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Minisini M, Cricchi E, Brancolini C. Acetylation and Phosphorylation in the Regulation of Hypoxia-Inducible Factor Activities: Additional Options to Modulate Adaptations to Changes in Oxygen Levels. Life (Basel) 2023; 14:20. [PMID: 38276269 PMCID: PMC10821055 DOI: 10.3390/life14010020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 12/13/2023] [Accepted: 12/20/2023] [Indexed: 01/27/2024] Open
Abstract
O2 is essential for the life of eukaryotic cells. The ability to sense oxygen availability and initiate a response to adapt the cell to changes in O2 levels is a fundamental achievement of evolution. The key switch for adaptation consists of the transcription factors HIF1A, HIF2A and HIF3A. Their levels are tightly controlled by O2 through the involvement of the oxygen-dependent prolyl hydroxylase domain-containing enzymes (PHDs/EGNLs), the von Hippel-Lindau tumour suppressor protein (pVHL) and the ubiquitin-proteasome system. Furthermore, HIF1A and HIF2A are also under the control of additional post-translational modifications (PTMs) that positively or negatively regulate the activities of these transcription factors. This review focuses mainly on two PTMs of HIF1A and HIF2A: phosphorylation and acetylation.
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Affiliation(s)
| | | | - Claudio Brancolini
- Lab of Epigenomics, Department of Medicine, Università degli Studi di Udine, 33100 Udine, Italy; (M.M.); (E.C.)
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2
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Yuan J, Mo Y, Zhang Y, Zhang Y, Zhang Q. Nickel nanoparticles induce epithelial-mesenchymal transition in human bronchial epithelial cells via the HIF-1α/HDAC3 pathway. Nanotoxicology 2022; 16:695-712. [PMID: 36345150 PMCID: PMC9892310 DOI: 10.1080/17435390.2022.2142169] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 10/26/2022] [Indexed: 11/11/2022]
Abstract
We and others have previously demonstrated that exposure to nickel nanoparticles (Nano-Ni) caused fibrogenic and carcinogenic effects; however, the underlying mechanisms are still not fully understood. This study aimed to investigate the effects of Nano-Ni on epithelial-mesenchymal transition (EMT) in human bronchial epithelial cells (BEAS-2B) and its underlying mechanisms since EMT is involved in both cancer pathogenesis and tissue fibrosis. Our results showed that exposure to Nano-Ni, compared to the control Nano-TiO2, caused a remarkable decrease in the expression of E-cadherin and an increase in the expression of vimentin and α-SMA, indicating an inducible role of Nano-Ni in EMT development in human bronchial epithelial cells. HIF-1α nuclear accumulation, HDAC3 upregulation, and decreased histone acetylation were also observed in the cells exposed to Nano-Ni, but not in those exposed to Nano-TiO2. Pretreatment of the cells with a specific HIF-1α inhibitor, CAY10585, or HIF-1α-specific siRNA transfection prior to Nano-Ni exposure resulted in the restoration of E-cadherin and abolished Nano-Ni-induced upregulation of vimentin and α-SMA, suggesting a crucial role of HIF-1α in Nano-Ni-induced EMT development. CAY10585 pretreatment also attenuated the HDAC3 upregulation and increased histone acetylation. Inhibition of HDAC3 with specific siRNA significantly restrained Nano-Ni-induced reduction in histone acetylation and restored EMT-related protein expression to near control levels. In summary, our findings suggest that exposure to Nano-Ni promotes the development of EMT in human bronchial epithelial cells by decreasing histone acetylation through HIF-1α-mediated HDAC3 upregulation. Our findings may provide information for further understanding of the molecular mechanisms of Nano-Ni-induced fibrosis and carcinogenesis.
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Affiliation(s)
| | | | - Yuanbao Zhang
- Department of Epidemiology and Population Health, School of Public Health and Information Sciences, University of Louisville, 485 E. Gray Street, Louisville, KY 40209, USA
| | - Yue Zhang
- Department of Epidemiology and Population Health, School of Public Health and Information Sciences, University of Louisville, 485 E. Gray Street, Louisville, KY 40209, USA
| | - Qunwei Zhang
- Department of Epidemiology and Population Health, School of Public Health and Information Sciences, University of Louisville, 485 E. Gray Street, Louisville, KY 40209, USA
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3
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Kim J, Lee H, Yi SJ, Kim K. Gene regulation by histone-modifying enzymes under hypoxic conditions: a focus on histone methylation and acetylation. Exp Mol Med 2022; 54:878-889. [PMID: 35869366 PMCID: PMC9355978 DOI: 10.1038/s12276-022-00812-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 04/30/2022] [Accepted: 05/10/2022] [Indexed: 12/12/2022] Open
Abstract
Oxygen, which is necessary for sustaining energy metabolism, is consumed in many biochemical reactions in eukaryotes. When the oxygen supply is insufficient for maintaining multiple homeostatic states at the cellular level, cells are subjected to hypoxic stress. Hypoxia induces adaptive cellular responses mainly through hypoxia-inducible factors (HIFs), which are stabilized and modulate the transcription of various hypoxia-related genes. In addition, many epigenetic regulators, such as DNA methylation, histone modification, histone variants, and adenosine triphosphate-dependent chromatin remodeling factors, play key roles in gene expression. In particular, hypoxic stress influences the activity and gene expression of histone-modifying enzymes, which controls the posttranslational modification of HIFs and histones. This review covers how histone methylation and histone acetylation enzymes modify histone and nonhistone proteins under hypoxic conditions and surveys the impact of epigenetic modifications on gene expression. In addition, future directions in this area are discussed. New sequencing technologies are revealing how cells respond to hypoxia, insufficient oxygen, by managing gene activation. In multicellular organisms, gene activation is managed by how tightly a section of DNA is wound around proteins called histones; genes in tightly packed regions are inaccessible and inactive, whereas those in looser regions can be activated. Kyunghwan Kim, Sun-Ju Yi, and co-workers at Chungbuk National University in South Korea have reviewed recent data on how cells regulate gene activity under hypoxic conditions. Advances in sequencing technology have allowed genome-wide studies of how hypoxia affects DNA structure and gene activation, revealing that gene-specific modifications may be more important than genome-wide modifications. Hypoxia is implicated in several diseases, such as cancer and chronic metabolic diseases, and a better understanding of how it affects gene activation may help identify new treatments for hypoxia-related diseases.
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Li J, Shi J, Pan Y, Zhao Y, Yan F, Li H, Lei L. Transcription modulation by CDK9 regulates inflammatory genes and RIPK3-MLKL-mediated necroptosis in periodontitis progression. Sci Rep 2019; 9:17369. [PMID: 31758083 PMCID: PMC6874675 DOI: 10.1038/s41598-019-53910-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 11/06/2019] [Indexed: 02/07/2023] Open
Abstract
Cyclin-dependent kinase 9 (CDK9), one crucial molecule in promoting the transition from transcription pausing to elongation, is a critical modulator of cell survival and death. However, the pathological function of CDK9 in bacterial inflammatory diseases has never been explored. CDK9 inhibition or knock-down attenuated Porphyromonas gingivalis-triggered inflammatory gene expression. Gene-expression microarray analysis of monocytes revealed that knock-down of CDK9 not only affected inflammatory responses, but also impacted cell death network, especially the receptor-interacting protein kinase 3 (RIPK3)-mixed lineage kinase domain-like (MLKL)-mediated necroptosis after P. gingivalis infection. Inhibition of CDK9 significantly decreased necroptosis with downregulation of both MLKL and phosphorylated MLKL. By regulating caspase-8 and cellular FLICE inhibitory protein (cFLIP), key molecules in regulating cell survival and death, CDK9 affected not only the classic RIPK1-RIPK3-mediated necroptosis, but also the alternate TIR-domain-containing adapter-inducing interferon-β-RIPK3-mediated necroptosis. CDK9 inhibition dampened pro-inflammatory gene production in the acute infection process in the subcutaneous chamber model in vivo. Moreover, CDK9 inhibition contributed to the decreased periodontal bone loss and inflammatory response induced by P. gingivalis in the periodontal micro-environment. In conclusion, by modulating the RIPK3-MLKL-mediated necroptosis, CDK9 inhibition provided a novel mechanism to impact the progress of bacterial infection in the periodontal milieu.
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Affiliation(s)
- Jiao Li
- Department of Orthodontics, Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, China
- Central Laboratory of Stomatology, Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, China
| | - Jiahong Shi
- Central Laboratory of Stomatology, Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, China
- Department of Periodontics, Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, China
| | - Yue Pan
- Central Laboratory of Stomatology, Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, China
| | - Yunhe Zhao
- Central Laboratory of Stomatology, Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, China
| | - Fuhua Yan
- Central Laboratory of Stomatology, Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, China
- Department of Periodontics, Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, China
| | - Houxuan Li
- Central Laboratory of Stomatology, Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, China.
- Department of Periodontics, Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, China.
| | - Lang Lei
- Department of Orthodontics, Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, China.
- Central Laboratory of Stomatology, Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, China.
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5
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Increase in HDAC9 suppresses myoblast differentiation via epigenetic regulation of autophagy in hypoxia. Cell Death Dis 2019; 10:552. [PMID: 31320610 PMCID: PMC6639330 DOI: 10.1038/s41419-019-1763-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 06/11/2019] [Accepted: 06/19/2019] [Indexed: 02/08/2023]
Abstract
Extremely reduced oxygen (O2) levels are detrimental to myogenic differentiation and multinucleated myotube formation, and chronic exposure to high-altitude hypoxia has been reported to be an important factor in skeletal muscle atrophy. However, how chronic hypoxia causes muscle dysfunction remains unknown. In the present study, we found that severe hypoxia (1% O2) significantly inhibited the function of C2C12 cells (from a myoblast cell line). Importantly, the impairment was continuously manifested even during culture under normoxic conditions for several passages. Mechanistically, we revealed that histone deacetylases 9 (HDAC9), a member of the histone deacetylase family, was significantly increased in C2C12 cells under hypoxic conditions, thereby inhibiting intracellular autophagy levels by directly binding to the promoter regions of Atg7, Beclin1, and LC3. This phenomenon resulted in the sequential dephosphorylation of GSK3β and inactivation of the canonical Wnt pathway, impairing the function of the C2C12 cells. Taken together, our results suggest that hypoxia-induced myoblast dysfunction is due to aberrant epigenetic regulation of autophagy, and our experimental evidence reveals the possible molecular pathogenesis responsible for some muscle diseases caused by chronic hypoxia and suggests a potential therapeutic option.
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Epigenetics: A Potential Mechanism Involved in the Pathogenesis of Various Adverse Consequences of Obstructive Sleep Apnea. Int J Mol Sci 2019; 20:ijms20122937. [PMID: 31208080 PMCID: PMC6627863 DOI: 10.3390/ijms20122937] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Revised: 06/09/2019] [Accepted: 06/13/2019] [Indexed: 12/14/2022] Open
Abstract
Epigenetics is defined as the heritable phenotypic changes which do not involve alterations in the DNA sequence, including histone modifications, non-coding RNAs, and DNA methylation. Recently, much attention has been paid to the role of hypoxia-mediated epigenetic regulation in cancer, pulmonary hypertension, adaptation to high altitude, and cardiorenal disease. In contrast to sustained hypoxia, chronic intermittent hypoxia with re-oxygenation (IHR) plays a major role in the pathogenesis of various adverse consequences of obstructive sleep apnea (OSA), resembling ischemia re-perfusion injury. Nevertheless, the role of epigenetics in the pathogenesis of OSA is currently underexplored. This review proposes that epigenetic processes are involved in the development of various adverse consequences of OSA by influencing adaptive potential and phenotypic variability under conditions of chronic IHR. Improved understanding of the interaction between genetic and environmental factors through epigenetic regulations holds great value to give deeper insight into the mechanisms underlying IHR-related low-grade inflammation, oxidative stress, and sympathetic hyperactivity, and clarify their implications for biomedical research.
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Lorén V, Garcia-Jaraquemada A, Naves JE, Carmona X, Mañosa M, Aransay AM, Lavin JL, Sánchez I, Cabré E, Manyé J, Domènech E. ANP32E, a Protein Involved in Steroid-Refractoriness in Ulcerative Colitis, Identified by a Systems Biology Approach. J Crohns Colitis 2019; 13:351-361. [PMID: 30329026 DOI: 10.1093/ecco-jcc/jjy171] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
BACKGROUND AND AIMS Steroid-refractoriness is a common and unpredictable phenomenon in ulcerative colitis [UC], but there are no conclusive studies on the molecular functions involved. We aimed to assess the mechanism of action related to steroid failure by integrating transcriptomic data from UC patients, and updated molecular data on UC and glucocorticoids. METHODS MicroRNA [miRNA] and mRNA expression were evaluated by sequencing and microarrays, respectively, from rectal biopsies of patients with moderately-to-severe active UC, obtained before and on the third day of steroid treatment. The differential results were integrated into the mathematical models generated by a systems biology approach. RESULTS This computational approach identified 18 proteins that stand out either by being associated with the mechanism of action or by providing a means to classify the patients according to steroid response. Their biological functions have been linked to inflammation, glucocorticoid-induced transcription and angiogenesis. All the selected proteins except ANP32E [a chaperone which has been linked to the exchange of H2A.z histone and promotes glucocorticoid receptor-induced transcription] had previously been related to UC and/or glucocorticoid-induced biological actions. Western blot and immunofluorescence assays confirmed the implication of this chaperone in steroid failure in patients with active UC. CONCLUSIONS A systems biology approach allowed us to identify a comprehensive mechanism of action of steroid-refractoriness, highlighting the key role of steroid-induced transcription and the potential implication of ANP32E in this phenomenon.
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Affiliation(s)
- V Lorén
- IBD Research Group, Germans Trias i Pujol Research Institute (IGTP), Badalona, Catalonia, Spain.,Centro de Investigación Biomédica en Red (CIBER), Madrid, Spain
| | - A Garcia-Jaraquemada
- IBD Research Group, Germans Trias i Pujol Research Institute (IGTP), Badalona, Catalonia, Spain
| | - J E Naves
- IBD Research Group, Germans Trias i Pujol Research Institute (IGTP), Badalona, Catalonia, Spain
| | - X Carmona
- IBD Research Group, Germans Trias i Pujol Research Institute (IGTP), Badalona, Catalonia, Spain
| | - M Mañosa
- IBD Research Group, Germans Trias i Pujol Research Institute (IGTP), Badalona, Catalonia, Spain.,Centro de Investigación Biomédica en Red (CIBER), Madrid, Spain.,Gastroenterology Department, Germans Trias i Pujol University Hospital, Badalona, Catalonia, Spain
| | - A M Aransay
- Centro de Investigación Biomédica en Red (CIBER), Madrid, Spain.,Genome Analysis Platform, CIC bioGUNE, Derio, Bizkaia, Spain
| | - J L Lavin
- Genome Analysis Platform, CIC bioGUNE, Derio, Bizkaia, Spain
| | - I Sánchez
- Functional Biology and Experimental Therapeutics Laboratory, Functional and Translational Neurogenetics Unit, Department of Neurosciences, Germans Trias i Pujol Research Institute, Badalona, Catalonia, Spain
| | - E Cabré
- IBD Research Group, Germans Trias i Pujol Research Institute (IGTP), Badalona, Catalonia, Spain.,Centro de Investigación Biomédica en Red (CIBER), Madrid, Spain.,Gastroenterology Department, Germans Trias i Pujol University Hospital, Badalona, Catalonia, Spain
| | - J Manyé
- IBD Research Group, Germans Trias i Pujol Research Institute (IGTP), Badalona, Catalonia, Spain.,Centro de Investigación Biomédica en Red (CIBER), Madrid, Spain
| | - E Domènech
- IBD Research Group, Germans Trias i Pujol Research Institute (IGTP), Badalona, Catalonia, Spain.,Centro de Investigación Biomédica en Red (CIBER), Madrid, Spain.,Gastroenterology Department, Germans Trias i Pujol University Hospital, Badalona, Catalonia, Spain
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Gatla HR, Muniraj N, Thevkar P, Yavvari S, Sukhavasi S, Makena MR. Regulation of Chemokines and Cytokines by Histone Deacetylases and an Update on Histone Decetylase Inhibitors in Human Diseases. Int J Mol Sci 2019; 20:E1110. [PMID: 30841513 PMCID: PMC6429312 DOI: 10.3390/ijms20051110] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 02/26/2019] [Accepted: 02/28/2019] [Indexed: 12/12/2022] Open
Abstract
Histone acetyltransferases (HATs) and histone deacetylases (HDACs) counteract with each other to regulate gene expression by altering chromatin structure. Aberrant HDAC activity was reported in many human diseases including wide range of cancers, viral infections, cardiovascular complications, auto-immune diseases and kidney diseases. HDAC inhibitors are small molecules designed to block the malignant activity of HDACs. Chemokines and cytokines control inflammation, immunological and other key biological processes and are shown to be involved in various malignancies. Various HDACs and HDAC inhibitors were reported to regulate chemokines and cytokines. Even though HDAC inhibitors have remarkable anti-tumor activity in hematological cancers, they are not effective in treating many diseases and many patients relapse after treatment. However, the role of HDACs and cytokines in regulating these diseases still remain unclear. Therefore, understanding exact mechanisms and effector functions of HDACs are urgently needed to selectively inhibit them and to establish better a platform to combat various malignancies. In this review, we address regulation of chemokines and cytokines by HDACs and HDAC inhibitors and update on HDAC inhibitors in human diseases.
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Affiliation(s)
- Himavanth Reddy Gatla
- Department of Pediatric Oncology, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA.
| | - Nethaji Muniraj
- Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA.
| | - Prashanth Thevkar
- Department of Microbiology, New York University, New York, NY 10016, USA.
| | - Siddhartha Yavvari
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA.
| | - Sahithi Sukhavasi
- Center for Distance Learning, GITAM University, Visakhapatnam, AP 530045, India.
| | - Monish Ram Makena
- Department of Physiology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA.
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Batie M, Del Peso L, Rocha S. Hypoxia and Chromatin: A Focus on Transcriptional Repression Mechanisms. Biomedicines 2018; 6:biomedicines6020047. [PMID: 29690561 PMCID: PMC6027312 DOI: 10.3390/biomedicines6020047] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 03/26/2018] [Accepted: 04/19/2018] [Indexed: 12/20/2022] Open
Abstract
Hypoxia or reduced oxygen availability has been studied extensively for its ability to activate specific genes. Hypoxia-induced gene expression is mediated by the HIF transcription factors, but not exclusively so. Despite the extensive knowledge about how hypoxia activates genes, much less is known about how hypoxia promotes gene repression. In this review, we discuss the potential mechanisms underlying hypoxia-induced transcriptional repression responses. We highlight HIF-dependent and independent mechanisms as well as the potential roles of dioxygenases with functions at the nucleosome and DNA level. Lastly, we discuss recent evidence regarding the involvement of transcriptional repressor complexes in hypoxia.
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Affiliation(s)
- Michael Batie
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L697ZB, UK.
| | - Luis Del Peso
- Department of Biochemistry, Institute of Biomedical Research, Autonomous Madrid University, Arturo Duperier, 4. 28029 Madrid, Spain.
| | - Sonia Rocha
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L697ZB, UK.
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Ali I, Conrad RJ, Verdin E, Ott M. Lysine Acetylation Goes Global: From Epigenetics to Metabolism and Therapeutics. Chem Rev 2018; 118:1216-1252. [PMID: 29405707 PMCID: PMC6609103 DOI: 10.1021/acs.chemrev.7b00181] [Citation(s) in RCA: 232] [Impact Index Per Article: 38.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Post-translational acetylation of lysine residues has emerged as a key regulatory mechanism in all eukaryotic organisms. Originally discovered in 1963 as a unique modification of histones, acetylation marks are now found on thousands of nonhistone proteins located in virtually every cellular compartment. Here we summarize key findings in the field of protein acetylation over the past 20 years with a focus on recent discoveries in nuclear, cytoplasmic, and mitochondrial compartments. Collectively, these findings have elevated protein acetylation as a major post-translational modification, underscoring its physiological relevance in gene regulation, cell signaling, metabolism, and disease.
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Affiliation(s)
- Ibraheem Ali
- Gladstone Institute of Virology and Immunology, San Francisco, California 94158, United States
- University of California, San Francisco, Department of Medicine, San Francisco, California 94158, United States
| | - Ryan J. Conrad
- Gladstone Institute of Virology and Immunology, San Francisco, California 94158, United States
- University of California, San Francisco, Department of Medicine, San Francisco, California 94158, United States
| | - Eric Verdin
- Buck Institute for Research on Aging, Novato, California 94945, United States
| | - Melanie Ott
- Gladstone Institute of Virology and Immunology, San Francisco, California 94158, United States
- University of California, San Francisco, Department of Medicine, San Francisco, California 94158, United States
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11
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Kaikkonen MU, Halonen P, Liu OHF, Turunen TA, Pajula J, Moreau P, Selvarajan I, Tuomainen T, Aavik E, Tavi P, Ylä-Herttuala S. Genome-Wide Dynamics of Nascent Noncoding RNA Transcription in Porcine Heart After Myocardial Infarction. ACTA ACUST UNITED AC 2017; 10:CIRCGENETICS.117.001702. [DOI: 10.1161/circgenetics.117.001702] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 04/25/2017] [Indexed: 11/16/2022]
Abstract
Background—
Microarrays and RNA sequencing are widely used to profile transcriptome remodeling during myocardial ischemia. However, the steady-state RNA analysis lacks in sensitivity to detect all noncoding RNA species and does not provide separation between transcriptional and post-transcriptional regulations. Here, we provide the first comprehensive analysis of nascent RNA profiles of mRNAs, primary micro-RNAs, long noncoding RNAs, and enhancer RNAs in a large animal model of acute infarction.
Methods and Results—
Acute infarction was induced by cardiac catheterization of domestic swine. Nuclei isolated from healthy, border zone, and ischemic regions of the affected heart were subjected to global run-on sequencing. Global run-on sequencing analysis indicated that half of affected genes are regulated at the level of transcriptional pausing. A gradient of induction of inflammatory mediators and repression of peroxisome proliferator-activated receptor signaling and oxidative phosphorylation was detected when moving from healthy toward infarcted area. In addition, we interrogated the transcriptional regulation of primary micro-RNAs and provide evidence that several arrhythmia-related target genes exhibit repression at post-transcriptional level. We identified 450 long noncoding RNAs differently regulated by ischemia, including novel conserved long noncoding RNAs expressed in antisense orientation to myocardial transcription factors GATA-binding protein 4, GATA-binding protein 6, and Krüppel-like factor 6. Finally, characterization of enhancers exhibiting differential expression of enhancer RNAs pointed a central role for Krüppel-like factor, MEF2C, ETS, NFY, ATF, E2F2, and NRF1 transcription factors in determining transcriptional responses to ischemia.
Conclusions—
Global run-on sequencing allowed us to follow the gradient of gene expression occurring in the ischemic heart and identify novel noncoding RNAs regulated by oxygen deprivation. These findings highlight potential new targets for diagnosis and treatment of myocardial ischemia.
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Affiliation(s)
- Minna U. Kaikkonen
- From the Department of Biotechnology and Molecular Medicine, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio (M.U.K., P.H., O.H.-F.L., T.T., J.P., P.M., I.S., T.T., E.A., P.T., S.Y.-H.); and Heart Center and Gene Therapy Unit, Kuopio University Hospital, Finland (S.Y.-H.)
| | - Paavo Halonen
- From the Department of Biotechnology and Molecular Medicine, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio (M.U.K., P.H., O.H.-F.L., T.T., J.P., P.M., I.S., T.T., E.A., P.T., S.Y.-H.); and Heart Center and Gene Therapy Unit, Kuopio University Hospital, Finland (S.Y.-H.)
| | - Oscar Hsin-Fu Liu
- From the Department of Biotechnology and Molecular Medicine, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio (M.U.K., P.H., O.H.-F.L., T.T., J.P., P.M., I.S., T.T., E.A., P.T., S.Y.-H.); and Heart Center and Gene Therapy Unit, Kuopio University Hospital, Finland (S.Y.-H.)
| | - Tiia A. Turunen
- From the Department of Biotechnology and Molecular Medicine, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio (M.U.K., P.H., O.H.-F.L., T.T., J.P., P.M., I.S., T.T., E.A., P.T., S.Y.-H.); and Heart Center and Gene Therapy Unit, Kuopio University Hospital, Finland (S.Y.-H.)
| | - Juho Pajula
- From the Department of Biotechnology and Molecular Medicine, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio (M.U.K., P.H., O.H.-F.L., T.T., J.P., P.M., I.S., T.T., E.A., P.T., S.Y.-H.); and Heart Center and Gene Therapy Unit, Kuopio University Hospital, Finland (S.Y.-H.)
| | - Pierre Moreau
- From the Department of Biotechnology and Molecular Medicine, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio (M.U.K., P.H., O.H.-F.L., T.T., J.P., P.M., I.S., T.T., E.A., P.T., S.Y.-H.); and Heart Center and Gene Therapy Unit, Kuopio University Hospital, Finland (S.Y.-H.)
| | - Ilakya Selvarajan
- From the Department of Biotechnology and Molecular Medicine, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio (M.U.K., P.H., O.H.-F.L., T.T., J.P., P.M., I.S., T.T., E.A., P.T., S.Y.-H.); and Heart Center and Gene Therapy Unit, Kuopio University Hospital, Finland (S.Y.-H.)
| | - Tomi Tuomainen
- From the Department of Biotechnology and Molecular Medicine, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio (M.U.K., P.H., O.H.-F.L., T.T., J.P., P.M., I.S., T.T., E.A., P.T., S.Y.-H.); and Heart Center and Gene Therapy Unit, Kuopio University Hospital, Finland (S.Y.-H.)
| | - Einari Aavik
- From the Department of Biotechnology and Molecular Medicine, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio (M.U.K., P.H., O.H.-F.L., T.T., J.P., P.M., I.S., T.T., E.A., P.T., S.Y.-H.); and Heart Center and Gene Therapy Unit, Kuopio University Hospital, Finland (S.Y.-H.)
| | - Pasi Tavi
- From the Department of Biotechnology and Molecular Medicine, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio (M.U.K., P.H., O.H.-F.L., T.T., J.P., P.M., I.S., T.T., E.A., P.T., S.Y.-H.); and Heart Center and Gene Therapy Unit, Kuopio University Hospital, Finland (S.Y.-H.)
| | - Seppo Ylä-Herttuala
- From the Department of Biotechnology and Molecular Medicine, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio (M.U.K., P.H., O.H.-F.L., T.T., J.P., P.M., I.S., T.T., E.A., P.T., S.Y.-H.); and Heart Center and Gene Therapy Unit, Kuopio University Hospital, Finland (S.Y.-H.)
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Dehne N, Brüne B. Hypoxic inhibition of JMJD3 reduces H3K27me3 demethylation and induction of the STAT6 target gene CCL18. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1859:1490-1501. [PMID: 27737800 DOI: 10.1016/j.bbagrm.2016.10.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 09/23/2016] [Accepted: 10/07/2016] [Indexed: 01/12/2023]
Abstract
Hypoxia, by activating transcription factors induces transcription of some genes but it also reduces mRNA synthesis by mechanisms that are poorly defined. Activation of human macrophages with interleukin (IL)-4 showed that up-regulation of some IL-4 target genes was reduced when macrophages were incubated at 1% oxygen. Hypoxia impaired induction of chemokine (C-C motif) ligand 18 (CCL18), although IL-4-induced DNA binding of the transcription factor STAT6 remained intact. In contrast, induction of serine peptidase inhibitor, Kunitz type (SPINT)2, another IL-4/STAT6 target gene, was not affected by hypoxia. The repressive histone mark histone 3 lysine 27 trimethylation (H3K27me3), known to prevent chromatin remodelling and transcription, was removed from the SPINT2 but not the CCL18 gene locus under hypoxia or dimethyloxalylglycine-treatment. The H3K27me3 demethylase JMJD3 was required for CCL18 gene induction but dispensable for induction of SPINT2. Our data indicate that hypoxic inhibition of JMJD3 activity reduces demethylation of H3K27me3, nucleosome removal, and hence induction of the STAT6 target gene CCL18, while induction of other STAT6-inducible genes such as SPINT2 remained unaffected by JMJD3. In contrast to mouse MΦ in human cells JMJD3 is not recruited by transcription factors like IRF4, KL4, or PPARγ to convey specificity in gene induction.
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Affiliation(s)
- Nathalie Dehne
- Institute of Biochemistry I, Faculty of Medicine, Goethe-University Frankfurt, 60590 Frankfurt am Main, Germany.
| | - Bernhard Brüne
- Institute of Biochemistry I, Faculty of Medicine, Goethe-University Frankfurt, 60590 Frankfurt am Main, Germany
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The Transcription Factor ZNF395 Is Required for the Maximal Hypoxic Induction of Proinflammatory Cytokines in U87-MG Cells. Mediators Inflamm 2015; 2015:804264. [PMID: 26229239 PMCID: PMC4502306 DOI: 10.1155/2015/804264] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 06/10/2015] [Indexed: 01/09/2023] Open
Abstract
Hypoxia activates the expression of proangiogenic and survival promoting factors as well as proinflammatory cytokines that support tissue inflammation. Hypoxia and inflammation are associated with tumor progression. The identification of the factors participating in the hypoxia associated inflammation is essential to develop strategies to control tumor hypoxia. The transcription factor ZNF395 was found to be overexpressed in various tumors including glioblastomas particularly in the network of a hypoxic response pointing to a functional role of ZNF395. On the other hand, ZNF395 was suggested to have tumor suppressor activities which may rely on its repression of proinflammatory factors. To address these conflictive observations, we investigated the role of ZNF395 in the expression of proinflammatory cytokines in the astrocytoma cell line U87-MG under hypoxia. We show that ZNF395 is a target gene of the hypoxia inducible factor HIF-1α. By gene expression analysis, RT-PCR and ELISA, we demonstrated that the siRNA-mediated suppression of ZNF395 impairs the hypoxic induction of IL-1β, IL-6, IL-8, and LIF in U87-MG cells. At ambient oxygen concentrations, ZNF395 had no enhancing effect, indicating that this transcriptional activation by ZNF395 is restricted to hypoxic conditions. Our results suggest that ZNF395 contributes to hypoxia associated inflammation by superactivating proinflammatory cytokines.
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Ye F, Karn J. Bacterial Short Chain Fatty Acids Push All The Buttons Needed To Reactivate Latent Viruses. ACTA ACUST UNITED AC 2015; 2. [PMID: 26029743 DOI: 10.14800/sce.532] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The genomes of herpesviruses and HIV become silent during latency through multiple chromatin silencing mechanisms including: histone deacetylation, repressive histone methylation, and DNA methylation. Reactivation of the latent virus requires removal of the chromatin silencing marks and their replacement by activating modifications such as histone acetylation and activating histone methylation. In a complementary mechanism, RNA Polymerase II (RNAP II) elongation is regulated by the positive transcription elongation factor b (P-TEFb)-dependent phosphorylation of Ser2 residues on its C-terminal domain. In resting T-cells latently infected by HIV, expression of P-TEFb is restricted. We found that a group of short chain fatty acids (SCFAs) produced by oral bacteria not only promote histone acetylation but also change the histone methylation dynamics by decreasing repressive histone methylation while increasing activating histone methylation. SCFAs also block DNA methylation and activate P-TEFb to enable elongation of stalled RNA polymerase II. Thus these molecules do not simply act as histone deacetylase (HDAC) inhibitors as previously claimed. Instead, they impact multiple complementary epigenetic regulatory mechanisms to promote highly efficient reactivation of latent viruses.
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Affiliation(s)
- Fengchun Ye
- Department of Biological Sciences, School of Dental Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106. USA
| | - Jonathan Karn
- Department of Molecular Biology & Microbiology, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106. USA
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