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Gantner BN, Palma FR, Kayzuka C, Lacchini R, Foltz DR, Backman V, Kelleher N, Shilatifard A, Bonini MG. Histone oxidation as a new mechanism of metabolic control over gene expression. Trends Genet 2024:S0168-9525(24)00134-3. [PMID: 38910033 DOI: 10.1016/j.tig.2024.05.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Revised: 05/30/2024] [Accepted: 05/30/2024] [Indexed: 06/25/2024]
Abstract
The emergence of aerobic respiration created unprecedented bioenergetic advantages, while imposing the need to protect critical genetic information from reactive byproducts of oxidative metabolism (i.e., reactive oxygen species, ROS). The evolution of histone proteins fulfilled the need to shield DNA from these potentially damaging toxins, while providing the means to compact and structure massive eukaryotic genomes. To date, several metabolism-linked histone post-translational modifications (PTMs) have been shown to regulate chromatin structure and gene expression. However, whether and how PTMs enacted by metabolically produced ROS regulate adaptive chromatin remodeling remain relatively unexplored. Here, we review novel mechanistic insights into the interactions of ROS with histones and their consequences for the control of gene expression regulation, cellular plasticity, and behavior.
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Affiliation(s)
- Benjamin N Gantner
- Department of Medicine, Division of Endocrinology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Flavio R Palma
- Division of Hematology Oncology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Cezar Kayzuka
- Division of Hematology Oncology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA; Department of Pharmacology, Ribeirao Preto Medical School, University of Sao Paulo, Sao Paulo, Brazil; Department of Psychiatric Nursing and Human Sciences, Ribeirao Preto College of Nursing, University of Sao Paulo, Sao Paulo, Brazil
| | - Riccardo Lacchini
- Department of Psychiatric Nursing and Human Sciences, Ribeirao Preto College of Nursing, University of Sao Paulo, Sao Paulo, Brazil
| | - Daniel R Foltz
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Vadim Backman
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA; Department of Bioengineering, McCormick School of Engineering, Northwestern University, Chicago, IL, USA
| | - Neil Kelleher
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA; Chemistry of Life Processes Institute, Northwestern University, Chicago, IL, USA
| | - Ali Shilatifard
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Marcelo G Bonini
- Division of Hematology Oncology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA; Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
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Bhagavan H, Wei AD, Oliveira LM, Aldinger KA, Ramirez JM. Chronic intermittent hypoxia elicits distinct transcriptomic responses among neurons and oligodendrocytes within the brainstem of mice. Am J Physiol Lung Cell Mol Physiol 2024; 326:L698-L712. [PMID: 38591125 DOI: 10.1152/ajplung.00320.2023] [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: 10/13/2023] [Revised: 01/22/2024] [Accepted: 03/26/2024] [Indexed: 04/10/2024] Open
Abstract
Chronic intermittent hypoxia (CIH) is a prevalent condition characterized by recurrent episodes of oxygen deprivation, linked to respiratory and neurological disorders. Prolonged CIH is known to have adverse effects, including endothelial dysfunction, chronic inflammation, oxidative stress, and impaired neuronal function. These factors can contribute to serious comorbidities, including metabolic disorders and cardiovascular diseases. To investigate the molecular impact of CIH, we examined male C57BL/6J mice exposed to CIH for 21 days, comparing with normoxic controls. We used single-nucleus RNA sequencing to comprehensively examine the transcriptomic impact of CIH on key cell classes within the brainstem, specifically excitatory neurons, inhibitory neurons, and oligodendrocytes. These cell classes regulate essential physiological functions, including autonomic tone, cardiovascular control, and respiration. Through analysis of 10,995 nuclei isolated from pontine-medullary tissue, we identified seven major cell classes, further subdivided into 24 clusters. Our findings among these cell classes, revealed significant differential gene expression, underscoring their distinct responses to CIH. Notably, neurons exhibited transcriptional dysregulation of genes associated with synaptic transmission, and structural remodeling. In addition, we found dysregulated genes encoding ion channels and inflammatory response. Concurrently, oligodendrocytes exhibited dysregulated genes associated with oxidative phosphorylation and oxidative stress. Utilizing CellChat network analysis, we uncovered CIH-dependent altered patterns of diffusible intercellular signaling. These insights offer a comprehensive transcriptomic cellular atlas of the pons-medulla and provide a fundamental resource for the analysis of molecular adaptations triggered by CIH.NEW & NOTEWORTHY This study on chronic intermittent hypoxia (CIH) from pons-medulla provides initial insights into the molecular effects on excitatory neurons, inhibitory neurons, and oligodendrocytes, highlighting our unbiased approach, in comparison with earlier studies focusing on single target genes. Our findings reveal that CIH affects cell classes distinctly, and the dysregulated genes in distinct cell classes are associated with synaptic transmission, ion channels, inflammation, oxidative stress, and intercellular signaling, advancing our understanding of CIH-induced molecular responses.
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Affiliation(s)
- Hemalatha Bhagavan
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, Washington, United States
| | - Aguan D Wei
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, Washington, United States
| | - Luiz M Oliveira
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, Washington, United States
| | - Kimberly A Aldinger
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, Washington, United States
- Department of Pediatrics, University of Washington, Seattle, Washington, United States
- Department of Neurology, University of Washington, Seattle, Washington, United States
| | - Jan-Marino Ramirez
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, Washington, United States
- Department of Pediatrics, University of Washington, Seattle, Washington, United States
- Department of Neurological Surgery, University of Washington, Seattle, Washington, United States
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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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Barth J, Loeffler I, Bondeva T, Liebisch M, Wolf G. The Role of Hypoxia on the Trimethylation of H3K27 in Podocytes. Biomedicines 2023; 11:2475. [PMID: 37760919 PMCID: PMC10525388 DOI: 10.3390/biomedicines11092475] [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: 08/01/2023] [Revised: 08/28/2023] [Accepted: 09/04/2023] [Indexed: 09/29/2023] Open
Abstract
Epigenetic alterations contribute to the pathogenesis of chronic diseases such as diabetes mellitus. Previous studies of our group showed that diabetic conditions reduce the trimethylation of H3K27 in podocytes in a NIPP1- (nuclear inhibitor of protein phosphatase 1) and EZH2- (enhancer of zeste homolog 2) dependent manner. It has been previously reported that in differentiated podocytes, hypoxia decreases the expression of slit diaphragm proteins and promotes foot process effacement, thereby contributing to the progression of renal disease. The exact mechanisms are, however, not completely understood. The aim of this study was to analyze the role of hypoxia and HIFs (hypoxia-inducible factor) on epigenetic changes in podocytes affecting NIPP1, EZH2 and H3K27me3, in vitro and in vivo. In vivo studies were performed with mice exposed to 10% systemic hypoxia for 3 days or injected with 3,4-DHB (dihydroxybenzoate), a PHD (prolyl hydroxylase) inhibitor, 24 h prior analyses. Immunodetection of H3K27me3, NIPP1 and EZH2 in glomerular podocytes revealed, to the best of our knowledge for the first time, that hypoxic conditions and pharmacological HIFs activation significantly reduce the expression of NIPP1 and EZH2 and diminish H3K27 trimethylation. These findings are also supported by in vitro studies using murine-differentiated podocytes.
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