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Vakayil M, Madani AY, Agha MV, Majeed Y, Hayat S, Yonuskunju S, Mohamoud YA, Malek J, Suhre K, Mazloum NA. The E3 ubiquitin-protein ligase UHRF1 promotes adipogenesis and limits fibrosis by suppressing GPNMB-mediated TGF-β signaling. Sci Rep 2024; 14:11886. [PMID: 38789534 PMCID: PMC11126700 DOI: 10.1038/s41598-024-62508-y] [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: 05/25/2023] [Accepted: 05/17/2024] [Indexed: 05/26/2024] Open
Abstract
The E3 ubiquitin-ligase UHRF1 is an epigenetic regulator coordinating DNA methylation and histone modifications. However, little is known about how it regulates adipogenesis or metabolism. In this study, we discovered that UHRF1 is a key regulatory factor for adipogenesis, and we identified the altered molecular pathways that UHRF1 targets. Using CRISPR/Cas9-based knockout strategies, we discovered the whole transcriptomic changes upon UHRF1 deletion. Bioinformatics analyses revealed that key adipogenesis regulators such PPAR-γ and C/EBP-α were suppressed, whereas TGF-β signaling and fibrosis markers were upregulated in UHRF1-depleted differentiating adipocytes. Furthermore, UHRF1-depleted cells showed upregulated expression and secretion of TGF-β1, as well as the glycoprotein GPNMB. Treating differentiating preadipocytes with recombinant GPNMB led to an increase in TGF-β protein and secretion levels, which was accompanied by an increase in secretion of fibrosis markers such as MMP13 and a reduction in adipogenic conversion potential. Conversely, UHRF1 overexpression studies in human cells demonstrated downregulated levels of GPNMB and TGF-β, and enhanced adipogenic potential. In conclusion, our data show that UHRF1 positively regulates 3T3-L1 adipogenesis and limits fibrosis by suppressing GPNMB and TGF-β signaling cascade, highlighting the potential relevance of UHRF1 and its targets to the clinical management of obesity and linked metabolic disorders.
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Affiliation(s)
- Muneera Vakayil
- College of Health and Life Sciences, Hamad Bin Khalifa University, Qatar Foundation, PO Box 34110, Doha, Qatar
- Department of Microbiology and Immunology, Weill Cornell Medicine-Qatar (WCM-Q), Qatar Foundation, PO Box 24144, Doha, Qatar
| | - Aisha Y Madani
- Department of Microbiology and Immunology, Weill Cornell Medicine-Qatar (WCM-Q), Qatar Foundation, PO Box 24144, Doha, Qatar
| | - Maha V Agha
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, PO Box 3050, Doha, Qatar
| | - Yasser Majeed
- Department of Microbiology and Immunology, Weill Cornell Medicine-Qatar (WCM-Q), Qatar Foundation, PO Box 24144, Doha, Qatar
| | - Shahina Hayat
- Department of Physiology and Biophysics, Weill Cornell Medicine-Qatar (WCM-Q), Qatar Foundation, PO Box 24144, Doha, Qatar
| | - Shameem Yonuskunju
- Department of Genetic Medicine, Weill Cornell Medicine-Qatar (WCM-Q), Qatar Foundation, PO Box 24144, Doha, Qatar
| | - Yasmin Ali Mohamoud
- Department of Genetic Medicine, Weill Cornell Medicine-Qatar (WCM-Q), Qatar Foundation, PO Box 24144, Doha, Qatar
| | - Joel Malek
- Department of Genetic Medicine, Weill Cornell Medicine-Qatar (WCM-Q), Qatar Foundation, PO Box 24144, Doha, Qatar
| | - Karsten Suhre
- Department of Physiology and Biophysics, Weill Cornell Medicine-Qatar (WCM-Q), Qatar Foundation, PO Box 24144, Doha, Qatar
| | - Nayef A Mazloum
- Department of Microbiology and Immunology, Weill Cornell Medicine-Qatar (WCM-Q), Qatar Foundation, PO Box 24144, Doha, Qatar.
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2
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Meng H, Huan Y, Zhang K, Yi X, Meng X, Kang E, Wu S, Deng W, Wang Y. Quiescent Adult Neural Stem Cells: Developmental Origin and Regulatory Mechanisms. Neurosci Bull 2024:10.1007/s12264-024-01206-1. [PMID: 38656419 DOI: 10.1007/s12264-024-01206-1] [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: 09/26/2023] [Accepted: 01/02/2024] [Indexed: 04/26/2024] Open
Abstract
The existence of neural stem cells (NSCs) in the adult mammalian nervous system, although small in number and restricted to the sub-ventricular zone of the lateral ventricles, the dentate gyrus of the hippocampus, and the olfactory epithelium, is a gift of evolution for the adaptive brain function which requires persistent plastic changes of these regions. It is known that most adult NSCs are latent, showing long cell cycles. In the past decade, the concept of quiescent NSCs (qNSCs) has been widely accepted by researchers in the field, and great progress has been made in the biology of qNSCs. Although the spontaneous neuronal regeneration derived from adult NSCs is not significant, understanding how the behaviors of qNSCs are regulated sheds light on stimulating endogenous NSC-based neuronal regeneration. In this review, we mainly focus on the recent progress of the developmental origin and regulatory mechanisms that maintain qNSCs under normal conditions, and that mobilize qNSCs under pathological conditions, hoping to give some insights for future study.
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Affiliation(s)
- Han Meng
- Department of Neurobiology and Institute of Neurosciences, School of Basic Medicine, Fourth Military Medical University, Xi'an, 710032, China
| | - Yu Huan
- Department of Neurosurgery, General Hospital of Northern Theater Command, Shenyang, 110016, China
| | - Kun Zhang
- Department of Neurobiology and Institute of Neurosciences, School of Basic Medicine, Fourth Military Medical University, Xi'an, 710032, China
| | - Xuyang Yi
- Department of Neurobiology and Institute of Neurosciences, School of Basic Medicine, Fourth Military Medical University, Xi'an, 710032, China
| | - Xinyu Meng
- Department of Neurobiology and Institute of Neurosciences, School of Basic Medicine, Fourth Military Medical University, Xi'an, 710032, China
- School of Life Science and Research Center for Natural Peptide Drugs, Shaanxi Engineering and Technological Research Center for Conversation and Utilization of Regional Biological Resources, Yanan University, Yan'an, 716000, China
| | - Enming Kang
- Department of Neurobiology and Institute of Neurosciences, School of Basic Medicine, Fourth Military Medical University, Xi'an, 710032, China
| | - Shengxi Wu
- Department of Neurobiology and Institute of Neurosciences, School of Basic Medicine, Fourth Military Medical University, Xi'an, 710032, China.
| | - Wenbing Deng
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 510631, China.
| | - Yazhou Wang
- Department of Neurobiology and Institute of Neurosciences, School of Basic Medicine, Fourth Military Medical University, Xi'an, 710032, China.
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3
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Banazadeh M, Abiri A, Poortaheri MM, Asnaashari L, Langarizadeh MA, Forootanfar H. Unexplored power of CRISPR-Cas9 in neuroscience, a multi-OMICs review. Int J Biol Macromol 2024; 263:130413. [PMID: 38408576 DOI: 10.1016/j.ijbiomac.2024.130413] [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: 02/03/2023] [Revised: 05/27/2023] [Accepted: 02/21/2024] [Indexed: 02/28/2024]
Abstract
The neuroscience and neurobiology of gene editing to enhance learning and memory is of paramount interest to the scientific community. The advancements of CRISPR system have created avenues to treat neurological disorders by means of versatile modalities varying from expression to suppression of genes and proteins. Neurodegenerative disorders have also been attributed to non-canonical DNA secondary structures by affecting neuron activity through controlling gene expression, nucleosome shape, transcription, translation, replication, and recombination. Changing DNA regulatory elements which could contribute to the fate and function of neurons are thoroughly discussed in this review. This study presents the ability of CRISPR system to boost learning power and memory, treat or cure genetically-based neurological disorders, and alleviate psychiatric diseases by altering the activity and the irritability of the neurons at the synaptic cleft through DNA manipulation, and also, epigenetic modifications using Cas9. We explore and examine how each different OMIC techniques can come useful when altering DNA sequences. Such insight into the underlying relationship between OMICs and cellular behaviors leads us to better neurological and psychiatric therapeutics by intelligently designing and utilizing the CRISPR/Cas9 technology.
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Affiliation(s)
- Mohammad Banazadeh
- Pharmaceutical Sciences and Cosmetic Products Research Center, Kerman University of Medical Sciences, Kerman, Iran
| | - Ardavan Abiri
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA; Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, CT 06520, USA
| | | | - Lida Asnaashari
- Student Research Committee, Kerman Universiy of Medical Sciences, Kerman, Iran
| | - Mohammad Amin Langarizadeh
- Department of Medicinal Chemistry, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran
| | - Hamid Forootanfar
- Pharmaceutical Sciences and Cosmetic Products Research Center, Kerman University of Medical Sciences, Kerman, Iran.
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4
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Irwin RE, Scullion C, Thursby SJ, Sun M, Thakur A, Hilman L, Callaghan B, Thompson PD, McKenna DJ, Rothbart SB, Xu G, Walsh CP. The UHRF1 protein is a key regulator of retrotransposable elements and innate immune response to viral RNA in human cells. Epigenetics 2023; 18:2216005. [PMID: 37246786 PMCID: PMC10228402 DOI: 10.1080/15592294.2023.2216005] [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: 05/09/2022] [Accepted: 04/14/2023] [Indexed: 05/30/2023] Open
Abstract
While epigenetic mechanisms such as DNA methylation and histone modification are known to be important for gene suppression, relatively little is still understood about the interplay between these systems. The UHRF1 protein can interact with both DNA methylation and repressive chromatin marks, but its primary function in humans has been unclear. To determine what that was, we first established stable UHRF1 knockdowns (KD) in normal, immortalized human fibroblasts using targeting shRNA, since CRISPR knockouts (KO) were lethal. Although these showed a loss of DNA methylation across the whole genome, transcriptional changes were dominated by the activation of genes involved in innate immune signalling, consistent with the presence of viral RNA from retrotransposable elements (REs). We confirmed using mechanistic approaches that 1) REs were demethylated and transcriptionally activated; 2) this was accompanied by activation of interferons and interferon-stimulated genes and 3) the pathway was conserved across other adult cell types. Restoring UHRF1 in either transient or stable KD systems could abrogate RE reactivation and the interferon response. Notably, UHRF1 itself could also re-impose RE suppression independent of DNA methylation, but not if the protein contained point mutations affecting histone 3 with trimethylated lysine 9 (H3K9me3) binding. Our results therefore show for the first time that UHRF1 can act as a key regulator of retrotransposon silencing independent of DNA methylation.
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Affiliation(s)
- RE Irwin
- Biomedical Sciences, Ulster University, Coleraine, UK
| | - C Scullion
- Biomedical Sciences, Ulster University, Coleraine, UK
- Precision Nanosystems Inc, Vancouver, BC, Canada
| | - SJ Thursby
- Biomedical Sciences, Ulster University, Coleraine, UK
- State Key Laboratory of Molecular Biology, Shanghai Institutes of Biological Sciences, Shanghai, China
| | - M Sun
- Cellular and Molecular Medicine Program, Division of Oncology, Johns Hopkins School of Medicine, St., Baltimore, MD, USA
| | - A Thakur
- Biomedical Sciences, Ulster University, Coleraine, UK
- Department of Epigenetics, Van Andel Research Institute, Grand Rapids, MI, USA
| | - L Hilman
- Biomedical Sciences, Ulster University, Coleraine, UK
| | - B Callaghan
- Biomedical Sciences, Ulster University, Coleraine, UK
| | - PD Thompson
- Department of Epigenetics, Van Andel Research Institute, Grand Rapids, MI, USA
| | - DJ McKenna
- Biomedical Sciences, Ulster University, Coleraine, UK
| | - SB Rothbart
- Nutrition Innovation Centre for Food and Health, Biomedical Sciences, Ulster University, Coleraine, UK
| | - Guoliang Xu
- Cellular and Molecular Medicine Program, Division of Oncology, Johns Hopkins School of Medicine, St., Baltimore, MD, USA
| | - CP Walsh
- Biomedical Sciences, Ulster University, Coleraine, UK
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5
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Kotsakis Ruehlmann A, Sammallahti S, Cortés Hidalgo AP, Bakulski KM, Binder EB, Campbell ML, Caramaschi D, Cecil CAM, Colicino E, Cruceanu C, Czamara D, Dieckmann L, Dou J, Felix JF, Frank J, Håberg SE, Herberth G, Hoang TT, Houtepen LC, Hüls A, Koen N, London SJ, Magnus MC, Mancano G, Mulder RH, Page CM, Räikkönen K, Röder S, Schmidt RJ, Send TS, Sharp G, Stein DJ, Streit F, Tuhkanen J, Witt SH, Zar HJ, Zenclussen AC, Zhang Y, Zillich L, Wright R, Lahti J, Brunst KJ. Epigenome-wide meta-analysis of prenatal maternal stressful life events and newborn DNA methylation. Mol Psychiatry 2023; 28:5090-5100. [PMID: 36899042 DOI: 10.1038/s41380-023-02010-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 02/08/2023] [Accepted: 02/21/2023] [Indexed: 03/12/2023]
Abstract
Prenatal maternal stressful life events are associated with adverse neurodevelopmental outcomes in offspring. Biological mechanisms underlying these associations are largely unknown, but DNA methylation likely plays a role. This meta-analysis included twelve non-overlapping cohorts from ten independent longitudinal studies (N = 5,496) within the international Pregnancy and Childhood Epigenetics consortium to examine maternal stressful life events during pregnancy and DNA methylation in cord blood. Children whose mothers reported higher levels of cumulative maternal stressful life events during pregnancy exhibited differential methylation of cg26579032 in ALKBH3. Stressor-specific domains of conflict with family/friends, abuse (physical, sexual, and emotional), and death of a close friend/relative were also associated with differential methylation of CpGs in APTX, MyD88, and both UHRF1 and SDCCAG8, respectively; these genes are implicated in neurodegeneration, immune and cellular functions, regulation of global methylation levels, metabolism, and schizophrenia risk. Thus, differences in DNA methylation at these loci may provide novel insights into potential mechanisms of neurodevelopment in offspring.
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Affiliation(s)
- Anna Kotsakis Ruehlmann
- University of Cincinnati College of Medicine, Department of Environmental and Public Health Sciences, Cincinnati, OH, USA
| | - Sara Sammallahti
- Erasmus MC, University Medical Center Rotterdam, Department of Adolescent and Child Psychiatry and Psychology, Rotterdam, Netherlands
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
- Department of Obstetrics and Gynaecology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Andrea P Cortés Hidalgo
- Erasmus MC, University Medical Center Rotterdam, Department of Adolescent and Child Psychiatry and Psychology, Rotterdam, Netherlands
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Kelly M Bakulski
- University of Michigan, School of Public Health, Department of Epidemiology, Ann Arbor, MI, USA
| | - Elisabeth B Binder
- Max Planck Institute of Psychiatry, Department of Translational Research in Psychiatry, Munich, Germany
| | - Megan Loraine Campbell
- University of Cape Town, Department of Psychiatry and Mental Health, Cape Town, South Africa
| | - Doretta Caramaschi
- School of Psychology, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom
| | - Charlotte A M Cecil
- Erasmus MC, University Medical Center Rotterdam, Department of Adolescent and Child Psychiatry and Psychology, Rotterdam, Netherlands
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Elena Colicino
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Cristiana Cruceanu
- Max Planck Institute of Psychiatry, Department of Translational Research in Psychiatry, Munich, Germany
| | - Darina Czamara
- Max Planck Institute of Psychiatry, Department of Translational Research in Psychiatry, Munich, Germany
| | - Linda Dieckmann
- Max Planck Institute of Psychiatry, Department of Translational Research in Psychiatry, Munich, Germany
- International Max Planck Research School for Translational Psychiatry (IMPRS-TP), Munich, Germany
| | - John Dou
- University of Michigan, School of Public Health, Department of Epidemiology, Ann Arbor, MI, USA
| | - Janine F Felix
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Josef Frank
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Siri E Håberg
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Gunda Herberth
- Helmholtz Centre for Environmental Research - UFZ, Department of Environmental Immunology, Leipzig, Germany
| | - Thanh T Hoang
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, 27709, NC, USA
| | - Lotte C Houtepen
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom
| | - Anke Hüls
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, USA
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Nastassja Koen
- Department of Psychiatry and Mental Health, University of Cape Town, South Africa; and UCT Neuroscience Institute, Cape Town, South Africa
- South African Medical Research Council (SAMRC) Unit on Risk and Resilience in Mental Disorders, Cape Town, South Africa
| | - Stephanie J London
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, 27709, NC, USA
| | - Maria C Magnus
- Norwegian Institute of Public Health, Centre for Fertility and Health, Oslo, Norway
| | - Giulia Mancano
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom
| | - Rosa H Mulder
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Christian M Page
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
- Department of Mathematics, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
| | - Katri Räikkönen
- University of Helsinki, Faculty of Medicine, Department of Psychology and Logopedics, Helsinki, Finland
| | - Stefan Röder
- Helmholtz Centre for Environmental Research - UFZ, Department of Environmental Immunology, Leipzig, Germany
| | - Rebecca J Schmidt
- University of California-Davis, School of Medicine, Department of Public Health Sciences, Davis, CA, USA
| | - Tabea S Send
- Department of Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Gemma Sharp
- School of Psychology, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom
| | - Dan J Stein
- Department of Psychiatry and Mental Health, University of Cape Town, South Africa; and UCT Neuroscience Institute, Cape Town, South Africa
- South African Medical Research Council (SAMRC) Unit on Risk and Resilience in Mental Disorders, Cape Town, South Africa
| | - Fabian Streit
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Johanna Tuhkanen
- University of Helsinki, Faculty of Medicine, Department of Psychology and Logopedics, Helsinki, Finland
| | - Stephanie H Witt
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Heather J Zar
- Department of Paediatrics & Child Health & SA-MRC Unit on Child & Adolescent Health, University of Cape Town, Cape Town, South Africa
| | - Ana C Zenclussen
- Helmholtz Centre for Environmental Research - UFZ, Department of Environmental Immunology, Leipzig, Germany
| | - Yining Zhang
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Lea Zillich
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Rosalind Wright
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Kravis Children's Hospital, Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Institute for Exposomic Research, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jari Lahti
- University of Helsinki, Faculty of Medicine, Department of Psychology and Logopedics, Helsinki, Finland
| | - Kelly J Brunst
- University of Cincinnati College of Medicine, Department of Environmental and Public Health Sciences, Cincinnati, OH, USA.
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Choudalakis M, Kungulovski G, Mauser R, Bashtrykov P, Jeltsch A. Refined read-out: The hUHRF1 Tandem-Tudor domain prefers binding to histone H3 tails containing K4me1 in the context of H3K9me2/3. Protein Sci 2023; 32:e4760. [PMID: 37593997 PMCID: PMC10464304 DOI: 10.1002/pro.4760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 08/11/2023] [Accepted: 08/13/2023] [Indexed: 08/19/2023]
Abstract
UHRF1 is an essential chromatin protein required for DNA methylation maintenance, mammalian development, and gene regulation. We investigated the Tandem-Tudor domain (TTD) of human UHRF1 that is known to bind H3K9me2/3 histones and is a major driver of UHRF1 localization in cells. We verified binding to H3K9me2/3 but unexpectedly discovered stronger binding to H3 peptides and mononucleosomes containing K9me2/3 with additional K4me1. We investigated the combined binding of TTD to H3K4me1-K9me2/3 versus H3K9me2/3 alone, engineered mutants with specific and differential changes of binding, and discovered a novel read-out mechanism for H3K4me1 in an H3K9me2/3 context that is based on the interaction of R207 with the H3K4me1 methyl group and on counting the H-bond capacity of H3K4. Individual TTD mutants showed up to a 10,000-fold preference for the double-modified peptides, suggesting that after a conformational change, WT TTD could exhibit similar effects. The frequent appearance of H3K4me1-K9me2 regions in human chromatin demonstrated in our TTD chromatin pull-down and ChIP-western blot data suggests that it has specific biological roles. Chromatin pull-down of TTD from HepG2 cells and full-length murine UHRF1 ChIP-seq data correlate with H3K4me1 profiles indicating that the H3K4me1-K9me2/3 interaction of TTD influences chromatin binding of full-length UHRF1. We demonstrate the H3K4me1-K9me2/3 specific binding of UHRF1-TTD to enhancers and promoters of cell-type-specific genes at the flanks of cell-type-specific transcription factor binding sites, and provided evidence supporting an H3K4me1-K9me2/3 dependent and TTD mediated downregulation of these genes by UHRF1. All these findings illustrate the important physiological function of UHRF1-TTD binding to H3K4me1-K9me2/3 double marks in a cellular context.
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Affiliation(s)
- Michel Choudalakis
- Department of BiochemistryInstitute of Biochemistry and Technical Biochemistry, University of StuttgartStuttgartGermany
| | - Goran Kungulovski
- Department of BiochemistryInstitute of Biochemistry and Technical Biochemistry, University of StuttgartStuttgartGermany
| | - Rebekka Mauser
- Department of BiochemistryInstitute of Biochemistry and Technical Biochemistry, University of StuttgartStuttgartGermany
| | - Pavel Bashtrykov
- Department of BiochemistryInstitute of Biochemistry and Technical Biochemistry, University of StuttgartStuttgartGermany
| | - Albert Jeltsch
- Department of BiochemistryInstitute of Biochemistry and Technical Biochemistry, University of StuttgartStuttgartGermany
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7
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Kałuzińska-Kołat Ż, Kołat D, Kośla K, Płuciennik E, Bednarek AK. Delineating the glioblastoma stemness by genes involved in cytoskeletal rearrangements and metabolic alterations. World J Stem Cells 2023; 15:302-322. [PMID: 37342224 PMCID: PMC10277965 DOI: 10.4252/wjsc.v15.i5.302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 02/03/2023] [Accepted: 03/08/2023] [Indexed: 05/26/2023] Open
Abstract
Literature data on glioblastoma ongoingly underline the link between metabolism and cancer stemness, the latter is one responsible for potentiating the resistance to treatment, inter alia due to increased invasiveness. In recent years, glioblastoma stemness research has bashfully introduced a key aspect of cytoskeletal rearrangements, whereas the impact of the cytoskeleton on invasiveness is well known. Although non-stem glioblastoma cells are less invasive than glioblastoma stem cells (GSCs), these cells also acquire stemness with greater ease if characterized as invasive cells and not tumor core cells. This suggests that glioblastoma stemness should be further investigated for any phenomena related to the cytoskeleton and metabolism, as they may provide new invasion-related insights. Previously, we proved that interplay between metabolism and cytoskeleton existed in glioblastoma. Despite searching for cytoskeleton-related processes in which the investigated genes might have been involved, not only did we stumble across the relation to metabolism but also reported genes that were found to be implicated in stemness. Thus, dedicated research on these genes in GSCs seems justifiable and might reveal novel directions and/or biomarkers that could be utilized in the future. Herein, we review the previously identified cytoskeleton/metabolism-related genes through the prism of glioblastoma stemness.
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Affiliation(s)
- Żaneta Kałuzińska-Kołat
- Department of Experimental Surgery, Medical University of Lodz, Lodz 90-136, Lodzkie, Poland
- Department of Molecular Carcinogenesis, Medical University of Lodz, Lodz 90-752, Lodzkie, Poland
| | - Damian Kołat
- Department of Experimental Surgery, Medical University of Lodz, Lodz 90-136, Lodzkie, Poland
- Department of Molecular Carcinogenesis, Medical University of Lodz, Lodz 90-752, Lodzkie, Poland
| | - Katarzyna Kośla
- Department of Molecular Carcinogenesis, Medical University of Lodz, Lodz 90-752, Lodzkie, Poland
| | - Elżbieta Płuciennik
- Department of Functional Genomics, Medical University of Lodz, Lodz 90-752, Lodzkie, Poland
| | - Andrzej K Bednarek
- Department of Molecular Carcinogenesis, Medical University of Lodz, Lodz 90-752, Lodzkie, Poland
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8
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Seo BJ, Hong TK, Yoon SH, Song JH, Uhm SJ, Song H, Hong K, Schöler HR, Do JT. Embryonic Stem Cells Lacking DNA Methyltransferases Differentiate into Neural Stem Cells that Are Defective in Self-Renewal. Int J Stem Cells 2022; 16:44-51. [PMID: 36310027 PMCID: PMC9978838 DOI: 10.15283/ijsc22138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 09/27/2022] [Accepted: 09/30/2022] [Indexed: 03/01/2023] Open
Abstract
Background and Objectives DNA methyltransferases (Dnmts) play an important role in regulating DNA methylation during early developmental processes and cellular differentiation. In this study, we aimed to investigate the role of Dnmts in neural differentiation of embryonic stem cells (ESCs) and in maintenance of the resulting neural stem cells (NSCs). Methods and Results We used three types of Dnmt knockout (KO) ESCs, including Dnmt1 KO, Dnmt3a/3b double KO (Dnmt3 DKO), and Dnmt1/3a/3b triple KO (Dnmt TKO), to investigate the role of Dnmts in neural differentiation of ESCs. All three types of Dnmt KO ESCs could form neural rosette and differentiate into NSCs in vitro. Interestingly, however, after passage three, Dnmt KO ESC-derived NSCs could not maintain their self-renewal and differentiated into neurons and glial cells. Conclusions Taken together, the data suggested that, although deficiency of Dnmts had no effect on the differentiation of ESCs into NSCs, the latter had defective maintenance, thereby indicating that Dnmts are crucial for self-renewal of NSCs.
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Affiliation(s)
- Bong Jong Seo
- Department of Stem Cell and Regenerative Biotechnology, Konkuk Institute of Technology, Konkuk University, Seoul, Korea
| | - Tae Kyung Hong
- Department of Stem Cell and Regenerative Biotechnology, Konkuk Institute of Technology, Konkuk University, Seoul, Korea,3D Tissue Culture Research Center, Konkuk University, Seoul, Korea
| | - Sang Hoon Yoon
- Department of Stem Cell and Regenerative Biotechnology, Konkuk Institute of Technology, Konkuk University, Seoul, Korea,3D Tissue Culture Research Center, Konkuk University, Seoul, Korea
| | - Jae Hoon Song
- Department of Stem Cell and Regenerative Biotechnology, Konkuk Institute of Technology, Konkuk University, Seoul, Korea
| | - Sang Jun Uhm
- Department of Animal Science, Sangji University, Wonju, Korea
| | - Hyuk Song
- Department of Stem Cell and Regenerative Biotechnology, Konkuk Institute of Technology, Konkuk University, Seoul, Korea
| | - Kwonho Hong
- Department of Stem Cell and Regenerative Biotechnology, Konkuk Institute of Technology, Konkuk University, Seoul, Korea
| | - Hans Robert Schöler
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Jeong Tae Do
- Department of Stem Cell and Regenerative Biotechnology, Konkuk Institute of Technology, Konkuk University, Seoul, Korea,3D Tissue Culture Research Center, Konkuk University, Seoul, Korea,Correspondence to Jeong Tae Do, Department of Stem Cell and Regenerative Biotechnology, Konkuk Institute of Technology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea, Tel: +82-2-450-3673, Fax: +82-2-455-1044, E-mail:
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9
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Dominant role of DNA methylation over H3K9me3 for IAP silencing in endoderm. Nat Commun 2022; 13:5447. [PMID: 36123357 PMCID: PMC9485127 DOI: 10.1038/s41467-022-32978-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 08/25/2022] [Indexed: 12/03/2022] Open
Abstract
Silencing of endogenous retroviruses (ERVs) is largely mediated by repressive chromatin modifications H3K9me3 and DNA methylation. On ERVs, these modifications are mainly deposited by the histone methyltransferase Setdb1 and by the maintenance DNA methyltransferase Dnmt1. Knock-out of either Setdb1 or Dnmt1 leads to ERV de-repression in various cell types. However, it is currently not known if H3K9me3 and DNA methylation depend on each other for ERV silencing. Here we show that conditional knock-out of Setdb1 in mouse embryonic endoderm results in ERV de-repression in visceral endoderm (VE) descendants and does not occur in definitive endoderm (DE). Deletion of Setdb1 in VE progenitors results in loss of H3K9me3 and reduced DNA methylation of Intracisternal A-particle (IAP) elements, consistent with up-regulation of this ERV family. In DE, loss of Setdb1 does not affect H3K9me3 nor DNA methylation, suggesting Setdb1-independent pathways for maintaining these modifications. Importantly, Dnmt1 knock-out results in IAP de-repression in both visceral and definitive endoderm cells, while H3K9me3 is unaltered. Thus, our data suggest a dominant role of DNA methylation over H3K9me3 for IAP silencing in endoderm cells. Our findings suggest that Setdb1-meditated H3K9me3 is not sufficient for IAP silencing, but rather critical for maintaining high DNA methylation. Silencing of endogenous retroviruses is crucial for maintaining transcriptional and genomic integrity of cells and is maintained by histone H3K9 methylation and/or DNA methylation in various cell types. Here the authors show that loss of DNA methyltransferase DNMT1 in endoderm results in ERV derepression while H3K9me3 is unaltered.
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10
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Bhat A, Ghatage T, Bhan S, Lahane GP, Dhar A, Kumar R, Pandita RK, Bhat KM, Ramos KS, Pandita TK. Role of Transposable Elements in Genome Stability: Implications for Health and Disease. Int J Mol Sci 2022; 23:ijms23147802. [PMID: 35887150 PMCID: PMC9319628 DOI: 10.3390/ijms23147802] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 07/07/2022] [Accepted: 07/12/2022] [Indexed: 12/11/2022] Open
Abstract
Most living organisms have in their genome a sizable proportion of DNA sequences capable of mobilization; these sequences are commonly referred to as transposons, transposable elements (TEs), or jumping genes. Although long thought to have no biological significance, advances in DNA sequencing and analytical technologies have enabled precise characterization of TEs and confirmed their ubiquitous presence across all forms of life. These findings have ignited intense debates over their biological significance. The available evidence now supports the notion that TEs exert major influence over many biological aspects of organismal life. Transposable elements contribute significantly to the evolution of the genome by giving rise to genetic variations in both active and passive modes. Due to their intrinsic nature of mobility within the genome, TEs primarily cause gene disruption and large-scale genomic alterations including inversions, deletions, and duplications. Besides genomic instability, growing evidence also points to many physiologically important functions of TEs, such as gene regulation through cis-acting control elements and modulation of the transcriptome through epigenetic control. In this review, we discuss the latest evidence demonstrating the impact of TEs on genome stability and the underling mechanisms, including those developed to mitigate the deleterious impact of TEs on genomic stability and human health. We have also highlighted the potential therapeutic application of TEs.
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Affiliation(s)
- Audesh Bhat
- Centre for Molecular Biology, Central University of Jammu, Jammu 181143, India;
- Correspondence: (A.B.); (T.K.P.)
| | - Trupti Ghatage
- Department of Pharmacy, BITS-Pilani Hyderabad Campus, Hyderabad 500078, India; (T.G.); (G.P.L.); (A.D.)
| | - Sonali Bhan
- Centre for Molecular Biology, Central University of Jammu, Jammu 181143, India;
| | - Ganesh P. Lahane
- Department of Pharmacy, BITS-Pilani Hyderabad Campus, Hyderabad 500078, India; (T.G.); (G.P.L.); (A.D.)
| | - Arti Dhar
- Department of Pharmacy, BITS-Pilani Hyderabad Campus, Hyderabad 500078, India; (T.G.); (G.P.L.); (A.D.)
| | - Rakesh Kumar
- Department of Biotechnology, Shri Mata Vaishnav Devi University, Katra 182320, India;
| | - Raj K. Pandita
- Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA;
| | - Krishna M. Bhat
- Department of Molecular Medicine, University of South Florida, Tampa, FL 33612, USA;
| | - Kenneth S. Ramos
- Center for Genomics and Precision Medicine, Texas A&M College of Medicine, Houston, TX 77030, USA;
| | - Tej K. Pandita
- Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA;
- Center for Genomics and Precision Medicine, Texas A&M College of Medicine, Houston, TX 77030, USA;
- Correspondence: (A.B.); (T.K.P.)
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11
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Saeki N, Inoue K, Ideta-Otsuka M, Watamori K, Mizuki S, Takenaka K, Igarashi K, Miura H, Takeda S, Imai Y. Epigenetic regulator UHRF1 suppressively orchestrates pro-inflammatory gene expression in rheumatoid arthritis. J Clin Invest 2022; 132:150533. [PMID: 35472067 PMCID: PMC9151705 DOI: 10.1172/jci150533] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 04/19/2022] [Indexed: 11/17/2022] Open
Abstract
Rheumatoid arthritis (RA) is characterized by chronic synovial inflammation with aberrant epigenetic alterations, eventually leading to joint destruction. However, the epigenetic regulatory mechanisms underlying RA pathogenesis remain largely unknown. Here we showed that Ubiquitin-like containing PHD and RING finger domains 1 (UHRF1) is a central epigenetic regulator that suppressively orchestrates multiple pathogeneses in RA. UHRF1 expression was remarkably up-regulated in synovial fibroblasts (SF) from arthritis model mice and RA patients. Mice with SF-specific Uhrf1 conditional knockout showed more severe arthritic phenotypes than littermate control. Uhrf1-deficient SF also exhibited enhanced apoptosis resistance and up-regulated expression of several cytokines including Ccl20. In RA patients, DAS28, CRP, and Th17 accumulation as well as apoptosis resistance were negatively correlated with UHRF1 expression in synovium. Finally, Ryuvidine administration that stabilizes UHRF1 ameliorated arthritis pathogeneses in a mouse model of RA. This study demonstrated that UHRF1 expressed in RA SF can contribute to negative feedback mechanisms that suppress multiple pathogenic events in arthritis, suggesting that targeting UHRF1 could be one of the therapeutic strategies for RA.
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Affiliation(s)
- Noritaka Saeki
- Division of Laboratory Animal Research, Ehime University, Toon, Japan
| | - Kazuki Inoue
- Nankai International Advanced Research Institute (Shenzhen Futian), Nankai University, Shenzhen, China
| | - Maky Ideta-Otsuka
- Laboratory of Instrumental Analysis, School of Pharmacy and Pharmaceutical Sciences, Hoshi University, Tokyo, Japan
| | - Kunihiko Watamori
- Department of Bone and Joint Surgery, Ehime University Graduate School of Medicine, Ehime, Japan
| | - Shinichi Mizuki
- The Center for Rheumatic Diseases, Matsuyama Red Cross Hospital, Matsuyama, Japan
| | - Katsuto Takenaka
- Department of Hematology, Clinical Immunology and Infectious Diseases, Ehime University Graduate School of Medicine, Ehime, Japan
| | - Katsuhide Igarashi
- Laboratory of Biofunctional Science, School of Pharmacy and Pharmaceutical Sciences, Hoshi University, Tokyo, Japan
| | - Hiromasa Miura
- Department of Bone and Joint Surgery, Ehime University Graduate School of Medicine, Ehime, Japan
| | - Shu Takeda
- Division of Endocrinology, Toranomon Hospital Endocrine Center, Tokyo, Japan
| | - Yuuki Imai
- Division of Laboratory Animal Research, Ehime University, Toon, Japan
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12
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UHRF1 establishes crosstalk between somatic and germ cells in male reproduction. Cell Death Dis 2022; 13:377. [PMID: 35440090 PMCID: PMC9018721 DOI: 10.1038/s41419-022-04837-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 04/02/2022] [Accepted: 04/05/2022] [Indexed: 11/08/2022]
Abstract
AbstractSertoli cells (SCs) support and nourish germ cells (GCs) through their crosstalk during spermatogenesis. However, the underlying epigenetic mechanism that ensures SCs’ functions in this process remains unclear. Here, we report that UHRF1, a critical epigenetic regulator, is mainly expressed in human and mouse pre-mature SCs, and is essential for establishing Sertoli-Germ cell crosstalk. SC-specific UHRF1 knockout mice exhibit complete sterility with Sertoli cell (SC) proliferation and differentiation aberrance, blood-testis barrier (BTB) disruption, and immature germ cell (GC) sloughing. RNA sequencing and Whole Genome Bisulfite Sequencing (WGBS) revealed that many extracellular matrix (ECM)-related genes (e.g., Timp1, Trf, and Spp1) appeared upregulated with the DNA hypomethylation status in UHRF1-deficient SCs. Strikingly, overexpression of Timp1, Trf, and Spp1 in SCs in vitro and in vivo could phenocopy the SC-specific UHRF1-deficient mice. Our data demonstrated that UHRF1 regulates the transcriptional program of ECM-related genes in SCs and establishes SC-GC crosstalk.
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13
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Wang X, Sarver AL, Han Q, Seiler CL, Xie C, Lu H, Forster CL, Tretyakova NY, Hallstrom TC. UHRF2 regulates cell cycle, epigenetics and gene expression to control the timing of retinal progenitor and ganglion cell differentiation. Development 2022; 149:274710. [PMID: 35285483 PMCID: PMC8984156 DOI: 10.1242/dev.195644] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Accepted: 01/28/2022] [Indexed: 11/20/2022]
Abstract
Ubiquitin-like, containing PHD and RING finger domains 2 (UHRF2) regulates cell cycle and binds 5-hydroxymethylcytosine (5hmC) to promote completion of DNA demethylation. Uhrf2-/- mice are without gross phenotypic defects; however, the cell cycle and epigenetic regulatory functions of Uhrf2 during retinal tissue development are unclear. Retinal progenitor cells (RPCs) produce all retinal neurons and Müller glia in a predictable sequence controlled by the complex interplay between extrinsic signaling, cell cycle, epigenetic changes and cell-specific transcription factor activation. In this study, we find that UHRF2 accumulates in RPCs, and its conditional deletion from mouse RPCs reduced 5hmC, altered gene expressions and disrupted retinal cell proliferation and differentiation. Retinal ganglion cells were overproduced in Uhrf2-deficient retinae at the expense of VSX2+ RPCs. Most other cell types were transiently delayed in differentiation. Expression of each member of the Tet3/Uhrf2/Tdg active demethylation pathway was reduced in Uhrf2-deficient retinae, consistent with locally reduced 5hmC in their gene bodies. This study highlights a novel role of UHRF2 in controlling the transition from RPCs to differentiated cell by regulating cell cycle, epigenetic and gene expression decisions.
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Affiliation(s)
- Xiaohong Wang
- Department of Pediatrics, Division of Blood and Marrow Transplantation, 420 Delaware Street S.E., University of Minnesota, Minneapolis, MN 55455, USA
| | - Aaron L Sarver
- Institute for Health Informatics, Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Qiyuan Han
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Christopher L Seiler
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Chencheng Xie
- Department of Pediatrics, Division of Blood and Marrow Transplantation, 420 Delaware Street S.E., University of Minnesota, Minneapolis, MN 55455, USA
| | - Huarui Lu
- Department of Pediatrics, Division of Blood and Marrow Transplantation, 420 Delaware Street S.E., University of Minnesota, Minneapolis, MN 55455, USA
| | - Colleen L Forster
- BioNet, Academic Health Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Natalia Y Tretyakova
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Timothy C Hallstrom
- Department of Pediatrics, Division of Blood and Marrow Transplantation, 420 Delaware Street S.E., University of Minnesota, Minneapolis, MN 55455, USA
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14
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Sakai H, Sawada Y, Tokunaga N, Tanaka K, Nakagawa S, Sakakibara I, Ono Y, Fukada SI, Ohkawa Y, Kikugawa T, Saika T, Imai Y. Uhrf1 governs the proliferation and differentiation of muscle satellite cells. iScience 2022; 25:103928. [PMID: 35243267 PMCID: PMC8886052 DOI: 10.1016/j.isci.2022.103928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 12/06/2021] [Accepted: 02/10/2022] [Indexed: 11/19/2022] Open
Abstract
DNA methylation is an essential form of epigenetic regulation responsible for cellular identity. In muscle stem cells, termed satellite cells, DNA methylation patterns are tightly regulated during differentiation. However, it is unclear how these DNA methylation patterns affect the function of satellite cells. We demonstrate that a key epigenetic regulator, ubiquitin like with PHD and RING finger domains 1 (Uhrf1), is activated in proliferating myogenic cells but not expressed in quiescent satellite cells or differentiated myogenic cells in mice. Ablation of Uhrf1 in mouse satellite cells impairs their proliferation and differentiation, leading to failed muscle regeneration. Uhrf1-deficient myogenic cells exhibited aberrant upregulation of transcripts, including Sox9, with the reduction of DNA methylation level of their promoter and enhancer region. These findings show that Uhrf1 is a critical epigenetic regulator of proliferation and differentiation in satellite cells, by controlling cell-type-specific gene expression via maintenance of DNA methylation. Uhrf1 is activated in proliferating myogenic cells Uhrf1 in satellite cells is required for muscle regeneration Ablation of Uhrf1 in satellite cells impairs their proliferation and differentiation Uhrf1 controls cell-type-specific transcripts via maintenance of DNA methylation
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Affiliation(s)
- Hiroshi Sakai
- Division of Integrative Pathophysiology, Proteo-Science Center, Ehime University, Toon, Ehime 791-0295, Japan
- Department of Pathophysiology, Ehime University Graduate School of Medicine, Toon, Ehime 791-0295, Japan
- Corresponding author
| | - Yuichiro Sawada
- Department of Urology, Ehime University Graduate School of Medicine, Toon, Ehime 791-0295, Japan
| | - Naohito Tokunaga
- Division of Analytical Bio-Medicine, Advanced Research Support Center, Ehime University, Toon, Ehime 791-0295, Japan
| | - Kaori Tanaka
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, Higashi-ku, Fukuoka 812-0054, Japan
| | - So Nakagawa
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Kanagawa 259-1193, Japan
| | - Iori Sakakibara
- Department of Nutritional Physiology, Institute of Medical Nutrition, Tokushima University Graduate School, Kuramoto-cho, Tokushima 770-8503, Japan
| | - Yusuke Ono
- Department of Muscle Development and Regeneration, Institute of Molecular Embryology and Genetics, Kumamoto University, Honjo, Kumamoto 860-0811, Japan
| | - So-ichiro Fukada
- Project for Muscle Stem Cell Biology, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka 565-0871, Japan
| | - Yasuyuki Ohkawa
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, Higashi-ku, Fukuoka 812-0054, Japan
| | - Tadahiko Kikugawa
- Department of Urology, Ehime University Graduate School of Medicine, Toon, Ehime 791-0295, Japan
| | - Takashi Saika
- Department of Urology, Ehime University Graduate School of Medicine, Toon, Ehime 791-0295, Japan
| | - Yuuki Imai
- Division of Integrative Pathophysiology, Proteo-Science Center, Ehime University, Toon, Ehime 791-0295, Japan
- Department of Pathophysiology, Ehime University Graduate School of Medicine, Toon, Ehime 791-0295, Japan
- Corresponding author
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15
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Evidence that direct inhibition of transcription factor binding is the prevailing mode of gene and repeat repression by DNA methylation. Nat Genet 2022; 54:1895-1906. [PMID: 36471082 PMCID: PMC9729108 DOI: 10.1038/s41588-022-01241-6] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 10/24/2022] [Indexed: 12/12/2022]
Abstract
Cytosine methylation efficiently silences CpG-rich regulatory regions of genes and repeats in mammalian genomes. To what extent this entails direct inhibition of transcription factor (TF) binding versus indirect inhibition via recruitment of methyl-CpG-binding domain (MBD) proteins is unclear. Here we show that combinatorial genetic deletions of all four proteins with functional MBDs in mouse embryonic stem cells, derived neurons or a human cell line do not reactivate genes or repeats with methylated promoters. These do, however, become activated by methylation-restricted TFs if DNA methylation is removed. We identify several causal TFs in neurons, including ONECUT1, which is methylation sensitive only at a motif variant. Rampantly upregulated retrotransposons in methylation-free neurons feature a CRE motif, which activates them in the absence of DNA methylation via methylation-sensitive binding of CREB1. Our study reveals methylation-sensitive TFs in vivo and argues that direct inhibition, rather than indirect repression by the tested MBD proteins, is the prevailing mechanism of methylation-mediated repression at regulatory regions and repeats.
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16
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Morc3 silences endogenous retroviruses by enabling Daxx-mediated histone H3.3 incorporation. Nat Commun 2021; 12:5996. [PMID: 34650047 PMCID: PMC8516933 DOI: 10.1038/s41467-021-26288-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 09/22/2021] [Indexed: 11/08/2022] Open
Abstract
Endogenous retroviruses (ERVs) comprise a significant portion of mammalian genomes. Although specific ERV loci feature regulatory roles for host gene expression, most ERV integrations are transcriptionally repressed by Setdb1-mediated H3K9me3 and DNA methylation. However, the protein network which regulates the deposition of these chromatin modifications is still incompletely understood. Here, we perform a genome-wide single guide RNA (sgRNA) screen for genes involved in ERV silencing and identify the GHKL ATPase protein Morc3 as a top-scoring hit. Morc3 knock-out (ko) cells display de-repression, reduced H3K9me3, and increased chromatin accessibility of distinct ERV families. We find that the Morc3 ATPase cycle and Morc3 SUMOylation are important for ERV chromatin regulation. Proteomic analyses reveal that Morc3 mutant proteins fail to interact with the histone H3.3 chaperone Daxx. This interaction depends on Morc3 SUMOylation and Daxx SUMO binding. Notably, in Morc3 ko cells, we observe strongly reduced histone H3.3 on Morc3 binding sites. Thus, our data demonstrate Morc3 as a critical regulator of Daxx-mediated histone H3.3 incorporation to ERV regions. Endogenous retroviruses (ERVs) compose a significant portion of mammalian genomes; however, how ERVs are regulated is not well known. Here the authors performed a genome-wide sgRNA screen to identify Morc3 as a mediator of ERV silencing. They show Morc3 associates with the H3.3 chaperone Daxx, and that loss of Morc3 leads to reduced H3.3 at ERVs.
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17
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Newkirk SJ, An W. UHRF1: a jack of all trades, and a master epigenetic regulator during spermatogenesis. Biol Reprod 2021; 102:1147-1152. [PMID: 32101289 DOI: 10.1093/biolre/ioaa026] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 02/26/2020] [Indexed: 01/03/2023] Open
Affiliation(s)
- Simon J Newkirk
- Department of Pharmaceutical Sciences, South Dakota State University, Brookings, SD, USA
| | - Wenfeng An
- Department of Pharmaceutical Sciences, South Dakota State University, Brookings, SD, USA
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18
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Magnani E, Macchi F, Madakashira BP, Zhang C, Alaydaroos F, Sadler KC. uhrf1 and dnmt1 Loss Induces an Immune Response in Zebrafish Livers Due to Viral Mimicry by Transposable Elements. Front Immunol 2021; 12:627926. [PMID: 33854502 PMCID: PMC8039153 DOI: 10.3389/fimmu.2021.627926] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 02/23/2021] [Indexed: 12/13/2022] Open
Abstract
Activation of transposable elements (TEs) can cause cellular damage. Cytoplasmic nucleic acid sensing pathways evolved to detect pathogens, but can also serve to cull cells with inappropriate TE activation as TEs can be viral mimetics. Epigenetic silencing of TEs is mediated in part by DNA methylation, but it is not clear if TE activation or the immune system contribute to the cellular damage caused by loss of DNA methylation. Here, we provide mechanistic insight into the observation of an activated interferon response in the liver of zebrafish larvae with deletion in critical components of the DNA methylation machinery, uhrf1 and dnmt1. We focus on dissecting the relationship between DNA methylation, TE activation and induction of an immune response through cytoplasmic DNA and double stranded RNA sensing pathways and identify tnfa as a mediator of cell death in the liver of these mutants. Integrated RNAseq and methylome analysis identified LTR transposons as the most upregulated in these mutants and also the most methylated in control larvae, indicating a direct role of DNA methylation in suppressing this TE subclass. RNAseq analysis from these same samples revealed expression signatures of a type-I interferon response and of tnfa activation, mimicking the pattern of gene expression in virally infected cells. CRISPR/Cas9 mediated depletion of the cellular antiviral sensors sting and mavs reduced expression of interferon response genes and tnfa depletion dramatically reduced cell death in uhrf1 mutant livers. This suggests that the antiviral response induced by DNA hypomethylation and TE activation in the liver is mediated by the signaling pathways activated by both cytoplasmic double stranded RNA and DNA and that tnfa mediates cell death as a potential mechanism to eliminate these damaged cells.
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Affiliation(s)
- Elena Magnani
- Program in Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Filippo Macchi
- Program in Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | | | - Chi Zhang
- Program in Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Fatima Alaydaroos
- Program in Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Kirsten C Sadler
- Program in Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
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19
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MacArthur IC, Dawlaty MM. TET Enzymes and 5-Hydroxymethylcytosine in Neural Progenitor Cell Biology and Neurodevelopment. Front Cell Dev Biol 2021; 9:645335. [PMID: 33681230 PMCID: PMC7930563 DOI: 10.3389/fcell.2021.645335] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 02/01/2021] [Indexed: 12/19/2022] Open
Abstract
Studies of tissue-specific epigenomes have revealed 5-hydroxymethylcytosine (5hmC) to be a highly enriched and dynamic DNA modification in the metazoan nervous system, inspiring interest in the function of this epigenetic mark in neurodevelopment and brain function. 5hmC is generated by oxidation of 5-methylcytosine (5mC), a process catalyzed by the ten–eleven translocation (TET) enzymes. 5hmC serves not only as an intermediate in DNA demethylation but also as a stable epigenetic mark. Here, we review the known functions of 5hmC and TET enzymes in neural progenitor cell biology and embryonic and postnatal neurogenesis. We also discuss how TET enzymes and 5hmC regulate neuronal activity and brain function and highlight their implications in human neurodevelopmental and neurodegenerative disorders. Finally, we present outstanding questions in the field and envision new research directions into the roles of 5hmC and TET enzymes in neurodevelopment.
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Affiliation(s)
- Ian C MacArthur
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, United States.,Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY, United States.,Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Meelad M Dawlaty
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, United States.,Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY, United States.,Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, Bronx, NY, United States
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20
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Wu Y, Dong J, Feng S, Zhao Q, Duan P, Xiong M, Wen Y, Lv C, Wang X, Yuan S. Maternal UHRF1 Is Essential for Transcription Landscapes and Repression of Repetitive Elements During the Maternal-to-Zygotic Transition. Front Cell Dev Biol 2021; 8:610773. [PMID: 33634103 PMCID: PMC7902027 DOI: 10.3389/fcell.2020.610773] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 12/31/2020] [Indexed: 11/21/2022] Open
Abstract
Maternal factors that modulate maternal-to-zygotic transition (MZT) are essential for the growth from specialized oocytes to totipotent embryos. Despite several studies, the mechanisms regulating epigenetic reprogramming during MZT remain largely elusive. UHRF1 plays a role in maintaining GC methylation in oocytes and early embryos. However, little is known about its role in mouse MZT. Here, we explored the function of maternal UHRF1 in zygotic genome regulation during early embryonic development in mice. We showed that the conditional knockout (cKO) of UHRF1 in either primordial or growing oocytes causes infertility but differentially affects early embryonic development. UHRF1 deficiency in primordial oocytes led to early embryonic developmental arrest at the two-cell stage, accompanied by significant alterations in global DNA and H3K4me3 methylation patterns. In comparison, UHRF1 ablation in growing oocytes significantly reduced developmental competence from two-cell embryos to blastocysts. At the transcriptional level, the absence of maternal UHRF1 led to aberrant transcriptional regulation of the zygotic genome during MZT at the two-cell stage. Furthermore, we observed that retrotransposable elements in UHRF1-deficient oocytes and embryos were not silenced properly; in particular, the LINE-1 and long terminal repeat (LTR) subfamily were activated abnormally. Collectively, the findings of our study reveal that maternal UHRF1 plays a critical role in establishing the correct epigenetic chromatin reprogramming of early embryos, regulating essential genes during MZT, and preserving genome integrity that drives early embryonic development in mice.
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Affiliation(s)
- Yanqing Wu
- Tongji Medical College, Institute Reproductive Health, Huazhong University of Science and Technology, Wuhan, China
| | - Juan Dong
- Tongji Medical College, Institute Reproductive Health, Huazhong University of Science and Technology, Wuhan, China.,Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shenglei Feng
- Tongji Medical College, Institute Reproductive Health, Huazhong University of Science and Technology, Wuhan, China
| | - Qiang Zhao
- Central Laboratory, Xiangyang No.1 People's Hospital, Hubei University of Medicine, Xiangyang, China
| | - Peng Duan
- Laboratory of Gynecological Oncology and Reproductive Health, Department of Obstetrics and Gynaecology, Xiangyang No.1 People's Hospital, Hubei University of Medicine, Xiangyang, China
| | - Mengneng Xiong
- Tongji Medical College, Institute Reproductive Health, Huazhong University of Science and Technology, Wuhan, China
| | - Yujiao Wen
- Tongji Medical College, Institute Reproductive Health, Huazhong University of Science and Technology, Wuhan, China
| | - Chunyu Lv
- Tongji Medical College, Institute Reproductive Health, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaoli Wang
- Tongji Medical College, Institute Reproductive Health, Huazhong University of Science and Technology, Wuhan, China
| | - Shuiqiao Yuan
- Tongji Medical College, Institute Reproductive Health, Huazhong University of Science and Technology, Wuhan, China.,Shenzhen Huazhong University of Science and Technology Research Institute, Shenzhen, China
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21
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Abstract
The mammalian cerebral cortex is the pinnacle of brain evolution, reaching its maximum complexity in terms of neuron number, diversity and functional circuitry. The emergence of this outstanding complexity begins during embryonic development, when a limited number of neural stem and progenitor cells manage to generate myriads of neurons in the appropriate numbers, types and proportions, in a process called neurogenesis. Here we review the current knowledge on the regulation of cortical neurogenesis, beginning with a description of the types of progenitor cells and their lineage relationships. This is followed by a review of the determinants of neuron fate, the molecular and genetic regulatory mechanisms, and considerations on the evolution of cortical neurogenesis in vertebrates leading to humans. We finish with an overview on how dysregulation of neurogenesis is a leading cause of human brain malformations and functional disabilities.
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Affiliation(s)
- Ana Villalba
- Instituto de Neurociencias, Consejo Superior de Investigaciones Científicas & Universidad Miguel Hernández, Sant Joan d'Alacant, Spain
| | - Magdalena Götz
- Institute for Stem Cell Research, Helmholtz Zentrum München & Biomedical Center, Ludwig-Maximilians Universitaet, Planegg-Martinsried, Germany
| | - Víctor Borrell
- Instituto de Neurociencias, Consejo Superior de Investigaciones Científicas & Universidad Miguel Hernández, Sant Joan d'Alacant, Spain.
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22
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Kumari N, Karmakar A, Chakrabarti S, Ganesan SK. Integrative Computational Approach Revealed Crucial Genes Associated With Different Stages of Diabetic Retinopathy. Front Genet 2020; 11:576442. [PMID: 33304382 PMCID: PMC7693709 DOI: 10.3389/fgene.2020.576442] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 10/07/2020] [Indexed: 12/31/2022] Open
Abstract
The increased incidence of diabetic retinopathy (DR) and the legacy effect associated with it has raised a great concern toward the need to find early diagnostic and treatment strategies. Identifying alterations in genes and microRNAs (miRNAs) is one of the most critical steps toward understanding the mechanisms by which a disease progresses, and this can be further used in finding potential diagnostic and prognostic biomarkers and treatment methods. We selected different datasets to identify altered genes and miRNAs. The integrative analysis was employed to find potential candidate genes (differentially expressed and aberrantly methylated genes that are also the target of altered miRNAs) and early genes (genes showing altered expression and methylation pattern during early stage of DR) for DR. We constructed a protein-protein interaction (PPI) network to find hub genes (potential candidate genes showing a greater number of interactions) and modules. Gene ontologies and pathways associated with the identified genes were analyzed to determine their role in DR progression. A total of 271 upregulated-hypomethylated genes, 84 downregulated-hypermethylated genes, 11 upregulated miRNA, and 30 downregulated miRNA specific to DR were identified. 40 potential candidate genes and 9 early genes were also identified. PPI network analysis revealed 7 hub genes (number of interactions >5) and 1 module (score = 5.67). Gene ontology and pathway analysis predicted enrichment of genes in oxidoreductase activity, binding to extracellular matrix, immune responses, leukocyte migration, cell adhesion, PI3K-Akt signaling pathway, ECM receptor interaction, etc., and thus their association with DR pathogenesis. In conclusion, we identified 7 hub genes and 9 early genes that could act as a potential prognostic, diagnostic, or therapeutic target for DR, and a few early genes could also play a role in metabolic memory phenomena.
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Affiliation(s)
- Nidhi Kumari
- Department of Structural Biology & Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India.,CSIR-IICB Translational Research Unit of Excellence (TRUE), Kolkata, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Aditi Karmakar
- Department of Structural Biology & Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India.,CSIR-IICB Translational Research Unit of Excellence (TRUE), Kolkata, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Saikat Chakrabarti
- Department of Structural Biology & Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India.,CSIR-IICB Translational Research Unit of Excellence (TRUE), Kolkata, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Senthil Kumar Ganesan
- Department of Structural Biology & Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India.,CSIR-IICB Translational Research Unit of Excellence (TRUE), Kolkata, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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23
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Adam MA, Harwell CC. Epigenetic regulation of cortical neurogenesis; orchestrating fate switches at the right time and place. Curr Opin Neurobiol 2020; 63:146-153. [PMID: 32428815 PMCID: PMC7483903 DOI: 10.1016/j.conb.2020.03.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 03/23/2020] [Accepted: 03/24/2020] [Indexed: 12/21/2022]
Abstract
Over the last several decades the field has made tremendous progress in understanding the proliferative behavior of cortical progenitors and the lineage relationships of their clonal progeny. The genetic and epigenetic mechanisms that control the dynamic patterns of gene expression during cortical development are only beginning to be characterized. In this review we highlight the most well characterized epigenetic modifications and their influence on progenitor proliferation and cortical neuron cell fate.
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Affiliation(s)
- Manal A Adam
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, United States
| | - Corey C Harwell
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, United States.
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24
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dnmt1 function is required to maintain retinal stem cells within the ciliary marginal zone of the zebrafish eye. Sci Rep 2020; 10:11293. [PMID: 32647199 PMCID: PMC7347529 DOI: 10.1038/s41598-020-68016-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 05/15/2020] [Indexed: 12/22/2022] Open
Abstract
The ciliary marginal zone (CMZ) of the zebrafish retina contains a population of actively proliferating resident stem cells, which generate retinal neurons throughout life. The maintenance methyltransferase, dnmt1, is expressed within the CMZ. Loss of dnmt1 function results in gene misregulation and cell death in a variety of developmental contexts, however, its role in retinal stem cell (RSC) maintenance is currently unknown. Here, we demonstrate that zebrafish dnmt1s872 mutants possess severe defects in RSC maintenance within the CMZ. Using a combination of immunohistochemistry, in situ hybridization, and a transgenic reporter assay, our results demonstrate a requirement for dnmt1 activity in the regulation of RSC proliferation, gene expression and in the repression of endogenous retroelements (REs). Ultimately, cell death is elevated in the dnmt1−/− CMZ, but in a p53-independent manner. Using a transgenic reporter for RE transposition activity, we demonstrate increased transposition in the dnmt1−/− CMZ. Taken together our data identify a critical role for dnmt1 function in RSC maintenance in the vertebrate eye.
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25
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Abstract
Multiple sclerosis (MS), a chronic inflammatory demyelinating and neurodegenerative disease of the central nervous system, is today a leading cause of unpredictable lifelong disability in young adults. The treatment of patients in progressive stages remains highly challenging, alluding to our limited understanding of the underlying pathological processes. In this review, we provide insights into the mechanisms underpinning MS progression from a perspective of epigenetics, that refers to stable and mitotically heritable, yet reversible, changes in the genome activity and gene expression. We first recapitulate findings from epigenetic studies examining the brain tissue of progressive MS patients, which support a contribution of DNA and histone modifications in impaired oligodendrocyte differentiation, defective myelination/remyelination and sustained neuro-axonal vulnerability. We next explore possibilities for identifying factors affecting progression using easily accessible tissues such as blood by comparing epigenetic signatures in peripheral immune cells and brain tissue. Despite minor overlap at individual methylation sites, nearly 30% of altered genes reported in peripheral immune cells of progressive MS patients were found in brain tissue, jointly converging on alterations of neuronal functions. We further speculate about the mechanisms underlying shared epigenetic patterns between blood and brain, which likely imply the influence of internal (genetic control) and/or external (e.g. smoking and ageing) factors imprinting a common signature in both compartments. Overall, we propose that epigenetics might shed light on clinically relevant mechanisms involved in disease progression and open new avenues for the treatment of progressive MS patients in the future.
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Affiliation(s)
- L Kular
- From the, Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - M Jagodic
- From the, Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
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26
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UHRF1-repressed 5'-hydroxymethylcytosine is essential for the male meiotic prophase I. Cell Death Dis 2020; 11:142. [PMID: 32081844 PMCID: PMC7035279 DOI: 10.1038/s41419-020-2333-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 01/29/2020] [Accepted: 01/30/2020] [Indexed: 12/23/2022]
Abstract
5’-hydroxymethylcytosine (5hmC), an important 5’-cytosine modification, is altered highly in order in male meiotic prophase. However, the regulatory mechanism of this dynamic change and the function of 5hmC in meiosis remain largely unknown. Using a knockout mouse model, we showed that UHRF1 regulated male meiosis. UHRF1 deficiency led to failure of meiosis and male infertility. Mechanistically, the deficiency of UHRF1 altered significantly the meiotic gene profile of spermatocytes. Uhrf1 knockout induced an increase of the global 5hmC level. The enrichment of hyper-5hmC at transcriptional start sites (TSSs) was highly associated with gene downregulation. In addition, the elevated level of the TET1 enzyme might have contributed to the higher 5hmC level in the Uhrf1 knockout spermatocytes. Finally, we reported Uhrf1, a key gene in male meiosis, repressed hyper-5hmC by downregulating TET1. Furthermore, UHRF1 facilitated RNA polymerase II (RNA-pol2) loading to promote gene transcription. Thus our study demonstrated a potential regulatory mechanism of 5hmC dynamic change and its involvement in epigenetic regulation in male meiosis.
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27
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Dong J, Wang X, Cao C, Wen Y, Sakashita A, Chen S, Zhang J, Zhang Y, Zhou L, Luo M, Liu M, Liao A, Namekawa SH, Yuan S. UHRF1 suppresses retrotransposons and cooperates with PRMT5 and PIWI proteins in male germ cells. Nat Commun 2019; 10:4705. [PMID: 31624244 PMCID: PMC6797737 DOI: 10.1038/s41467-019-12455-4] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Accepted: 09/11/2019] [Indexed: 11/20/2022] Open
Abstract
DNA methylation, repressive histone marks, and PIWI-interacting RNA (piRNA) are essential for the control of retrotransposon silencing in the mammalian germline. However, it remains unknown how these repressive epigenetic pathways crosstalk to ensure retrotransposon silencing in the male germline. Here, we show that UHRF1 is responsible for retrotransposon silencing and cooperates with repressive epigenetic pathways in male germ cells. Conditional loss of UHRF1 in postnatal germ cells causes DNA hypomethylation, upregulation of retrotransposons, the activation of a DNA damage response, and switches in the global chromatin status, leading to complete male sterility. Furthermore, we show that UHRF1 interacts with PRMT5, an arginine methyltransferase, to regulate the repressive histone arginine modifications (H4R3me2s and H3R2me2s), and cooperates with the PIWI pathway during spermatogenesis. Collectively, UHRF1 regulates retrotransposon silencing in male germ cells and provides a molecular link between DNA methylation, histone modification, and the PIWI pathway in the germline.
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Affiliation(s)
- Juan Dong
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Xiaoli Wang
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Congcong Cao
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Yujiao Wen
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Akihiko Sakashita
- Division of Reproductive Sciences, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Si Chen
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Jin Zhang
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Yue Zhang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 210029, China
| | - Liquan Zhou
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Mengcheng Luo
- Department of Tissue and Embryology, School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, China
- Hubei Provincial Key Laboratory of Developmentally Originated Disease, Wuhan, 430071, China
| | - Mingxi Liu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 210029, China
| | - Aihua Liao
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Satoshi H Namekawa
- Division of Reproductive Sciences, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Shuiqiao Yuan
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
- Shenzhen Huazhong University of Science and Technology Research Institute, Shenzhen, 518057, China.
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28
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Abstract
Facioscapulohumeral muscular dystrophy (FSHD), a progressive myopathy that afflicts individuals of all ages, provides a powerful model of the complex interplay between genetic and epigenetic mechanisms of chromatin regulation. FSHD is caused by dysregulation of a macrosatellite repeat, either by contraction of the repeat or by mutations in silencing proteins. Both cases lead to chromatin relaxation and, in the context of a permissive allele, aberrant expression of the DUX4 gene in skeletal muscle. DUX4 is a pioneer transcription factor that activates a program of gene expression during early human development, after which its expression is silenced in most somatic cells. When misexpressed in FSHD skeletal muscle, the DUX4 program leads to accumulated muscle pathology. Epigenetic regulators of the disease locus represent particularly attractive therapeutic targets for FSHD, as many are not global modifiers of the genome, and altering their expression or activity should allow correction of the underlying defect.
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MESH Headings
- CRISPR-Cas Systems
- Chromatin/chemistry
- Chromosomal Proteins, Non-Histone/genetics
- Chromosomal Proteins, Non-Histone/metabolism
- Chromosomes, Human, Pair 4
- DNA (Cytosine-5-)-Methyltransferases/genetics
- DNA (Cytosine-5-)-Methyltransferases/metabolism
- DNA Methylation
- Epigenesis, Genetic
- Gene Editing
- Genetic Loci
- Genome, Human
- Homeodomain Proteins/genetics
- Homeodomain Proteins/metabolism
- Humans
- Muscle, Skeletal/metabolism
- Muscle, Skeletal/pathology
- Muscular Dystrophy, Facioscapulohumeral/classification
- Muscular Dystrophy, Facioscapulohumeral/genetics
- Muscular Dystrophy, Facioscapulohumeral/metabolism
- Muscular Dystrophy, Facioscapulohumeral/pathology
- Mutation
- Severity of Illness Index
- DNA Methyltransferase 3B
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Affiliation(s)
- Charis L Himeda
- Department of Pharmacology, School of Medicine, University of Nevada, Reno, Nevada 89557, USA;
| | - Peter L Jones
- Department of Pharmacology, School of Medicine, University of Nevada, Reno, Nevada 89557, USA;
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29
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UHRF1 Promotes Proliferation of Human Adipose-Derived Stem Cells and Suppresses Adipogenesis via Inhibiting Peroxisome Proliferator-Activated Receptor γ. BIOMED RESEARCH INTERNATIONAL 2019; 2019:9456847. [PMID: 31428652 PMCID: PMC6681597 DOI: 10.1155/2019/9456847] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 06/11/2019] [Accepted: 06/24/2019] [Indexed: 12/11/2022]
Abstract
Once the adipose tissue is enlarged for the purpose of saving excess energy intake, obesity may be observed. Ubiquitin-like with PHD and RING Finger domains 1 (UHRF1) is helpful in repairing damaged DNA as it increases the resistance of cancer cells against cytocidal drugs. Peroxisome proliferator-activated receptor γ (PPARγ), an important nucleus transcription factor participating in adipogenesis, has been extensively reported. To date, no study has indicated whether UHRF1 can regulate proliferation and differentiation of human adipose-derived stem cells (hADSCs). Hence, this study aimed to utilize overexpression or downregulation of UHRF1 to explore the possible mechanism of proliferation and differentiation of hADSCs. We here used lentivirus, containing UHRF1 (LV-UHRF1) and siRNA-UHRF1 to transfect hADSCs, on which Cell Counting Kit-8 (CCK-8), cell growth curve, colony formation assay, and EdU proliferation assay were applied to evaluate proliferation of hADSCs, cells cycle was investigated by flow cytometry, and adipogenesis was detected by Oil Red O staining and Western blotting. Our results showed that UHRF1 can promote proliferation of hADSCs after overexpression of UHRF1, while proliferation of hADSCs was reduced through downregulation of UHRF1, and UHRF1 can control proliferation of hADSCs through transition from G1-phase to S-phase; besides, we found that UHRF1 negatively regulates adipogenesis of hADSCs via PPARγ. In summary, the results may provide a new insight regarding the role of UHRF1 on regulating proliferation and differentiation of hADSCs.
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30
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Jönsson ME, Ludvik Brattås P, Gustafsson C, Petri R, Yudovich D, Pircs K, Verschuere S, Madsen S, Hansson J, Larsson J, Månsson R, Meissner A, Jakobsson J. Activation of neuronal genes via LINE-1 elements upon global DNA demethylation in human neural progenitors. Nat Commun 2019; 10:3182. [PMID: 31320637 PMCID: PMC6639357 DOI: 10.1038/s41467-019-11150-8] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 06/20/2019] [Indexed: 01/14/2023] Open
Abstract
DNA methylation contributes to the maintenance of genomic integrity in somatic cells, in part through the silencing of transposable elements. In this study, we use CRISPR-Cas9 technology to delete DNMT1, the DNA methyltransferase key for DNA methylation maintenance, in human neural progenitor cells (hNPCs). We observe that inactivation of DNMT1 in hNPCs results in viable, proliferating cells despite a global loss of DNA CpG-methylation. DNA demethylation leads to specific transcriptional activation and chromatin remodeling of evolutionarily young, hominoid-specific LINE-1 elements (L1s), while older L1s and other classes of transposable elements remain silent. The activated L1s act as alternative promoters for many protein-coding genes involved in neuronal functions, revealing a hominoid-specific L1-based transcriptional network controlled by DNA methylation that influences neuronal protein-coding genes. Our results provide mechanistic insight into the role of DNA methylation in silencing transposable elements in somatic human cells, as well as further implicating L1s in human brain development and disease. DNA methylation plays an important role in silencing transposable elements. Here the authors find that loss of DNMT1 and DNA methylation leads to transcriptional activation and chromatin remodelling of evolutionarily young—hominoid-specific —LINE-1 elements which then act as alternative promoters for neuronal genes.
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Affiliation(s)
- Marie E Jönsson
- Wallenberg Neuroscience Center and Lund Stem Cell Center, Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, BMC A11, Lund University, 221 84, Lund, Sweden
| | - Per Ludvik Brattås
- Wallenberg Neuroscience Center and Lund Stem Cell Center, Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, BMC A11, Lund University, 221 84, Lund, Sweden
| | - Charlotte Gustafsson
- Center for Hematology and Regenerative Medicine Huddinge, Karolinska Institute, 141 52, Stockholm, Sweden
| | - Rebecca Petri
- Wallenberg Neuroscience Center and Lund Stem Cell Center, Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, BMC A11, Lund University, 221 84, Lund, Sweden
| | - David Yudovich
- Division of Molecular Medicine and Gene Therapy, Department of Laboratory Medicine and Lund Stem Cell Center, BMC A12, Lund University, 221 84, Lund, Sweden
| | - Karolina Pircs
- Wallenberg Neuroscience Center and Lund Stem Cell Center, Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, BMC A11, Lund University, 221 84, Lund, Sweden
| | - Shana Verschuere
- Wallenberg Neuroscience Center and Lund Stem Cell Center, Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, BMC A11, Lund University, 221 84, Lund, Sweden
| | - Sofia Madsen
- Wallenberg Neuroscience Center and Lund Stem Cell Center, Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, BMC A11, Lund University, 221 84, Lund, Sweden
| | - Jenny Hansson
- Laboratory of Proteomic Hematology, Department of Laboratory Medicine and Lund Stem Cell Center, BMC B12, Lund University, 221 84, Lund, Sweden
| | - Jonas Larsson
- Division of Molecular Medicine and Gene Therapy, Department of Laboratory Medicine and Lund Stem Cell Center, BMC A12, Lund University, 221 84, Lund, Sweden
| | - Robert Månsson
- Center for Hematology and Regenerative Medicine Huddinge, Karolinska Institute, 141 52, Stockholm, Sweden
| | - Alexander Meissner
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, 14195, Berlin, Germany
| | - Johan Jakobsson
- Wallenberg Neuroscience Center and Lund Stem Cell Center, Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, BMC A11, Lund University, 221 84, Lund, Sweden.
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31
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Wang S, Zhang C, Hasson D, Desai A, SenBanerjee S, Magnani E, Ukomadu C, Lujambio A, Bernstein E, Sadler KC. Epigenetic Compensation Promotes Liver Regeneration. Dev Cell 2019; 50:43-56.e6. [PMID: 31231040 PMCID: PMC6615735 DOI: 10.1016/j.devcel.2019.05.034] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 04/02/2019] [Accepted: 05/16/2019] [Indexed: 12/19/2022]
Abstract
Two major functions of the epigenome are to regulate gene expression and to suppress transposons. It is unclear how these functions are balanced during physiological challenges requiring tissue regeneration, where exquisite coordination of gene expression is essential. Transcriptomic analysis of seven time points following partial hepatectomy identified the epigenetic regulator UHRF1, which is essential for DNA methylation, as dynamically expressed during liver regeneration in mice. UHRF1 deletion in hepatocytes (Uhrf1HepKO) caused genome-wide DNA hypomethylation but, surprisingly, had no measurable effect on gene or transposon expression or liver homeostasis. Partial hepatectomy of Uhrf1HepKO livers resulted in early and sustained activation of proregenerative genes and enhanced liver regeneration. This was attributed to redistribution of H3K27me3 from promoters to transposons, effectively silencing them and, consequently, alleviating repression of liver regeneration genes, priming them for expression in Uhrf1HepKO livers. Thus, epigenetic compensation safeguards the genome against transposon activation, indirectly affecting gene regulation.
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Affiliation(s)
- Shuang Wang
- Department of Medicine/Division of Liver Diseases, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Chi Zhang
- Program in Biology, New York University Abu Dhabi, Abu Dhabi, P.O. Box 129188, United Arab Emirates
| | - Dan Hasson
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Anal Desai
- Division of Gastroenterology, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Sucharita SenBanerjee
- Division of Gastroenterology, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; College of Arts and Sciences, Wentworth Institute of Technology, 504 Parker St., Boston, MA 02115, USA
| | - Elena Magnani
- Program in Biology, New York University Abu Dhabi, Abu Dhabi, P.O. Box 129188, United Arab Emirates
| | - Chinweike Ukomadu
- Division of Gastroenterology, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Amaia Lujambio
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Liver Cancer Program, Division of Liver Diseases, Department of Medicine, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Emily Bernstein
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Kirsten C Sadler
- Department of Medicine/Division of Liver Diseases, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Program in Biology, New York University Abu Dhabi, Abu Dhabi, P.O. Box 129188, United Arab Emirates.
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32
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Kular L, Needhamsen M, Adzemovic MZ, Kramarova T, Gomez-Cabrero D, Ewing E, Piket E, Tegnér J, Beck S, Piehl F, Brundin L, Jagodic M. Neuronal methylome reveals CREB-associated neuro-axonal impairment in multiple sclerosis. Clin Epigenetics 2019; 11:86. [PMID: 31146783 PMCID: PMC6543588 DOI: 10.1186/s13148-019-0678-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 04/30/2019] [Indexed: 11/21/2022] Open
Abstract
Background Due to limited access to brain tissue, the precise mechanisms underlying neuro-axonal dysfunction in neurological disorders such as multiple sclerosis (MS) are largely unknown. In that context, profiling DNA methylation, which is a stable and cell type-specific regulatory epigenetic mark of genome activity, offers a unique opportunity to characterize the molecular mechanisms underpinning brain pathology in situ. We examined DNA methylation patterns of neuronal nuclei isolated from post-mortem brain tissue to infer processes that occur in neurons of MS patients. Results We isolated subcortical neuronal nuclei from post-mortem white matter tissue of MS patients and non-neurological controls using flow cytometry. We examined bulk DNA methylation changes (total n = 29) and further disentangled true DNA methylation (5mC) from neuron-specific DNA hydroxymethylation (5hmC) (n = 17), using Illumina Infinium 450K arrays. We performed neuronal sub-type deconvolution using glutamate and GABA methylation profiles to further reduce neuronal sample heterogeneity. In total, we identified 2811 and 1534 significant (genome-wide adjusted P value < 0.05) differentially methylated and hydroxymethylated positions between MS patients and controls. We found striking hypo-5mC and hyper-5hmC changes occurring mainly within gene bodies, which correlated with reduced transcriptional activity, assessed using published RNAseq data from bulk brain tissue of MS patients and controls. Pathway analyses of the two cohorts implicated dysregulation of genes involved in axonal guidance and synaptic plasticity, with meta-analysis confirming CREB signalling as the most highly enriched pathway underlying these processes. We functionally investigated DNA methylation changes of CREB signalling-related genes by immunohistofluoresence of phosphorylated CREB in neurons from brain sections of a subcohort of MS patients and controls (n = 15). Notably, DNA methylation changes associated with a reduction of CREB activity in white matter neurons of MS patients compared to controls. Conclusions Our data demonstrate that investigating 5mC and 5hmC modifications separately allows the discovery of a substantial fraction of changes occurring in neurons, which can escape traditional bisulfite-based DNA methylation analysis. Collectively, our findings indicate that neurons of MS patients acquire sustained hypo-5mC and hyper-5hmC, which may impair CREB-mediated neuro-axonal integrity, in turn relating to clinical symptoms. Electronic supplementary material The online version of this article (10.1186/s13148-019-0678-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lara Kular
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Maria Needhamsen
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Milena Z Adzemovic
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Tatiana Kramarova
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - David Gomez-Cabrero
- Department of Medicine, Unit of Computational Medicine, Center for Molecular Medicine, Karolinska Institutet, Solna, Sweden.,Mucosal and Salivary Biology Division, King's College London Dental Institute, London, SE1 9RT, UK.,Translational Bioinformatics Unit, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), IdiSNA, Pamplona, Spain
| | - Ewoud Ewing
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Eliane Piket
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Jesper Tegnér
- Department of Medicine, Unit of Computational Medicine, Center for Molecular Medicine, Karolinska Institutet, Solna, Sweden.,Biological and Environmental Sciences and Engineering Division, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Stephan Beck
- Medical Genomics, UCL Cancer Institute, University College London, London, UK
| | - Fredrik Piehl
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Neurology, Karolinska University Hospital, Stockholm, Sweden
| | - Lou Brundin
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Neurology, Karolinska University Hospital, Stockholm, Sweden
| | - Maja Jagodic
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.
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33
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Martinez-Redondo P, Izpisua Belmonte JC. Tailored chromatin modulation to promote tissue regeneration. Semin Cell Dev Biol 2019; 97:3-15. [PMID: 31028854 DOI: 10.1016/j.semcdb.2019.04.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 04/22/2019] [Accepted: 04/22/2019] [Indexed: 12/16/2022]
Abstract
Epigenetic regulation of gene expression is fundamental in the maintenance of cellular identity and the regulation of cellular plasticity during tissue repair. In fact, epigenetic modulation is associated with the processes of cellular de-differentiation, proliferation, and re-differentiation that takes place during tissue regeneration. In here we explore the epigenetic events that coordinate tissue repair in lower vertebrates with high regenerative capacity, and in mammalian adult stem cells, which are responsible for the homeostasis maintenance of most of our tissues. Finally we summarize promising CRISPR-based editing technologies developed during the last years, which look as promising tools to not only study but also promote specific events during tissue regeneration.
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Affiliation(s)
- Paloma Martinez-Redondo
- Gene Expression Laboratory, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA, 92037, United States
| | - Juan Carlos Izpisua Belmonte
- Gene Expression Laboratory, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA, 92037, United States.
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34
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Abstract
Transposable elements (TEs) are low-complexity elements (e.g., LINEs, SINEs, SVAs, and HERVs) that make up to two-thirds of the human genome. There is mounting evidence that TEs play an essential role in molecular functions that influence genomic plasticity and gene expression regulation. With the advent of next-generation sequencing approaches, our understanding of the relationship between TEs and psychiatric disorders will greatly improve. In this chapter, the Authors comprehensively summarize the state-of the-art of TE research in animal models and humans supporting a framework in which TEs play a functional role in mechanisms affecting a variety of behaviors, including neurodevelopmental, neuropsychiatric, and neurodegenerative disorders. Finally, the Authors discuss recent therapeutic applications raised from the increasing experimental evidence on TE functional mechanisms.
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Affiliation(s)
- G Guffanti
- McLean Hospital - Harvard Medical School, Belmont, MA, USA.
| | - A Bartlett
- Department of Psychology, University of Massachusetts, Boston, Boston, MA, USA
| | - P DeCrescenzo
- McLean Hospital - Harvard Medical School, Belmont, MA, USA
| | - F Macciardi
- Department of Psychiatry and Human Behavior, University of California, Irvine, Irvine, CA, USA
| | - R Hunter
- Department of Psychology, University of Massachusetts, Boston, Boston, MA, USA
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35
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Epigenetic regulator UHRF1 inactivates REST and growth suppressor gene expression via DNA methylation to promote axon regeneration. Proc Natl Acad Sci U S A 2018; 115:E12417-E12426. [PMID: 30530687 DOI: 10.1073/pnas.1812518115] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Injured peripheral sensory neurons switch to a regenerative state after axon injury, which requires transcriptional and epigenetic changes. However, the roles and mechanisms of gene inactivation after injury are poorly understood. Here, we show that DNA methylation, which generally leads to gene silencing, is required for robust axon regeneration after peripheral nerve lesion. Ubiquitin-like containing PHD ring finger 1 (UHRF1), a critical epigenetic regulator involved in DNA methylation, increases upon axon injury and is required for robust axon regeneration. The increased level of UHRF1 results from a decrease in miR-9. The level of another target of miR-9, the transcriptional regulator RE1 silencing transcription factor (REST), transiently increases after injury and is required for axon regeneration. Mechanistically, UHRF1 interacts with DNA methyltransferases (DNMTs) and H3K9me3 at the promoter region to repress the expression of the tumor suppressor gene phosphatase and tensin homolog (PTEN) and REST. Our study reveals an epigenetic mechanism that silences tumor suppressor genes and restricts REST expression in time after injury to promote axon regeneration.
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36
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Blanchart A, Navis AC, Assaife-Lopes N, Usoskin D, Aranda S, Sontheimer J, Ernfors P. UHRF1 Licensed Self-Renewal of Active Adult Neural Stem Cells. Stem Cells 2018; 36:1736-1751. [PMID: 29999568 DOI: 10.1002/stem.2889] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 06/04/2018] [Accepted: 06/23/2018] [Indexed: 12/12/2022]
Abstract
Adult neurogenesis in the brain continuously seeds new neurons throughout life, but how homeostasis of adult neural stem cells (NSCs) is maintained is incompletely understood. Here, we demonstrate that the DNA methylation adapter ubiquitin-like, containing PHD and RING finger domains-1 (UHRF1) is expressed in, and regulates proliferation of, the active but not quiescent pool of adult neural progenitor cells. Mice with a neural stem cell-specific deficiency in UHRF1 exhibit a massive depletion of neurogenesis resulting in a collapse of formation of new neurons. In the absence of UHRF1, NSCs unexpectedly remain in the cell cycle but with a 17-fold increased cell cycle length due to a failure of replication phase entry caused by promoter demethylation and derepression of Cdkn1a, which encodes the cyclin-dependent kinase inhibitor p21. UHRF1 does not affect the proportion progenitor cells active within the cell cycle but among these cells, UHRF1 is critical for licensing replication re-entry. Therefore, this study shows that a UHRF1-Cdkn1a axis is essential for the control of stem cell self-renewal and neurogenesis in the adult brain. Stem Cells 2018;36:1736-1751.
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Affiliation(s)
- Albert Blanchart
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Anna C Navis
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Natalia Assaife-Lopes
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Dmitry Usoskin
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Sergi Aranda
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Jana Sontheimer
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Patrik Ernfors
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
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37
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Uhrf1 regulates active transcriptional marks at bivalent domains in pluripotent stem cells through Setd1a. Nat Commun 2018; 9:2583. [PMID: 29968706 PMCID: PMC6030064 DOI: 10.1038/s41467-018-04818-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 05/23/2018] [Indexed: 11/18/2022] Open
Abstract
Embryonic stem cells (ESCs) maintain pluripotency through unique epigenetic states. When ESCs commit to a specific lineage, epigenetic changes in histones and DNA accompany the transition to specialized cell types. Investigating how epigenetic regulation controls lineage specification is critical in order to generate the required cell types for clinical applications. Uhrf1 is a widely known hemi-methylated DNA-binding protein, playing a role in DNA methylation through the recruitment of Dnmt1 and in heterochromatin formation alongside G9a, Trim28, and HDACs. Although Uhrf1 is not essential in ESC self-renewal, it remains elusive how Uhrf1 regulates cell specification. Here we report that Uhrf1 forms a complex with the active trithorax group, the Setd1a/COMPASS complex, to maintain bivalent histone marks, particularly those associated with neuroectoderm and mesoderm specification. Overall, our data demonstrate that Uhrf1 safeguards proper differentiation via bivalent histone modifications. Uhrf1 is a known regulator of heterochromatin and DNA methylation in embryonic stem cells (ESCs). Here, the authors demonstrate that Uhrf1 acts together with the Set1/COMPASS complex regulator of active transcription to promote H3K4 methylation at bivalent loci and Uhrf1 loss results in disruption of differentiation.
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38
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Np95/Uhrf1 regulates tumor suppressor gene expression of neural stem/precursor cells, contributing to neurogenesis in the adult mouse brain. Neurosci Res 2018; 143:31-43. [PMID: 29859850 DOI: 10.1016/j.neures.2018.05.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 05/29/2018] [Accepted: 05/30/2018] [Indexed: 01/30/2023]
Abstract
Adult neurogenesis is a process of generating new neurons from neural stem/precursor cells (NS/PCs) in restricted adult brain regions throughout life. It is now generally known that adult neurogenesis in the hippocampal dentate gyrus (DG) and subventricular zone participates in various higher brain functions, such as learning and memory formation, olfactory discrimination and repair after brain injury. However, the mechanisms underlying adult neurogenesis remain to be fully understood. Here, we show that Nuclear protein 95 KDa (Np95, also known as UHRF1 or ICBP90), which is an essential protein for maintaining DNA methylation during cell division, is involved in multiple processes of adult neurogenesis. Specific ablation of Np95 in adult NS/PCs (aNS/PCs) led to a decrease in their proliferation and an impairment of neuronal differentiation and to suppression of neuronal maturation associated with the impairment of dendritic formation in the hippocampal DG. We also found that deficiency of Np95 in NS/PCs increased the expression of tumor suppressor genes p16 and p53, and confirmed that expression of these genes in NS/PCs recapitulates the phenotype of Np95-deficient NS/PCs. Taken together, our findings suggest that Np95 plays an essential role in proliferation and differentiation of aNS/PCs through the regulation of tumor suppressor gene expression in adult neurogenesis.
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39
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Cui D, Xu X. DNA Methyltransferases, DNA Methylation, and Age-Associated Cognitive Function. Int J Mol Sci 2018; 19:E1315. [PMID: 29710796 PMCID: PMC5983821 DOI: 10.3390/ijms19051315] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 04/20/2018] [Accepted: 04/20/2018] [Indexed: 12/16/2022] Open
Abstract
Ageing, a leading cause of the decline/deficits in human learning, memory, and cognitive abilities, is a major risk factor for age-associated neurodegenerative disorders such as Alzheimer’s disease. Emerging evidence suggests that epigenetics, an inheritable but reversible biochemical process, plays a crucial role in the pathogenesis of age-related neurological disorders. DNA methylation, the best-known epigenetic mark, has attracted most attention in this regard. DNA methyltransferases (DNMTs) are key enzymes in mediating the DNA methylation process, by which a methyl group is transferred, faithfully or anew, to genomic DNA sequences. Biologically, DNMTs are important for gene imprinting. Accumulating evidence suggests that DNMTs not only play critical roles, including gene imprinting and transcription regulation, in early development stages of the central nervous system (CNS), but also are indispensable in adult learning, memory, and cognition. Therefore, the impact of DNMTs and DNA methylation on age-associated cognitive functions and neurodegenerative diseases has emerged as a pivotal topic in the field. In this review, the effects of each DNMT on CNS development and healthy and pathological ageing are discussed.
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Affiliation(s)
- Di Cui
- Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany.
| | - Xiangru Xu
- Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany.
- Department of Anesthesiology, Yale University School of Medicine, New Haven, CT 06520, USA.
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40
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Dubnau J. The Retrotransposon storm and the dangers of a Collyer's genome. Curr Opin Genet Dev 2018; 49:95-105. [PMID: 29705598 PMCID: PMC5975205 DOI: 10.1016/j.gde.2018.04.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 03/08/2018] [Accepted: 04/11/2018] [Indexed: 12/13/2022]
Abstract
Like the famous Collyer's mansion in NY, our genomes have accumulated vast quantities of sequences that have been referred to as 'junk DNA,' much of which consists of retrotransposons (RTEs). A recent literature establishes the phenomenology that many RTEs become expressed at progressively higher levels during the course of normal aging. This seems to reflect gradual loss of heterochromatin in old age. In addition, RTEs appear to be precociously expressed in brains of younger animals that are experiencing neurodegenerative decline. Although it is difficult to distinguish cause from consequence, several recent studies support the contention that RTE expression, and even perhaps transposition, causally contribute to both the normal deterioration seen with age and to the precipitous decline in some neurodegenerative disorders. This may reflect a two hit model in which normal age-dependent loss of heterochromatin synergizes with a disruption to posttranscriptional silencing of RTEs caused by genetic and environmental stress.
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Affiliation(s)
- Josh Dubnau
- Department of Anesthesiology, State University of New York at Stony Brook, Stony Brook, NY 11794-8480, United States; Department of Neurobiology & Behavior, Stony Brook University & Stony Brook School of Medicine, Stony Brook, NY 11794-8480, United States.
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41
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Zhou H, Wang B, Sun H, Xu X, Wang Y. Epigenetic Regulations in Neural Stem Cells and Neurological Diseases. Stem Cells Int 2018; 2018:6087143. [PMID: 29743892 PMCID: PMC5878882 DOI: 10.1155/2018/6087143] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2017] [Accepted: 01/08/2018] [Indexed: 12/17/2022] Open
Abstract
Among the regulatory mechanisms of the renewal and differentiation of neural stem cells, recent evidences support that epigenetic modifications such as DNA methylation, histone modification, and noncoding RNAs play critical roles in the regulation on the proliferation and differentiation of neural stem cells. In this review, we discussed recent advances of DNA modifications on the regulative mechanisms of neural stem cells. Among these epigenetic modifications, DNA 5-hydroxymethylcytosine (5hmC) modification is emerging as an important modulator on the proliferation and differentiation of neural stem cells. At the same time, Ten-eleven translocation (Tet) methylcytosine dioxygenases, the rate-limiting enzyme for the 5-hydroxymethylation reaction from 5-methylcytosine to 5-hydroxymethylcytosine, play a critical role in the tumorigenesis and the proliferation and differentiation of stem cells. The functions of 5hmC and TET proteins on neural stem cells and their roles in neurological diseases are discussed.
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Affiliation(s)
- Hang Zhou
- Department of Neurology, The Second Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Neuroscience, Soochow University, Suzhou, China
| | - Bin Wang
- Institute of Neuroscience, Soochow University, Suzhou, China
| | - Hao Sun
- Department of Orthopedics, Clinical Medical School, Yangzhou University, Northern Jiangsu People's Hospital, Yangzhou 225001, China
| | - Xingshun Xu
- Department of Neurology, The Second Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Neuroscience, Soochow University, Suzhou, China
| | - Yongxiang Wang
- Department of Orthopedics, Clinical Medical School, Yangzhou University, Northern Jiangsu People's Hospital, Yangzhou 225001, China
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42
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Stricker SH, Götz M. DNA-Methylation: Master or Slave of Neural Fate Decisions? Front Neurosci 2018; 12:5. [PMID: 29449798 PMCID: PMC5799221 DOI: 10.3389/fnins.2018.00005] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 01/04/2018] [Indexed: 01/05/2023] Open
Abstract
The pristine formation of complex organs depends on sharp temporal and spatial control of gene expression. Therefore, epigenetic mechanisms have been frequently attributed a central role in controlling cell fate determination. A prime example for this is the first discovered and still most studied epigenetic mark, DNA methylation, and the development of the most complex mammalian organ, the brain. Recently, the field of epigenetics has advanced significantly: new DNA modifications were discovered, epigenomic profiling became widely accessible, and methods for targeted epigenomic manipulation have been developed. Thus, it is time to challenge established models of epigenetic gene regulation. Here, we review the current state of knowledge about DNA modifications, their epigenomic distribution, and their regulatory role. We will summarize the evidence suggesting they possess crucial roles in neurogenesis and discuss whether this likely includes lineage choice regulation or rather effects on differentiation. Finally, we will attempt an outlook on how questions, which remain unresolved, could be answered soon.
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Affiliation(s)
- Stefan H Stricker
- MCN Junior Research Group, Munich Center for Neurosciences, Ludwig-Maximilian-Universität, Munich, Germany.,Physiological Genomics, BioMedical Center, Munich, Germany.,German Research Center for Environmental Health, Ingolstädter Landstrasse 1, Germany and Biomedical Center, Institute of Stem Cell Research, Helmholtz Zentrum, Ludwig-Maximilian-Universität, Munich, Germany
| | - Magdalena Götz
- Physiological Genomics, BioMedical Center, Munich, Germany.,German Research Center for Environmental Health, Ingolstädter Landstrasse 1, Germany and Biomedical Center, Institute of Stem Cell Research, Helmholtz Zentrum, Ludwig-Maximilian-Universität, Munich, Germany.,German Excellence Cluster of Systems Neurology, Munich, Germany
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43
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Ye J, Zhang Y, Liang W, Huang J, Wang L, Zhong X. UHRF1 is an Independent Prognostic Factor and a Potential Therapeutic Target of Esophageal Squamous Cell Carcinoma. J Cancer 2017; 8:4027-4039. [PMID: 29187878 PMCID: PMC5706005 DOI: 10.7150/jca.21256] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 10/10/2017] [Indexed: 12/15/2022] Open
Abstract
Purpose: Ubiquitin-like with plant homeodomain and ring-finger domains 1 (UHRF1) plays an essential role in DNA methylation, and the overexpression of UHRF1 is associated with poor prognosis in various cancers. Esophageal squamous cell carcinoma (ESCC) accounts for approximately 90% of esophageal cancer cases in China, but the five-year survival rate for patients is less than 10% due to limited clinical approaches for early diagnosis and treatment. The present research aimed to investigate the expression of UHRF1 in ESCC and its biological role in ESCC development. Methods: UHRF1 expression in ESCC and normal esophageal tissues was examined using immunohistochemical staining, followed by analysis of the correlation between UHRF1 expression and clinical features. In addition, the effects of lentivirus-mediated RNA interference of UHRF1 on global DNA methylation, cell proliferation, cell cycle progression and apoptosis and were investigated in ESCC cells. Results: UHRF1 was overexpressed in ESCC tissues and was an independent prognostic factor for ESCC patients. In ESCC cells, knockdown of UHRF1 caused global DNA hypomethylation, inhibited cell proliferation and induced apoptosis. Furthermore, UHRF1 depletion induced cell cycle arrest at the G2/M phase, accompanied by activation of Wee1 and DNA damage response pathway. Conclusions: Our findings identify UHRF1 as a promising prognostic marker for ESCC and suggest that UHRF1 may be a potential therapy target for ESCC patients with elevated UHRF1 expression.
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Affiliation(s)
- Jiecheng Ye
- Department of Pathology, Medical College, Jinan University, Guangzhou 510632, China.,Guangdong Province Key Laboratory of Molecular Immunology and Antibody Engineering, Jinan University, Guangzhou 510632, China
| | - Yong Zhang
- Institute of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Weiye Liang
- Department of Pathology, Medical College, Jinan University, Guangzhou 510632, China.,Guangdong Province Key Laboratory of Molecular Immunology and Antibody Engineering, Jinan University, Guangzhou 510632, China
| | - Jianxian Huang
- Department of Pathology, Medical College, Jinan University, Guangzhou 510632, China.,Guangdong Province Key Laboratory of Molecular Immunology and Antibody Engineering, Jinan University, Guangzhou 510632, China
| | - Lihui Wang
- Department of Pathology, Medical College, Jinan University, Guangzhou 510632, China.,Guangdong Province Key Laboratory of Molecular Immunology and Antibody Engineering, Jinan University, Guangzhou 510632, China
| | - Xueyun Zhong
- Department of Pathology, Medical College, Jinan University, Guangzhou 510632, China.,Guangdong Province Key Laboratory of Molecular Immunology and Antibody Engineering, Jinan University, Guangzhou 510632, China
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44
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Chernyavskaya Y, Mudbhary R, Zhang C, Tokarz D, Jacob V, Gopinath S, Sun X, Wang S, Magnani E, Madakashira BP, Yoder JA, Hoshida Y, Sadler KC. Loss of DNA methylation in zebrafish embryos activates retrotransposons to trigger antiviral signaling. Development 2017; 144:2925-2939. [PMID: 28698226 DOI: 10.1242/dev.147629] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 07/02/2017] [Indexed: 12/19/2022]
Abstract
Complex cytoplasmic nucleotide-sensing mechanisms can recognize foreign DNA based on a lack of methylation and initiate an immune response to clear the infection. Zebrafish embryos with global DNA hypomethylation caused by mutations in the ubiquitin-like with PHD and ring finger domains 1 (uhrf1) or DNA methyltransferase 1 (dnmt1) genes exhibit a robust interferon induction characteristic of the first line of defense against viral infection. We found that this interferon induction occurred in non-immune cells and examined whether intracellular viral sensing pathways in these cells were the trigger. RNA-seq analysis of uhrf1 and dnmt1 mutants revealed widespread induction of Class I retrotransposons and activation of cytoplasmic DNA viral sensors. Attenuating Sting, phosphorylated Tbk1 and, importantly, blocking reverse transcriptase activity suppressed the expression of interferon genes in uhrf1 mutants. Thus, activation of transposons in cells with global DNA hypomethylation mimics a viral infection by activating cytoplasmic DNA sensors. This suggests that antiviral pathways serve as surveillance of cells that have derepressed intragenomic parasites due to DNA hypomethylation.
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Affiliation(s)
- Yelena Chernyavskaya
- Division of Liver Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, Box 1020, New York, NY 10029, USA.,Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, Box 1020, New York, NY 10029, USA.,Program in Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Raksha Mudbhary
- Division of Liver Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, Box 1020, New York, NY 10029, USA.,Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, Box 1020, New York, NY 10029, USA.,Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, Box 1020, New York, NY 10029, USA
| | - Chi Zhang
- Division of Liver Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, Box 1020, New York, NY 10029, USA.,Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, Box 1020, New York, NY 10029, USA.,Program in Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Debra Tokarz
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, NC 27607, USA.,Center for Comparative Medicine and Translational Research, North Carolina State University, Raleigh, NC 27607, USA
| | - Vinitha Jacob
- Division of Liver Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, Box 1020, New York, NY 10029, USA.,Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, Box 1020, New York, NY 10029, USA.,Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, Box 1020, New York, NY 10029, USA
| | - Smita Gopinath
- Division of Liver Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, Box 1020, New York, NY 10029, USA.,Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, Box 1020, New York, NY 10029, USA
| | - Xiaochen Sun
- Division of Liver Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, Box 1020, New York, NY 10029, USA.,Liver Cancer Program, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, Box 1020, New York, NY 10029, USA
| | - Shuang Wang
- Division of Liver Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, Box 1020, New York, NY 10029, USA.,Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, Box 1020, New York, NY 10029, USA
| | - Elena Magnani
- Division of Liver Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, Box 1020, New York, NY 10029, USA.,Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, Box 1020, New York, NY 10029, USA.,Program in Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | | | - Jeffrey A Yoder
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, NC 27607, USA.,Center for Comparative Medicine and Translational Research, North Carolina State University, Raleigh, NC 27607, USA
| | - Yujin Hoshida
- Division of Liver Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, Box 1020, New York, NY 10029, USA.,Program in Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates.,Liver Cancer Program, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, Box 1020, New York, NY 10029, USA
| | - Kirsten C Sadler
- Division of Liver Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, Box 1020, New York, NY 10029, USA .,Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, Box 1020, New York, NY 10029, USA.,Program in Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates.,Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, Box 1020, New York, NY 10029, USA
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Abstract
Cellular senescence is a cell fate characterized by an irreversible cell cycle arrest, but the molecular mechanism underlying this senescence hallmark remains poorly understood. Through an unbiased search for novel senescence regulators in airway basal cells, we discovered that the epigenetic regulator ubiquitin-like with PHD and ring finger domain-containing protein 1 (UHRF1) is critical for regulating cell cycle progression. Upon injury, basal cells in the mouse airway rapidly induce the expression of UHRF1 in order to stimulate stem cell proliferation and tissue repair. Targeted depletion of Uhrf1 specifically in airway basal cells causes a profound defect in cell cycle progression. Consistently, cultured primary human basal cells lacking UHRF1 do not exhibit cell death or differentiation phenotypes but undergo a spontaneous program of senescence. Mechanistically, UHRF1 loss induces G1 cell cycle arrest by abrogating DNA replication factory formation as evidenced by loss of proliferating cell nuclear antigen (PCNA) puncta and an inability to enter the first cell cycle. This proliferation defect is partially mediated by the p15 pathway. Overall, our study provides the first evidence of an indispensable role of UHRF1 in somatic stem cells proliferation during the process of airway regeneration.
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PIM1 induces cellular senescence through phosphorylation of UHRF1 at Ser311. Oncogene 2017; 36:4828-4842. [PMID: 28394343 DOI: 10.1038/onc.2017.96] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2016] [Revised: 01/23/2017] [Accepted: 02/26/2017] [Indexed: 12/13/2022]
Abstract
PIM1 is a proto-oncogene, encoding a serine/threonine protein kinase that regulates cell proliferation, survival, differentiation and apoptosis. Previous reports suggest that overexpression of PIM1 can induce cellular senescence. However, the molecular mechanism underlying this process is not fully understood. Here we report that UHRF1 is a novel substrate of PIM1 kinase, which could be phosphorylated at Ser311 and therefore promoted to degradation. Our data demonstrates that PIM1 destabilizes UHRF1, leading to DNA hypomethylation, which consequently results in genomic instability, increased p16 expression and subsequent induction of cellular senescence. Taken together, our results suggest that down-regulation of UHRF1 is an important mechanism of PIM1-mediated cellular senescence.
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