexed: 11/18/2022] Open
Abstract
It is believed that insulin regulates metabolic functions of white adipose tissue primarily at the post-translational level via the PI3K-Akt-mediated pathway. Still, changes in transcription also play an important role in the response of white adipocytes to insulin and environmental signals. One transcription factor that is dramatically and rapidly induced in adipocytes by insulin and nutrients is called Early Growth Response 1, or Egr1. Among other functions, it directly binds to promoters of leptin and ATGL stimulating the former and inhibiting the latter. Furthermore, expression of Egr1 in adipocytes demonstrates cell autonomous circadian pattern suggesting that Egr1 not only mediates the effect of insulin and nutrients on lipolysis and leptin production but also, coordinates insulin action with endogenous circadian rhythms of adipose tissue.
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Affiliation(s)
- A. B. Meriin
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, United States
| | - N. Zaarur
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, United States
| | - D. Roy
- Department of Neuroscience, The Ohio State University, Columbus, OH, United States
| | - K. V. Kandror
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, United States
- *Correspondence: K. V. Kandror,
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31
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Santoleri D, Lim HW, Emmett MJ, Stoute J, Gavin MJ, Sostre-Colón J, Uehara K, Welles JE, Liu KF, Lazar MA, Titchenell PM. Global-run on sequencing identifies Gm11967 as an Akt-dependent long noncoding RNA involved in insulin sensitivity. iScience 2022; 25:104410. [PMID: 35663017 PMCID: PMC9156944 DOI: 10.1016/j.isci.2022.104410] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 03/18/2022] [Accepted: 05/11/2022] [Indexed: 01/07/2023] Open
Abstract
The insulin responsive Akt and FoxO1 signaling axis is a key regulator of the hepatic transcriptional response to nutrient intake. Here, we used global run-on sequencing (GRO-seq) to measure the nascent transcriptional response to fasting and refeeding as well as define the specific role of hepatic Akt and FoxO1 signaling in mediating this response. We identified 599 feeding-regulated transcripts, as well as over 6,000 eRNAs, and mapped their dependency on Akt and FoxO1 signaling. Further, we identified several feeding-regulated lncRNAs, including the lncRNA Gm11967, whose expression was dependent upon the liver Akt-FoxO1 axis. Restoring Gm11967 expression in mice lacking liver Akt improved insulin sensitivity and induced glucokinase protein expression, indicating that Akt-dependent control of Gm11967 contributes to the translational control of glucokinase. More broadly, we have generated a unique genome-wide dataset that defines the feeding and Akt/FoxO1-dependent transcriptional changes in response to nutrient availability.
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Affiliation(s)
- Dominic Santoleri
- Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania Biomedical Graduate Studies, Philadelphia, PA 19104, USA
- Institute of Diabetes, Obesity and Metabolism, Smilow Center for Translational Research, University of Pennsylvania Perelman School of Medicine, 3400 Civic Center Blvd, Building 421, Philadelphia, PA 19104, USA
| | - Hee-Woong Lim
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
- Department of Pediatrics, University of Cincinnati, Cincinnati, OH 45229, USA
| | - Matthew J. Emmett
- Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Julian Stoute
- Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania Biomedical Graduate Studies, Philadelphia, PA 19104, USA
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Matthew J. Gavin
- Institute of Diabetes, Obesity and Metabolism, Smilow Center for Translational Research, University of Pennsylvania Perelman School of Medicine, 3400 Civic Center Blvd, Building 421, Philadelphia, PA 19104, USA
| | - Jaimarie Sostre-Colón
- Institute of Diabetes, Obesity and Metabolism, Smilow Center for Translational Research, University of Pennsylvania Perelman School of Medicine, 3400 Civic Center Blvd, Building 421, Philadelphia, PA 19104, USA
| | - Kahealani Uehara
- Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania Biomedical Graduate Studies, Philadelphia, PA 19104, USA
- Institute of Diabetes, Obesity and Metabolism, Smilow Center for Translational Research, University of Pennsylvania Perelman School of Medicine, 3400 Civic Center Blvd, Building 421, Philadelphia, PA 19104, USA
| | - Jaclyn E. Welles
- Institute of Diabetes, Obesity and Metabolism, Smilow Center for Translational Research, University of Pennsylvania Perelman School of Medicine, 3400 Civic Center Blvd, Building 421, Philadelphia, PA 19104, USA
| | - Kathy Fange Liu
- Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania Biomedical Graduate Studies, Philadelphia, PA 19104, USA
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Mitchell A. Lazar
- Institute of Diabetes, Obesity and Metabolism, Smilow Center for Translational Research, University of Pennsylvania Perelman School of Medicine, 3400 Civic Center Blvd, Building 421, Philadelphia, PA 19104, USA
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Paul M. Titchenell
- Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania Biomedical Graduate Studies, Philadelphia, PA 19104, USA
- Institute of Diabetes, Obesity and Metabolism, Smilow Center for Translational Research, University of Pennsylvania Perelman School of Medicine, 3400 Civic Center Blvd, Building 421, Philadelphia, PA 19104, USA
- Department of Physiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
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32
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Hetman M, Slomnicki L, Hodges E, Ohri SS, Whittemore SR. Role of circadian rhythms in pathogenesis of acute CNS injuries: Insights from experimental studies. Exp Neurol 2022; 353:114080. [DOI: 10.1016/j.expneurol.2022.114080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 03/28/2022] [Accepted: 04/05/2022] [Indexed: 11/16/2022]
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Laitinen P, Väänänen MA, Kolari IL, Mäkinen PI, Kaikkonen MU, Weinberg MS, Morris KV, Korhonen P, Malm T, Ylä-Herttuala S, Roberts TC, Turunen MP, Turunen TA. Nuclear microRNA-466c regulates Vegfa expression in response to hypoxia. PLoS One 2022; 17:e0265948. [PMID: 35358280 PMCID: PMC8975276 DOI: 10.1371/journal.pone.0265948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 03/10/2022] [Indexed: 11/18/2022] Open
Abstract
MicroRNAs are well characterized in their role in silencing gene expression by targeting 3´-UTR of mRNAs in cytoplasm. However, recent studies have shown that miRNAs have a role in the regulation of genes in the nucleus, where they are abundantly located. We show here that in mouse endothelial cell line (C166), nuclear microRNA miR-466c participates in the regulation of vascular endothelial growth factor a (Vegfa) gene expression in hypoxia. Upregulation of Vegfa expression in response to hypoxia was significantly compromised after removal of miR-466c with CRISPR-Cas9 genomic deletion. We identified a promoter-associated long non-coding RNA on mouse Vegfa promoter and show that miR-466c directly binds to this transcript to modulate Vegfa expression. Collectively, these observations suggest that miR-466c regulates Vegfa gene transcription in the nucleus by targeting the promoter, and expands on our understanding of the role of miRNAs well beyond their canonical role.
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Affiliation(s)
- Pia Laitinen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
- RNatives Oy, Kuopio, Finland
| | - Mari-Anna Väänänen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Ida-Liisa Kolari
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Petri I. Mäkinen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Minna U. Kaikkonen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Marc S. Weinberg
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California, United States of America
- Wits/SAMRC Antiviral Gene Therapy Research Unit, School of Pathology, University of the Witwaterstrand, Witwaterstrand, South Africa
| | - Kevin V. Morris
- Center for Gene Therapy, City of Hope–Beckman Research Institute at the City of Hope, Duarte, California, United States of America
- Menzies Health Institute Queensland, School of Medical Science Griffith University, Gold Coast Campus, Queensland, Australia
| | - Paula Korhonen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Tarja Malm
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Seppo Ylä-Herttuala
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
- Heart Center and Gene Therapy Unit, Kuopio University Hospital, Kuopio, Finland
| | - Thomas C. Roberts
- Department of Paediatrics, University of Oxford, Oxford, United Kingdom
- MDUK Oxford Neuromuscular Centre, Oxford, United Kingdom
| | - Mikko P. Turunen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
- RNatives Oy, Kuopio, Finland
- * E-mail:
| | - Tiia A. Turunen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
- RNatives Oy, Kuopio, Finland
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Kim JY, Yang IS, Kim HJ, Yoon JY, Han YH, Seong JK, Lee MO. RORα contributes to the maintenance of genome ploidy in the liver of mice with diet-induced nonalcoholic steatohepatitis. Am J Physiol Endocrinol Metab 2022; 322:E118-E131. [PMID: 34894722 DOI: 10.1152/ajpendo.00309.2021] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Hepatic polyploidization is closely linked to the progression of nonalcoholic fatty liver disease (NAFLD); however, the underlying molecular mechanism is not clearly understood. In this study, we demonstrated the role of retinoic acid-related orphan receptor α (RORα) in the maintenance of genomic integrity, particularly in the pathogenesis of NAFLD, using the high-fat diet (HFD)-fed liver-specific RORα knockout (RORα-LKO) mouse model. First, we observed that the loss of hepatic retinoic acid receptor-related orphan receptor α (RORα) accelerated hepatocyte nuclear polyploidization after HFD feeding. In 70% partial hepatectomy experiments, enrichment of hepatocyte polyploidy was more obvious in the RORα-LKO animals, which was accompanied by early progression to the S phase and blockade of the G2/M transition, suggesting a potential role of RORα in suppressing hepatocyte polyploidization in the regenerating liver. An analysis of a publicly available RNA sequencing (RNA-seq) and chromatin immunoprecipitation-seq dataset, together with the Search Tool of the Retrieval of Interacting Genes/Proteins database resource, revealed that DNA endoreplication was the top-enriched biological process Gene Ontology term. Furthermore, we found that E2f7 and E2f8, which encode key transcription factors for DNA endoreplication, were the downstream targets of RORα-induced transcriptional repression. Finally, we showed that the administration of JC1-40, an RORα activator (5 mg/kg body wt), significantly reduced hepatic nuclear polyploidization in the HFD-fed mice. Together, our observations suggest that the RORα-induced suppression of hepatic polyploidization may provide new insights into the pathological polyploidy of NAFLD and may contribute to the development of therapeutic strategies for the treatment of NAFLD.NEW & NOTEWORTHY It has been reported that hepatic polyploidization is closely linked to the progression of NAFLD. Here, we showed that the genetic depletion of hepatic RORα in mice accelerated hepatocyte polyploidization after high-fat diet feeding. The mechanism could be the RORα-mediated repression of E2f7 and E2f8, key transcription factors for DNA endoreplication. Thus, preservation of genome integrity by RORα could provide a new insight for developing therapeutics against the disease.
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Affiliation(s)
- Ju-Yeon Kim
- College of Pharmacy, Seoul National University, Seoul, South Korea
| | - In Sook Yang
- College of Veterinary Medicine, Seoul National University, Seoul, South Korea
| | - Hyeon-Ji Kim
- College of Pharmacy, Seoul National University, Seoul, South Korea
- Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, South Korea
| | - Jae-Yeun Yoon
- College of Pharmacy, Seoul National University, Seoul, South Korea
| | - Yong-Hyun Han
- College of Pharmacy, Kangwon National University, Chuncheon, South Korea
| | - Je Kyung Seong
- College of Veterinary Medicine, Seoul National University, Seoul, South Korea
- Research Institute of Veterinary Science, Seoul National University, Seoul, South Korea
- Korea Mouse Phenotyping Center, Seoul National University, Seoul, South Korea
| | - Mi-Ock Lee
- College of Pharmacy, Seoul National University, Seoul, South Korea
- Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, South Korea
- Bio-MAX Institute, Seoul National University, Seoul, South Korea
- Korea Mouse Phenotyping Center, Seoul National University, Seoul, South Korea
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35
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Jiang C, Liu P, La CM, Guan D. In silico integrative analysis of multi-omics reveals regulatory layers for diurnal gene expression in mouse liver. Front Endocrinol (Lausanne) 2022; 13:955070. [PMID: 35937828 PMCID: PMC9353712 DOI: 10.3389/fendo.2022.955070] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 06/27/2022] [Indexed: 11/25/2022] Open
Abstract
Diurnal oscillation persists throughout the body and plays an essential role in maintaining physiological homeostasis. Disruption of diurnal rhythm contributes to many diseases including type 2 diabetes. The regulatory mechanism of the transcription-translation feedback loop (TTFL) of core clock genes is well-established, while a systematic study across all regulatory layers of gene expression, including gene transcription, RNA translation, and DNA binding protein (DBP) activities, is still lacking. We comprehensively bioinformatics analyzed the rhythmicity of gene transcription, mature RNA abundance, protein abundance and DBP activity using publicly available omic-datasets from mouse livers. We found that the core clock genes, Bmal1 and Rev-erbα, persistently retained rhythmicity in all stages, which supported the essential rhythmic function along with the TTFL. Interestingly, there were many layer-specific rhythmic genes playing layer-specific rhythmic functions. The systematic analysis of gene transcription rate, RNA translation efficiency, and post-translation modification of DBP were incorporated to determine the potential mechanisms for layer-specific rhythmic genes. We observed the gene with rhythmic expression in both mature RNA and protein layers were largely due to relatively consistent translation rate. In addition, rhythmic translation rate induced the rhythms of protein whose mature RNA levels were not rhythmic. Further analysis revealed a phosphorylation-mediated and an enhancer RNA-mediated cycling regulation between the corresponding layers. This study presents a global view of the oscillating genes in multiple layers via a systematical analysis and indicates the complexity of regulatory mechanisms across different layers for further functional study.
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Greulich F, Bielefeld KA, Scheundel R, Mechtidou A, Strickland B, Uhlenhaut NH. Enhancer RNA Expression in Response to Glucocorticoid Treatment in Murine Macrophages. Cells 2021; 11:28. [PMID: 35011590 PMCID: PMC8744892 DOI: 10.3390/cells11010028] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/17/2021] [Accepted: 12/20/2021] [Indexed: 12/15/2022] Open
Abstract
Glucocorticoids are potent anti-inflammatory drugs; however, their molecular mode of action remains complex and elusive. They bind to the glucocorticoid receptor (GR), a nuclear receptor that controls gene expression in almost all tissues in a cell type-specific manner. While GR's transcriptional targets mediate beneficial reactions in immune cells, they also harbor the potential of adverse metabolic effects in other cell types such as hepatocytes. Here, we have profiled nascent transcription upon glucocorticoid stimulation in LPS-activated primary murine macrophages using 4sU-seq. We compared our results to publicly available nascent transcriptomics data from murine liver and bioinformatically identified non-coding RNAs transcribed from intergenic GR binding sites in a tissue-specific fashion. These tissue-specific enhancer RNAs (eRNAs) correlate with target gene expression, reflecting cell type-specific glucocorticoid responses. We further associate GR-mediated eRNA expression with changes in H3K27 acetylation and BRD4 recruitment in inflammatory macrophages upon glucocorticoid treatment. In summary, we propose a common mechanism by which GR-bound enhancers regulate target gene expression by changes in histone acetylation, BRD4 recruitment and eRNA expression. We argue that local eRNAs are potential therapeutic targets downstream of GR signaling which may modulate glucocorticoid response in a cell type-specific way.
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Affiliation(s)
- Franziska Greulich
- Metabolic Programming, TUM School of Life Sciences, ZIEL Institute for Food & Health, Gregor-Mendel-Strasse 2, 85354 Freising, Germany; (F.G.); (R.S.); (B.S.)
- Helmholtz Diabetes Center (IDO, IDC, IDE), Helmholtz Center Munich HMGU, Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany; (K.A.B.); (A.M.)
| | - Kirsten Adele Bielefeld
- Helmholtz Diabetes Center (IDO, IDC, IDE), Helmholtz Center Munich HMGU, Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany; (K.A.B.); (A.M.)
| | - Ronny Scheundel
- Metabolic Programming, TUM School of Life Sciences, ZIEL Institute for Food & Health, Gregor-Mendel-Strasse 2, 85354 Freising, Germany; (F.G.); (R.S.); (B.S.)
| | - Aikaterini Mechtidou
- Helmholtz Diabetes Center (IDO, IDC, IDE), Helmholtz Center Munich HMGU, Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany; (K.A.B.); (A.M.)
| | - Benjamin Strickland
- Metabolic Programming, TUM School of Life Sciences, ZIEL Institute for Food & Health, Gregor-Mendel-Strasse 2, 85354 Freising, Germany; (F.G.); (R.S.); (B.S.)
| | - Nina Henriette Uhlenhaut
- Metabolic Programming, TUM School of Life Sciences, ZIEL Institute for Food & Health, Gregor-Mendel-Strasse 2, 85354 Freising, Germany; (F.G.); (R.S.); (B.S.)
- Helmholtz Diabetes Center (IDO, IDC, IDE), Helmholtz Center Munich HMGU, Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany; (K.A.B.); (A.M.)
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Brown MR, Sen SK, Mazzone A, Her TK, Xiong Y, Lee JH, Javeed N, Colwell CS, Rakshit K, LeBrasseur NK, Gaspar-Maia A, Ordog T, Matveyenko AV. Time-restricted feeding prevents deleterious metabolic effects of circadian disruption through epigenetic control of β cell function. SCIENCE ADVANCES 2021; 7:eabg6856. [PMID: 34910509 PMCID: PMC8673777 DOI: 10.1126/sciadv.abg6856] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 10/28/2021] [Indexed: 05/30/2023]
Abstract
Circadian rhythm disruption (CD) is associated with impaired glucose homeostasis and type 2 diabetes mellitus (T2DM). While the link between CD and T2DM remains unclear, there is accumulating evidence that disruption of fasting/feeding cycles mediates metabolic dysfunction. Here, we used an approach encompassing analysis of behavioral, physiological, transcriptomic, and epigenomic effects of CD and consequences of restoring fasting/feeding cycles through time-restricted feeding (tRF) in mice. Results show that CD perturbs glucose homeostasis through disruption of pancreatic β cell function and loss of circadian transcriptional and epigenetic identity. In contrast, restoration of fasting/feeding cycle prevented CD-mediated dysfunction by reestablishing circadian regulation of glucose tolerance, β cell function, transcriptional profile, and reestablishment of proline and acidic amino acid–rich basic leucine zipper (PAR bZIP) transcription factor DBP expression/activity. This study provides mechanistic insights into circadian regulation of β cell function and corresponding beneficial effects of tRF in prevention of T2DM.
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Affiliation(s)
- Matthew R. Brown
- Department of Physiology and Biomedical Engineering, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
| | - Satish K. Sen
- Department of Physiology and Biomedical Engineering, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
| | - Amelia Mazzone
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
- Epigenomics Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Tracy K. Her
- Department of Physiology and Biomedical Engineering, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
| | - Yuning Xiong
- Epigenomics Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
| | - Jeong-Heon Lee
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
- Epigenomics Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
| | - Naureen Javeed
- Department of Physiology and Biomedical Engineering, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
| | - Christopher S. Colwell
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Kuntol Rakshit
- Department of Physiology and Biomedical Engineering, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
| | - Nathan K. LeBrasseur
- Department of Physical Medicine and Rehabilitation, Mayo Clinic, Rochester, MN, USA
| | - Alexandre Gaspar-Maia
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
- Epigenomics Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Tamas Ordog
- Department of Physiology and Biomedical Engineering, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
- Epigenomics Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
- Division of Gastroenterology and Hepatology, Department of Medicine, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
| | - Aleksey V. Matveyenko
- Department of Physiology and Biomedical Engineering, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
- Division of Endocrinology, Metabolism, Diabetes, and Nutrition, Department of Medicine, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
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Razi Soofiyani S, Ahangari H, Soleimanian A, Babaei G, Ghasemnejad T, Safavi SE, Eyvazi S, Tarhriz V. The role of circadian genes in the pathogenesis of colorectal cancer. Gene 2021; 804:145894. [PMID: 34418469 DOI: 10.1016/j.gene.2021.145894] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 04/07/2021] [Accepted: 08/06/2021] [Indexed: 02/07/2023]
Abstract
Colorectal cancer (CRC) is the third most frequent cancer in human beings and is also the major cause of death among the other gastrointestinal cancers. The exact mechanisms of CRC development in most patients remains unclear. So far, several genetically, environmental and epigenetically risk factors have been identified for CRC development. The circadian rhythm is a 24-h rhythm that drives several biologic processes. The circadian system is guided by a central pacemaker which is located in the suprachiasmatic nucleus (SCN) in the hypothalamus. Circadian rhythm is regulated by circadian clock genes, cytokines and hormones like melatonin. Disruptions in biological rhythms are known to be strongly associated with several diseases, including cancer. The role of the different circadian genes has been verified in various cancers, however, the pathways of different circadian genes in the pathogenesis of CRC are less investigated. Identification of the details of the pathways in CRC helps researchers to explore new therapies for the malignancy.
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Affiliation(s)
- Saiedeh Razi Soofiyani
- Clinical Research Development Unit of Sina Educational, Research and Treatment Center, Tabriz University of Medical Sciences, Tabriz, Iran; Molecular Medicine Research Center, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hossein Ahangari
- Department of Food Science and Technology, Faculty of Nutrition and Food Science, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Alireza Soleimanian
- Department of Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | - Ghader Babaei
- Department of Clinical Biochemistry, Urmia University of Medical Sciences, Urmia, Iran
| | - Tohid Ghasemnejad
- Molecular Medicine Research Center, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Seyed Esmaeil Safavi
- Faculty of Veternary Medicine, Tabriz Branch, Islamic Azad University, Tabriz, Iran; Biotechnology Research Center, Tabriz Branch, Islamic Azad University, Tabriz, Iran
| | - Shirin Eyvazi
- Biotechnology Research Center, Tabriz Branch, Islamic Azad University, Tabriz, Iran; Department of Biology, Tabriz Branch, Islamic Azad University, Tabriz, Iran.
| | - Vahideh Tarhriz
- Molecular Medicine Research Center, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran.
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Azzimato V, Chen P, Barreby E, Morgantini C, Levi L, Vankova A, Jager J, Sulen A, Diotallevi M, Shen JX, Miller A, Ellis E, Rydén M, Näslund E, Thorell A, Lauschke VM, Channon KM, Crabtree MJ, Haschemi A, Craige SM, Mori M, Spallotta F, Aouadi M. Hepatic miR-144 Drives Fumarase Activity Preventing NRF2 Activation During Obesity. Gastroenterology 2021; 161:1982-1997.e11. [PMID: 34425095 DOI: 10.1053/j.gastro.2021.08.030] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 08/04/2021] [Accepted: 08/15/2021] [Indexed: 12/11/2022]
Abstract
BACKGROUND AND AIMS Oxidative stress plays a key role in the development of metabolic complications associated with obesity, including insulin resistance and the most common chronic liver disease worldwide, nonalcoholic fatty liver disease. We have recently discovered that the microRNA miR-144 regulates protein levels of the master mediator of the antioxidant response, nuclear factor erythroid 2-related factor 2 (NRF2). On miR-144 silencing, the expression of NRF2 target genes was significantly upregulated, suggesting that miR-144 controls NRF2 at the level of both protein expression and activity. Here we explored a mechanism whereby hepatic miR-144 inhibited NRF2 activity upon obesity via the regulation of the tricarboxylic acid (TCA) metabolite, fumarate, a potent activator of NRF2. METHODS We performed transcriptomic analysis in liver macrophages (LMs) of obese mice and identified the immuno-responsive gene 1 (Irg1) as a target of miR-144. IRG1 catalyzes the production of a TCA derivative, itaconate, an inhibitor of succinate dehydrogenase (SDH). TCA enzyme activities and kinetics were analyzed after miR-144 silencing in obese mice and human liver organoids using single-cell activity assays in situ and molecular dynamic simulations. RESULTS Increased levels of miR-144 in obesity were associated with reduced expression of Irg1, which was restored on miR-144 silencing in vitro and in vivo. Furthermore, miR-144 overexpression reduces Irg1 expression and the production of itaconate in vitro. In alignment with the reduction in IRG1 levels and itaconate production, we observed an upregulation of SDH activity during obesity. Surprisingly, however, fumarate hydratase (FH) activity was also upregulated in obese livers, leading to the depletion of its substrate fumarate. miR-144 silencing selectively reduced the activities of both SDH and FH resulting in the accumulation of their related substrates succinate and fumarate. Moreover, molecular dynamics analyses revealed the potential role of itaconate as a competitive inhibitor of not only SDH but also FH. Combined, these results demonstrate that silencing of miR-144 inhibits the activity of NRF2 through decreased fumarate production in obesity. CONCLUSIONS Herein we unravel a novel mechanism whereby miR-144 inhibits NRF2 activity through the consumption of fumarate by activation of FH. Our study demonstrates that hepatic miR-144 triggers a hyperactive FH in the TCA cycle leading to an impaired antioxidant response in obesity.
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Affiliation(s)
- Valerio Azzimato
- Center for Infectious Medicine (CIM), Department of Medicine, Karolinska Institutet, Huddinge, Sweden.
| | - Ping Chen
- Center for Infectious Medicine (CIM), Department of Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Emelie Barreby
- Center for Infectious Medicine (CIM), Department of Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Cecilia Morgantini
- Center for Infectious Medicine (CIM), Department of Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Laura Levi
- Center for Infectious Medicine (CIM), Department of Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Ana Vankova
- Center for Infectious Medicine (CIM), Department of Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Jennifer Jager
- Université Côte d'Azur, Inserm, Centre Méditerranéen de Médecine Moléculaire (C3M), Team « Cellular and Molecular Pathophysiology of Obesity and Diabetes,» Côte d'Azur, France
| | - André Sulen
- Center for Infectious Medicine (CIM), Department of Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Marina Diotallevi
- BHF Centre of Research Excellence, Division of Cardiovascular Medicine, Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK; Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Joanne X Shen
- Department of Physiology and Pharmacology, Karolinska Institutet, Solna, Sweden
| | - Anne Miller
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Ewa Ellis
- Division of Transplantation Surgery, Department of Clinical Science, Intervention and Technology (CLINTEC), Karolinska Institutet, Stockholm, Sweden
| | - Mikael Rydén
- Department of Medicine (H7), Karolinska Institutet, Huddinge, Sweden
| | - Erik Näslund
- Department of Clinical Sciences, Danderyd Hospital, Karolinska Institutet, Stockholm, Sweden
| | - Anders Thorell
- Department of Clinical Sciences, Danderyd Hospital, Karolinska Institutet, Stockholm, Sweden; Department of Surgery, Ersta Hospital, Karolinska Institutet, Stockholm, Sweden
| | - Volker M Lauschke
- Department of Physiology and Pharmacology, Karolinska Institutet, Solna, Sweden; Dr Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany
| | - Keith M Channon
- BHF Centre of Research Excellence, Division of Cardiovascular Medicine, Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK; Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Mark J Crabtree
- BHF Centre of Research Excellence, Division of Cardiovascular Medicine, Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK; Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Arvand Haschemi
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Siobhan M Craige
- Department of Human Nutrition, Foods, and Exercise, Virginia Tech, Blacksburg, Virginia
| | - Mattia Mori
- Department of Biotechnology, Chemistry, and Pharmacy, University of Siena, Siena, Italy
| | - Francesco Spallotta
- Institute for Systems Analysis and Computer Science "A. Ruberti," National Research Council (IASI - CNR), Rome, Italy
| | - Myriam Aouadi
- Center for Infectious Medicine (CIM), Department of Medicine, Karolinska Institutet, Huddinge, Sweden.
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Kim H, Han Y, Kim J, Lee M. RORα Enhances Lysosomal Acidification and Autophagic Flux in the Hepatocytes. Hepatol Commun 2021; 5:2121-2138. [PMID: 34558854 PMCID: PMC8631090 DOI: 10.1002/hep4.1785] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 05/25/2021] [Accepted: 06/24/2021] [Indexed: 12/30/2022] Open
Abstract
Lysosomes are intracellular acidic organelles with catabolic functions that contribute to the activation of autophagy. Although autophagy abnormality is associated with defects in lysosomal acidification during the progression of nonalcoholic fatty liver disease (NAFLD), the mechanisms of control of lysosomal acidification are not well understood at the molecular level. Thus, we aimed to elucidate the role of the orphan nuclear receptor retinoic acid-related orphan receptor α (RORα) in lysosomal acidification and autophagic flux, particularly in nutrition-enriched hepatocytes. First, lysosomal acidity was much lower in the hepatocytes obtained from hepatocyte-specific RORα-deleted (RORα-LKO) mice, whereas the infusion of an adenovirus encoding RORα in wild-type hepatocytes increased lysosomal acidity, as determined by LysoSensor. Second, the lysosomal translocation of the mechanistic target of rapamycin was increased and immature cathepsin D was accumulated in the liver of RORα-LKO mice. Third, the accumulation of LC3-II, p62/sequestosome 1 (SQSTM1), and neighbor of BRCA1 gene 1 (NBR1) was increased in the livers of RORα-LKO mice, indicating an impaired autophagic flux in the livers. Consistently, the number of autolysosomes containing mitochondria and lipid droplets was dramatically reduced in the RORα-deleted hepatocytes. Finally, we found that RORα induced the transcription of genes involved in lysosomal function, such as Atp6v1g1, a vacuolar H+ -ATPase (v-ATPase) subunit, which were largely down-regulated in the livers of mice with high-fat diet-induced NAFLD and patients with hepatitis. Conclusion: Targeting RORα may be a potential therapeutic strategy to restore lysosomal acidification, which inhibits the progression of NAFLD.
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Affiliation(s)
- Hyeon‐Ji Kim
- College of PharmacySeoul National UniversitySeoulKorea
| | - Yong‐Hyun Han
- Laboratory of Pathology and PhysiologyCollege of PharmacyKangwon National UniversityChuncheonSouth Korea
| | - Ju‐Yeon Kim
- College of PharmacySeoul National UniversitySeoulKorea
| | - Mi‐Ock Lee
- College of PharmacySeoul National UniversitySeoulKorea
- Bio‐MAX InstituteSeoul National UniversitySeoulKorea
- Research Institute of Pharmaceutical SciencesSeoulKorea
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41
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Circadian clock and cell cycle: Cancer and chronotherapy. Acta Histochem 2021; 123:151816. [PMID: 34800857 DOI: 10.1016/j.acthis.2021.151816] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 10/25/2021] [Accepted: 11/05/2021] [Indexed: 01/03/2023]
Abstract
The circadian clock is an endogenous timing system that ensures that various physiological processes have nearly 24 h circadian rhythms, including cell metabolism, division, apoptosis, and tumor production. In addition, results from animal models and molecular studies underscore emerging links between the cell cycle and the circadian clock. Mutations in the core genes of the circadian clock' can disrupt the cell cycle, which in turn increases the possibility of tumors. At present, tumor chronotherapy, which relies on a circadian clock mechanism, is developing rapidly for optimizing the time of drug administration in tumor treatment to improve drug efficacy and safety. However, the relationship between the circadian clock and the cell cycle is extremely complicated. This review summarizes the possible connection between the circadian clock and the cell cycle. In addition, the review provides evidence of the influence of the circadian clock on senescence and cancer.
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42
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Qu M, Qu H, Jia Z, Kay SA. HNF4A defines tissue-specific circadian rhythms by beaconing BMAL1::CLOCK chromatin binding and shaping the rhythmic chromatin landscape. Nat Commun 2021; 12:6350. [PMID: 34732735 PMCID: PMC8566521 DOI: 10.1038/s41467-021-26567-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 10/12/2021] [Indexed: 11/30/2022] Open
Abstract
Transcription modulated by the circadian clock is diverse across cell types, underlying circadian control of peripheral metabolism and its observed perturbation in human diseases. We report that knockout of the lineage-specifying Hnf4a gene in mouse liver causes associated reductions in the genome-wide distribution of core clock component BMAL1 and accessible chromatin marks (H3K4me1 and H3K27ac). Ectopically expressing HNF4A remodels chromatin landscape and nucleates distinct tissue-specific BMAL1 chromatin binding events, predominantly in enhancer regions. Circadian rhythms are disturbed in Hnf4a knockout liver and HNF4A-MODY diabetic model cells. Additionally, the epigenetic state and accessibility of the liver genome dynamically change throughout the day, synchronized with chromatin occupancy of HNF4A and clustered expression of circadian outputs. Lastly, Bmal1 knockout attenuates HNF4A genome-wide binding in the liver, likely due to downregulated Hnf4a transcription. Our results may provide a general mechanism for establishing circadian rhythm heterogeneity during development and disease progression, governed by chromatin structure.
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Affiliation(s)
- Meng Qu
- Department of Neurology, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA.
| | - Han Qu
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
| | - Zhenyu Jia
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
- Graduate Program in Genetics, Genomics, and Bioinformatics, University of California, Riverside, CA, 92521, USA
| | - Steve A Kay
- Department of Neurology, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA.
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Adlanmerini M, Krusen BM, Nguyen HCB, Teng CW, Woodie LN, Tackenberg MC, Geisler CE, Gaisinsky J, Peed LC, Carpenter BJ, Hayes MR, Lazar MA. REV-ERB nuclear receptors in the suprachiasmatic nucleus control circadian period and restrict diet-induced obesity. SCIENCE ADVANCES 2021; 7:eabh2007. [PMID: 34705514 PMCID: PMC8550249 DOI: 10.1126/sciadv.abh2007] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 09/07/2021] [Indexed: 05/28/2023]
Abstract
Circadian disruption, as occurs in shift work, is associated with metabolic diseases often attributed to a discordance between internal clocks and environmental timekeepers. REV-ERB nuclear receptors are key components of the molecular clock, but their specific role in the SCN master clock is unknown. We report here that mice lacking circadian REV-ERB nuclear receptors in the SCN maintain free-running locomotor and metabolic rhythms, but these rhythms are notably shortened by 3 hours. When housed under a 24-hour light:dark cycle and fed an obesogenic diet, these mice gained excess weight and accrued more liver fat than controls. These metabolic disturbances were corrected by matching environmental lighting to the shortened endogenous 21-hour clock period, which decreased food consumption. Thus, SCN REV-ERBs are not required for rhythmicity but determine the free-running period length. Moreover, these results support the concept that dissonance between environmental conditions and endogenous time periods causes metabolic disruption.
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Affiliation(s)
- Marine Adlanmerini
- Institute for Diabetes, Obesity, and Metabolism and Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Brianna M. Krusen
- Institute for Diabetes, Obesity, and Metabolism and Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Hoang C. B. Nguyen
- Institute for Diabetes, Obesity, and Metabolism and Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Clare W. Teng
- Institute for Diabetes, Obesity, and Metabolism and Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Lauren N. Woodie
- Institute for Diabetes, Obesity, and Metabolism and Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Michael C. Tackenberg
- Institute for Diabetes, Obesity, and Metabolism and Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Caroline E. Geisler
- Department of Psychiatry, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Jane Gaisinsky
- Department of Psychiatry, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Lindsey C. Peed
- Institute for Diabetes, Obesity, and Metabolism and Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Bryce J. Carpenter
- Institute for Diabetes, Obesity, and Metabolism and Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Matthew R. Hayes
- Institute for Diabetes, Obesity, and Metabolism and Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
- Department of Psychiatry, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Mitchell A. Lazar
- Institute for Diabetes, Obesity, and Metabolism and Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
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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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Guan D, Lazar MA. Interconnections between circadian clocks and metabolism. J Clin Invest 2021; 131:e148278. [PMID: 34338232 DOI: 10.1172/jci148278] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Circadian rhythms evolved through adaptation to daily light/dark changes in the environment; they are believed to be regulated by the core circadian clock interlocking feedback loop. Recent studies indicate that each core component executes general and specific functions in metabolism. Here, we review the current understanding of the role of these core circadian clock genes in the regulation of metabolism using various genetically modified animal models. Additionally, emerging evidence shows that exposure to environmental stimuli, such as artificial light, unbalanced diet, mistimed eating, and exercise, remodels the circadian physiological processes and causes metabolic disorders. This Review summarizes the reciprocal regulation between the circadian clock and metabolism, highlights remaining gaps in knowledge about the regulation of circadian rhythms and metabolism, and examines potential applications to human health and disease.
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Affiliation(s)
- Dongyin Guan
- Institute for Diabetes, Obesity, and Metabolism.,Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, and
| | - Mitchell A Lazar
- Institute for Diabetes, Obesity, and Metabolism.,Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, and.,Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
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46
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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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47
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Judd J, Sanderson H, Feschotte C. Evolution of mouse circadian enhancers from transposable elements. Genome Biol 2021; 22:193. [PMID: 34187518 PMCID: PMC8240256 DOI: 10.1186/s13059-021-02409-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 06/10/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Transposable elements are increasingly recognized as a source of cis-regulatory variation. Previous studies have revealed that transposons are often bound by transcription factors and some have been co-opted into functional enhancers regulating host gene expression. However, the process by which transposons mature into complex regulatory elements, like enhancers, remains poorly understood. To investigate this process, we examined the contribution of transposons to the cis-regulatory network controlling circadian gene expression in the mouse liver, a well-characterized network serving an important physiological function. RESULTS ChIP-seq analyses reveal that transposons and other repeats contribute ~ 14% of the binding sites for core circadian regulators (CRs) including BMAL1, CLOCK, PER1/2, and CRY1/2, in the mouse liver. RSINE1, an abundant murine-specific SINE, is the only transposon family enriched for CR binding sites across all datasets. Sequence analyses and reporter assays reveal that the circadian regulatory activity of RSINE1 stems from the presence of imperfect CR binding motifs in the ancestral RSINE1 sequence. These motifs matured into canonical motifs through point mutations after transposition. Furthermore, maturation occurred preferentially within elements inserted in the proximity of ancestral CR binding sites. RSINE1 also acquired motifs that recruit nuclear receptors known to cooperate with CRs to regulate circadian gene expression specifically in the liver. CONCLUSIONS Our results suggest that the birth of enhancers from transposons is predicated both by the sequence of the transposon and by the cis-regulatory landscape surrounding their genomic integration site.
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Affiliation(s)
- Julius Judd
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14853, USA
| | - Hayley Sanderson
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT, 84112, USA
| | - Cédric Feschotte
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14853, USA.
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48
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Azzimato V, Jager J, Chen P, Morgantini C, Levi L, Barreby E, Sulen A, Oses C, Willerbrords J, Xu C, Li X, Shen JX, Akbar N, Haag L, Ellis E, Wålhen K, Näslund E, Thorell A, Choudhury RP, Lauschke VM, Rydén M, Craige SM, Aouadi M. Liver macrophages inhibit the endogenous antioxidant response in obesity-associated insulin resistance. Sci Transl Med 2021; 12:12/532/eaaw9709. [PMID: 32102936 DOI: 10.1126/scitranslmed.aaw9709] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 02/06/2020] [Indexed: 12/22/2022]
Abstract
Obesity and insulin resistance are risk factors for nonalcoholic fatty liver disease (NAFLD), the most common chronic liver disease worldwide. Because no approved medication nor an accurate and noninvasive diagnosis is currently available for NAFLD, there is a clear need to better understand the link between obesity and NAFLD. Lipid accumulation during obesity is known to be associated with oxidative stress and inflammatory activation of liver macrophages (LMs). However, we show that although LMs do not become proinflammatory during obesity, they display signs of oxidative stress. In livers of both humans and mice, antioxidant nuclear factor erythroid 2-related factor 2 (NRF2) was down-regulated with obesity and insulin resistance, yielding an impaired response to lipid accumulation. At the molecular level, a microRNA-targeting NRF2 protein, miR-144, was elevated in the livers of obese insulin-resistant humans and mice, and specific silencing of miR-144 in murine and human LMs was sufficient to restore NRF2 protein expression and the antioxidant response. These results highlight the pathological role of LMs and their therapeutic potential to restore the impaired endogenous antioxidant response in obesity-associated NAFLD.
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Affiliation(s)
- Valerio Azzimato
- Integrated Cardio Metabolic Center, Department of Medicine, Karolinska Institutet, 141 57 Huddinge, Sweden
| | - Jennifer Jager
- Université Côte d'Azur, Inserm U1065, C3M, Team Cellular and Molecular Physiopathology of Obesity, 06000 Nice, France
| | - Ping Chen
- Integrated Cardio Metabolic Center, Department of Medicine, Karolinska Institutet, 141 57 Huddinge, Sweden
| | - Cecilia Morgantini
- Integrated Cardio Metabolic Center, Department of Medicine, Karolinska Institutet, 141 57 Huddinge, Sweden
| | - Laura Levi
- Integrated Cardio Metabolic Center, Department of Medicine, Karolinska Institutet, 141 57 Huddinge, Sweden
| | - Emelie Barreby
- Integrated Cardio Metabolic Center, Department of Medicine, Karolinska Institutet, 141 57 Huddinge, Sweden
| | - André Sulen
- Integrated Cardio Metabolic Center, Department of Medicine, Karolinska Institutet, 141 57 Huddinge, Sweden
| | - Carolina Oses
- Integrated Cardio Metabolic Center, Department of Medicine, Karolinska Institutet, 141 57 Huddinge, Sweden
| | - Joost Willerbrords
- Integrated Cardio Metabolic Center, Department of Medicine, Karolinska Institutet, 141 57 Huddinge, Sweden
| | - Connie Xu
- Integrated Cardio Metabolic Center, Department of Medicine, Karolinska Institutet, 141 57 Huddinge, Sweden
| | - Xidan Li
- Integrated Cardio Metabolic Center, Department of Medicine, Karolinska Institutet, 141 57 Huddinge, Sweden
| | - Joanne X Shen
- Section of Pharmacogenetics, Department of Physiology and Pharmacology, Karolinska Institutet, 171 77 Solna, Sweden
| | - Naveed Akbar
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, OX3 9DU Oxford, UK
| | - Lars Haag
- Department of Laboratory Medicine, Laboratory Medicine, Karolinska Institutet, 141 57 Huddinge, Sweden
| | - Ewa Ellis
- Division of Transplantation Surgery, Clinical Science, Intervention and Technology (CLINTEC), Karolinska Institutet, 141 57 Huddinge, Sweden
| | - Kerstin Wålhen
- Unit of Endocrinology Department of Medicine, Karolinska Institutet, 141 57 Huddinge, Sweden
| | - Erik Näslund
- Division of Surgery, Department of Clinical Sciences, Danderyd Hospital, Karolinska Institutet, 182 88 Stockholm, Sweden
| | - Anders Thorell
- Division of Surgery, Department of Clinical Sciences, Danderyd Hospital, Karolinska Institutet, 182 88 Stockholm, Sweden.,Department of Surgery, Ersta Hospital, Karolinska Institutet, 116 28 Stockholm, Sweden
| | - Robin P Choudhury
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, OX3 9DU Oxford, UK
| | - Volker M Lauschke
- Section of Pharmacogenetics, Department of Physiology and Pharmacology, Karolinska Institutet, 171 77 Solna, Sweden
| | - Mikael Rydén
- Unit of Endocrinology Department of Medicine, Karolinska Institutet, 141 57 Huddinge, Sweden
| | - Siobhan M Craige
- Human Nutrition, Food, and Exercise Department, Virginia Tech, Blacksburg, VA 24060, USA
| | - Myriam Aouadi
- Integrated Cardio Metabolic Center, Department of Medicine, Karolinska Institutet, 141 57 Huddinge, Sweden.
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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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50
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Furlan-Magaril M, Ando-Kuri M, Arzate-Mejía RG, Morf J, Cairns J, Román-Figueroa A, Tenorio-Hernández L, Poot-Hernández AC, Andrews S, Várnai C, Virk B, Wingett SW, Fraser P. The global and promoter-centric 3D genome organization temporally resolved during a circadian cycle. Genome Biol 2021; 22:162. [PMID: 34099014 PMCID: PMC8185950 DOI: 10.1186/s13059-021-02374-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 05/05/2021] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Circadian gene expression is essential for organisms to adjust their physiology and anticipate daily changes in the environment. The molecular mechanisms controlling circadian gene transcription are still under investigation. In particular, how chromatin conformation at different genomic scales and regulatory elements impact rhythmic gene expression has been poorly characterized. RESULTS Here we measure changes in the spatial chromatin conformation in mouse liver using genome-wide and promoter-capture Hi-C alongside daily oscillations in gene transcription. We find topologically associating domains harboring circadian genes that switch assignments between the transcriptionally active and inactive compartment at different hours of the day, while their boundaries stably maintain their structure over time. To study chromatin contacts of promoters at high resolution over time, we apply promoter capture Hi-C. We find circadian gene promoters displayed a maximal number of chromatin contacts at the time of their peak transcriptional output. Furthermore, circadian genes, as well as contacted and transcribed regulatory elements, reach maximal expression at the same timepoints. Anchor sites of circadian gene promoter loops are enriched in DNA binding sites for liver nuclear receptors and other transcription factors, some exclusively present in either rhythmic or stable contacts. Finally, by comparing the interaction profiles between core clock and output circadian genes, we show that core clock interactomes are more dynamic compared to output circadian genes. CONCLUSION Our results identify chromatin conformation dynamics at different scales that parallel oscillatory gene expression and characterize the repertoire of regulatory elements that control circadian gene transcription through rhythmic or stable chromatin configurations.
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Affiliation(s)
- Mayra Furlan-Magaril
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico.
| | - Masami Ando-Kuri
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, CB2 0RE, UK
| | - Rodrigo G Arzate-Mejía
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
- Laboratory of Neuroepigenetics, Medical Faculty of the University of Zurich and Department of Health Science and Technology of the Swiss Federal Institute of Technology, Neuroscience Center Zurich, Zurich, Switzerland
| | - Jörg Morf
- Nuclear Dynamics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, CB2 0AW, UK
| | - Jonathan Cairns
- Nuclear Dynamics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK
| | - Abraham Román-Figueroa
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Luis Tenorio-Hernández
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - A César Poot-Hernández
- Unidad de Bioinformática y Manejo de Información, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Simon Andrews
- Bioinformatics Group, The Babraham Institute, Cambridge, CB22 3AT, UK
| | - Csilla Várnai
- Nuclear Dynamics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK
- Centre for Computational Biology, University of Birmingham, Birmingham, B15 2FG, UK
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, B15 2SY, UK
| | - Boo Virk
- Bioinformatics Group, The Babraham Institute, Cambridge, CB22 3AT, UK
| | - Steven W Wingett
- Bioinformatics Group, The Babraham Institute, Cambridge, CB22 3AT, UK
- Cell Biology Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0QH, UK
| | - Peter Fraser
- Nuclear Dynamics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
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