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Pratx L, Crawford T, Bäurle I. Mechanisms of heat stress-induced transcriptional memory. CURRENT OPINION IN PLANT BIOLOGY 2024; 81:102590. [PMID: 38968911 DOI: 10.1016/j.pbi.2024.102590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 05/29/2024] [Accepted: 06/07/2024] [Indexed: 07/07/2024]
Abstract
Transcriptional memory allows organisms to store information about transcriptional reprogramming in response to a stimulus. In plants, this often involves the response to an abiotic stress, which in nature may be cyclical or recurring. Such transcriptional memory confers sustained induction or enhanced re-activation in response to a recurrent stimulus, which may increase chances of survival and fitness. Heat stress (HS) has emerged as an excellent model system to study transcriptional memory in plants, and much progress has been made in elucidating the molecular mechanisms underlying this phenomenon. Here, we review how histone turnover and transcriptional co-regulator complexes contribute to reprogramming of transcriptional responses.
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Affiliation(s)
- Loris Pratx
- University of Potsdam, Institute for Biochemistry and Biology, Karl-Liebknecht-Str. 24-25, D-14476 Potsdam, Germany
| | - Tim Crawford
- University of Potsdam, Institute for Biochemistry and Biology, Karl-Liebknecht-Str. 24-25, D-14476 Potsdam, Germany
| | - Isabel Bäurle
- University of Potsdam, Institute for Biochemistry and Biology, Karl-Liebknecht-Str. 24-25, D-14476 Potsdam, Germany.
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2
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Carrasco-Wong I, Längst G, Sobrevia L, Casanello P. Nrf2 pre-recruitment at Enhancer 2 is a hallmark of H 2 O 2 -induced epigenetic transcriptional memory in the HMOX1 gene in human umbilical artery endothelial cells. J Cell Physiol 2024. [PMID: 38465708 DOI: 10.1002/jcp.31243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 02/01/2024] [Accepted: 02/26/2024] [Indexed: 03/12/2024]
Abstract
Maternal obesity (MO) is a significant cause of increased cardiometabolic risk in offspring, who present endothelial dysfunction at birth. Alterations in physiologic and cellular redox status are strongly associated with altered gene regulation in arterial endothelium. However, specific mechanisms by which the pro-oxidant fetal environment in MO could modulate the vascular gene expression and function during the offspring's postnatal life are elusive. We tested if oxidative stress could reprogram the antioxidant-coding gene's response to a pro-oxidant challenge through an epigenetic transcriptional memory (ETM) mechanism. A pro-oxidant double-hit protocol was applied to human umbilical artery endothelial cells (HUAECs) and EA.hy 926 endothelial cell lines. The ETM acquisition in the HMOX1 gene was analyzed by RT-qPCR. HMOX1 mRNA decay was evaluated by Actinomycin-D treatment and RT-qPCR. To assess the chromatin accessibility and the enrichment of NRF2, RNAP2, and phosphorylation at serin-5 of RNAP2, at HMOX1 gene regulatory regions, were used DNase HS-qPCR and ChIP-qPCR assays, respectively. The CpG methylation pattern at the HMOX1 core promoter was analyzed by DNA bisulfite conversion and Sanger sequencing. Data were analyzed using two-way ANOVA, and p < 0.05 was statistically significant. Using a pro-oxidant double-hit protocol, we found that the Heme Oxygenase gene (HMOX1) presents an ETM response associated with changes in the chromatin structure at the promoter and gene regulatory regions. The ETM response was characterized by a paused-RNA Polymerase 2 and NRF2 enrichment at the transcription start site and Enhancer 2 of the HMOX1 gene, respectively. Changes in DNA methylation pattern at the HMOX1 promoter were not a hallmark of this oxidative stress-induced ETM. These data suggest that a pro-oxidant milieu could trigger an ETM at the vascular level, indicating a potential epigenetic mechanism involved in the increased cardiovascular risk in the offspring of women with obesity.
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Affiliation(s)
- Ivo Carrasco-Wong
- Cellular Signaling and Differentiation Laboratory (CSDL), School of Medical Technology, Medicine and Science Faculty, Universidad San Sebastian, Santiago, Chile
| | - Gernot Längst
- Biochemistry III, Biochemistry Centre Regensburg (BCR), University of Regensburg, Regensburg, Germany
| | - Luis Sobrevia
- Cellular and Molecular Physiology Laboratory (CMPL), Department of Obstetrics, Division of Obstetrics and Gynecology, School of Medicine, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
- Department of Physiology, Faculty of Pharmacy, Universidad de Sevilla, Seville, Spain
- Medical School, Faculty of Medicine, Sao Paulo State University (UNESP), Sao Paulo, Sao Paulo, Brazil
- University of Queensland Centre for Clinical Research (UQCCR), Faculty of Medicine and Biomedical Sciences, University of Queensland, Herston, Brisbane, Queensland, Australia
- Division of Pathology, Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen (UMCG), Groningen, the Netherlands
- Faculty of Excellence, Institute for Obesity Research, School of Medicine and Health Sciences, Monterrey, Nuevo León, Mexico, Tecnologico de Monterrey, Monterrey, Nuevo León, Mexico
| | - Paola Casanello
- Division of Pathology, Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen (UMCG), Groningen, the Netherlands
- Department of Neonatology, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
- Department of Obstetrics, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
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Dastidar SG, De Kumar B, Lauckner B, Parrello D, Perley D, Vlasenok M, Tyagi A, Koney NKK, Abbas A, Nechaev S. Transcriptional responses of cancer cells to heat shock-inducing stimuli involve amplification of robust HSF1 binding. Nat Commun 2023; 14:7420. [PMID: 37973875 PMCID: PMC10654513 DOI: 10.1038/s41467-023-43157-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 11/01/2023] [Indexed: 11/19/2023] Open
Abstract
Responses of cells to stimuli are increasingly discovered to involve the binding of sequence-specific transcription factors outside of known target genes. We wanted to determine to what extent the genome-wide binding and function of a transcription factor are shaped by the cell type versus the stimulus. To do so, we induced the Heat Shock Response pathway in two different cancer cell lines with two different stimuli and related the binding of its master regulator HSF1 to nascent RNA and chromatin accessibility. Here, we show that HSF1 binding patterns retain their identity between basal conditions and under different magnitudes of activation, so that common HSF1 binding is globally associated with distinct transcription outcomes. HSF1-induced increase in DNA accessibility was modest in scale, but occurred predominantly at remote genomic sites. Apart from regulating transcription at existing elements including promoters and enhancers, HSF1 binding amplified during responses to stimuli may engage inactive chromatin.
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Affiliation(s)
- Sayantani Ghosh Dastidar
- Department of Biomedical Sciences, University of North Dakota School of Medicine, Grand Forks, ND, 58202, USA
- Illumina, Inc., San Diego, CA, 92122, USA
| | - Bony De Kumar
- Department of Biomedical Sciences, University of North Dakota School of Medicine, Grand Forks, ND, 58202, USA
- Yale Center for Genome Analysis, Department of Genetics, Yale University School of Medicine, New Haven, CT, 06510, USA
| | - Bo Lauckner
- Department of Biomedical Sciences, University of North Dakota School of Medicine, Grand Forks, ND, 58202, USA
| | - Damien Parrello
- Department of Biomedical Sciences, University of North Dakota School of Medicine, Grand Forks, ND, 58202, USA
| | - Danielle Perley
- Department of Biomedical Sciences, University of North Dakota School of Medicine, Grand Forks, ND, 58202, USA
- Canadian Centre for Computational Genomics, McGill Genome Centre, Montreal, QC, H3A0G1, Canada
| | - Maria Vlasenok
- Department of Biomedical Sciences, University of North Dakota School of Medicine, Grand Forks, ND, 58202, USA
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow, 121205, Russia
| | - Antariksh Tyagi
- Department of Biomedical Sciences, University of North Dakota School of Medicine, Grand Forks, ND, 58202, USA
- Yale Center for Genome Analysis, Department of Genetics, Yale University School of Medicine, New Haven, CT, 06510, USA
| | - Nii Koney-Kwaku Koney
- Department of Biomedical Sciences, University of North Dakota School of Medicine, Grand Forks, ND, 58202, USA
- University of Ghana Medical School, University of Ghana, Accra, Ghana
| | - Ata Abbas
- Department of Biomedical Sciences, University of North Dakota School of Medicine, Grand Forks, ND, 58202, USA
- Department of Biochemistry, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Sergei Nechaev
- Department of Biomedical Sciences, University of North Dakota School of Medicine, Grand Forks, ND, 58202, USA.
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4
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Tehrani SSH, Kogan A, Mikulski P, Jansen LET. Remembering foods and foes: emerging principles of transcriptional memory. Cell Death Differ 2023:10.1038/s41418-023-01200-6. [PMID: 37563261 DOI: 10.1038/s41418-023-01200-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 07/20/2023] [Accepted: 08/01/2023] [Indexed: 08/12/2023] Open
Abstract
Transcriptional memory is characterized by a primed cellular state, induced by an external stimulus that results in an altered expression of primed genes upon re-exposure to the inducing signal. Intriguingly, the primed state is heritably maintained across somatic cell divisions even after the initial stimulus and target gene transcription cease. This phenomenon is widely observed across various organisms and appears to enable cells to retain a memory of external signals, thereby adapting to environmental changes. Signals range from nutrient supplies (food) to a variety of stress signals, including exposure to pathogens (foes), leading to long-term memory such as in the case of trained immunity in plants and mammals. Here, we review these priming phenomena and our current understanding of transcriptional memory. We consider different mechanistic models for how memory can work and discuss existing evidence for potential carriers of memory. Key molecular signatures include: the poising of RNA polymerase II machinery, maintenance of histone marks, as well as alterations in nuclear positioning and long-range chromatin interactions. Finally, we discuss the potential adaptive roles of transcriptional memory in the organismal response to its environment from nutrient sensing to trained immunity.
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Affiliation(s)
- Sahar S H Tehrani
- Department of Biochemistry, University of Oxford, OX1 3QU, Oxford, UK
| | - Anna Kogan
- Department of Biochemistry, University of Oxford, OX1 3QU, Oxford, UK
| | - Pawel Mikulski
- Department of Biochemistry, University of Oxford, OX1 3QU, Oxford, UK.
| | - Lars E T Jansen
- Department of Biochemistry, University of Oxford, OX1 3QU, Oxford, UK.
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Jin HL, Duan S, Zhang P, Yang Z, Zeng Y, Chen Z, Hong L, Li M, Luo L, Chang Z, Hu J, Wang HB. Dual roles for CND1 in maintenance of nuclear and chloroplast genome stability in plants. Cell Rep 2023; 42:112268. [PMID: 36933214 DOI: 10.1016/j.celrep.2023.112268] [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: 12/23/2021] [Revised: 12/19/2022] [Accepted: 02/28/2023] [Indexed: 03/19/2023] Open
Abstract
The coordination of chloroplast and nuclear genome status is critical for plant cell function. Here, we report that Arabidopsis CHLOROPLAST AND NUCLEUS DUAL-LOCALIZED PROTEIN 1 (CND1) maintains genome stability in the chloroplast and the nucleus. CND1 localizes to both compartments, and complete loss of CND1 results in embryo lethality. Partial loss of CND1 disturbs nuclear cell-cycle progression and photosynthetic activity. CND1 binds to nuclear pre-replication complexes and DNA replication origins and regulates nuclear genome stability. In chloroplasts, CND1 interacts with and facilitates binding of the regulator of chloroplast genome stability WHY1 to chloroplast DNA. The defects in nuclear cell-cycle progression and photosynthesis of cnd1 mutants are respectively rescued by compartment-restricted CND1 localization. Light promotes the association of CND1 with HSP90 and its import into chloroplasts. This study provides a paradigm of the convergence of genome status across organelles to coordinately regulate cell cycle to control plant growth and development.
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Affiliation(s)
- Hong-Lei Jin
- Institute of Medical Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, People's Republic of China; Guangzhou Key Laboratory of Chinese Medicine Research on Prevention and Treatment of Osteoporosis, The Third Affiliated Hospital of Guangzhou University of Chinese Medicine, No. 263, Longxi Avenue, Guangzhou, China.
| | - Sujuan Duan
- Institute of Medical Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, People's Republic of China
| | - Pengxiang Zhang
- Institute of Medical Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, People's Republic of China
| | - Ziyue Yang
- Institute of Medical Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, People's Republic of China
| | - Yunping Zeng
- Institute of Medical Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, People's Republic of China
| | - Ziqi Chen
- Institute of Medical Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, People's Republic of China
| | - Liu Hong
- Institute of Medical Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, People's Republic of China
| | - Mengshu Li
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, People's Republic of China
| | - Lujun Luo
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, People's Republic of China
| | - Zhenyi Chang
- Institute of Medical Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, People's Republic of China
| | - Jiliang Hu
- Institute of Medical Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, People's Republic of China
| | - Hong-Bin Wang
- Institute of Medical Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, People's Republic of China; Key Laboratory of Chinese Medicinal Resource from Lingnan (Guangzhou University of Chinese Medicine), Ministry of Education, Guangzhou, China; State Key Laboratory of Dampness Syndrome of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China.
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6
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van Dijk A, Anten J, Bakker A, Evers N, Hoekstra AT, Chang JC, Scheenstra MR, Veldhuizen EJA, Netea MG, Berkers CR, Haagsman HP. Innate Immune Training of Human Macrophages by Cathelicidin Analogs. Front Immunol 2022; 13:777530. [PMID: 35958593 PMCID: PMC9360325 DOI: 10.3389/fimmu.2022.777530] [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: 09/15/2021] [Accepted: 02/15/2022] [Indexed: 11/21/2022] Open
Abstract
Trained innate immunity can be induced in human macrophages by microbial ligands, but it is unknown if exposure to endogenous alarmins such as cathelicidins can have similar effects. Previously, we demonstrated sustained protection against infection by the chicken cathelicidin-2 analog DCATH-2. Thus, we assessed the capacity of cathelicidins to induce trained immunity. PMA-differentiated THP-1 (dTHP1) cells were trained with cathelicidin analogs for 24 hours and restimulated after a 3-day rest period. DCATH-2 training of dTHP-1 cells amplified their proinflammatory cytokine response when restimulated with TLR2/4 agonists. Trained cells displayed a biased cellular metabolism towards mTOR-dependent aerobic glycolysis and long-chain fatty acid accumulation and augmented microbicidal activity. DCATH-2-induced trained immunity was inhibited by histone acetylase inhibitors, suggesting epigenetic regulation, and depended on caveolae/lipid raft-mediated uptake, MAPK p38 and purinergic signaling. To our knowledge, this is the first report of trained immunity by host defense peptides.
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Affiliation(s)
- Albert van Dijk
- Division Infectious Diseases and Immunology, Department Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
- *Correspondence: Albert van Dijk,
| | - Jennifer Anten
- Division Infectious Diseases and Immunology, Department Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Anne Bakker
- Division Infectious Diseases and Immunology, Department Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Noah Evers
- Division Infectious Diseases and Immunology, Department Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Anna T. Hoekstra
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, Netherlands
| | - Jung-Chin Chang
- Division Cell Biology, Metabolism & Cancer, Department Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Maaike R. Scheenstra
- Division Infectious Diseases and Immunology, Department Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Edwin J. A. Veldhuizen
- Division Infectious Diseases and Immunology, Department Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Mihai G. Netea
- Department of Internal Medicine, Radboud Center for Infectious Diseases (RCI), Radboud University Nijmegen Medical Centre, Nijmegen, Netherlands
| | - Celia R. Berkers
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, Netherlands
- Division Cell Biology, Metabolism & Cancer, Department Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Henk P. Haagsman
- Division Infectious Diseases and Immunology, Department Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
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7
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Venkatachalam V, Jambhekar A, Lahav G. Reading oscillatory instructions: How cells achieve time-dependent responses to oscillating transcription factors. Curr Opin Cell Biol 2022; 77:102099. [PMID: 35690043 DOI: 10.1016/j.ceb.2022.102099] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 03/16/2022] [Accepted: 04/24/2022] [Indexed: 11/16/2022]
Affiliation(s)
- Veena Venkatachalam
- Department of Systems Biology, Blavatnik Institute at Harvard Medical School, 210 Longwood Avenue, Boston, MA 02115, USA; Department of Radiation Oncology, Dana-Farber Brigham Cancer Center, 75 Francis St, Boston, MA 02115, USA
| | - Ashwini Jambhekar
- Department of Systems Biology, Blavatnik Institute at Harvard Medical School, 210 Longwood Avenue, Boston, MA 02115, USA; Ludwig Center at Harvard, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02215, USA
| | - Galit Lahav
- Department of Systems Biology, Blavatnik Institute at Harvard Medical School, 210 Longwood Avenue, Boston, MA 02115, USA; Ludwig Center at Harvard, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02215, USA.
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8
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Hamelin Morrissette J, Tremblay D, Marcotte-Chénard A, Lizotte F, Brunet MA, Laurent B, Riesco E, Geraldes P. Transcriptomic modulation in response to high-intensity interval training in monocytes of older women with type 2 diabetes. Eur J Appl Physiol 2022; 122:1085-1095. [PMID: 35182182 DOI: 10.1007/s00421-022-04911-9] [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: 10/07/2021] [Accepted: 02/04/2022] [Indexed: 11/03/2022]
Abstract
PURPOSE Type 2 diabetes is associated with a higher risk of cardiovascular diseases, lowering the quality of life and increasing mortality rates of affected individuals. Circulating monocytes are tightly involved in the atherosclerosis process leading to cardiovascular diseases (CVD), and their inflammatory profile can be modified by exercise. The objective was to exploratory identify genes associated with CVD that could be regulated by high-intensity interval training (HIIT) in monocytes of type 2 diabetes patients. METHODS Next-generation RNA sequencing (RNA-seq) analyses were conducted on isolated circulating monocytes (CD14+) of six women aged 60 and over with type 2 diabetes who completed a 12-week supervised HIIT intervention on a treadmill. RESULTS Following the intervention, a reduction of resting diastolic blood pressure was observed. Concomitant with this result, 56 genes were found to be downregulated following HIIT intervention in isolated monocytes. A large proportion of the regulated genes was involved in cellular adhesion, migration and differentiation into an "atherosclerosis-specific" macrophage phenotype. CONCLUSION The downregulation of transcripts in monocytes globally suggests a favorable cardiovascular effect of the HIIT in older women with type 2 diabetes. In the context of precision medicine and personalized exercise prescription, shedding light on the fundamental mechanisms underlying HIIT effects on the gene profile of immune cells is essential to develop efficient nonpharmacological strategies to prevent CVD in high-risk population.
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Affiliation(s)
| | - Dominic Tremblay
- Faculty of Medicine and Health Sciences, Research Center of the Centre Hospitalier Universitaire de Sherbrooke (CHUS), 3001 12e Avenue N, Sherbrooke, QC, J1H 5H3, Canada
| | | | - Farah Lizotte
- Faculty of Medicine and Health Sciences, Research Center of the Centre Hospitalier Universitaire de Sherbrooke (CHUS), 3001 12e Avenue N, Sherbrooke, QC, J1H 5H3, Canada
| | - Marie A Brunet
- Faculty of Medicine and Health Sciences, Research Center of the Centre Hospitalier Universitaire de Sherbrooke (CHUS), 3001 12e Avenue N, Sherbrooke, QC, J1H 5H3, Canada.,Medical Genetics Service, Department of Pediatrics, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Benoit Laurent
- Research Center on Aging, CIUSSS de l'Estrie-CHUS, Sherbrooke, QC, J1H 4C4, Canada.,Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, J1H 5N4, Canada
| | - Eléonor Riesco
- Research Center on Aging, CIUSSS de l'Estrie-CHUS, Sherbrooke, QC, J1H 4C4, Canada.,Faculty of Physical Activity Sciences, Université de Sherbrooke, Sherbrooke, QC, J1K 2R1, Canada
| | - Pedro Geraldes
- Faculty of Medicine and Health Sciences, Research Center of the Centre Hospitalier Universitaire de Sherbrooke (CHUS), 3001 12e Avenue N, Sherbrooke, QC, J1H 5H3, Canada. .,Division of Endocrinology, Department of Medicine, Faculty of Medicine and Health Sciences, University of Sherbrooke, Sherbrooke, QC, J1H 5N4, Canada.
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9
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Choi J, Lysakovskaia K, Stik G, Demel C, Söding J, Tian TV, Graf T, Cramer P. Evidence for additive and synergistic action of mammalian enhancers during cell fate determination. eLife 2021; 10:e65381. [PMID: 33770473 PMCID: PMC8004103 DOI: 10.7554/elife.65381] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 03/14/2021] [Indexed: 12/18/2022] Open
Abstract
Enhancer activity drives cell differentiation and cell fate determination, but it remains unclear how enhancers cooperate during these processes. Here we investigate enhancer cooperation during transdifferentiation of human leukemia B-cells to macrophages. Putative enhancers are established by binding of the pioneer factor C/EBPα followed by chromatin opening and enhancer RNA (eRNA) synthesis from H3K4-monomethylated regions. Using eRNA synthesis as a proxy for enhancer activity, we find that most putative enhancers cooperate in an additive way to regulate transcription of assigned target genes. However, transcription from 136 target genes depends exponentially on the summed activity of its putative paired enhancers, indicating that these enhancers cooperate synergistically. The target genes are cell type-specific, suggesting that enhancer synergy can contribute to cell fate determination. Enhancer synergy appears to depend on cell type-specific transcription factors, and such interacting enhancers are not predicted from occupancy or accessibility data that are used to detect superenhancers.
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Affiliation(s)
- Jinmi Choi
- Max Planck Institute for Biophysical Chemistry, Department of Molecular BiologyGöttingenGermany
| | - Kseniia Lysakovskaia
- Max Planck Institute for Biophysical Chemistry, Department of Molecular BiologyGöttingenGermany
| | - Gregoire Stik
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG)BarcelonaSpain
| | - Carina Demel
- Max Planck Institute for Biophysical Chemistry, Department of Molecular BiologyGöttingenGermany
| | - Johannes Söding
- Max Planck Institute for Biophysical Chemistry, Quantitative Biology and BioinformaticsGöttingenGermany
| | - Tian V Tian
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG)BarcelonaSpain
| | - Thomas Graf
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG)BarcelonaSpain
| | - Patrick Cramer
- Max Planck Institute for Biophysical Chemistry, Department of Molecular BiologyGöttingenGermany
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10
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Wan QL, Meng X, Dai W, Luo Z, Wang C, Fu X, Yang J, Ye Q, Zhou Q. N 6-methyldeoxyadenine and histone methylation mediate transgenerational survival advantages induced by hormetic heat stress. SCIENCE ADVANCES 2021; 7:eabc3026. [PMID: 33523838 PMCID: PMC7775758 DOI: 10.1126/sciadv.abc3026] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 10/20/2020] [Indexed: 05/05/2023]
Abstract
Environmental stress can induce survival advantages that are passed down to multiple generations, representing an evolutionarily advantageous adaptation at the species level. Using the nematode worm Caenorhabditis elegans as a model, we found that heat shock experienced in either parent could increase the longevity of themselves and up to the fifth generation of descendants. Mechanistic analyses revealed that transcription factor DAF-16/FOXO, heat shock factor HSF-1, and nuclear receptor DAF-12/FXR functioned transgenerationally to implement the hormetic stress response. Histone H3K9me3 methyltransferases SET-25 and SET-32 and DNA N6-methyl methyltransferase DAMT-1 participated in transmitting high-temperature memory across generations. H3K9me3 and N6-methyladenine could mark heat stress response genes and promote their transcription in progeny to extend life span. We dissected the mechanisms responsible for implementing and transmitting environmental memories in descendants from heat-shocked parents and demonstrated that hormetic stress caused survival benefits could be transmitted to multiple generations through H3K9me3 and N6-mA modifications.
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Affiliation(s)
- Qin-Li Wan
- Zhuhai Precision Medical Center, Zhuhai People’s Hospital (Zhuhai Hospital Affiliated with Jinan University), Jinan University, Guangzhou, Guangdong 510632, China
- Biomedical Translational Research Institute, Jinan University, Guangzhou, Guangdong 510632, China
| | - Xiao Meng
- Zhuhai Precision Medical Center, Zhuhai People’s Hospital (Zhuhai Hospital Affiliated with Jinan University), Jinan University, Guangzhou, Guangdong 510632, China
- Biomedical Translational Research Institute, Jinan University, Guangzhou, Guangdong 510632, China
- The First Affiliated Hospital, Jinan University, Guangzhou, Guangdong 510632, China
| | - Wenyu Dai
- Zhuhai Precision Medical Center, Zhuhai People’s Hospital (Zhuhai Hospital Affiliated with Jinan University), Jinan University, Guangzhou, Guangdong 510632, China
- Biomedical Translational Research Institute, Jinan University, Guangzhou, Guangdong 510632, China
- The First Affiliated Hospital, Jinan University, Guangzhou, Guangdong 510632, China
| | - Zhenhuan Luo
- Zhuhai Precision Medical Center, Zhuhai People’s Hospital (Zhuhai Hospital Affiliated with Jinan University), Jinan University, Guangzhou, Guangdong 510632, China
- Biomedical Translational Research Institute, Jinan University, Guangzhou, Guangdong 510632, China
- The First Affiliated Hospital, Jinan University, Guangzhou, Guangdong 510632, China
| | - Chongyang Wang
- Zhuhai Precision Medical Center, Zhuhai People’s Hospital (Zhuhai Hospital Affiliated with Jinan University), Jinan University, Guangzhou, Guangdong 510632, China
- Biomedical Translational Research Institute, Jinan University, Guangzhou, Guangdong 510632, China
- The First Affiliated Hospital, Jinan University, Guangzhou, Guangdong 510632, China
| | - Xiaodie Fu
- Zhuhai Precision Medical Center, Zhuhai People’s Hospital (Zhuhai Hospital Affiliated with Jinan University), Jinan University, Guangzhou, Guangdong 510632, China
- Biomedical Translational Research Institute, Jinan University, Guangzhou, Guangdong 510632, China
- The First Affiliated Hospital, Jinan University, Guangzhou, Guangdong 510632, China
| | - Jing Yang
- Zhuhai Precision Medical Center, Zhuhai People’s Hospital (Zhuhai Hospital Affiliated with Jinan University), Jinan University, Guangzhou, Guangdong 510632, China
- Biomedical Translational Research Institute, Jinan University, Guangzhou, Guangdong 510632, China
- The First Affiliated Hospital, Jinan University, Guangzhou, Guangdong 510632, China
| | - Qunshan Ye
- Zhuhai Precision Medical Center, Zhuhai People’s Hospital (Zhuhai Hospital Affiliated with Jinan University), Jinan University, Guangzhou, Guangdong 510632, China
- Biomedical Translational Research Institute, Jinan University, Guangzhou, Guangdong 510632, China
- The First Affiliated Hospital, Jinan University, Guangzhou, Guangdong 510632, China
| | - Qinghua Zhou
- Biomedical Translational Research Institute, Jinan University, Guangzhou, Guangdong 510632, China
- The First Affiliated Hospital, Jinan University, Guangzhou, Guangdong 510632, China
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Single-cell analysis of clonal maintenance of transcriptional and epigenetic states in cancer cells. Nat Genet 2020; 52:709-718. [PMID: 32601473 PMCID: PMC7610382 DOI: 10.1038/s41588-020-0645-y] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Accepted: 05/12/2020] [Indexed: 12/28/2022]
Abstract
Propagation of clonal regulatory programs contributes to cancer development. It is poorly understood how epigenetic mechanisms interact with genetic drivers to shape this process. Here, we combine single-cell analysis of transcription and DNA methylation with a Luria-Delbrück experimental design to demonstrate the existence of clonally stable epigenetic memory in multiple types of cancer cells. Longitudinal transcriptional and genetic analysis of clonal colon cancer cell populations reveals a slowly drifting spectrum of epithelial-to-mesenchymal transcriptional identities that is seemingly independent of genetic variation. DNA methylation landscapes correlate with these identities but also reflect an independent clock-like methylation loss process. Methylation variation can be explained as an effect of global trans-acting factors in most cases. However, for a specific class of promoters-in particular, cancer-testis antigens-de-repression is correlated with and probably driven by loss of methylation in cis. This study indicates how genetic sub-clonal structure in cancer cells can be diversified by epigenetic memory.
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Bheda P, Aguilar-Gómez D, Becker NB, Becker J, Stavrou E, Kukhtevich I, Höfer T, Maerkl S, Charvin G, Marr C, Kirmizis A, Schneider R. Single-Cell Tracing Dissects Regulation of Maintenance and Inheritance of Transcriptional Reinduction Memory. Mol Cell 2020; 78:915-925.e7. [DOI: 10.1016/j.molcel.2020.04.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 02/15/2020] [Accepted: 04/15/2020] [Indexed: 10/24/2022]
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