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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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Kar A, Alvarez M, Garske KM, Huang H, Lee SHT, Deal M, Das SS, Koka A, Jamal Z, Mohlke KL, Laakso M, Heinonen S, Pietiläinen KH, Pajukanta P. Age-dependent genes in adipose stem and precursor cells affect regulation of fat cell differentiation and link aging to obesity via cellular and genetic interactions. Genome Med 2024; 16:19. [PMID: 38297378 PMCID: PMC10829214 DOI: 10.1186/s13073-024-01291-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 01/19/2024] [Indexed: 02/02/2024] Open
Abstract
BACKGROUND Age and obesity are dominant risk factors for several common cardiometabolic disorders, and both are known to impair adipose tissue function. However, the underlying cellular and genetic factors linking aging and obesity on adipose tissue function have remained elusive. Adipose stem and precursor cells (ASPCs) are an understudied, yet crucial adipose cell type due to their deterministic adipocyte differentiation potential, which impacts the capacity to store fat in a metabolically healthy manner. METHODS We integrated subcutaneous adipose tissue (SAT) bulk (n=435) and large single-nucleus RNA sequencing (n=105) data with the UK Biobank (UKB) (n=391,701) data to study age-obesity interactions originating from ASPCs by performing cell-type decomposition, differential expression testing, cell-cell communication analyses, and construction of polygenic risk scores for body mass index (BMI). RESULTS We found that the SAT ASPC proportions significantly decrease with age in an obesity-dependent way consistently in two independent cohorts, both showing that the age dependency of ASPC proportions is abolished by obesity. We further identified 76 genes (72 SAT ASPC marker genes and 4 transcription factors regulating ASPC marker genes) that are differentially expressed by age in SAT and functionally enriched for developmental processes and adipocyte differentiation (i.e., adipogenesis). The 76 age-perturbed ASPC genes include multiple negative regulators of adipogenesis, such as RORA, SMAD3, TWIST2, and ZNF521, form tight clusters of longitudinally co-expressed genes during human adipogenesis, and show age-based differences in cellular interactions between ASPCs and adipose cell types. Finally, our genetic data demonstrate that cis-regional variants of these genes interact with age as predictors of BMI in an obesity-dependent way in the large UKB, while no such gene-age interaction on BMI is observed with non-age-dependent ASPC marker genes, thus independently confirming our cellular ASPC results at the biobank level. CONCLUSIONS Overall, we discover that obesity prematurely induces a decrease in ASPC proportions and identify 76 developmentally important ASPC genes that implicate altered negative regulation of fat cell differentiation as a mechanism for aging and directly link aging to obesity via significant cellular and genetic interactions.
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Affiliation(s)
- Asha Kar
- Department of Human Genetics, David Geffen School of Medicine at UCLA, University of California, Los Angeles (UCLA), Gonda Center, Room 6357B, 695 Charles E. Young Drive South, Los Angeles, CA, 90095-7088, USA
| | - Marcus Alvarez
- Department of Human Genetics, David Geffen School of Medicine at UCLA, University of California, Los Angeles (UCLA), Gonda Center, Room 6357B, 695 Charles E. Young Drive South, Los Angeles, CA, 90095-7088, USA
| | - Kristina M Garske
- Department of Human Genetics, David Geffen School of Medicine at UCLA, University of California, Los Angeles (UCLA), Gonda Center, Room 6357B, 695 Charles E. Young Drive South, Los Angeles, CA, 90095-7088, USA
| | - Huiling Huang
- Department of Human Genetics, David Geffen School of Medicine at UCLA, University of California, Los Angeles (UCLA), Gonda Center, Room 6357B, 695 Charles E. Young Drive South, Los Angeles, CA, 90095-7088, USA
- Bioinformatics Interdepartmental Program, UCLA, Los Angeles, USA
| | - Seung Hyuk T Lee
- Department of Human Genetics, David Geffen School of Medicine at UCLA, University of California, Los Angeles (UCLA), Gonda Center, Room 6357B, 695 Charles E. Young Drive South, Los Angeles, CA, 90095-7088, USA
| | - Milena Deal
- Department of Human Genetics, David Geffen School of Medicine at UCLA, University of California, Los Angeles (UCLA), Gonda Center, Room 6357B, 695 Charles E. Young Drive South, Los Angeles, CA, 90095-7088, USA
| | - Sankha Subhra Das
- Department of Human Genetics, David Geffen School of Medicine at UCLA, University of California, Los Angeles (UCLA), Gonda Center, Room 6357B, 695 Charles E. Young Drive South, Los Angeles, CA, 90095-7088, USA
| | - Amogha Koka
- Department of Human Genetics, David Geffen School of Medicine at UCLA, University of California, Los Angeles (UCLA), Gonda Center, Room 6357B, 695 Charles E. Young Drive South, Los Angeles, CA, 90095-7088, USA
| | - Zoeb Jamal
- Department of Human Genetics, David Geffen School of Medicine at UCLA, University of California, Los Angeles (UCLA), Gonda Center, Room 6357B, 695 Charles E. Young Drive South, Los Angeles, CA, 90095-7088, USA
| | - Karen L Mohlke
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Markku Laakso
- Department of Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - Sini Heinonen
- Obesity Research Unit, Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Kirsi H Pietiläinen
- Obesity Research Unit, Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- HealthyWeightHub, Endocrinology, Abdominal Center, Helsinki University Central Hospital and University of Helsinki, Helsinki, Finland
| | - Päivi Pajukanta
- Department of Human Genetics, David Geffen School of Medicine at UCLA, University of California, Los Angeles (UCLA), Gonda Center, Room 6357B, 695 Charles E. Young Drive South, Los Angeles, CA, 90095-7088, USA.
- Bioinformatics Interdepartmental Program, UCLA, Los Angeles, USA.
- Institute for Precision Health, David Geffen School of Medicine at UCLA, Los Angeles, USA.
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3
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Suzuki T, Komatsu T, Shibata H, Tanioka A, Vargas D, Kawabata-Iwakawa R, Miura F, Masuda S, Hayashi M, Tanimura-Inagaki K, Morita S, Kohmaru J, Adachi K, Tobo M, Obinata H, Hirayama T, Kimura H, Sakai J, Nagasawa H, Itabashi H, Hatada I, Ito T, Inagaki T. Crucial role of iron in epigenetic rewriting during adipocyte differentiation mediated by JMJD1A and TET2 activity. Nucleic Acids Res 2023; 51:6120-6142. [PMID: 37158274 PMCID: PMC10325906 DOI: 10.1093/nar/gkad342] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 04/10/2023] [Accepted: 04/21/2023] [Indexed: 05/10/2023] Open
Abstract
Iron metabolism is closely associated with the pathogenesis of obesity. However, the mechanism of the iron-dependent regulation of adipocyte differentiation remains unclear. Here, we show that iron is essential for rewriting of epigenetic marks during adipocyte differentiation. Iron supply through lysosome-mediated ferritinophagy was found to be crucial during the early stage of adipocyte differentiation, and iron deficiency during this period suppressed subsequent terminal differentiation. This was associated with demethylation of both repressive histone marks and DNA in the genomic regions of adipocyte differentiation-associated genes, including Pparg, which encodes PPARγ, the master regulator of adipocyte differentiation. In addition, we identified several epigenetic demethylases to be responsible for iron-dependent adipocyte differentiation, with the histone demethylase jumonji domain-containing 1A and the DNA demethylase ten-eleven translocation 2 as the major enzymes. The interrelationship between repressive histone marks and DNA methylation was indicated by an integrated genome-wide association analysis, and was also supported by the findings that both histone and DNA demethylation were suppressed by either the inhibition of lysosomal ferritin flux or the knockdown of iron chaperone poly(rC)-binding protein 2. In summary, epigenetic regulations through iron-dependent control of epigenetic enzyme activities play an important role in the organized gene expression mechanisms of adipogenesis.
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Affiliation(s)
- Tomohiro Suzuki
- Laboratory of Epigenetics and Metabolism, Institute for Molecular and Cellular Regulation, Gunma University, Gunma371-8512, Japan
| | - Tetsuro Komatsu
- Laboratory of Epigenetics and Metabolism, Institute for Molecular and Cellular Regulation, Gunma University, Gunma371-8512, Japan
| | - Hiroshi Shibata
- Laboratory of Epigenetics and Metabolism, Institute for Molecular and Cellular Regulation, Gunma University, Gunma371-8512, Japan
| | - Akiko Tanioka
- Laboratory of Epigenetics and Metabolism, Institute for Molecular and Cellular Regulation, Gunma University, Gunma371-8512, Japan
| | - Diana Vargas
- Laboratory of Epigenetics and Metabolism, Institute for Molecular and Cellular Regulation, Gunma University, Gunma371-8512, Japan
| | - Reika Kawabata-Iwakawa
- Division of Integrated Oncology Research, Gunma University Initiative for Advanced Research, Gunma University, Gunma371-8511, Japan
| | - Fumihito Miura
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, Fukuoka 812-8582, Japan
| | - Shinnosuke Masuda
- Laboratory of Epigenetics and Metabolism, Institute for Molecular and Cellular Regulation, Gunma University, Gunma371-8512, Japan
| | - Mayuko Hayashi
- Laboratory of Epigenetics and Metabolism, Institute for Molecular and Cellular Regulation, Gunma University, Gunma371-8512, Japan
| | - Kyoko Tanimura-Inagaki
- Laboratory of Epigenetics and Metabolism, Institute for Molecular and Cellular Regulation, Gunma University, Gunma371-8512, Japan
- Department of Endocrinology, Metabolism and Nephrology, Graduate School of Medicine, Nippon Medical School, Tokyo 113-8602, Japan
| | - Sumiyo Morita
- Laboratory of Genome Science, Biosignal Genome Resource Center, Institute for Molecular and Cellular Regulation, Gunma University, Gunma371-8512, Japan
| | - Junki Kohmaru
- Institute for Molecular and Cellular Regulation Joint Usage/Research Support Center, Gunma University, Gunma371-8512, Japan
| | - Koji Adachi
- Kaihin Makuhari Laboratory, PerkinElmer Japan Co., Ltd., Chiba261-8501, Japan
| | - Masayuki Tobo
- Institute for Molecular and Cellular Regulation Joint Usage/Research Support Center, Gunma University, Gunma371-8512, Japan
| | - Hideru Obinata
- Education and Research Support Center, Gunma University Graduate School of Medicine, Gunma371-8511, Japan
| | - Tasuku Hirayama
- Laboratory of Pharmaceutical and Medicinal Chemistry, Gifu Pharmaceutical University, Gifu501-1196, Japan
| | - Hiroshi Kimura
- Cell Biology Center, Tokyo Institute of Technology, Kanagawa226-8503, Japan
| | - Juro Sakai
- Division of Metabolic Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo153-8904, Japan
- Division of Molecular Physiology and Metabolism, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan
| | - Hideko Nagasawa
- Laboratory of Pharmaceutical and Medicinal Chemistry, Gifu Pharmaceutical University, Gifu501-1196, Japan
| | - Hideyuki Itabashi
- Graduate School of Science and Technology, Gunma University, Gunma376-8515, Japan
| | - Izuho Hatada
- Laboratory of Genome Science, Biosignal Genome Resource Center, Institute for Molecular and Cellular Regulation, Gunma University, Gunma371-8512, Japan
- Viral Vector Core, Gunma University Initiative for Advanced Research, Gunma371-8511, Japan
| | - Takashi Ito
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, Fukuoka 812-8582, Japan
| | - Takeshi Inagaki
- Laboratory of Epigenetics and Metabolism, Institute for Molecular and Cellular Regulation, Gunma University, Gunma371-8512, Japan
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4
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MYPT1-PP1β phosphatase negatively regulates both chromatin landscape and co-activator recruitment for beige adipogenesis. Nat Commun 2022; 13:5715. [PMID: 36175407 PMCID: PMC9523048 DOI: 10.1038/s41467-022-33363-0] [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: 03/27/2022] [Accepted: 09/14/2022] [Indexed: 12/05/2022] Open
Abstract
Protein kinase A promotes beige adipogenesis downstream from β-adrenergic receptor signaling by phosphorylating proteins, including histone H3 lysine 9 (H3K9) demethylase JMJD1A. To ensure homeostasis, this process needs to be reversible however, this step is not well understood. We show that myosin phosphatase target subunit 1- protein phosphatase 1β (MYPT1-PP1β) phosphatase activity is inhibited via PKA-dependent phosphorylation, which increases phosphorylated JMJD1A and beige adipogenesis. Mechanistically, MYPT1-PP1β depletion results in JMJD1A-mediated H3K9 demethylation and activation of the Ucp1 enhancer/promoter regions. Interestingly, MYPT1-PP1β also dephosphorylates myosin light chain which regulates actomyosin tension-mediated activation of YAP/TAZ which directly stimulates Ucp1 gene expression. Pre-adipocyte specific Mypt1 deficiency increases cold tolerance with higher Ucp1 levels in subcutaneous white adipose tissues compared to control mice, confirming this regulatory mechanism in vivo. Thus, we have uncovered regulatory cross-talk involved in beige adipogenesis that coordinates epigenetic regulation with direct activation of the mechano-sensitive YAP/TAZ transcriptional co-activators. How β-AR signaling coordinates epigenetic and transcriptional pathways is unknown. Here the authors show that cold-induced β-AR signaling negatively regulates MYPT1-PP1β phosphatase activity to orchestrate both pathways for beige adipogenesis.
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5
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Suzuki T, Hayashi M, Komatsu T, Tanioka A, Nagasawa M, Tanimura-Inagaki K, Rahman MS, Masuda S, Yusa K, Sakai J, Shibata H, Inagaki T. Measurement of the nuclear concentration of α-ketoglutarate during adipocyte differentiation by using a fluorescence resonance energy transfer-based biosensor with nuclear localization signals. Endocr J 2021; 68:1429-1438. [PMID: 34261826 DOI: 10.1507/endocrj.ej21-0255] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
α-Ketoglutarate (α-KG) also known as 2-oxoglutarate (2-OG) is an intermediate metabolite in the tricarboxylic acid (TCA) cycle and is also produced by the deamination of glutamate. It is an indispensable cofactor for a series of 2-oxoglutarate-dependent oxygenases including epigenetic modifiers such as ten-eleven translocation DNA demethylases (TETs) and JmjC domain-containing histone demethylases (JMJDs). Since these epigenetic enzymes target genomic DNA and histone in the nucleus, the nuclear concentration of α-KG would affect the levels of transcription by modulating the activity of the epigenetic enzymes. Thus, it is of great interest to measure the nuclear concentration of α-KG to elucidate the regulatory mechanism of these enzymes. Here, we report a novel fluorescence resonance energy transfer (FRET)-based biosensor with multiple nuclear localization signals (NLSs) to measure the nuclear concentration of α-KG. The probe contains the α-KG-binding GAF domain of NifA protein from Azotobacter vinelandii fused with EYFP and ECFP. Treatment of 3T3-L1 preadipocytes expressing this probe with either dimethyl-2-oxoglutarate (dimethyl-2-OG), a cell-permeable 2-OG derivative, or citrate elicited time- and dose-dependent changes in the FRET ratio, proving that this probe functions as an α-KG sensor. Measurement of the nuclear α-KG levels in the 3T3-L1 cells stably expressing the probe during adipocyte differentiation revealed that the nuclear concentration of α-KG increased in the early stage of differentiation and remained high thereafter. Thus, this nuclear-localized α-KG probe is a powerful tool for real-time monitoring of α-KG concentrations with subcellular resolution in living cells and is useful for elucidating the regulatory mechanisms of epigenetic enzymes.
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Affiliation(s)
- Tomohiro Suzuki
- Laboratory of Epigenetics and Metabolism, Institute for Molecular and Cellular Regulation, Gunma University, Gunma 371-8512, Japan
| | - Mayuko Hayashi
- Laboratory of Epigenetics and Metabolism, Institute for Molecular and Cellular Regulation, Gunma University, Gunma 371-8512, Japan
| | - Tetsuro Komatsu
- Laboratory of Epigenetics and Metabolism, Institute for Molecular and Cellular Regulation, Gunma University, Gunma 371-8512, Japan
| | - Akiko Tanioka
- Laboratory of Epigenetics and Metabolism, Institute for Molecular and Cellular Regulation, Gunma University, Gunma 371-8512, Japan
| | - Masahiro Nagasawa
- Laboratory of Epigenetics and Metabolism, Institute for Molecular and Cellular Regulation, Gunma University, Gunma 371-8512, Japan
| | - Kyoko Tanimura-Inagaki
- Laboratory of Epigenetics and Metabolism, Institute for Molecular and Cellular Regulation, Gunma University, Gunma 371-8512, Japan
- Division of Diabetes, Endocrinology, and Metabolism, Department of Medicine, Nippon Medical School, Tokyo 113-8602, Japan
| | - Mohammad Sharifur Rahman
- Laboratory of Epigenetics and Metabolism, Institute for Molecular and Cellular Regulation, Gunma University, Gunma 371-8512, Japan
| | - Shinnosuke Masuda
- Laboratory of Epigenetics and Metabolism, Institute for Molecular and Cellular Regulation, Gunma University, Gunma 371-8512, Japan
| | - Kosuke Yusa
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan
| | - Juro Sakai
- Division of Metabolic Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo 153-8904, Japan
- Division of Molecular Physiology and Metabolism, Tohoku University Graduate School of Medicine, Sendai 980-8574, Japan
| | - Hiroshi Shibata
- Laboratory of Epigenetics and Metabolism, Institute for Molecular and Cellular Regulation, Gunma University, Gunma 371-8512, Japan
| | - Takeshi Inagaki
- Laboratory of Epigenetics and Metabolism, Institute for Molecular and Cellular Regulation, Gunma University, Gunma 371-8512, Japan
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6
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Wei Z, Luo L, Hu S, Tian R, Liu Z. KDM2B overexpression prevents myocardial ischemia‑reperfusion injury in rats through regulating inflammatory response via the TLR4/NF‑κB p65 axis. Exp Ther Med 2021; 23:154. [PMID: 35069835 PMCID: PMC8753960 DOI: 10.3892/etm.2021.11077] [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: 08/13/2021] [Accepted: 10/19/2021] [Indexed: 11/05/2022] Open
Abstract
Histone modifier lysine-specific demethylase 2B (KDM2B) has been previously reported to activate the inflammatory response by transcription initiation of the IL-6 gene. However, the effects of KDM2B on the inflammatory response during myocardial ischemia-reperfusion (I/R) injury and corresponding mechanisms remain poorly understood. The present study aimed to investigate the role and mechanism of KDM2B in myocardial I/R injury. Therefore, a myocardial I/R injury model was established in rats through coronary artery ligation. Adeno-associated virus-encoding KDM2B and small interfering RNA-KDM2B were designed to determine the effects of KDM2B on myocardial I/R injury using H&E staining and a TUNEL assay in the myocardial tissues. Reverse transcription-quantitative PCR and western blotting were performed to detect the mRNA and protein expression levels of KDM2B, toll-like receptor 4 (TLR4), NF-κB p65 and NOD-, LRR- and pyrin domain-containing protein 3 (NLRP3). ELISA was used to detect the levels of TNF-α, IL-6 and IL-1β in the peripheral blood samples. Pathological analysis demonstrated that the cells in the model group were disordered, with a large area of necrosis and neutrophil infiltration. Knocking down KDM2B expression significantly upregulated the mRNA and protein expression levels of TLR4, NLRP3, NF-κB p65 and the ratio of phosphorylated (p)-p65 to p65. KDM2B knockdown also significantly increased the levels of IL-1β, IL-6 and TNF-α in the peripheral blood, which aggravated myocardial injury and promoted the apoptosis of myocardial cells. However, overexpression of KDM2B downregulated the mRNA and protein expression levels of TLR4, NLRP3, NF-κB P65, the ratio of p-p65 to p65 whilst reducing the levels of IL-1β, IL-6 and TNF-α in the peripheral blood, which markedly improved myocardial injury and significantly inhibited the apoptosis of cells in myocardial tissue. In conclusion, the results indicated that overexpression of KDM2B may prevent myocardial I/R injury in rats by reducing the inflammatory response through regulation of the TLR4/NF-κB p65 axis.
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Affiliation(s)
- Zijie Wei
- Department of Cardiac Intensive Care, The First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi 341000, P.R. China
| | - Lihua Luo
- Department of Nephrology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi 341000, P.R. China
| | - Shuo Hu
- Department of Cardiac Surgery, The First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi 341000, P.R. China
| | - Rongcheng Tian
- Department of Emergency, The First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi 341000, P.R. China
| | - Ziyou Liu
- Department of Cardiac Surgery, The First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi 341000, P.R. China
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7
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Matsumura Y, Ito R, Yajima A, Yamaguchi R, Tanaka T, Kawamura T, Magoori K, Abe Y, Uchida A, Yoneshiro T, Hirakawa H, Zhang J, Arai M, Yang C, Yang G, Takahashi H, Fujihashi H, Nakaki R, Yamamoto S, Ota S, Tsutsumi S, Inoue SI, Kimura H, Wada Y, Kodama T, Inagaki T, Osborne TF, Aburatani H, Node K, Sakai J. Spatiotemporal dynamics of SETD5-containing NCoR-HDAC3 complex determines enhancer activation for adipogenesis. Nat Commun 2021; 12:7045. [PMID: 34857762 PMCID: PMC8639990 DOI: 10.1038/s41467-021-27321-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 11/09/2021] [Indexed: 01/03/2023] Open
Abstract
Enhancer activation is essential for cell-type specific gene expression during cellular differentiation, however, how enhancers transition from a hypoacetylated "primed" state to a hyperacetylated-active state is incompletely understood. Here, we show SET domain-containing 5 (SETD5) forms a complex with NCoR-HDAC3 co-repressor that prevents histone acetylation of enhancers for two master adipogenic regulatory genes Cebpa and Pparg early during adipogenesis. The loss of SETD5 from the complex is followed by enhancer hyperacetylation. SETD5 protein levels were transiently increased and rapidly degraded prior to enhancer activation providing a mechanism for the loss of SETD5 during the transition. We show that induction of the CDC20 co-activator of the ubiquitin ligase leads to APC/C mediated degradation of SETD5 during the transition and this operates as a molecular switch that facilitates adipogenesis.
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Affiliation(s)
- Yoshihiro Matsumura
- Division of Metabolic Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan.
| | - Ryo Ito
- grid.69566.3a0000 0001 2248 6943Division of Molecular Physiology and Metabolism, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Ayumu Yajima
- grid.26999.3d0000 0001 2151 536XDivision of Metabolic Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan ,grid.412339.e0000 0001 1172 4459Department of Cardiovascular Medicine, Saga University, Saga, Japan
| | - Rei Yamaguchi
- grid.69566.3a0000 0001 2248 6943Division of Molecular Physiology and Metabolism, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Toshiya Tanaka
- grid.26999.3d0000 0001 2151 536XDepartment of Nuclear Receptor Medicine, Laboratories for Systems Biology and Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Takeshi Kawamura
- grid.26999.3d0000 0001 2151 536XIsotope Science Center, The University of Tokyo, Tokyo, Japan
| | - Kenta Magoori
- grid.26999.3d0000 0001 2151 536XDivision of Metabolic Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Yohei Abe
- grid.26999.3d0000 0001 2151 536XDivision of Metabolic Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Aoi Uchida
- grid.26999.3d0000 0001 2151 536XDivision of Metabolic Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Takeshi Yoneshiro
- grid.26999.3d0000 0001 2151 536XDivision of Metabolic Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Hiroyuki Hirakawa
- grid.26999.3d0000 0001 2151 536XDivision of Metabolic Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan ,grid.265073.50000 0001 1014 9130Department of Physiology and Cell Biology, Tokyo Medical and Dental University (TMDU), Graduate School, Tokyo, Japan
| | - Ji Zhang
- grid.26999.3d0000 0001 2151 536XDivision of Metabolic Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan ,grid.69566.3a0000 0001 2248 6943Division of Molecular Physiology and Metabolism, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Makoto Arai
- grid.26999.3d0000 0001 2151 536XDivision of Metabolic Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan ,grid.69566.3a0000 0001 2248 6943Division of Molecular Physiology and Metabolism, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Chaoran Yang
- grid.69566.3a0000 0001 2248 6943Division of Molecular Physiology and Metabolism, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Ge Yang
- grid.69566.3a0000 0001 2248 6943Division of Molecular Physiology and Metabolism, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Hiroki Takahashi
- grid.69566.3a0000 0001 2248 6943Division of Molecular Physiology and Metabolism, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Hitomi Fujihashi
- grid.26999.3d0000 0001 2151 536XDivision of Metabolic Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Ryo Nakaki
- grid.26999.3d0000 0001 2151 536XGenome Science Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan ,Rhelixa Inc, Tokyo, Japan
| | - Shogo Yamamoto
- grid.26999.3d0000 0001 2151 536XGenome Science Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Satoshi Ota
- grid.26999.3d0000 0001 2151 536XGenome Science Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Shuichi Tsutsumi
- grid.26999.3d0000 0001 2151 536XGenome Science Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Shin-ichi Inoue
- grid.69566.3a0000 0001 2248 6943Division of Molecular Physiology and Metabolism, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Hiroshi Kimura
- grid.32197.3e0000 0001 2179 2105Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Youichiro Wada
- grid.26999.3d0000 0001 2151 536XIsotope Science Center, The University of Tokyo, Tokyo, Japan
| | - Tatsuhiko Kodama
- grid.26999.3d0000 0001 2151 536XDepartment of Nuclear Receptor Medicine, Laboratories for Systems Biology and Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Takeshi Inagaki
- grid.26999.3d0000 0001 2151 536XDivision of Metabolic Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan ,grid.256642.10000 0000 9269 4097Laboratory of Epigenetics and Metabolism, Institute for Molecular and Cellular Regulation, Gunma University, Gunma, Japan
| | - Timothy F. Osborne
- grid.21107.350000 0001 2171 9311Institute for Fundamental Biomedical Research, Johns Hopkins All Children’s Hospital, and Medicine in the Division of Endocrinology, Diabetes and Metabolism of the Johns Hopkins University School of Medicine, Petersburg, FL USA
| | - Hiroyuki Aburatani
- grid.26999.3d0000 0001 2151 536XGenome Science Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Koichi Node
- grid.412339.e0000 0001 1172 4459Department of Cardiovascular Medicine, Saga University, Saga, Japan
| | - Juro Sakai
- Division of Metabolic Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan. .,Division of Molecular Physiology and Metabolism, Tohoku University Graduate School of Medicine, Sendai, Japan.
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8
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Postnatal exercise protects offspring from high-fat diet-induced reductions in subcutaneous adipocyte beiging in C57Bl6/J mice. J Nutr Biochem 2021; 99:108853. [PMID: 34517093 PMCID: PMC9040048 DOI: 10.1016/j.jnutbio.2021.108853] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 06/11/2021] [Accepted: 07/29/2021] [Indexed: 12/05/2022]
Abstract
Maternal low-protein and postnatal high-fat (HF) diets program offspring obesity and type 2 diabetes mellitus (T2DM) risk by epigenetically reducing beige adipocytes (BAs) via increased G9a protein expression (Histone3 Lysine9 dimethyl transferase), an inhibitor of the BA marker fibroblast growth factor 21 (FGF21). Conversely, offspring exercise reduces fat mass and white adipocytes, but the mechanisms are not yet understood. This work investigated whether exercise reduces offspring obesity and T2DM risk caused by a maternal HF diet via regulation of G9a and FGF21 expression that would convert white to BA. Two-month-old female C57Bl/6J mice (F0) were fed a 16% (normal fat; NF) or a 45% HF diet for 3 months prior to breeding, and subsequent gestation and lactation. Male offspring (F1) were fed the same NF and HF diets and further divided into either sedentary (S) or voluntary wheel running (Ex) groups for an additional 3 months yielding eight groups: NF (maternal treatment condition)-NF-S (postweaning treatment conditions), NF-HF-S, NF-NF-Ex, NF-HF-Ex, HF-NF-S, HF-HF-S, HF-NF-Ex, and HF-HF-Ex. Subcutaneous adipose tissue was collected for protein and mRNA analysis of FGF21, peroxisome proliferator-activated receptor-gamma coactivator (PGC-1 alpha, inducer of FGF21), G9a, E4BP4 (G9a coactivator), and protein expression of H3K9 demethylases (KDM4C). Postnatal HF diet decreased FGF21 positive BA numbers regardless of maternal diets and postnatal exercise. Under sedentary conditions, postnatal HF diet increased protein expression of FGF21 transcription inhibitors G9a and E4BP4 compared to NF diet resulting in decreased FGF21 expression. In contrast, postnatal HF diet and exercise decreased G9a and E4BP4 protein expression while decreasing FGF21 expression compared to NF diet. Under exercised condition, postnatal HF diet-induced KDM4C protein expression while no changes in KDM4C protein expression were induced by postnatal HF diet under sedentary conditions. These findings suggest that the postnatal diet exerts a greater impact on offspring adiposity and BA numbers than maternal diets. These data also suggest that offspring exercise induces KDM4C to counter the increase in G9a that was triggered by maternal and postnatal HF diets. Future studies need to determine whether KDM4C induces methylation status of G9a to alter thermogenic function of BA.
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9
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Zhang J, Matsumura Y, Kano Y, Yoshida A, Kawamura T, Hirakawa H, Inagaki T, Tanaka T, Kimura H, Yanagi S, Fukami K, Doi T, Osborne TF, Kodama T, Aburatani H, Sakai J. Ubiquitination-dependent and -independent repression of target genes by SETDB1 reveal a context-dependent role for its methyltransferase activity during adipogenesis. Genes Cells 2021; 26:513-529. [PMID: 33971063 DOI: 10.1111/gtc.12868] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 04/28/2021] [Accepted: 04/29/2021] [Indexed: 12/12/2022]
Abstract
The lysine methyltransferase SETDB1, an enzyme responsible for methylation of histone H3 at lysine 9, plays a key role in H3K9 tri-methylation-dependent silencing of endogenous retroviruses and developmental genes. Recent studies have shown that ubiquitination of human SETDB1 complements its catalytic activity and the silencing of endogenous retroviruses in human embryonic stem cells. However, it is not known whether SETDB1 ubiquitination is essential for its other major role in epigenetic silencing of developmental gene programs. We previously showed that SETDB1 contributes to the formation of H3K4/H3K9me3 bivalent chromatin domains that keep adipogenic Cebpa and Pparg genes in a poised state for activation and restricts the differentiation potential of pre-adipocytes. Here, we show that ubiquitin-resistant K885A mutant of SETDB1 represses adipogenic genes and inhibits pre-adipocyte differentiation similar to wild-type SETDB1. We show this was due to a compensation mechanism for H3K9me3 chromatin modifications on the Cebpa locus by other H3K9 methyltransferases Suv39H1 and Suv39H2. In contrast, the K885A mutant did not repress other SETDB1 target genes such as Tril and Gas6 suggesting SETDB1 represses its target genes by two mechanisms; one that requires its ubiquitination and another that still requires SETDB1 but not its enzyme activity.
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Affiliation(s)
- Ji Zhang
- Division of Metabolic Medicine, Research Center for Advanced Science and Technology, University of Tokyo, Tokyo, Japan.,Division of Molecular Physiology and Metabolism, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Yoshihiro Matsumura
- Division of Metabolic Medicine, Research Center for Advanced Science and Technology, University of Tokyo, Tokyo, Japan
| | - Yuka Kano
- Division of Metabolic Medicine, Research Center for Advanced Science and Technology, University of Tokyo, Tokyo, Japan.,Laboratory of Molecular Biochemistry, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, Japan
| | - Ayano Yoshida
- Division of Metabolic Medicine, Research Center for Advanced Science and Technology, University of Tokyo, Tokyo, Japan.,Laboratory of Genome and Biosignal, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, Japan
| | - Takeshi Kawamura
- Laboratory of Systems Biology and Medicine, Research Center for Advanced Science and Technology, University of Tokyo, Tokyo, Japan.,Proteomics Laboratory, Isotope Science Center, University of Tokyo, Tokyo, Japan
| | - Hiroyuki Hirakawa
- Division of Metabolic Medicine, Research Center for Advanced Science and Technology, University of Tokyo, Tokyo, Japan.,Department of Physiology and Cell Biology, Tokyo Medical and Dental University (TMDU), Graduate School, Tokyo, Japan
| | - Takeshi Inagaki
- Division of Metabolic Medicine, Research Center for Advanced Science and Technology, University of Tokyo, Tokyo, Japan
| | - Toshiya Tanaka
- Laboratory of Systems Biology and Medicine, Research Center for Advanced Science and Technology, University of Tokyo, Tokyo, Japan
| | - Hiroshi Kimura
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Shigeru Yanagi
- Laboratory of Molecular Biochemistry, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, Japan
| | - Kiyoko Fukami
- Laboratory of Genome and Biosignal, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, Japan
| | - Takefumi Doi
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Japan
| | - Timothy F Osborne
- Institute for Fundamental Biomedical Research, Johns Hopkins All Children's Hospital, and Medicine in the Division of Endocrinology, Diabetes and Metabolism, Johns Hopkins University School of Medicine, St. Petersburg, FL, USA
| | - Tatsuhiko Kodama
- Laboratory of Systems Biology and Medicine, Research Center for Advanced Science and Technology, University of Tokyo, Tokyo, Japan
| | - Hiroyuki Aburatani
- Genome Science Division, Research Center for Advanced Science and Technology, University of Tokyo, Tokyo, Japan
| | - Juro Sakai
- Division of Metabolic Medicine, Research Center for Advanced Science and Technology, University of Tokyo, Tokyo, Japan.,Division of Molecular Physiology and Metabolism, Tohoku University Graduate School of Medicine, Sendai, Japan
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10
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KDM2B Overexpression Facilitates Lytic De Novo KSHV Infection by Inducing AP-1 Activity Through Interaction with the SCF E3 Ubiquitin Ligase Complex. J Virol 2021; 95:JVI.00331-21. [PMID: 33692209 PMCID: PMC8139688 DOI: 10.1128/jvi.00331-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
It is still largely unknown what host factors are involved in controlling the expression of the lytic viral gene RTA during primary infection, which determines if Kaposi's sarcoma-associated herpesvirus (KSHV) establishes latent or lytic infection. We have recently identified the histone demethylase KDM2B as a repressor of RTA expression during both de novo KSHV infection and latency based on an epigenetic factor siRNA screen. Here, we report that surprisingly, KDM2B overexpression can promote lytic de novo infection by using a mechanism that differs from what is needed for its repressor function. Our study revealed that while the DNA-binding and demethylase activities of KDM2B linked to its transcription repressive function are dispensable, its C-terminal F-box and LRR domains are required for the lytic infection-inducing function of KDM2B. We found that overexpressed KDM2B increases the half-life of the AP-1 subunit c-Jun protein and induces the AP-1 signaling pathway. This effect is dependent upon the binding of KDM2B to the SKP1-CUL1-F-box (SCF) E3 ubiquitin ligase complex via its F-box domain. Importantly, the inhibition of AP-1 reduces KDM2B-mediated lytic de novo KSHV infection. Overall, our findings indicate that KDM2B may induce the degradation of some host factors by using the SCF complex resulting in the enrichment of c-Jun. This leads to increased AP-1 transcriptional activity, which facilitates lytic gene expression following de novo infection interfering with the establishment of viral latency.SignificanceThe expression of epigenetic factors is often dysregulated in cancers or upon specific stress signals, which often results in a display of non-canonical functions of the epigenetic factors that are independent from their chromatin-modifying roles. We have previously demonstrated that KDM2B normally inhibits KSHV lytic cycle using its histone demethylase activity. Surprisingly, we found that KDM2B overexpression can promote lytic de novo infection, which does not require its histone demethylase or DNA-binding functions. Instead, KDM2B uses the SKP1-CUL1-F-box (SCF) E3 ubiquitin ligase complex to induce AP-1 transcriptional activity, which promotes lytic gene expression. This is the first report that demonstrates a functional link between SFCKDM2B and AP-1 in the regulation of KSHV lytic cycle.
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11
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SRF is a nonhistone methylation target of KDM2B and SET7 in the regulation of skeletal muscle differentiation. Exp Mol Med 2021; 53:250-263. [PMID: 33564100 PMCID: PMC8080764 DOI: 10.1038/s12276-021-00564-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 11/19/2020] [Accepted: 12/14/2020] [Indexed: 12/19/2022] Open
Abstract
The demethylation of histone lysine residues, one of the most important modifications in transcriptional regulation, is associated with various physiological states. KDM2B is a demethylase of histones H3K4, H3K36, and H3K79 and is associated with the repression of transcription. Here, we present a novel mechanism by which KDM2B demethylates serum response factor (SRF) K165 to negatively regulate muscle differentiation, which is counteracted by the histone methyltransferase SET7. We show that KDM2B inhibited skeletal muscle differentiation by inhibiting the transcription of SRF-dependent genes. Both KDM2B and SET7 regulated the balance of SRF K165 methylation. SRF K165 methylation was required for the transcriptional activation of SRF and for the promoter occupancy of SRF-dependent genes. SET7 inhibitors blocked muscle cell differentiation. Taken together, these data indicate that SRF is a nonhistone target of KDM2B and that the methylation balance of SRF as maintained by KDM2B and SET7 plays an important role in muscle cell differentiation. The balance between the opposing actions of two enzymes that, respectively, inhibit or activate the same gene-regulating protein plays a key role in the differentiation of skeletal muscle cells. A South Korean team led by Hyun Koon at Chonnam National University, Hwasun, and Sang-Beom Seo at Chung-Ang University, Seoul, studied the effect of the enzymes on cultured human muscle-forming cells. One enzyme, KDM2B, inhibits the differentiation of the cells by removing methyl groups (CH3) from a protein called serum response factor (SRF). A second enzyme, SET7, activates differentiation by adding methyl groups to SRF. The SRF protein controls the activity of many genes required for cell differentiation. This work reveals SRF as a previously unidentified target for KDM2B, and provides new insights into skeletal muscle development in health and disease.
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12
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Ahmed M, Min DS, Kim DR. Curated gene expression dataset of differentiating 3T3-L1 adipocytes under pharmacological and genetic perturbations. Adipocyte 2020; 9:600-608. [PMID: 33016192 PMCID: PMC7553567 DOI: 10.1080/21623945.2020.1829852] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The 3T3-L1 cell line is used as an adipocyte differentiation model for the analysis of genes specifically expressed during the differentiation course. This cell model has several applications in obesity and insulin resistance research. We built a data resource to model gene expression of differentiating and mature adipocytes in response to several drugs and gene manipulations. We surveyed the literature survey for microarray datasets of differentiating 3T3-L1 cell line sampled at one or more time points under genetic or pharmacological perturbations. Data and metadata were obtained from the gene expression omnibus. The metadata were manually curated using unified language across the studies. Probe intensities were mapped and collapsed to genes using a reproducible pipeline. Samples were classified into none, genetically or pharmacologically modified. In addition to the clean datasets, two aggregated sets were further homogenized for illustration purposes. The curated datasets are available as an R/Bioconductor experimental data package curatedAdipoArray. The package documents the source code of the data collection, curation and processing. Finally, we used a subset of the data to effectively remove batch effects and reproduce biological observations. Database URL https://bioconductor.org/packages/curatedAdipoArray
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Affiliation(s)
- Mahmoud Ahmed
- Department of Biochemistry and Convergence Medical Sciences and Institute of Health Sciences, Gyeongsang National University School of Medicine, Jinju, Republic of Korea
| | - Do Sik Min
- College of Pharmacy, Yonsei University, Incheon, Republic of Korea
| | - Deok Ryong Kim
- Department of Biochemistry and Convergence Medical Sciences and Institute of Health Sciences, Gyeongsang National University School of Medicine, Jinju, Republic of Korea
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13
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Geng Z, Gao Z. Mammalian PRC1 Complexes: Compositional Complexity and Diverse Molecular Mechanisms. Int J Mol Sci 2020; 21:E8594. [PMID: 33202645 PMCID: PMC7697839 DOI: 10.3390/ijms21228594] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 11/04/2020] [Accepted: 11/05/2020] [Indexed: 12/13/2022] Open
Abstract
Polycomb group (PcG) proteins function as vital epigenetic regulators in various biological processes, including pluripotency, development, and carcinogenesis. PcG proteins form multicomponent complexes, and two major types of protein complexes have been identified in mammals to date, Polycomb Repressive Complexes 1 and 2 (PRC1 and PRC2). The PRC1 complexes are composed in a hierarchical manner in which the catalytic core, RING1A/B, exclusively interacts with one of six Polycomb group RING finger (PCGF) proteins. This association with specific PCGF proteins allows for PRC1 to be subdivided into six distinct groups, each with their own unique modes of action arising from the distinct set of associated proteins. Historically, PRC1 was considered to be a transcription repressor that deposited monoubiquitylation of histone H2A at lysine 119 (H2AK119ub1) and compacted local chromatin. More recently, there is increasing evidence that demonstrates the transcription activation role of PRC1. Moreover, studies on the higher-order chromatin structure have revealed a new function for PRC1 in mediating long-range interactions. This provides a different perspective regarding both the transcription activation and repression characteristics of PRC1. This review summarizes new advancements regarding the composition of mammalian PRC1 and accompanying explanations of how diverse PRC1-associated proteins participate in distinct transcription regulation mechanisms.
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Affiliation(s)
- Zhuangzhuang Geng
- Departments of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, PA 17033, USA;
| | - Zhonghua Gao
- Departments of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, PA 17033, USA;
- Penn State Hershey Cancer Institute, Hershey, PA 17033, USA
- The Stem Cell and Regenerative Biology Program, Penn State College of Medicine, Hershey, PA 17033, USA
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14
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Arifuzzaman S, Khatun MR, Khatun R. Emerging of lysine demethylases (KDMs): From pathophysiological insights to novel therapeutic opportunities. Biomed Pharmacother 2020; 129:110392. [PMID: 32574968 DOI: 10.1016/j.biopha.2020.110392] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 06/06/2020] [Accepted: 06/09/2020] [Indexed: 12/12/2022] Open
Abstract
In recent years, there have been remarkable scientific advancements in the understanding of lysine demethylases (KDMs) because of their demethylation of diverse substrates, including nucleic acids and proteins. Novel structural architectures, physiological roles in the gene expression regulation, and ability to modify protein functions made KDMs the topic of interest in biomedical research. These structural diversities allow them to exert their function either alone or in complex with numerous other bio-macromolecules. Impressive number of studies have demonstrated that KDMs are localized dynamically across the cellular and tissue microenvironment. Their dysregulation is often associated with human diseases, such as cancer, immune disorders, neurological disorders, and developmental abnormalities. Advancements in the knowledge of the underlying biochemistry and disease associations have led to the development of a series of modulators and technical compounds. Given the distinct biophysical and biochemical properties of KDMs, in this review we have focused on advances related to the structure, function, disease association, and therapeutic targeting of KDMs highlighting improvements in both the specificity and efficacy of KDM modulation.
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Affiliation(s)
- Sarder Arifuzzaman
- Department of Pharmacy, Jahangirnagar University, Dhaka-1342, Bangladesh; Everest Pharmaceuticals Ltd., Dhaka-1208, Bangladesh.
| | - Mst Reshma Khatun
- Department of Pharmacy, Jahangirnagar University, Dhaka-1342, Bangladesh
| | - Rabeya Khatun
- Department of Pediatrics, TMSS Medical College and Rafatullah Community Hospital, Gokul, Bogura, 5800, Bangladesh
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15
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Vacík T, Lađinović D, Raška I. KDM2A/B lysine demethylases and their alternative isoforms in development and disease. Nucleus 2019; 9:431-441. [PMID: 30059280 PMCID: PMC7000146 DOI: 10.1080/19491034.2018.1498707] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Aberrant levels of histone modifications lead to chromatin malfunctioning and consequently to various developmental defects and human diseases. Therefore, the proteins bearing the ability to modify histones have been extensively studied and the molecular mechanisms of their action are now fairly well understood. However, little attention has been paid to naturally occurring alternative isoforms of chromatin modifying proteins and to their biological roles. In this review, we focus on mammalian KDM2A and KDM2B, the only two lysine demethylases whose genes have been described to produce also an alternative isoform lacking the N-terminal demethylase domain. These short KDM2A/B-SF isoforms arise through alternative promoter usage and seem to play important roles in development and disease. We hypothesise about the biological significance of these alternative isoforms, which might represent a more common evolutionarily conserved regulatory mechanism.
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Affiliation(s)
- Tomáš Vacík
- a Institute of Biology and Medical Genetics, First Faculty of Medicine , Charles University and General University Hospital in Prague , Praha 2 , Czech Republic
| | - Dijana Lađinović
- a Institute of Biology and Medical Genetics, First Faculty of Medicine , Charles University and General University Hospital in Prague , Praha 2 , Czech Republic
| | - Ivan Raška
- a Institute of Biology and Medical Genetics, First Faculty of Medicine , Charles University and General University Hospital in Prague , Praha 2 , Czech Republic
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16
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Nic-Can GI, Rodas-Junco BA, Carrillo-Cocom LM, Zepeda-Pedreguera A, Peñaloza-Cuevas R, Aguilar-Ayala FJ, Rojas-Herrera RA. Epigenetic Regulation of Adipogenic Differentiation by Histone Lysine Demethylation. Int J Mol Sci 2019; 20:E3918. [PMID: 31408999 PMCID: PMC6719019 DOI: 10.3390/ijms20163918] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 07/29/2019] [Indexed: 12/13/2022] Open
Abstract
Obesity is a rising public health problem that contributes to the development of several metabolic diseases and cancer. Adipocyte precursors outside of adipose depots that expand due to overweight and obesity may have a negative impact on human health. Determining how progenitor cells acquire a preadipocyte commitment and become mature adipocytes remains a significant challenge. Over the past several years, we have learned that the establishment of cellular identity is widely influenced by changes in histone marks, which in turn modulate chromatin structure. In this regard, histone lysine demethylases (KDMs) are now emerging as key players that shape chromatin through their ability to demethylate almost all major histone methylation sites. Recent research has shown that KDMs orchestrate the chromatin landscape, which mediates the activation of adipocyte-specific genes. In addition, KDMs have functions in addition to their enzymatic activity, which are beginning to be revealed, and their dysregulation seems to be related to the development of metabolic disorders. In this review, we highlight the biological functions of KDMs that contribute to the establishment of a permissive or repressive chromatin environment during the mesenchymal stem cell transition into adipocytes. Understanding how KDMs regulate adipogenesis might prompt the development of new strategies for fighting obesity-related diseases.
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Affiliation(s)
- Geovanny I Nic-Can
- CONACYT-Facultad de Ingeniería Química, Universidad Autónoma de Yucatán.; Periférico Norte Kilómetro 33.5, Tablaje Catastral 13615, Chuburná de Hidalgo Inn, Mérida 97203, Yucatán, Mexico.
- Laboratorio Translacional de Células Troncales-Facultad de Odontología, Universidad Autónoma de Yucatán, Calle 61-A X Av, Itzaes Costado Sur "Parque de la Paz", Col. Centro, Mérida 97000, Yucatán, Mexico.
| | - Beatriz A Rodas-Junco
- CONACYT-Facultad de Ingeniería Química, Universidad Autónoma de Yucatán.; Periférico Norte Kilómetro 33.5, Tablaje Catastral 13615, Chuburná de Hidalgo Inn, Mérida 97203, Yucatán, Mexico
- Laboratorio Translacional de Células Troncales-Facultad de Odontología, Universidad Autónoma de Yucatán, Calle 61-A X Av, Itzaes Costado Sur "Parque de la Paz", Col. Centro, Mérida 97000, Yucatán, Mexico
| | - Leydi M Carrillo-Cocom
- Facultad de Ingeniería Química, Universidad Autónoma de Yucatán.; Periférico Norte Kilómetro 33.5, Tablaje Catastral 13615, Chuburná de Hidalgo Inn, Mérida 97203, Yucatán, Mexico
| | - Alejandro Zepeda-Pedreguera
- Facultad de Ingeniería Química, Universidad Autónoma de Yucatán.; Periférico Norte Kilómetro 33.5, Tablaje Catastral 13615, Chuburná de Hidalgo Inn, Mérida 97203, Yucatán, Mexico
| | - Ricardo Peñaloza-Cuevas
- Laboratorio Translacional de Células Troncales-Facultad de Odontología, Universidad Autónoma de Yucatán, Calle 61-A X Av, Itzaes Costado Sur "Parque de la Paz", Col. Centro, Mérida 97000, Yucatán, Mexico
| | - Fernando J Aguilar-Ayala
- Laboratorio Translacional de Células Troncales-Facultad de Odontología, Universidad Autónoma de Yucatán, Calle 61-A X Av, Itzaes Costado Sur "Parque de la Paz", Col. Centro, Mérida 97000, Yucatán, Mexico
| | - Rafael A Rojas-Herrera
- Facultad de Ingeniería Química, Universidad Autónoma de Yucatán.; Periférico Norte Kilómetro 33.5, Tablaje Catastral 13615, Chuburná de Hidalgo Inn, Mérida 97203, Yucatán, Mexico
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17
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Tanimura K, Suzuki T, Vargas D, Shibata H, Inagaki T. Epigenetic regulation of beige adipocyte fate by histone methylation. Endocr J 2019; 66:115-125. [PMID: 30606913 DOI: 10.1507/endocrj.ej18-0442] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Adipose tissue harbors plasticity to adapt to environmental thermal changes. While brown adipocyte is a thermogenic cell which produces heat acutely in response to cold stimuli, beige (or brite) adipocyte is an inducible form of thermogenic adipocytes which emerges in the white adipose depots in response to chronic cold exposure. Such adaptability of adipocytes is regulated by epigenetic mechanisms. Among them, histone methylation is chemically stable and thus is an appropriate epigenetic mark for mediating cellular memory to induce and maintain the beige adipocyte characteristics. The enzymes that catalyze the methylation or demethylation of H3K27 and H3K9 regulate brown adipocyte biogenesis through their catalytic activity-dependent and -independent mechanisms. Resolving the bivalency of H3K4me3 and H3K27me3 as well as "opening" the chromatin structure by demethylation of H3K9 both mediate beige adipogenesis. In addition, it is recently reported that maintenance of beige adipocyte, beige-to-white transition, and cellular memory of prior cold exposure in beige adipocyte are also regulated by histone methylation. A further understanding of the epigenetic mechanism of beige adipocyte biogenesis would unravel the mechanism of the cellular memory of environmental stimuli and provide a novel therapeutics for the metabolic disorders such as obesity and diabetes that are influenced by environmental factors.
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Affiliation(s)
- Kyoko Tanimura
- Laboratory of Epigenetics and Metabolism, Institute for Molecular and Cellular Regulation, Gunma University, Gunma 371-8512, Japan
- Department of Diabetes, Endocrinology, and Metabolism, Nippon Medical School, Tokyo 113-8603, Japan
| | - Tomohiro Suzuki
- Laboratory of Epigenetics and Metabolism, Institute for Molecular and Cellular Regulation, Gunma University, Gunma 371-8512, Japan
| | - Diana Vargas
- Laboratory of Epigenetics and Metabolism, Institute for Molecular and Cellular Regulation, Gunma University, Gunma 371-8512, Japan
| | - Hiroshi Shibata
- Laboratory of Epigenetics and Metabolism, Institute for Molecular and Cellular Regulation, Gunma University, Gunma 371-8512, Japan
| | - Takeshi Inagaki
- Laboratory of Epigenetics and Metabolism, Institute for Molecular and Cellular Regulation, Gunma University, Gunma 371-8512, Japan
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Domizi P, Malizia F, Chazarreta-Cifre L, Diacovich L, Banchio C. KDM2B regulates choline kinase expression and neuronal differentiation of neuroblastoma cells. PLoS One 2019; 14:e0210207. [PMID: 30629659 PMCID: PMC6328129 DOI: 10.1371/journal.pone.0210207] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 12/18/2018] [Indexed: 12/30/2022] Open
Abstract
The process of neuronal differentiation is associated with neurite elongation and membrane biogenesis, and phosphatidylcholine (PtdCho) is the major membrane phospholipid in mammalian cells. During neuroblast differentiation, the transcription of two genes involved in PtdCho biosynthesis are stimulated: Chka gene for choline kinase (CK) alpha isoform and Pcyt1a gene for CTP:phosphocholine cytidylyltransferase (CCT) alpha isoform. Here we show that CKα is essential for neuronal differentiation. In addition, we demonstrated that KDM2B regulates CKα expression and, as a consequence, neuronal differentiation. This factor is up-regulated in the course of the neuroblasts proliferative and undifferentiated state and down-regulated during differentiation induced by retinoic acid (RA). During proliferation, KDM2B binds to the Box2 located in the Chka promoter repressing its transcription. Interestingly, KDM2B knockdown enhances the levels of CKα expression in neuroblast cells and induces neuronal differentiation even in the absence of RA. These results suggest that KDM2B is required for the appropriate regulation of CKα during neuronal differentiation and to the maintaining of the undifferentiated stage of neuroblast cells.
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Affiliation(s)
- Pablo Domizi
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET) Ocampo y Esmeralda, Predio CONICET and Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Florencia Malizia
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET) Ocampo y Esmeralda, Predio CONICET and Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Lorena Chazarreta-Cifre
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET) Ocampo y Esmeralda, Predio CONICET and Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Lautaro Diacovich
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET) Ocampo y Esmeralda, Predio CONICET and Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Claudia Banchio
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET) Ocampo y Esmeralda, Predio CONICET and Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
- * E-mail:
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19
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Yan M, Yang X, Wang H, Shao Q. The critical role of histone lysine demethylase KDM2B in cancer. Am J Transl Res 2018; 10:2222-2233. [PMID: 30210666 PMCID: PMC6129528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 07/05/2018] [Indexed: 06/08/2023]
Abstract
The discovery of histone demethylases has revealed the dynamic nature of the regulation of histone methylation. KDM2B is an important histone lysine demethylase that removes methyl from H3K36me2 and H3K4me3. It participates in many aspects of normal cellular processes such as cell senescence, cell differentiation and stem cell self-renewal. Recent studies also showed that KDM2B was overexpressed in various types of cancers. This review focuses primarily on the current knowledge of KDM2B and its function in cancer development.
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Affiliation(s)
- Meina Yan
- Department of Immunology, Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University Zhenjiang 212013, Jiangsu, China
| | - Xinxin Yang
- Department of Immunology, Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University Zhenjiang 212013, Jiangsu, China
| | - Hui Wang
- Department of Immunology, Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University Zhenjiang 212013, Jiangsu, China
| | - Qixiang Shao
- Department of Immunology, Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University Zhenjiang 212013, Jiangsu, China
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20
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Abstract
Conventional root canal therapies yield high success rates. The treatment outcomes are negatively affected by the presence of apical periodontitis (AP), which reflects active root canal infection and inflammatory responses. Also, cross-sectional studies revealed surprisingly high prevalence of AP in the general population, especially in those with prior endodontic treatments. Hence, AP is an ongoing disease entity in endodontics that needs further understanding of the pathogenesis and disease progression. The current Chapter will discuss the basic mechanisms of AP with emphasis on emerging role of epigenetic regulators in regulation of inflammatory mediators.
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21
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Rona G, Roberti D, Yin Y, Pagan JK, Homer H, Sassani E, Zeke A, Busino L, Rothenberg E, Pagano M. PARP1-dependent recruitment of the FBXL10-RNF68-RNF2 ubiquitin ligase to sites of DNA damage controls H2A.Z loading. eLife 2018; 7:e38771. [PMID: 29985131 PMCID: PMC6037479 DOI: 10.7554/elife.38771] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 06/21/2018] [Indexed: 12/05/2022] Open
Abstract
The mammalian FBXL10-RNF68-RNF2 ubiquitin ligase complex (FRRUC) mono-ubiquitylates H2A at Lys119 to repress transcription in unstressed cells. We found that the FRRUC is rapidly and transiently recruited to sites of DNA damage in a PARP1- and TIMELESS-dependent manner to promote mono-ubiquitylation of H2A at Lys119, a local decrease of H2A levels, and an increase of H2A.Z incorporation. Both the FRRUC and H2A.Z promote transcriptional repression, double strand break signaling, and homologous recombination repair (HRR). All these events require both the presence and activity of the FRRUC. Moreover, the FRRUC and its activity are required for the proper recruitment of BMI1-RNF2 and MEL18-RNF2, two other ubiquitin ligases that mono-ubiquitylate Lys119 in H2A upon genotoxic stress. Notably, whereas H2A.Z is not required for H2A mono-ubiquitylation, impairment of the latter results in the inhibition of H2A.Z incorporation. We propose that the recruitment of the FRRUC represents an early and critical regulatory step in HRR.
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Affiliation(s)
- Gergely Rona
- Department of Biochemistry and Molecular PharmacologyNew York University School of MedicineNew YorkUnited States
- Perlmutter Cancer CenterNew York University School of MedicineNew YorkUnited States
| | - Domenico Roberti
- Department of Biochemistry and Molecular PharmacologyNew York University School of MedicineNew YorkUnited States
- Perlmutter Cancer CenterNew York University School of MedicineNew YorkUnited States
| | - Yandong Yin
- Department of Biochemistry and Molecular PharmacologyNew York University School of MedicineNew YorkUnited States
- Perlmutter Cancer CenterNew York University School of MedicineNew YorkUnited States
| | - Julia K Pagan
- Department of Biochemistry and Molecular PharmacologyNew York University School of MedicineNew YorkUnited States
- Perlmutter Cancer CenterNew York University School of MedicineNew YorkUnited States
| | - Harrison Homer
- Department of Biochemistry and Molecular PharmacologyNew York University School of MedicineNew YorkUnited States
- Perlmutter Cancer CenterNew York University School of MedicineNew YorkUnited States
| | - Elizabeth Sassani
- Department of Biochemistry and Molecular PharmacologyNew York University School of MedicineNew YorkUnited States
- Perlmutter Cancer CenterNew York University School of MedicineNew YorkUnited States
| | - Andras Zeke
- Institute of Enzymology, Research Center for Natural SciencesHungarian Academy of SciencesBudapestHungary
| | - Luca Busino
- Department of Biochemistry and Molecular PharmacologyNew York University School of MedicineNew YorkUnited States
- Perlmutter Cancer CenterNew York University School of MedicineNew YorkUnited States
| | - Eli Rothenberg
- Department of Biochemistry and Molecular PharmacologyNew York University School of MedicineNew YorkUnited States
- Perlmutter Cancer CenterNew York University School of MedicineNew YorkUnited States
| | - Michele Pagano
- Department of Biochemistry and Molecular PharmacologyNew York University School of MedicineNew YorkUnited States
- Perlmutter Cancer CenterNew York University School of MedicineNew YorkUnited States
- Howard Hughes Medical Institute, New York University School of MedicineNew YorkUnited States
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Crujeiras AB, Pissios P, Moreno-Navarrete JM, Diaz-Lagares A, Sandoval J, Gomez A, Ricart W, Esteller M, Casanueva FF, Fernandez-Real JM. An Epigenetic Signature in Adipose Tissue Is Linked to Nicotinamide N-Methyltransferase Gene Expression. Mol Nutr Food Res 2018; 62:e1700933. [PMID: 29688621 DOI: 10.1002/mnfr.201700933] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 03/19/2018] [Indexed: 01/24/2023]
Abstract
SCOPE The enzyme nicotinamide N-methyltransferase (NNMT) is a major methyltransferase in adipose tissue. We hypothesized an epigenetic signature in association with NNMT gene expression in adipose tissue. METHODS AND RESULTS The global human methylome was analyzed in visceral adipose tissue (VAT) from morbidly obese patients using the Infinium Human Methylation 450 BeadChip array (discovery cohort: n = 11). The findings were confirmed in two additional independent cohorts (cohort 1: n = 60; BMI 20-60 kg m-2 and cohort 2: n = 40; BMI > 40 kg m-2 ) and validated after weight loss (using microarray data). Among the genes associated with the largest methylation fold change were genes related to metabolic processes, proliferation, inflammation, and extracellular matrix remodeling, such as COL23A1, PLEC1, FBXO21, STEAP3, RGS12, IGDCC3, FOXK2, and ORAI2. In fact, the results showed 577 differentially methylated CpG sites (DMCpGs) associated with the NNMT expression levels, with low methylation levels paralleling high NNMT expression. The expression of FBXO21 and FOXK2 was specifically modified after weight loss concomitantly with a decrease in NNMT expression and inflammation-related genes. Interestingly, the adipose tissue NNMT gene expression correlated with markers of adipose tissue inflammation. CONCLUSIONS The expression of NNMT in VAT is associated with a specific methylome signature involving genes linked to adipose tissue metabolic pathophysiology.
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Affiliation(s)
- Ana B Crujeiras
- Laboratory of Molecular and Cellular Endocrinology, Instituto de Investigación Sanitaria (IDIS), Complejo Hospitalario Universitario de Santiago (CHUS/SERGAS) and Santiago de Compostela University (USC), Santiago de Compostela 15706, Spain, CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Madrid, 28029, Spain
| | - Pavlos Pissios
- Division of Endocrinology, Diabetes, and Metabolism, Beth Israel Deaconess Medical Center, Boston, MA, 02215, USA
| | - Jose M Moreno-Navarrete
- Department of Diabetes, Endocrinology and Nutrition, Institut d'Investigació Biomèdica de Girona, Girona, 77190 Spain, CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Madrid, 28029, Spain
| | - Angel Diaz-Lagares
- Translational Medical Oncology (Oncomet), Instituto de Investigación Sanitaria (IDIS), Complejo Hospitalario Universitario de Santiago (CHUS/SERGAS) and CIBERonc, Santiago de Compostela, 15706, Spain
| | - Juan Sandoval
- Laboratory of Personalized Medicine, Epigenomics Unit, Medical Research Institute La Fe, Valencia, 46026, Spain
| | - Antonio Gomez
- Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet, Catalonia, 08908, Spain
| | - Wilfredo Ricart
- Department of Diabetes, Endocrinology and Nutrition, Institut d'Investigació Biomèdica de Girona, Girona, 77190 Spain, CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Madrid, 28029, Spain
| | - Manel Esteller
- Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet, Catalonia 08908, Spain, Institucio Catalana de Recerca i Estudis Avançats (ICREA), Passeig de Lluís Companys, 23, Barcelona, 08010, Spain
| | - Felipe F Casanueva
- Laboratory of Molecular and Cellular Endocrinology, Instituto de Investigación Sanitaria (IDIS), Complejo Hospitalario Universitario de Santiago (CHUS/SERGAS) and Santiago de Compostela University (USC), Santiago de Compostela 15706, Spain, CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Madrid, 28029, Spain
| | - Jose M Fernandez-Real
- Department of Diabetes, Endocrinology and Nutrition, Institut d'Investigació Biomèdica de Girona, Girona, 77190 Spain, CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Madrid, 28029, Spain
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23
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Histone demethylase JMJD1A coordinates acute and chronic adaptation to cold stress via thermogenic phospho-switch. Nat Commun 2018; 9:1566. [PMID: 29674659 PMCID: PMC5908789 DOI: 10.1038/s41467-018-03868-8] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 03/19/2018] [Indexed: 12/13/2022] Open
Abstract
In acute cold stress in mammals, JMJD1A, a histone H3 lysine 9 (H3K9) demethylase, upregulates thermogenic gene expressions through β-adrenergic signaling in brown adipose tissue (BAT). Aside BAT-driven thermogenesis, mammals have another mechanism to cope with long-term cold stress by inducing the browning of the subcutaneous white adipose tissue (scWAT). Here, we show that this occurs through a two-step process that requires both β-adrenergic-dependent phosphorylation of S265 and demethylation of H3K9me2 by JMJD1A. The histone demethylation-independent acute Ucp1 induction in BAT and demethylation-dependent chronic Ucp1 expression in beige scWAT provides complementary molecular mechanisms to ensure an ordered transition between acute and chronic adaptation to cold stress. JMJD1A mediates two major signaling pathways, namely, β-adrenergic receptor and peroxisome proliferator-activated receptor-γ (PPARγ) activation, via PRDM16-PPARγ-P-JMJD1A complex for beige adipogenesis. S265 phosphorylation of JMJD1A, and the following demethylation of H3K9me2 might prove to be a novel molecular target for the treatment of metabolic disorders, via promoting beige adipogenesis. JMJD1A is essential for thermogenic gene induction in brown adipose tissue. Here the authors show that white adipose tissue beige-ing requires both β-adrenergic-dependent phosphorylation of S265 and demethylation activity of JMJD1A while brown adipose tissue-driven thermogenesis requires β-adrenergic dependent phosphorylation of S265 but is independent of H3K9me2 demethylation.
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24
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Staberg M, Rasmussen RD, Michaelsen SR, Pedersen H, Jensen KE, Villingshøj M, Skjoth-Rasmussen J, Brennum J, Vitting-Seerup K, Poulsen HS, Hamerlik P. Targeting glioma stem-like cell survival and chemoresistance through inhibition of lysine-specific histone demethylase KDM2B. Mol Oncol 2018; 12:406-420. [PMID: 29360266 PMCID: PMC5830623 DOI: 10.1002/1878-0261.12174] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 12/18/2017] [Accepted: 01/03/2018] [Indexed: 12/30/2022] Open
Abstract
Glioblastoma (GBM) ranks among the most lethal cancers, with current therapies offering only palliation. Inter‐ and intrapatient heterogeneity is a hallmark of GBM, with epigenetically distinct cancer stem‐like cells (CSCs) at the apex. Targeting GSCs remains a challenging task because of their unique biology, resemblance to normal neural stem/progenitor cells, and resistance to standard cytotoxic therapy. Here, we find that the chromatin regulator, JmjC domain histone H3K36me2/me1 demethylase KDM2B, is highly expressed in glioblastoma surgical specimens compared to normal brain. Targeting KDM2B function genetically or pharmacologically impaired the survival of patient‐derived primary glioblastoma cells through the induction of DNA damage and apoptosis, sensitizing them to chemotherapy. KDM2B loss decreased the GSC pool, which was potentiated by coadministration of chemotherapy. Collectively, our results demonstrate KDM2B is crucial for glioblastoma maintenance, with inhibition causing loss of GSC survival, genomic stability, and chemoresistance.
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Affiliation(s)
- Mikkel Staberg
- Department of Radiation Biology, The Finsen Center, Copenhagen University Hospital, Denmark.,Brain Tumor Biology Group, Danish Cancer Society Research Center, Copenhagen, Denmark
| | | | - Signe Regner Michaelsen
- Department of Radiation Biology, The Finsen Center, Copenhagen University Hospital, Denmark.,Brain Tumor Biology Group, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Henriette Pedersen
- Brain Tumor Biology Group, Danish Cancer Society Research Center, Copenhagen, Denmark
| | | | - Mette Villingshøj
- Department of Radiation Biology, The Finsen Center, Copenhagen University Hospital, Denmark
| | | | - Jannick Brennum
- Department of Neurosurgery, Copenhagen University Hospital, Denmark
| | | | - Hans Skovgaard Poulsen
- Department of Radiation Biology, The Finsen Center, Copenhagen University Hospital, Denmark
| | - Petra Hamerlik
- Brain Tumor Biology Group, Danish Cancer Society Research Center, Copenhagen, Denmark
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25
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Kuang Y, Lu F, Guo J, Xu H, Wang Q, Xu C, Zeng L, Yi S. Histone demethylase KDM2B upregulates histone methyltransferase EZH2 expression and contributes to the progression of ovarian cancer in vitro and in vivo. Onco Targets Ther 2017; 10:3131-3144. [PMID: 28706445 PMCID: PMC5495092 DOI: 10.2147/ott.s134784] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Aberrant histone methylation contributes to the progression and development of many tumors. Histone methylation is a dynamic process regulated by both histone demethylase and histone methyltransferase, which ultimately alters the levels of gene transcription. However, the relationship between histone demethylase and histone methyltransferase, as well as their regulatory mechanisms in ovarian cancer development, is still unclear. Lysine-specific demethylase 2B (KDM2B) is a key demethylase of H3K36me3 and H3K4me3 that regulates gene expression and plays a role in tumorigenesis via epigenetic mechanisms. To determine the expression pattern of KDM2B in ovarian neoplasms, we analyzed the mRNA and protein levels of KDM2B and the histone methyltransferase enhancer of zester homolog 2 (EZH2) in normal, benign, borderline, and malignant ovarian tissue samples. We found that KDM2B expression was gradually increased in ovarian tumors, with the highest expression found in the malignant ovarian tissues, and the differences in KDM2B expression among the different International Federation of Gynecology and Obstetrics stages and pathological grades/types were statistically significant. Moreover, KDM2B expression was positively correlated with EZH2 expression in ovarian tissues. To determine the role of KDM2B in tumorigenesis in vitro and in vivo, we silenced KDM2B expression in ovarian cancer cells using the KDM2B short hairpin RNA expression lentivirus and established a nude mouse xenograft model. Downregulation of endogenous KDM2B decreased the expression of EZH2 and reduced the proliferation and migration of ovarian cancer cells. Loss of KDM2B suppressed ovarian tumor formation in vivo. Our results suggest that KDM2B plays an important role in the tumorigenesis of ovarian cancer, with a possible mechanism of increasing the expression of the oncogene EZH2; this indicates that certain histone methyltransferase may be positively regulated by certain histone demethylase in the epigenetic regulation of ovarian tumors. KDM2B may be a novel therapeutic target for the clinical treatment of ovarian cancer.
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Affiliation(s)
- Yan Kuang
- Department of Obstetrics and Gynecology, First Affiliated Hospital of Guangxi Medical University, Nanning
| | - Fangfang Lu
- Department of Obstetrics and Gynecology, First Affiliated Hospital of Guangxi Medical University, Nanning
| | - Jianfeng Guo
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Hong Xu
- Department of Obstetrics and Gynecology, First Affiliated Hospital of Guangxi Medical University, Nanning
| | - Qi Wang
- Department of Obstetrics and Gynecology, First Affiliated Hospital of Guangxi Medical University, Nanning
| | - Chaohuan Xu
- Department of Obstetrics and Gynecology, First Affiliated Hospital of Guangxi Medical University, Nanning
| | - Longjia Zeng
- Department of Obstetrics and Gynecology, First Affiliated Hospital of Guangxi Medical University, Nanning
| | - Suyi Yi
- Department of Obstetrics and Gynecology, First Affiliated Hospital of Guangxi Medical University, Nanning
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26
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Metabolism and chromatin dynamics in health and disease. Mol Aspects Med 2017; 54:1-15. [DOI: 10.1016/j.mam.2016.09.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Revised: 09/22/2016] [Accepted: 09/27/2016] [Indexed: 01/04/2023]
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27
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Lysine-Specific Histone Demethylases Contribute to Cellular Differentiation and Carcinogenesis. EPIGENOMES 2017. [DOI: 10.3390/epigenomes1010004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
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28
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Lewis ZA. Polycomb Group Systems in Fungi: New Models for Understanding Polycomb Repressive Complex 2. Trends Genet 2017; 33:220-231. [DOI: 10.1016/j.tig.2017.01.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 01/16/2017] [Accepted: 01/17/2017] [Indexed: 02/03/2023]
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29
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Yu P, Ji L, Lee KJ, Yu M, He C, Ambati S, McKinney EC, Jackson C, Baile CA, Schmitz RJ, Meagher RB. Subsets of Visceral Adipose Tissue Nuclei with Distinct Levels of 5-Hydroxymethylcytosine. PLoS One 2016; 11:e0154949. [PMID: 27171244 PMCID: PMC4865362 DOI: 10.1371/journal.pone.0154949] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 04/21/2016] [Indexed: 12/11/2022] Open
Abstract
The reprogramming of cellular memory in specific cell types, and in visceral adipocytes in particular, appears to be a fundamental aspect of obesity and its related negative health outcomes. We explored the hypothesis that adipose tissue contains epigenetically distinct subpopulations of adipocytes that are differentially potentiated to record cellular memories of their environment. Adipocytes are large, fragile, and technically difficult to efficiently isolate and fractionate. We developed fluorescence nuclear cytometry (FNC) and fluorescence activated nuclear sorting (FANS) of cellular nuclei from visceral adipose tissue (VAT) using the levels of the pan-adipocyte protein, peroxisome proliferator-activated receptor gamma-2 (PPARg2), to distinguish classes of PPARg2-Positive (PPARg2-Pos) adipocyte nuclei from PPARg2-Negative (PPARg2-Neg) leukocyte and endothelial cell nuclei. PPARg2-Pos nuclei were 10-fold enriched for most adipocyte marker transcripts relative to PPARg2-Neg nuclei. PPARg2-Pos nuclei showed 2- to 50-fold higher levels of transcripts encoding most of the chromatin-remodeling factors assayed, which regulate the methylation of histones and DNA cytosine (e.g., DNMT1, TET1, TET2, KDM4A, KMT2C, SETDB1, PAXIP1, ARID1A, JMJD6, CARM1, and PRMT5). PPARg2-Pos nuclei were large with decondensed chromatin. TAB-seq demonstrated 5-hydroxymethylcytosine (5hmC) levels were remarkably dynamic in gene bodies of various classes of VAT nuclei, dropping 3.8-fold from the highest quintile of expressed genes to the lowest. In short, VAT-derived adipocytes appear to be more actively remodeling their chromatin than non-adipocytes.
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Affiliation(s)
- Ping Yu
- Department of Genetics, University of Georgia, 120 East Green Street, Athens, GA, 30602, United States of America
| | - Lexiang Ji
- Institute of Bioinformatics, University of Georgia, 120 East Green Street, Athens, GA, 30602, United States of America
| | - Kevin J. Lee
- Department of Genetics, University of Georgia, 120 East Green Street, Athens, GA, 30602, United States of America
- GRU-UGA Medical Partnership, University of Georgia Health Sciences Campus, Prince Avenue, Athens, GA, 30602, United States of America
| | - Miao Yu
- Department of Chemistry, University of Chicago, 5735 S Ellis Ave, Chicago, IL, 60637 USA
| | - Chuan He
- Department of Chemistry, University of Chicago, 5735 S Ellis Ave, Chicago, IL, 60637 USA
| | - Suresh Ambati
- Department of Genetics, University of Georgia, 120 East Green Street, Athens, GA, 30602, United States of America
| | - Elizabeth C. McKinney
- Department of Genetics, University of Georgia, 120 East Green Street, Athens, GA, 30602, United States of America
| | - Crystal Jackson
- Abeome Corporation, Athens, GA, 111 Riverbend Road, 30602, United States of America
| | - Clifton A. Baile
- Department of Foods and Nutrition, University of Georgia, 305 Sanford Dr, Athens, GA, 30602, United States of America
| | - Robert J. Schmitz
- Department of Genetics, University of Georgia, 120 East Green Street, Athens, GA, 30602, United States of America
| | - Richard B. Meagher
- Department of Genetics, University of Georgia, 120 East Green Street, Athens, GA, 30602, United States of America
- * E-mail:
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30
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Matsumura Y, Nakaki R, Inagaki T, Yoshida A, Kano Y, Kimura H, Tanaka T, Tsutsumi S, Nakao M, Doi T, Fukami K, Osborne TF, Kodama T, Aburatani H, Sakai J. H3K4/H3K9me3 Bivalent Chromatin Domains Targeted by Lineage-Specific DNA Methylation Pauses Adipocyte Differentiation. Mol Cell 2016; 60:584-96. [PMID: 26590716 DOI: 10.1016/j.molcel.2015.10.025] [Citation(s) in RCA: 152] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Revised: 08/11/2015] [Accepted: 10/12/2015] [Indexed: 12/29/2022]
Abstract
Bivalent H3K4me3 and H3K27me3 chromatin domains in embryonic stem cells keep active developmental regulatory genes expressed at very low levels and poised for activation. Here, we show an alternative and previously unknown bivalent modified histone signature in lineage-committed mesenchymal stem cells and preadipocytes that pairs H3K4me3 with H3K9me3 to maintain adipogenic master regulatory genes (Cebpa and Pparg) expressed at low levels yet poised for activation when differentiation is required. We show lineage-specific gene-body DNA methylation recruits H3K9 methyltransferase SETDB1, which methylates H3K9 immediately downstream of transcription start sites marked with H3K4me3 to establish the bivalent domain. At the Cebpa locus, this prevents transcription factor C/EBPβ binding, histone acetylation, and further H3K4me3 deposition and is associated with pausing of RNA polymerase II, which limits Cebpa gene expression and adipogenesis.
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Affiliation(s)
- Yoshihiro Matsumura
- Division of Metabolic Medicine, The University of Tokyo, 4-6-1, Komaba, Meguro-ku, Tokyo 153-8904, Japan; The Translational Systems Biology and Medicine Initiative (TSBMI), Center for Disease Biology and Integrative Medicine, Faculty of Medicine, The University of Tokyo, Tokyo 113-8655, Japan.
| | - Ryo Nakaki
- Genome Science Division, The University of Tokyo, 4-6-1, Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | - Takeshi Inagaki
- Division of Metabolic Medicine, The University of Tokyo, 4-6-1, Komaba, Meguro-ku, Tokyo 153-8904, Japan; The Translational Systems Biology and Medicine Initiative (TSBMI), Center for Disease Biology and Integrative Medicine, Faculty of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Ayano Yoshida
- Division of Metabolic Medicine, The University of Tokyo, 4-6-1, Komaba, Meguro-ku, Tokyo 153-8904, Japan; Laboratory of Genome and Biosignals, Tokyo University of Pharmacy and Life Science, Tokyo 192-0392, Japan
| | - Yuka Kano
- Division of Metabolic Medicine, The University of Tokyo, 4-6-1, Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | - Hiroshi Kimura
- Department of Biological Sciences, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Toshiya Tanaka
- Division of Metabolic Medicine, The University of Tokyo, 4-6-1, Komaba, Meguro-ku, Tokyo 153-8904, Japan; Laboratory for Systems Biology and Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1, Komaba, Meguro-ku, Tokyo 153-8904, Japan; The Translational Systems Biology and Medicine Initiative (TSBMI), Center for Disease Biology and Integrative Medicine, Faculty of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Shuichi Tsutsumi
- Genome Science Division, The University of Tokyo, 4-6-1, Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | - Mitsuyoshi Nakao
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto 860-0811, Japan
| | - Takefumi Doi
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka 565-0871, Japan
| | - Kiyoko Fukami
- Laboratory of Genome and Biosignals, Tokyo University of Pharmacy and Life Science, Tokyo 192-0392, Japan
| | - Timothy F Osborne
- Metabolic Disease Program, Sanford-Burnham Medical Research Institute, Orlando, FL 32827, USA
| | - Tatsuhiko Kodama
- Laboratory for Systems Biology and Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1, Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | - Hiroyuki Aburatani
- Genome Science Division, The University of Tokyo, 4-6-1, Komaba, Meguro-ku, Tokyo 153-8904, Japan; The Translational Systems Biology and Medicine Initiative (TSBMI), Center for Disease Biology and Integrative Medicine, Faculty of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Juro Sakai
- Division of Metabolic Medicine, The University of Tokyo, 4-6-1, Komaba, Meguro-ku, Tokyo 153-8904, Japan; The Translational Systems Biology and Medicine Initiative (TSBMI), Center for Disease Biology and Integrative Medicine, Faculty of Medicine, The University of Tokyo, Tokyo 113-8655, Japan.
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