1
|
Mondal AK, Gaur M, Advani J, Swaroop A. Epigenome-metabolism nexus in the retina: implications for aging and disease. Trends Genet 2024:S0168-9525(24)00099-4. [PMID: 38782642 DOI: 10.1016/j.tig.2024.04.012] [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: 03/18/2024] [Revised: 04/22/2024] [Accepted: 04/23/2024] [Indexed: 05/25/2024]
Abstract
Intimate links between epigenome modifications and metabolites allude to a crucial role of cellular metabolism in transcriptional regulation. Retina, being a highly metabolic tissue, adapts by integrating inputs from genetic, epigenetic, and extracellular signals. Precise global epigenomic signatures guide development and homeostasis of the intricate retinal structure and function. Epigenomic and metabolic realignment are hallmarks of aging and highlight a link of the epigenome-metabolism nexus with aging-associated multifactorial traits affecting the retina, including age-related macular degeneration and glaucoma. Here, we focus on emerging principles of epigenomic and metabolic control of retinal gene regulation, with emphasis on their contribution to human disease. In addition, we discuss potential mitigation strategies involving lifestyle changes that target the epigenome-metabolome relationship for maintaining retinal function.
Collapse
Affiliation(s)
- Anupam K Mondal
- Neurobiology, Neurodegeneration, and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mohita Gaur
- Neurobiology, Neurodegeneration, and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jayshree Advani
- Neurobiology, Neurodegeneration, and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Anand Swaroop
- Neurobiology, Neurodegeneration, and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| |
Collapse
|
2
|
Yu G, Chen D, Ye M, Wu X, Zhu Z, Shen Y, Mehareb EM, Esh A, Raza G, Wang K, Wang Q, Jin JB. H3K27 demethylase SsJMJ4 negatively regulates drought-stress responses in sugarcane. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:3040-3053. [PMID: 38310636 DOI: 10.1093/jxb/erae037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 02/02/2024] [Indexed: 02/06/2024]
Abstract
Sugarcane (Saccharum spp.), a leading sugar and energy crop, is seriously impacted by drought stress. However, the molecular mechanisms underlying sugarcane drought resistance, especially the functions of epigenetic regulators, remain elusive. Here, we show that a S. spontaneum KDM4/JHDM3 group JmjC protein, SsJMJ4, negatively regulates drought-stress responses through its H3K27me3 demethylase activity. Ectopic overexpression of SsJMJ4 in Arabidopsis reduced drought resistance possibly by promoting expression of AtWRKY54 and AtWRKY70, encoding two negative regulators of drought stress. SsJMJ4 directly bound to AtWRKY54 and AtWRKY70, and reduced H3K27me3 levels at these loci to ensure their proper transcription under normal conditions. Drought stress down-regulated both transcription and protein abundance of SsJMJ4, which was correlated with the reduced occupancy of SsJMJ4 at AtWRKY54 and AtWRKY70 chromatin, increased H3K27me3 levels at these loci, as well as reduced transcription levels of these genes. In S. spontaneum, drought stress-repressed transcription of SsWRKY122, an ortholog of AtWRKY54 and AtWRKY70, was associated with increased H3K27me3 levels at these loci. Transient overexpression of SsJMJ4 in S. spontaneum protoplasts raised transcription of SsWRKY122, paralleled with reduced H3K27me3 levels at its loci. These results suggest that the SsJMJ4-mediated dynamic deposition of H3K27me3 is required for an appropriate response to drought stress.
Collapse
Affiliation(s)
- Guangrun Yu
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
- School of Life Sciences, Nantong University, Nantong 226019, China
| | - Daoqian Chen
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Meiling Ye
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Xiaoge Wu
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Zhiying Zhu
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Yan Shen
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Eid M Mehareb
- Sugar Crops Research Institute, Agricultural Research Center, Giza 12619, Egypt
| | - Ayman Esh
- Sugar Crops Research Institute, Agricultural Research Center, Giza 12619, Egypt
| | - Ghulam Raza
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, 38000, Pakistan
| | - Kai Wang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
- School of Life Sciences, Nantong University, Nantong 226019, China
| | - Qiongli Wang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Jing Bo Jin
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- China National Botanical Garden, Beijing, China
- University of the Chinese Academy of Sciences, Beijing, China
- Academician Workstation of Agricultural High-tech Industrial Area of the Yellow River Delta, National Center of Technology Innovation for Comprehensive Utilization of Saline-Alkali Land, Dongying, Shandong, China
| |
Collapse
|
3
|
Pinto TS, Feltran GDS, Fernandes CJDC, de Camargo Andrade AF, Coque ADC, Silva SL, Abuderman AA, Zambuzzi WF, Foganholi da Silva RA. Epigenetic changes in shear-stressed endothelial cells. Cell Biol Int 2024; 48:665-681. [PMID: 38420868 DOI: 10.1002/cbin.12138] [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: 03/19/2023] [Revised: 01/18/2024] [Accepted: 01/28/2024] [Indexed: 03/02/2024]
Abstract
Epigenetic changes, particularly histone compaction modifications, have emerged as critical regulators in the epigenetic pathway driving endothelial cell phenotype under constant exposure to laminar forces induced by blood flow. However, the underlying epigenetic mechanisms governing endothelial cell behavior in this context remain poorly understood. To address this knowledge gap, we conducted in vitro experiments using human umbilical vein endothelial cells subjected to various tensional forces simulating pathophysiological blood flow shear stress conditions, ranging from normotensive to hypertensive forces. Our study uncovers a noteworthy observation wherein endothelial cells exposed to high shear stress demonstrate a decrease in the epigenetic marks H3K4ac and H3K27ac, accompanied by significant alterations in the levels of HDAC (histone deacetylase) proteins. Moreover, we demonstrate a negative regulatory effect of increased shear stress on HOXA13 gene expression and a concomitant increase in the expression of the long noncoding RNA, HOTTIP, suggesting a direct association with the suppression of HOXA13. Collectively, these findings represent the first evidence of the role of histone-related epigenetic modifications in modulating chromatin compaction during mechanosignaling of endothelial cells in response to elevated shear stress forces. Additionally, our results highlight the importance of understanding the physiological role of HOXA13 in vascular biology and hypertensive patients, emphasizing the potential for developing small molecules to modulate its activity. These findings warrant further preclinical investigations and open new avenues for therapeutic interventions targeting epigenetic mechanisms in hypertensive conditions.
Collapse
Affiliation(s)
- Thaís Silva Pinto
- Lab. of Bioassays and Cellular Dynamics, Department of Chemical and Biological Sciences, Institute of Biosciences, Paulista State University-UNESP, Botucatu, São Paulo, Brazil
| | - Geórgia da Silva Feltran
- Lab. of Bioassays and Cellular Dynamics, Department of Chemical and Biological Sciences, Institute of Biosciences, Paulista State University-UNESP, Botucatu, São Paulo, Brazil
| | - Célio Júnior da C Fernandes
- Lab. of Bioassays and Cellular Dynamics, Department of Chemical and Biological Sciences, Institute of Biosciences, Paulista State University-UNESP, Botucatu, São Paulo, Brazil
| | - Amanda Fantini de Camargo Andrade
- Lab. of Bioassays and Cellular Dynamics, Department of Chemical and Biological Sciences, Institute of Biosciences, Paulista State University-UNESP, Botucatu, São Paulo, Brazil
| | - Alex de Camargo Coque
- Epigenetic Study Center and Gene Regulation-CEEpiRG, Program in Environmental and Experimental Pathology, Paulista University, São Paulo, São Paulo, Brazil
| | - Simone L Silva
- School of Dentistry, University of Taubaté, Taubaté, São Paulo, Brazil
| | - Abdulwahab A Abuderman
- Department of Basic Medical Sciences, College of Medicine, Prince Sattam bin Abdulaziz University, Riyadh, Saudi Arabia
| | - Willian F Zambuzzi
- Lab. of Bioassays and Cellular Dynamics, Department of Chemical and Biological Sciences, Institute of Biosciences, Paulista State University-UNESP, Botucatu, São Paulo, Brazil
| | - Rodrigo A Foganholi da Silva
- Epigenetic Study Center and Gene Regulation-CEEpiRG, Program in Environmental and Experimental Pathology, Paulista University, São Paulo, São Paulo, Brazil
- School of Dentistry, University of Taubaté, Taubaté, São Paulo, Brazil
| |
Collapse
|
4
|
Jia J, Luo Y, Wu Z, Ji Y, Liu S, Shu J, Chen B, Liu J. OsJMJ718, a histone demethylase gene, positively regulates seed germination in rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:191-202. [PMID: 38116956 DOI: 10.1111/tpj.16600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 11/27/2023] [Accepted: 12/09/2023] [Indexed: 12/21/2023]
Abstract
Seed vigor has major impact on the rate and uniformity of seedling growth, crop yield, and quality. However, the epigenetic regulatory mechanism of crop seed vigor remains unclear. In this study, a (jumonji C) JmjC gene of the histone lysine demethylase OsJMJ718 was cloned in rice, and its roles in seed germination and its epigenetic regulation mechanism were investigated. OsJMJ718 was located in the nucleus and was engaged in H3K9 methylation. Histochemical GUS staining analysis revealed OsJMJ718 was highly expressed in seed embryos. Abiotic stress strongly induced the OsJMJ718 transcriptional accumulation level. Germination percentage and seedling vigor index of OsJMJ718 knockout lines (OsJMJ718-CR) were lower than those of the wild type (WT). Chromatin immunoprecipitation followed by sequencing (ChIP-seq) of seeds imbibed for 24 h showed an increase in H3K9me3 deposition of thousands of genes in OsJMJ718-CR. ChIP-seq results and transcriptome analysis showed that differentially expressed genes were enriched in ABA and ethylene signal transduction pathways. The content of ABA in OsJMJ718-CR was higher than that in WT seeds. OsJMJ718 overexpression enhanced sensitivity to ABA during germination and early seedling growth. In the seed imbibition stage, ABA and ethylene content diminished and augmented, separately, suggesting that OsJMJ718 may adjust rice seed germination through the ABA and ethylene signal transduction pathways. This study displayed the important function of OsJMJ718 in adjusting rice seed germination and vigor, which will provide an essential reference for practical issues, such as improving rice vigor and promoting direct rice sowing production.
Collapse
Affiliation(s)
- Junting Jia
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Yongjian Luo
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Zhiyuan Wu
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Yufang Ji
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Shuangxing Liu
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Jie Shu
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Bingxian Chen
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Jun Liu
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| |
Collapse
|
5
|
Cai F, Yang X, Ma G, Wang P, Zhang M, Zhang N, Zhang R, Liang H, Nie Y, Dong C, Deng J. EGLN3 attenuates gastric cancer cell malignant characteristics by inhibiting JMJD8/NF-κB signalling activation independent of hydroxylase activity. Br J Cancer 2024; 130:597-612. [PMID: 38184692 PMCID: PMC10876699 DOI: 10.1038/s41416-023-02546-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: 07/11/2023] [Revised: 12/07/2023] [Accepted: 12/08/2023] [Indexed: 01/08/2024] Open
Abstract
BACKGROUND The expression of Egl-9 family hypoxia-inducible factor 3 (EGLN3) is notably decreased in various malignancies, including gastric cancer (GC). While the predominant focus has been on the hydroxylase activity of EGLN3 for its antitumour effects, recent findings have suggested nonenzymatic roles for EGLN3. METHODS This study assessed the clinical significance of EGLN3 expression in GC and explored the connection between EGLN3 DNA promoter methylation and transcriptional silencing. To investigate the effect of EGLN3 on GC cells, a gain-of-function strategy was adopted. RNA sequencing was conducted to identify the key effector molecules and signalling pathways associated with EGLN3. RESULTS EGLN3 expression was significantly reduced in GC tissues, correlating with poorer patient prognosis. EGLN3 hypermethylation disrupts transcriptional equilibrium, contributing to deeper tumour invasion and lymph node metastasis, thus exacerbating GC progression. Conversely, restoration of EGLN3 expression in GC cells substantially inhibited cell proliferation and metastasis. EGLN3 was also found to impede the malignant progression of GC cells by downregulating Jumonji C domain-containing protein 8-mediated activation of the NF-κB pathway, independent of its hydroxylase activity. CONCLUSIONS EGLN3 has the potential to hinder the spread of GC cells through a nonenzymatic mechanism, thereby shedding light on the complex nature of GC progression.
Collapse
Affiliation(s)
- Fenglin Cai
- Department of Gastric Surgery, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin Key Laboratory of Digestive Cancer; Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Haihe Laboratory of Cell Ecosystem, School of Basic Medical Sciences, Tianjin Medical University, 300070, Tianjin, China
- Department of Biochemistry and Molecular Biology, Tianjin Medical University, 300070, Tianjin, China
| | - Xiuding Yang
- Department of Gastric Surgery, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin Key Laboratory of Digestive Cancer; Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China
| | - Gang Ma
- Department of Gastric Surgery, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin Key Laboratory of Digestive Cancer; Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China
| | - Pengliang Wang
- Department of Gastrointestinal Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, China
| | - Mengmeng Zhang
- Department of Gastric Surgery, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin Key Laboratory of Digestive Cancer; Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China
| | - Nannan Zhang
- State Key Laboratory of Cancer Biology and National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an, China
| | - Rupeng Zhang
- Department of Gastric Surgery, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin Key Laboratory of Digestive Cancer; Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China
| | - Han Liang
- Department of Gastric Surgery, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin Key Laboratory of Digestive Cancer; Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China
| | - Yongzhan Nie
- State Key Laboratory of Cancer Biology and National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an, China
| | - Cheng Dong
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Haihe Laboratory of Cell Ecosystem, School of Basic Medical Sciences, Tianjin Medical University, 300070, Tianjin, China.
- Department of Biochemistry and Molecular Biology, Tianjin Medical University, 300070, Tianjin, China.
| | - Jingyu Deng
- Department of Gastric Surgery, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin Key Laboratory of Digestive Cancer; Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China.
| |
Collapse
|
6
|
Yin J, Gu T, Chaudhry N, Davidson NE, Huang Y. Epigenetic modulation of antitumor immunity and immunotherapy response in breast cancer: biological mechanisms and clinical implications. Front Immunol 2024; 14:1325615. [PMID: 38268926 PMCID: PMC10806158 DOI: 10.3389/fimmu.2023.1325615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Accepted: 12/22/2023] [Indexed: 01/26/2024] Open
Abstract
Breast cancer (BC) is the most common non-skin cancer and the second leading cause of cancer death in American women. The initiation and progression of BC can proceed through the accumulation of genetic and epigenetic changes that allow transformed cells to escape the normal cell cycle checkpoint control. Unlike nucleotide mutations, epigenetic changes such as DNA methylation, histone posttranslational modifications (PTMs), nucleosome remodeling and non-coding RNAs are generally reversible and therefore potentially responsive to pharmacological intervention. Epigenetic dysregulations are critical mechanisms for impaired antitumor immunity, evasion of immune surveillance, and resistance to immunotherapy. Compared to highly immunogenic tumor types, such as melanoma or lung cancer, breast cancer has been viewed as an immunologically quiescent tumor which displays a relatively low population of tumor-infiltrating lymphocytes (TIL), low tumor mutational burden (TMB) and modest response rates to immune checkpoint inhibitors (ICI). Emerging evidence suggests that agents targeting aberrant epigenetic modifiers may augment host antitumor immunity in BC via several interrelated mechanisms such as enhancing tumor antigen presentation, activation of cytotoxic T cells, inhibition of immunosuppressive cells, boosting response to ICI, and induction of immunogenic cell death (ICD). These discoveries have established a highly promising basis for using combinatorial approaches of epigenetic drugs with immunotherapy as an innovative paradigm to improve outcomes of BC patients. In this review, we summarize the current understanding of how epigenetic processes regulate immune cell function and antitumor immunogenicity in the context of the breast tumor microenvironment. Moreover, we discuss the therapeutic potential and latest clinical trials of the combination of immune checkpoint blockers with epigenetic agents in breast cancer.
Collapse
Affiliation(s)
- Jun Yin
- The University of Pittsburgh Medical Center (UPMC) Hillman Cancer Center, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Tiezheng Gu
- The University of Pittsburgh Medical Center (UPMC) Hillman Cancer Center, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Norin Chaudhry
- Department of Internal Medicine, Division of Hematology, Oncology, and Blood and Marrow Transplantation, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
| | - Nancy E. Davidson
- Fred Hutchinson Cancer Center, University of Washington, Seattle, WA, United States
| | - Yi Huang
- Department of Internal Medicine, Division of Hematology, Oncology, and Blood and Marrow Transplantation, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA, United States
| |
Collapse
|
7
|
Jin W, Yan W, Ma M, Hasi A, Che G. Genome-wide identification and expression analysis of the JMJ-C gene family in melon (Cucumis melo L.) reveals their potential role in fruit development. BMC Genomics 2023; 24:771. [PMID: 38093236 PMCID: PMC10720240 DOI: 10.1186/s12864-023-09868-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 12/03/2023] [Indexed: 12/17/2023] Open
Abstract
BACKGROUND Proteins with the jumonji (JMJ)-C domain belong to the histone demethylase family and contribute to reverse histone methylation. Although JMJ-C family genes have an essential role in regulating plant growth and development, the characterization of the JMJ-C family genes in melon has not been uncovered. RESULTS In this study, a total of 17 JMJ-C proteins were identified in melon (Cucumis melo L.). CmJMJs were categorized into five subfamilies based on the specific conserved domain: KDM4/JHDM3, KDM5/JARID1, JMJD6, KDM3/JHDM2, and JMJ-C domain-only. The chromosome localization analyses showed that 17 CmJMJs were distributed on nine chromosomes. Cis-acting element analyses of the 17 CmJMJ genes showed numerous hormone, light, and stress response elements distributed in the promoter region. Covariance analysis revealed one pair of replicated fragments (CmJMJ3a and CmJMJ3b) in 17 CmJMJ genes. We investigated the expression profile of 17 CmJMJ genes in different lateral organs and four developmental stages of fruit by RNA-seq transcriptome analysis and RT-qPCR. The results revealed that most CmJMJ genes were prominently expressed in female flowers, ovaries, and developing fruits, suggesting their active role in melon fruit development. Subcellular localization showed that the fruit-related CmJMJ5a protein is specifically localized in the cell nucleus. CONCLUSIONS This study provides a comprehensive understanding of the gene structure, classification, and evolution of JMJ-C in melon and supports the clarification of the JMJ-C functions in further research.
Collapse
Affiliation(s)
- Wuyun Jin
- Key Laboratory of Herbage & Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Wei Yan
- Key Laboratory of Herbage & Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Ming Ma
- Key Laboratory of Herbage & Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Agula Hasi
- Key Laboratory of Herbage & Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China.
| | - Gen Che
- Key Laboratory of Herbage & Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China.
| |
Collapse
|
8
|
Szczepanek J, Tretyn A. MicroRNA-Mediated Regulation of Histone-Modifying Enzymes in Cancer: Mechanisms and Therapeutic Implications. Biomolecules 2023; 13:1590. [PMID: 38002272 PMCID: PMC10669115 DOI: 10.3390/biom13111590] [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: 09/21/2023] [Revised: 10/22/2023] [Accepted: 10/26/2023] [Indexed: 11/26/2023] Open
Abstract
In the past decade, significant advances in molecular research have provided a deeper understanding of the intricate regulatory mechanisms involved in carcinogenesis. MicroRNAs, short non-coding RNA sequences, exert substantial influence on gene expression by repressing translation or inducing mRNA degradation. In the context of cancer, miRNA dysregulation is prevalent and closely associated with various stages of carcinogenesis, including initiation, progression, and metastasis. One crucial aspect of the cancer phenotype is the activity of histone-modifying enzymes that govern chromatin accessibility for transcription factors, thus impacting gene expression. Recent studies have revealed that miRNAs play a significant role in modulating these histone-modifying enzymes, leading to significant implications for genes related to proliferation, differentiation, and apoptosis in cancer cells. This article provides an overview of current research on the mechanisms by which miRNAs regulate the activity of histone-modifying enzymes in the context of cancer. Both direct and indirect mechanisms through which miRNAs influence enzyme expression are discussed. Additionally, potential therapeutic implications arising from miRNA manipulation to selectively impact histone-modifying enzyme activity are presented. The insights from this analysis hold significant therapeutic promise, suggesting the utility of miRNAs as tools for the precise regulation of chromatin-related processes and gene expression. A contemporary focus on molecular regulatory mechanisms opens therapeutic pathways that can effectively influence the control of tumor cell growth and dissemination.
Collapse
Affiliation(s)
- Joanna Szczepanek
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, ul. Wilenska 4, 87-100 Torun, Poland
| | - Andrzej Tretyn
- Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, ul. Lwowska 1, 87-100 Torun, Poland;
| |
Collapse
|
9
|
Lu CF, Zhou YN, Zhang J, Su S, Liu Y, Peng GH, Zang W, Cao J. The role of epigenetic methylation/demethylation in the regulation of retinal photoreceptors. Front Cell Dev Biol 2023; 11:1149132. [PMID: 37305686 PMCID: PMC10251769 DOI: 10.3389/fcell.2023.1149132] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 05/09/2023] [Indexed: 06/13/2023] Open
Abstract
Photoreceptors are integral and crucial for the retina, as they convert light into electrical signals. Epigenetics plays a vital role in determining the precise expression of genetic information in space and time during the development and maturation of photoreceptors, cell differentiation, degeneration, death, and various pathological processes. Epigenetic regulation has three main manifestations: histone modification, DNA methylation, and RNA-based mechanisms, where methylation is involved in two regulatory mechanisms-histone methylation and DNA methylation. DNA methylation is the most studied form of epigenetic modification, while histone methylation is a relatively stable regulatory mechanism. Evidence suggests that normal methylation regulation is essential for the growth and development of photoreceptors and the maintenance of their functions, while abnormal methylation can lead to many pathological forms of photoreceptors. However, the role of methylation/demethylation in regulating retinal photoreceptors remains unclear. Therefore, this study aims to review the role of methylation/demethylation in regulating photoreceptors in various physiological and pathological situations and discuss the underlying mechanisms involved. Given the critical role of epigenetic regulation in gene expression and cellular differentiation, investigating the specific molecular mechanisms underlying these processes in photoreceptors may provide valuable insights into the pathogenesis of retinal diseases. Moreover, understanding these mechanisms could lead to the development of novel therapies that target the epigenetic machinery, thereby promoting the maintenance of retinal function throughout an individual's lifespan.
Collapse
Affiliation(s)
- Chao-Fan Lu
- Department of Anatomy, Basic Medical College, Zhengzhou University, Zhengzhou, China
| | - Ya-Nan Zhou
- Department of Anatomy, Basic Medical College, Zhengzhou University, Zhengzhou, China
| | - Jingjing Zhang
- Department of Anatomy, Basic Medical College, Zhengzhou University, Zhengzhou, China
| | - Songxue Su
- Department of Anatomy, Basic Medical College, Zhengzhou University, Zhengzhou, China
| | - Yupeng Liu
- Department of Anatomy, Basic Medical College, Zhengzhou University, Zhengzhou, China
| | - Guang-Hua Peng
- Department of Pathophysiology, Basic Medical College, Zhengzhou University, Zhengzhou, China
- Laboratory of Visual Cell Differentiation and Regulation, Basic Medical College, Zhengzhou University, Zhengzhou, China
| | - Weidong Zang
- Department of Anatomy, Basic Medical College, Zhengzhou University, Zhengzhou, China
| | - Jing Cao
- Department of Anatomy, Basic Medical College, Zhengzhou University, Zhengzhou, China
| |
Collapse
|
10
|
Zeng J, Jiang G, Liang H, Yan H, Kong X, Duan X, Li Z. Histone demethylase MaJMJ15 is involved in the regulation of postharvest banana fruit ripening. Food Chem 2023; 407:135102. [PMID: 36495744 DOI: 10.1016/j.foodchem.2022.135102] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 11/05/2022] [Accepted: 11/25/2022] [Indexed: 12/03/2022]
Abstract
Histone methylation plays important roles in plant development. However, the role of histone methylation in fruit ripening remains unclear. Here, a total of 16 Jumonji domain-containing proteins (JMJs) were identified from banana genome. During fruit ripening, expression of MaJMJ15 was significantly upregulated. Exogenous ethylene accelerated the upregulation whereas 1-methylcyclopropene delayed the process, suggesting that MaJMJ15 positively regulates banana fruit ripening. MaJMJ15 is an H3K27me3 site-specific demethylase. Transient overexpression of MaJMJ15 promoted banana fruit ripening. Moreover, the global H3K27me3 was decreased by MaJMJ15. Furthermore, MaJMJ15 directly targeted several key ripening-related genes (RRGs) in banana including NAC transcription factor 1/2 (MaNAC1/2), 1-aminocyclopropane-1-carboxylate synthase 1 (MaACS1), 1-aminocyclopropane-1-carboxylate oxidase 1 (MaACO1) and expansin 2 (MaEXP2), removed H3K27me3 from their chromatin, and activated their expression. Our data suggest that MaJMJ15 is an H3K27me3 demethylase, which is involved in the regulation of banana fruit ripening by activating expression of key RRGs via removal of H3K27me3.
Collapse
Affiliation(s)
- Jing Zeng
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guoxiang Jiang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hanzhi Liang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huiling Yan
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiangjin Kong
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xuewu Duan
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou 510650, China; University of Chinese Academy of Sciences, Beijing 100049, China; Agro-food Science and Technology Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China.
| | - Zhiwei Li
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| |
Collapse
|
11
|
Zuo Y, Zhan L, Wen H, Xue J, Tan Y, Sun W, Xu E. Stabilization of nuclear β-catenin by inhibiting KDM2A mediates cerebral ischemic tolerance. FASEB J 2023; 37:e22796. [PMID: 36723950 DOI: 10.1096/fj.202201657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 01/18/2023] [Indexed: 02/02/2023]
Abstract
Hypoxic postconditioning (HPC) with 8% oxygen increases nuclear accumulation of β-catenin through activating the classical Wnt pathway, thereby alleviating transient global cerebral ischemia (tGCI)-induced neuronal damage in the hippocampal CA1 subregion of adult rats. However, little is understood about the regulatory mechanism of nuclear β-catenin in HPC-mediated cerebral ischemic tolerance. Although lysine(K)-specific demethylase 2A (KDM2A) has been known as a crucial regulator of nuclear β-catenin destabilization, whether it plays an important role through modulating nuclear β-catenin in cerebral ischemic tolerance induced by HPC remains unknown. In this study, we explored the molecular mechanism of stabilizing nuclear β-catenin by inhibiting KDM2A-mediated demethylation in the HPC-offered neuroprotection against tGCI. In addition, we confirmed that nuclear methylated-β-catenin in CA1 decreased and nuclear β-catenin turnover increased after tGCI, which were reversed by HPC. The administration with methyltransferase inhibitor AdOx abrogated HPC-induced methylation and stabilization of nuclear β-catenin in CA1, as well as the neuroprotection against tGCI. Notably, HPC downregulated the expression of KDM2A in CA1 and reduced the interaction between KDM2A and β-catenin in the nucleus after tGCI. The knockdown of KDM2A with small-interfering RNA could upregulate nuclear methylated-β-catenin and stabilize β-catenin, thereby increasing survivin in CA1 and improving the cognitive function of rats after tGCI. Opposite results were observed by the administration of KDM2A-carried adenovirus vector. Furthermore, we demonstrated that KDM2A mediates the demethylation of nuclear β-catenin through jumonji C (JmjC) domain of KDM2A in HEK-293T and SH-SY5Y cells. Our data support that the inhibition of KDM2A-mediated demethylation of nuclear β-catenin contributes to HPC-induced neuroprotection against tGCI.
Collapse
Affiliation(s)
- Yunyan Zuo
- Department of Neurology, Institute of Neurosciences, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Lixuan Zhan
- Department of Neurology, Institute of Neurosciences, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Haixia Wen
- Department of Neurology, Institute of Neurosciences, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China.,Department of Neurology, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| | - Jiahui Xue
- Department of Neurology, Institute of Neurosciences, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Yafu Tan
- Department of Neurology, Institute of Neurosciences, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China.,Department of Neurology, the First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Weiwen Sun
- Department of Neurology, Institute of Neurosciences, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - En Xu
- Department of Neurology, Institute of Neurosciences, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| |
Collapse
|
12
|
He C, Liu W, Sun J, Zhang D, Li B. Jumonji domain-containing protein RIOX2 is overexpressed and associated with worse survival outcomes in prostate cancers. Front Oncol 2023; 13:1087082. [PMID: 36776320 PMCID: PMC9911806 DOI: 10.3389/fonc.2023.1087082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 01/09/2023] [Indexed: 01/28/2023] Open
Abstract
Background Histone demethylase RIOX2 was cloned as a c-Myc downstream gene involved in cell proliferation and has been implicated as an oncogenic factor in multiple tumor types. Its expression profiles and correlation with disease progression in prostate cancers are unknown. Methods Transcriptomic profiles of Jumanji domain-containing protein genes were assessed using multiple public expression datasets generated from RNA-seq and cDNA microarray assays. RIOX2 protein expression was assessed using an immunohistochemistry approach on a tissue section array from benign and malignant prostate tissues. Gene expression profiles were analyzed using the bioinformatics software R package. Western blot assay examined androgen stimulation on RIOX2 protein expression in LNCaP cells. Results Among 35 Jumanji domain-containing protein genes, 12 genes were significantly upregulated in prostate cancers compared to benign compartments. COX regression analysis identified that the ribosomal oxygenase 2 (RIOX2) gene was the only one significantly associated with disease-specific survival outcomes in prostate cancer patients. RIOX2 upregulation was confirmed at the protein levels using immunohistochemical assays on prostate cancer tissue sections. Meanwhile, RIOX2 upregulation was associated with clinicopathological features, including late-stage diseases, adverse Gleason scores, TP53 gene mutation, and disease-free status. In castration-resistant prostate cancers (CRPC), RIOX2 expression was positively correlated with AR signaling index but negatively correlated with the neuroendocrinal progression index. However, androgen treatment had no significant stimulatory effect on RIOX2 expression, indicating a parallel but not a causative effect of androgen signaling on RIOX2 gene expression. Further analysis discovered that RIOX2 expression was tightly correlated with its promoter hypomethylation and MYC gene expression, consistent with the notion that RIOX2 was a c-Myc target gene. Conclusion The Jumanji domain-containing protein RIOX2 was significantly overexpressed in prostate cancer, possibly due to c-Myc upregulation. RIOX2 upregulation was identified as an independent prognostic factor for disease-specific survival.
Collapse
Affiliation(s)
- Chenchen He
- Department of Radiation Oncology, The First Affiliated Hospital, Xi’an Jiaotong University, Xi’an, China
| | - Wang Liu
- Department of Urology, The University of Kansas Medical Center, Kansas City, KS, United States
| | - Jiahao Sun
- Department of Radiation Oncology, The First Affiliated Hospital, Xi’an Jiaotong University, Xi’an, China
| | - Da Zhang
- Department of Pathology & Laboratory Medicine, The University of Kansas Medical Center, Kansas City, KS, United States
| | - Benyi Li
- Department of Urology, The University of Kansas Medical Center, Kansas City, KS, United States,Department of Pathology & Laboratory Medicine, The University of Kansas Medical Center, Kansas City, KS, United States,*Correspondence: Benyi Li,
| |
Collapse
|
13
|
Phylogenomic and Evolutionary Analyses Reveal Diversifications of SET-Domain Proteins in Fungi. J Fungi (Basel) 2022; 8:jof8111159. [DOI: 10.3390/jof8111159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 10/28/2022] [Accepted: 10/28/2022] [Indexed: 11/06/2022] Open
Abstract
In recent years, many publications have established histone lysine methylation as a central epigenetic modification in the regulation of chromatin and transcription. The histone lysine methyltransferases contain a conserved SET domain and are widely distributed in various organisms. However, a comprehensive study on the origin and diversification of the SET-domain-containing genes in fungi has not been conducted. In this study, a total of 3816 SET-domain-containing genes, which were identified and characterized using HmmSearch from 229 whole genomes sequenced fungal species, were used to ascertain their evolution and diversification in fungi. Using the CLANS program, all the SET-domain-containing genes were grouped into three main clusters, and each cluster contains several groups. Domain organization analysis showed that genes belonging to the same group have similar sequence structures. In contrast, different groups process domain organizations or locations differently, suggesting the SET-domain-containing genes belonging to different groups may have obtained distinctive regulatory mechanisms during their evolution. These genes that conduct the histone methylations (such as H3K4me, H3K9me, H3K27me, H4K20me, H3K36me) are mainly grouped into Cluster 1 while the other genes grouped into Clusters 2 and 3 are still functionally undetermined. Our results also showed that numerous gene duplication and loss events have happened during the evolution of those fungal SET-domain-containing proteins. Our results provide novel insights into the roles of SET-domain genes in fungal evolution and pave a fundamental path to further understanding the epigenetic basis of gene regulation in fungi.
Collapse
|
14
|
Roessner A, Franke S, Schreier J, Ullmann S, Karras F, Jechorek D. Genetics and epigenetics in conventional chondrosarcoma with focus on non-coding RNAs. Pathol Res Pract 2022; 239:154172. [DOI: 10.1016/j.prp.2022.154172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 10/14/2022] [Accepted: 10/14/2022] [Indexed: 11/09/2022]
|
15
|
Elhossaini H, Hamad M, Irhimeh MR, Nakhla S, Rajarathnam GP, Abbas A. Combined hypoxia hypercapnia delays apoptosis and maintains CD34 cell surface antigen. Biochem Eng J 2022. [DOI: 10.1016/j.bej.2022.108650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
16
|
Vicioso-Mantis M, Aguirre S, Martínez-Balbás MA. JmjC Family of Histone Demethylases Form Nuclear Condensates. Int J Mol Sci 2022; 23:ijms23147664. [PMID: 35887017 PMCID: PMC9319511 DOI: 10.3390/ijms23147664] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 07/08/2022] [Accepted: 07/08/2022] [Indexed: 12/16/2022] Open
Abstract
The Jumonji-C (JmjC) family of lysine demethylases (KDMs) (JMJC-KDMs) plays an essential role in controlling gene expression and chromatin structure. In most cases, their function has been attributed to the demethylase activity. However, accumulating evidence demonstrates that these proteins play roles distinct from histone demethylation. This raises the possibility that they might share domains that contribute to their functional outcome. Here, we show that the JMJC-KDMs contain low-complexity domains and intrinsically disordered regions (IDR), which in some cases reached 70% of the protein. Our data revealed that plant homeodomain finger protein (PHF2), KDM2A, and KDM4B cluster by phase separation. Moreover, our molecular analysis implies that PHF2 IDR contributes to transcription regulation. These data suggest that clustering via phase separation is a common feature that JMJC-KDMs utilize to facilitate their functional responses. Our study uncovers a novel potential function for the JMJC-KDM family that sheds light on the mechanisms to achieve the competent concentration of molecules in time and space within the cell nucleus.
Collapse
|
17
|
Zhao W, Wang X, Zhang Q, Zheng Q, Yao H, Gu X, Liu D, Tian X, Wang X, Li Y, Zhu Z. H3K36 demethylase JMJ710 negatively regulates drought tolerance by suppressing MYB48-1 expression in rice. PLANT PHYSIOLOGY 2022; 189:1050-1064. [PMID: 35253881 PMCID: PMC9157158 DOI: 10.1093/plphys/kiac095] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 01/31/2022] [Indexed: 05/14/2023]
Abstract
The homeostasis of histone methylation is maintained by histone methyltransferases and demethylases, which are important for the regulation of gene expression. Here, we report a histone demethylase from rice (Oryza sativa), Jumonji C domain-containing protein (JMJ710), which belongs to the JMJD6 group and plays an important role in the response to drought stress. Overexpression of JMJ710 causes a drought-sensitive phenotype, while RNAi and clustered regularly interspaced short palindromic repeats (CRISPR)-knockout mutant lines show drought tolerance. In vitro and in vivo assays showed that JMJ710 is a histone demethylase. It targets to MYB TRANSCRIPTION FACTOR 48 (MYB48-1) chromatin, demethylates H3K36me2, and negatively regulates the expression of MYB48-1, a positive regulator of drought tolerance. Under drought stress, JMJ710 is downregulated and the expression of MYB48-1 increases, and the subsequent activation of its downstream drought-responsive genes leads to drought tolerance. This research reports a negative regulator of drought stress-responsive genes, JMJ710, that ensures that the drought tolerance mechanism is not mis-activated under normal conditions but allows quick activation upon drought stress.
Collapse
Affiliation(s)
- Weijie Zhao
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Xiaoyan Wang
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Qian Zhang
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Qian Zheng
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Haitao Yao
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Xiangyang Gu
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Dongliang Liu
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Xuemin Tian
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Xiaoji Wang
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Yongqing Li
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhengge Zhu
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
- Author for correspondence:
| |
Collapse
|
18
|
Genome-wide identification, classification and expression analysis of the JmjC domain-containing histone demethylase gene family in Jatropha curcas L. Sci Rep 2022; 12:6543. [PMID: 35449230 PMCID: PMC9023485 DOI: 10.1038/s41598-022-10584-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 04/05/2022] [Indexed: 12/20/2022] Open
Abstract
JmjC domain-containing proteins, an important family of histone lysine demethylase, play significant roles in maintaining the homeostasis of histone methylation. In this study, we comprehensively analyzed the JmjC domain-containing gene family in Jatropha curcas and found 20 JmjC domain-containing genes (JcJMJ genes). Phylogenetic analysis revealed that these JcJMJ genes can be classified into five major subgroups, and genes in each subgroup had similar motif and domain composition. Cis-regulatory element analysis showed that the number and types of cis-regulatory elements owned by the promoter of JcJMJ genes in different subgroup were significantly different. Moreover, miRNA target prediction result revealed a complicated miRNA-mediated post-transcriptional regulatory network, in which JcJMJ genes were regulated by different numbers and types of miRNAs. Further analysis of the tissue and stress expression profiles showed that many JcJMJ genes had tissue and stress expression specificity. All these results provided valuable information for understanding the evolution of JcJMJ genes and the complex transcriptional and post transcriptional regulation involved, and laid the foundation for further functional analysis of JcJMJ genes.
Collapse
|
19
|
Zhao LF, Qi FY, Zhang JG, Pang JR, Ren HM, Shen DD, Zhao LJ, Qi L, Liu HM, Zheng YC. Identification of the upstream regulators of KDM5B in gastric cancer. Life Sci 2022; 298:120458. [DOI: 10.1016/j.lfs.2022.120458] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 02/19/2022] [Accepted: 03/01/2022] [Indexed: 02/03/2023]
|
20
|
Fischer S, Weber LM, Liefke R. Evolutionary adaptation of the Polycomb repressive complex 2. Epigenetics Chromatin 2022; 15:7. [PMID: 35193659 PMCID: PMC8864842 DOI: 10.1186/s13072-022-00439-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Accepted: 02/08/2022] [Indexed: 12/31/2022] Open
Abstract
The Polycomb repressive complex 2 (PRC2) is an essential chromatin regulatory complex involved in repressing the transcription of diverse developmental genes. PRC2 consists of a core complex; possessing H3K27 methyltransferase activity and various associated factors that are important to modulate its function. During evolution, the composition of PRC2 and the functionality of PRC2 components have changed considerably. Here, we compare the PRC2 complex members of Drosophila and mammals and describe their adaptation to altered biological needs. We also highlight how the PRC2.1 subcomplex has gained multiple novel functions and discuss the implications of these changes for the function of PRC2 in chromatin regulation.
Collapse
Affiliation(s)
- Sabrina Fischer
- Institute of Molecular Biology and Tumor Research (IMT), Philipps University of Marburg, 35043, Marburg, Germany
| | - Lisa Marie Weber
- Institute of Molecular Biology and Tumor Research (IMT), Philipps University of Marburg, 35043, Marburg, Germany
| | - Robert Liefke
- Institute of Molecular Biology and Tumor Research (IMT), Philipps University of Marburg, 35043, Marburg, Germany. .,Department of Hematology, Oncology, and Immunology, University Hospital Giessen and Marburg, 35043, Marburg, Germany.
| |
Collapse
|
21
|
Vogt PH, Zimmer J, Bender U, Strowitzki T. AZFa candidate gene UTY and its X homologue UTX are expressed in human germ cells. REPRODUCTION AND FERTILITY 2022; 2:151-160. [PMID: 35128450 PMCID: PMC8812439 DOI: 10.1530/raf-20-0049] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 05/11/2021] [Indexed: 12/15/2022] Open
Abstract
The Ubiquitous Transcribed Y (UTY a.k.a. KDM6C) AZFa candidate gene on the human Y chromosome and its paralog on the X chromosome, UTX (a.k.a. KDM6A), encode a histone lysine demethylase removing chromatin H3K27 methylation marks at genes transcriptional start sites for activation. Both proteins harbour the conserved Jumonji C (JmjC) domain, functional in chromatin metabolism, and an extended N-terminal tetratricopeptide repeat (TPR) block involved in specific protein interactions. Specific antisera for human UTY and UTX proteins were developed to distinguish the expression of both proteins in human germ cells by immunohistochemical experiments on appropriate tissue sections. In the male germ line, UTY was expressed in the fraction of A spermatogonia located at the basal membrane, probably including spermatogonia stem cells. UTX expression was more spread in all spermatogonia and in early spermatids. In female germ line, UTX expression was found in the primordial germ cells of the ovary. UTY was also expressed during fetal male germ cell development, whereas UTX expression was visible only at distinct gestation weeks. Based on these results and the conserved neighboured location of UTY and DDX3Y in Yq11 found in mammals of distinct lineages, we conclude that UTY, such as DDX3Y, is part of the Azoospermia factor a (AZFa) locus functioning in human spermatogonia to support the balance of their proliferation-differentiation rate before meiosis. Comparable UTY and DDX3Y expression was also found in gonadoblastoma and dysgerminoma cells found in germ cell nests of the dysgenetic gonads of individuals with disorders of sexual development and a Y chromosome in karyotype (DSD-XY). This confirms that AZFa overlaps with GBY, the Gonadoblastoma susceptibility Y locus, and includes the UTY gene.
Collapse
Affiliation(s)
- Peter H Vogt
- Division of Reproduction Genetics, Department of, Gynaecol. Endocrinology & Infertility Disorders, Women Hospital, University of Heidelberg, Germany
| | - Jutta Zimmer
- Division of Reproduction Genetics, Department of, Gynaecol. Endocrinology & Infertility Disorders, Women Hospital, University of Heidelberg, Germany
| | - Ulrike Bender
- Division of Reproduction Genetics, Department of, Gynaecol. Endocrinology & Infertility Disorders, Women Hospital, University of Heidelberg, Germany
| | - Thomas Strowitzki
- Department of Gynaecol. Endocrinology & Infertility Disorders, Women Hospital, University of Heidelberg, Germany
| |
Collapse
|
22
|
Atanasoff-Kardjalieff AK, Studt L. Secondary Metabolite Gene Regulation in Mycotoxigenic Fusarium Species: A Focus on Chromatin. Toxins (Basel) 2022; 14:96. [PMID: 35202124 PMCID: PMC8880415 DOI: 10.3390/toxins14020096] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/20/2022] [Accepted: 01/21/2022] [Indexed: 12/31/2022] Open
Abstract
Fusarium is a species-rich group of mycotoxigenic plant pathogens that ranks as one of the most economically important fungal genera in the world. During growth and infection, they are able to produce a vast spectrum of low-molecular-weight compounds, so-called secondary metabolites (SMs). SMs often comprise toxic compounds (i.e., mycotoxins) that contaminate precious food and feed sources and cause adverse health effects in humans and livestock. In this context, understanding the regulation of their biosynthesis is crucial for the development of cropping strategies that aim at minimizing mycotoxin contamination in the field. Nevertheless, currently, only a fraction of SMs have been identified, and even fewer are considered for regular monitoring by regulatory authorities. Limitations to exploit their full chemical potential arise from the fact that the genes involved in their biosynthesis are often silent under standard laboratory conditions and only induced upon specific stimuli mimicking natural conditions in which biosynthesis of the respective SM becomes advantageous for the producer. This implies a complex regulatory network. Several components of these gene networks have been studied in the past, thereby greatly advancing the understanding of SM gene regulation and mycotoxin biosynthesis in general. This review aims at summarizing the latest advances in SM research in these notorious plant pathogens with a focus on chromatin structure.
Collapse
Affiliation(s)
| | - Lena Studt
- Department of Applied Genetics and Cell Biology, Institute of Microbial Genetics, University of Natural Resources and Life Sciences, Vienna (BOKU), 3430 Tulln an der Donau, Austria;
| |
Collapse
|
23
|
Malbeteau L, Pham HT, Eve L, Stallcup MR, Poulard C, Le Romancer M. How Protein Methylation Regulates Steroid Receptor Function. Endocr Rev 2022; 43:160-197. [PMID: 33955470 PMCID: PMC8755998 DOI: 10.1210/endrev/bnab014] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Indexed: 02/06/2023]
Abstract
Steroid receptors (SRs) are members of the nuclear hormonal receptor family, many of which are transcription factors regulated by ligand binding. SRs regulate various human physiological functions essential for maintenance of vital biological pathways, including development, reproduction, and metabolic homeostasis. In addition, aberrant expression of SRs or dysregulation of their signaling has been observed in a wide variety of pathologies. SR activity is tightly and finely controlled by post-translational modifications (PTMs) targeting the receptors and/or their coregulators. Whereas major attention has been focused on phosphorylation, growing evidence shows that methylation is also an important regulator of SRs. Interestingly, the protein methyltransferases depositing methyl marks are involved in many functions, from development to adult life. They have also been associated with pathologies such as inflammation, as well as cardiovascular and neuronal disorders, and cancer. This article provides an overview of SR methylation/demethylation events, along with their functional effects and biological consequences. An in-depth understanding of the landscape of these methylation events could provide new information on SR regulation in physiology, as well as promising perspectives for the development of new therapeutic strategies, illustrated by the specific inhibitors of protein methyltransferases that are currently available.
Collapse
Affiliation(s)
- Lucie Malbeteau
- Université de Lyon, F-69000 Lyon, France.,Inserm U1052, Centre de Recherche en Cancérologie de Lyon, F-69000 Lyon, France.,CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, F-69000 Lyon, France
| | - Ha Thuy Pham
- Université de Lyon, F-69000 Lyon, France.,Inserm U1052, Centre de Recherche en Cancérologie de Lyon, F-69000 Lyon, France.,CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, F-69000 Lyon, France
| | - Louisane Eve
- Université de Lyon, F-69000 Lyon, France.,Inserm U1052, Centre de Recherche en Cancérologie de Lyon, F-69000 Lyon, France.,CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, F-69000 Lyon, France
| | - Michael R Stallcup
- Department of Biochemistry and Molecular Medicine, Norris Comprehensive Center, University of Southern California, Los Angeles, CA 90089, USA
| | - Coralie Poulard
- Université de Lyon, F-69000 Lyon, France.,Inserm U1052, Centre de Recherche en Cancérologie de Lyon, F-69000 Lyon, France.,CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, F-69000 Lyon, France
| | - Muriel Le Romancer
- Université de Lyon, F-69000 Lyon, France.,Inserm U1052, Centre de Recherche en Cancérologie de Lyon, F-69000 Lyon, France.,CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, F-69000 Lyon, France
| |
Collapse
|
24
|
Lee HW, Jose CC, Cuddapah S. Epithelial-mesenchymal transition: Insights into nickel-induced lung diseases. Semin Cancer Biol 2021; 76:99-109. [PMID: 34058338 PMCID: PMC8627926 DOI: 10.1016/j.semcancer.2021.05.020] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 05/14/2021] [Accepted: 05/17/2021] [Indexed: 02/06/2023]
Abstract
Nickel compounds are environmental toxicants, prevalent in the atmosphere due to their widespread use in several industrial processes, extensive consumption of nickel containing products, as well as burning of fossil fuels. Exposure to nickel is associated with a multitude of chronic inflammatory lung diseases including asthma, chronic obstructive pulmonary disease (COPD) and pulmonary fibrosis. In addition, nickel exposure is implicated in the development of nasal and lung cancers. Interestingly, a common pathogenic mechanism underlying the development of diseases associated with nickel exposure is epithelial-mesenchymal transition (EMT). EMT is a process by which the epithelial cells lose their junctions and polarity and acquire mesenchymal traits, including increased ability to migrate and invade. EMT is a normal and essential physiological process involved in differentiation, development and wound healing. However, EMT also contributes to a number of pathological conditions, including fibrosis, cancer and metastasis. Growing evidence suggest that EMT induction could be an important outcome of nickel exposure. In this review, we discuss the role of EMT in nickel-induced lung diseases and the mechanisms associated with EMT induction by nickel exposure.
Collapse
Affiliation(s)
- Hyun-Wook Lee
- Department of Environmental Medicine, New York University School of Medicine, New York, NY, 10010, USA
| | - Cynthia C Jose
- Department of Environmental Medicine, New York University School of Medicine, New York, NY, 10010, USA
| | - Suresh Cuddapah
- Department of Environmental Medicine, New York University School of Medicine, New York, NY, 10010, USA.
| |
Collapse
|
25
|
Qin Z, Li Z, Yang S, Wang F, Gao T, Tao W, Zhou L, Wang D, Sun L. Genome-wide identification, evolution of histone lysine demethylases (KDM) genes and their expression during gonadal development in Nile tilapia. Comp Biochem Physiol B Biochem Mol Biol 2021; 257:110674. [PMID: 34624518 DOI: 10.1016/j.cbpb.2021.110674] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 09/29/2021] [Accepted: 09/30/2021] [Indexed: 12/16/2022]
Abstract
Histone lysine demethylases (KDM) are responsible for histone demethylation and are involved in gene expression regulation. Previous studies have shown that histone lysine demethylation plays an important role in gonadal development of vertebrates. The KDM family consists of eight subfamilies, i.e., kdm1, kdm2, kdm3, kdm4, kdm5, kdm6, kdm7 and JmjC-only subfamily. In this study, 13 to 63 KDM genes in 23 representative species were identified based on the available version of genome assembly. Phylogenetic relationships, domain architecture, and synteny of these genes were comprehensively analyzed and the results suggested KDM genes probably originated from the early diverging metazoan and significantly expanded in vertebrates with multiple whole genome duplication, especially in the third-round whole genome duplication (3R-WGD) and polyploidization of teleosts. The subfamilies of kdm2, kdm3, kdm4, kdm5, kdm6 and kdm7 were duplicated with 1R-2R events, and duplicates of kdm2a, kdm4a, kdm5b and kdm6b were resulted from 3R-WGD. Based on transcriptome data, the KDM genes were found to be dominantly expressed in the ovary and testis. More than 80% of KDM genes displayed sexual dimorphic expression, with 15 genes dominantly expressed in ovaries, and 12 genes dominantly expressed in testes. Importantly, from transcriptome data, qRT-PCR and fluorescence in situ hybridization during sex reversal, genes with higher expression in ovary than testis, such as kdm1b and two JmjC-only subfamily members hspbap1 and riox1, were downregulated, while other genes, such as kdm3c, kdm5bb, kdm6ba, kdm6bb and kdm7b, with higher expression in testis than ovary, were upregulated in ovotestis, indicating these genes play critical roles in the gonadal development and sex reversal. This study provided new insights into the evolution of the KDM genes and a fundamental clue for understanding their important roles in sex differentiation and gonadal development in teleosts.
Collapse
Affiliation(s)
- Zuliang Qin
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, 400715 Chongqing, PR China
| | - Zhiqiang Li
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, 400715 Chongqing, PR China
| | - Shuangyi Yang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, 400715 Chongqing, PR China
| | - Feilong Wang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, 400715 Chongqing, PR China
| | - Tian Gao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, 400715 Chongqing, PR China
| | - Wenjing Tao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, 400715 Chongqing, PR China
| | - Linyan Zhou
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, 400715 Chongqing, PR China
| | - Deshou Wang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, 400715 Chongqing, PR China
| | - Lina Sun
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, 400715 Chongqing, PR China.
| |
Collapse
|
26
|
Verdikt R, Allard P. Metabolo-epigenetics: the interplay of metabolism and epigenetics during early germ cells development. Biol Reprod 2021; 105:616-624. [PMID: 34132770 PMCID: PMC8444669 DOI: 10.1093/biolre/ioab118] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 06/09/2021] [Accepted: 06/11/2021] [Indexed: 12/26/2022] Open
Abstract
Metabolites control epigenetic mechanisms, and conversly, cell metabolism is regulated at the epigenetic level in response to changes in the cellular environment. In recent years, this metabolo-epigenetic control of gene expression has been implicated in the regulation of multiple stages of embryonic development. The developmental potency of stem cells and their embryonic counterparts is directly determined by metabolic rewiring. Here, we review the current knowledge on the interplay between epigenetics and metabolism in the specific context of early germ cell development. We explore the implications of metabolic rewiring in primordial germ cells in light of their epigenetic remodeling during cell fate determination. Finally, we discuss the relevance of concerted metabolic and epigenetic regulation of primordial germ cells in the context of mammalian transgenerational epigenetic inheritance.
Collapse
Affiliation(s)
- Roxane Verdikt
- Institute for Society and Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Patrick Allard
- Institute for Society and Genetics, University of California, Los Angeles, Los Angeles, CA, USA
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA
| |
Collapse
|
27
|
Dudek J, Kutschka I, Maack C. Metabolic and Redox Regulation of Cardiovascular Stem Cell Biology and Pathology. Antioxid Redox Signal 2021; 35:163-181. [PMID: 33121253 DOI: 10.1089/ars.2020.8201] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Significance: Cardiovascular stem cells are important for regeneration and repair of damaged tissue. Recent Advances: Pluripotent stem cells have a unique metabolism, which is adopted for their energetic and biosynthetic demand as rapidly proliferating cells. Stem cell differentiation requires an exceptional metabolic flexibility allowing for metabolic remodeling between glycolysis and oxidative phosphorylation. Critical Issues: Respiration is associated with the generation of reactive oxygen species (ROS) by the mitochondrial respiratory chain. But also the membrane-bound protein nicotinamide adenine dinucleotide phosphate oxidase (NADPH oxidase, NOX) contributes to ROS levels. ROS not only play a significant role in stem cell differentiation and tissue renewal but also cause senescence and contribute to tissue aging. Future Directions: For utilization of stem cells in therapeutic approaches, a deep understanding of the molecular mechanisms how metabolism and the cellular redox state regulate stem cell differentiation is required. Modulating the redox state of stem cells using antioxidative agents may be suitable to enhance activity of endothelial progenitor cells. Antioxid. Redox Signal. 35, 163-181.
Collapse
Affiliation(s)
- Jan Dudek
- Department of Translational Research, Comprehensive Heart Failure Center (CHFC), University Clinic Würzburg, Würzburg, Germany
| | - Ilona Kutschka
- Department of Translational Research, Comprehensive Heart Failure Center (CHFC), University Clinic Würzburg, Würzburg, Germany
| | - Christoph Maack
- Department of Translational Research, Comprehensive Heart Failure Center (CHFC), University Clinic Würzburg, Würzburg, Germany.,Department of Internal Medicine I, University Hospital Würzburg, Würzburg, Germany
| |
Collapse
|
28
|
Huppertz S, Senger K, Brown A, Leins H, Eiwen K, Mulaw MA, Geiger H, Becker M. KDM6A, a histone demethylase, regulates stress hematopoiesis and early B-cell differentiation. Exp Hematol 2021; 99:32-43.e13. [PMID: 34126175 DOI: 10.1016/j.exphem.2021.06.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 05/26/2021] [Accepted: 06/09/2021] [Indexed: 11/16/2022]
Abstract
Histone methylases and demethylases regulate gene expression programs in hematopoiesis. The molecular function of the demethylase KDM6A in normal hematopoiesis and, in particular, for the hematopoietic stem and progenitor cell (HSPC) compartment remains only partially understood. Female but not male Kdm6a-/- HSPCs were functionally impaired in adoptive transfer experiments as well as upon proliferative stress induced by 5-fluorouracil. Loss of Kdm6a affected primarily early B cells and erythroid and myeloid progenitor cells with respect to both number and function. Global gene expression analyses revealed a shared altered gene signature in Kdm6a-/- pro-B and pre-B cells that is also present in HSPCs, supporting that altered B-cell differentiation in Kdm6a-/- animals is already initiated in HSPCs. Interestingly, loss of KDM6A did not affect the global level of methylation of H3K27, its presumed target, in hematopoietic cells. Our data indicate a critical role for KDM6A in the regulation of hematopoietic differentiation and differentiation-specific gene expression programs, with a prominent role in early B-cell differentiation that is likely independent of H3K27 methylation status.
Collapse
Affiliation(s)
- Sascha Huppertz
- Institute for Medical Radiology and Cell Research (MSZ), Center of Experimental Molecular Medicine (ZEMM), Würzburg University, Würzburg, Germany
| | - Katharina Senger
- Institute of Molecular Medicine, Stem Cells and Aging, Aging Research Center, Ulm University, Ulm, Germany
| | - Andreas Brown
- Institute of Molecular Medicine, Stem Cells and Aging, Aging Research Center, Ulm University, Ulm, Germany
| | - Hanna Leins
- Institute of Molecular Medicine, Stem Cells and Aging, Aging Research Center, Ulm University, Ulm, Germany
| | - Karina Eiwen
- Institute of Molecular Medicine, Stem Cells and Aging, Aging Research Center, Ulm University, Ulm, Germany
| | - Medhanie A Mulaw
- Institute of Experimental Cancer Research, Ulm University, Ulm, Germany
| | - Hartmut Geiger
- Institute of Molecular Medicine, Stem Cells and Aging, Aging Research Center, Ulm University, Ulm, Germany
| | - Matthias Becker
- Institute for Medical Radiology and Cell Research (MSZ), Center of Experimental Molecular Medicine (ZEMM), Würzburg University, Würzburg, Germany.
| |
Collapse
|
29
|
Koleini N, Shapiro JS, Geier J, Ardehali H. Ironing out mechanisms of iron homeostasis and disorders of iron deficiency. J Clin Invest 2021; 131:e148671. [PMID: 34060484 DOI: 10.1172/jci148671] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Iron plays an important role in mammalian physiological processes. It is a critical component for the function of many proteins, including enzymes that require heme and iron-sulfur clusters. However, excess iron is also detrimental because of its ability to catalyze the formation of reactive oxygen species. As a result, cellular and systemic iron levels are tightly regulated to prevent oxidative damage. Iron deficiency can lead to a number of pathological conditions, the most prominent being anemia. Iron deficiency should be corrected to improve adult patients' symptoms and to facilitate normal growth during fetal development and childhood. However, inappropriate use of intravenous iron in chronic conditions, such as cancer and heart failure, in the absence of clear iron deficiency can lead to unwanted side effects. Thus, this form of therapy should be reserved for certain patients who cannot tolerate oral iron and need rapid iron replenishment. Here, we will review cellular and systemic iron homeostasis and will discuss complications of iron deficiency.
Collapse
|
30
|
Macchia PE, Nettore IC, Franchini F, Santana-Viera L, Ungaro P. Epigenetic regulation of adipogenesis by histone-modifying enzymes. Epigenomics 2021; 13:235-251. [PMID: 33502245 DOI: 10.2217/epi-2020-0304] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Many studies investigating the transcriptional control of adipogenesis have been published so far; recently the research is focusing on the role of epigenetic mechanisms in regulating the process of adipocyte development. Histone-modifying enzymes and the histone tails post-transcriptional modifications catalyzed by them, are fundamentally involved in the epigenetic regulation of adipogenesis. In our review, we will discuss recent advances in epigenomic regulation of adipogenesis with a focus on histone-modifying enzymes implicated in the various phases of adipocytes differentiation process from mesenchymal stem cells to mature adipocytes. Understanding adipogenesis, may provide new ways to treat obesity and related metabolic diseases.
Collapse
Affiliation(s)
- Paolo E Macchia
- Department of Clinical Medicine and Surgery, University of Naples Federico II, 80131 Napoli, Italy
| | - Immacolata C Nettore
- Department of Clinical Medicine and Surgery, University of Naples Federico II, 80131 Napoli, Italy
| | - Fabiana Franchini
- Department of Clinical Medicine and Surgery, University of Naples Federico II, 80131 Napoli, Italy
| | - Laura Santana-Viera
- National Research Council - Institute for Experimental Endocrinology & Oncology 'Gaetano Salvatore', 80145 Napoli, Italy
| | - Paola Ungaro
- National Research Council - Institute for Experimental Endocrinology & Oncology 'Gaetano Salvatore', 80145 Napoli, Italy
| |
Collapse
|
31
|
Zhang B, Zhang Y, Jiang X, Su H, Wang Q, Wudu M, Jiang J, Ren H, Xu Y, Liu Z, Qiu X. JMJD8 Promotes Malignant Progression of Lung Cancer by Maintaining EGFR Stability and EGFR/PI3K/AKT Pathway Activation. J Cancer 2021; 12:976-987. [PMID: 33442397 PMCID: PMC7797639 DOI: 10.7150/jca.50234] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 11/16/2020] [Indexed: 12/25/2022] Open
Abstract
JMJD8 is a JmjC domain-containing protein that has not been widely examined, despite its potential role in malignant tumor development. The underlying biological functions and molecular mechanisms of JMJD8 in non-small-cell lung cancer (NSCLC) remain unclear. Herein, we explored the relationship between JMJD8 and the activation of malignancy pathways in NSCLC. Immunohistochemical analyses revealed that high JMJD8 expression significantly correlated with cell differentiation and advanced TNM stages of NSCLC. The overexpression of JMJD8 promoted cell proliferation and invasion in vitro. Upon JMJD8 knockdown in lung cancer cell lines, cyclin B1, RhoA, RhoC, MMP9, and N-cadherin were down-regulated, and p21 and E-cadherin were conversely up-regulated. Key factors in the PI3K/AKT signaling pathway, such as p‑AKT, showed clear decreases in expression; additionally, the expression of epidermal growth factor receptor (EGFR), which functions upstream of PI3K, was altered. Co-immunoprecipitation experiments indicated that JMJD8 interacts with EGFR, and JMJD8 knockdown accelerated EGFR degradation. Our results suggested that JMJD8 functions as an oncogenic regulator in NSCLC. We found that JMJD8 promotes carcinogenic activity in NSCLC cells by facilitating EGFR stability, thereby activating the downstream PI3K/AKT signaling pathway. JMJD8 shows potential as a prognostic marker for lung cancer patients, providing a new target for therapeutic strategies.
Collapse
Affiliation(s)
- Bo Zhang
- Department of Pathology, First Affiliated Hospital and College of Basic Medical Sciences, China Medical University, Shenyang, China
| | - Yao Zhang
- Department of Pathology, First Affiliated Hospital and College of Basic Medical Sciences, China Medical University, Shenyang, China
| | - Xizi Jiang
- Department of Pathology, First Affiliated Hospital and College of Basic Medical Sciences, China Medical University, Shenyang, China
| | - Hongbo Su
- Department of Pathology, First Affiliated Hospital and College of Basic Medical Sciences, China Medical University, Shenyang, China
| | - Qiongzi Wang
- Department of Pathology, First Affiliated Hospital and College of Basic Medical Sciences, China Medical University, Shenyang, China
| | - Muli Wudu
- Department of Pathology, First Affiliated Hospital and College of Basic Medical Sciences, China Medical University, Shenyang, China
| | - Jun Jiang
- Department of Pathology, First Affiliated Hospital and College of Basic Medical Sciences, China Medical University, Shenyang, China
| | - Hongjiu Ren
- Department of Pathology, First Affiliated Hospital and College of Basic Medical Sciences, China Medical University, Shenyang, China
| | - Yitong Xu
- Department of Pathology, First Affiliated Hospital and College of Basic Medical Sciences, China Medical University, Shenyang, China
| | - Zongang Liu
- Department of Thoracic Surgical, Shengjing Hospital Affiliated with China Medical University, Shenyang, China
| | - Xueshan Qiu
- Department of Pathology, First Affiliated Hospital and College of Basic Medical Sciences, China Medical University, Shenyang, China
| |
Collapse
|
32
|
Wang Z, Liu D, Xu B, Tian R, Zuo Y. Modular arrangements of sequence motifs determine the functional diversity of KDM proteins. Brief Bioinform 2020; 22:5912575. [PMID: 32987405 DOI: 10.1093/bib/bbaa215] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Histone lysine demethylases (KDMs) play a vital role in regulating chromatin dynamics and transcription. KDM proteins are given modular activities by its sequence motifs with obvious roles division, which endow the complex and diverse functions. In our review, according to functional features, we classify sequence motifs into four classes: catalytic motifs, targeting motifs, regulatory motifs and potential motifs. JmjC, as the main catalytic motif, combines to Fe2+ and α-ketoglutarate by residues H-D/E-H and S-N-N/Y-K-N/Y-T/S. Targeting motifs make catalytic motifs recognize specific methylated lysines, such as PHD that helps KDM5 to demethylate H3K4me3. Regulatory motifs consist of a functional network. For example, NLS, Ser-rich, TPR and JmjN motifs regulate the nuclear localization. And interactions through the CW-type-C4H2C2-SWIRM are necessary to the demethylase activity of KDM1B. Additionally, many conservative domains that have potential functions but no deep exploration are reviewed for the first time. These conservative domains are usually amino acid-rich regions, which have great research value. The arrangements of four types of sequence motifs generate that KDM proteins diversify toward modular activities and biological functions. Finally, we draw a blueprint of functional mechanisms to discuss the modular activity of KDMs.
Collapse
Affiliation(s)
- Zerong Wang
- State key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of life sciences, Inner Mongolia University
| | - Dongyang Liu
- State key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of life sciences, Inner Mongolia University. He is now studying for a master's degree at the institute of botany of the Chinese Academy of Sciences. His research interests include bioinformatics and computational genomics
| | - Baofang Xu
- State key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of life sciences, Inner Mongolia University
| | - Ruixia Tian
- State key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of life sciences, Inner Mongolia University
| | - Yongchun Zuo
- State key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of life sciences, Inner Mongolia University. His research interests include bioinformatics and integration analysis of multiomics in cell reprogramming
| |
Collapse
|
33
|
Luz-Madrigal A, Grajales-Esquivel E, Tangeman J, Kosse S, Liu L, Wang K, Fausey A, Liang C, Tsonis PA, Del Rio-Tsonis K. DNA demethylation is a driver for chick retina regeneration. Epigenetics 2020; 15:998-1019. [PMID: 32290791 PMCID: PMC7518676 DOI: 10.1080/15592294.2020.1747742] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 02/26/2020] [Accepted: 03/09/2020] [Indexed: 01/01/2023] Open
Abstract
Cellular reprogramming resets the epigenetic landscape to drive shifts in transcriptional programmes and cell identity. The embryonic chick can regenerate a complete neural retina, after retinectomy, via retinal pigment epithelium (RPE) reprogramming in the presence of FGF2. In this study, we systematically analysed the reprogramming competent chick RPE prior to injury, and during different stages of reprogramming. In addition to changes in the expression of genes associated with epigenetic modifications during RPE reprogramming, we observed dynamic changes in histone marks associated with bivalent chromatin (H3K27me3/H3K4me3) and intermediates of the process of DNA demethylation including 5hmC and 5caC. Comprehensive analysis of the methylome by whole-genome bisulphite sequencing (WGBS) confirmed extensive rearrangements of DNA methylation patterns including differentially methylated regions (DMRs) found at promoters of genes associated with chromatin organization and fibroblast growth factor production. We also identified Tet methylcytosine dioxygenase 3 (TET3) as an important factor for DNA demethylation and retina regeneration, capable of reprogramming RPE in the absence of exogenous FGF2. In conclusion, we demonstrate that injury early in RPE reprogramming triggers genome-wide dynamic changes in chromatin, including bivalent chromatin and DNA methylation. In the presence of FGF2, these dynamic modifications are further sustained in the commitment to form a new retina. Our findings reveal active DNA demethylation as an important process that may be applied to remove the epigenetic barriers in order to regenerate retina in mammals. ABBREVIATIONS bp: Base pair; DMR: Differentially methylated region; DMC: Differentially methylated cytosines; GFP: Green fluorescent protein; PCR: Polymerase chain reaction. TET: Ten-eleven translocation; RPE: retinal pigment epithelium.
Collapse
Affiliation(s)
- Agustín Luz-Madrigal
- Department of Biology and Center for Visual Sciences at Miami University, Miami University, Oxford, OH, USA
- Department of Biology and Center for Stem Cell & Organoid Medicine (CuSTOM), Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Erika Grajales-Esquivel
- Department of Biology and Center for Visual Sciences at Miami University, Miami University, Oxford, OH, USA
| | - Jared Tangeman
- Department of Biology and Center for Visual Sciences at Miami University, Miami University, Oxford, OH, USA
| | - Sarah Kosse
- Department of Biology and Center for Visual Sciences at Miami University, Miami University, Oxford, OH, USA
| | - Lin Liu
- Department of Biology and Center for Visual Sciences at Miami University, Miami University, Oxford, OH, USA
| | - Kai Wang
- Department of Biology and Center for Visual Sciences at Miami University, Miami University, Oxford, OH, USA
| | - Andrew Fausey
- Department of Biology and Center for Visual Sciences at Miami University, Miami University, Oxford, OH, USA
| | - Chun Liang
- Department of Biology and Center for Visual Sciences at Miami University, Miami University, Oxford, OH, USA
- Department of Computer Science and Software Engineering, Miami University, Oxford, OH, USA
| | - Panagiotis A. Tsonis
- Department of Biology, University of Dayton and Center for Tissue Regeneration and Engineering at the University of Dayton (TREND), Dayton, OH, USA
| | - Katia Del Rio-Tsonis
- Department of Biology and Center for Visual Sciences at Miami University, Miami University, Oxford, OH, USA
| |
Collapse
|
34
|
Estrogen Induces Selective Transcription of Caveolin1 Variants in Human Breast Cancer through Estrogen Responsive Element-Dependent Mechanisms. Int J Mol Sci 2020; 21:ijms21175989. [PMID: 32825330 PMCID: PMC7503496 DOI: 10.3390/ijms21175989] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 08/13/2020] [Accepted: 08/19/2020] [Indexed: 02/07/2023] Open
Abstract
The estrogen receptor (ER) signaling regulates numerous physiological processes mainly through activation of gene transcription (genomic pathways). Caveolin1 (CAV1) is a membrane-resident protein that behaves as platform to enable different signaling molecules and receptors for membrane-initiated pathways. CAV1 directly interacts with ERs and allows their localization on membrane with consequent activation of ER-non-genomic pathways. Loss of CAV1 function is a common feature of different types of cancers, including breast cancer. Two protein isoforms, CAV1α and CAV1β, derived from two alternative translation initiation sites, are commonly described for this gene. However, the exact transcriptional regulation underlying CAV1 expression pattern is poorly elucidated. In this study, we dissect the molecular mechanism involved in selective expression of CAV1β isoform, induced by estrogens and downregulated in breast cancer. Luciferase assays and Chromatin immunoprecipitation demonstrate that transcriptional activation is triggered by estrogen-responsive elements embedded in CAV1 intragenic regions and DNA-binding of estrogen-ER complexes. This regulatory control is dynamically established by local chromatin changes, as proved by the occurrence of histone H3 methylation/demethylation events and association of modifier proteins as well as modification of H3 acetylation status. Thus, we demonstrate for the first time, an estrogen-ERs-dependent regulatory circuit sustaining selective CAV1β expression.
Collapse
|
35
|
LY75 Ablation Mediates Mesenchymal-Epithelial Transition (MET) in Epithelial Ovarian Cancer (EOC) Cells Associated with DNA Methylation Alterations and Suppression of the Wnt/β-Catenin Pathway. Int J Mol Sci 2020; 21:ijms21051848. [PMID: 32156068 PMCID: PMC7084525 DOI: 10.3390/ijms21051848] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 02/26/2020] [Accepted: 03/05/2020] [Indexed: 02/07/2023] Open
Abstract
Growing evidence demonstrates that epithelial-mesenchymal transition (EMT) plays an important role in epithelial ovarian cancer (EOC) progression and spreading; however, its molecular mechanisms remain poorly defined. We have previously shown that the antigen receptor LY75 can modulate EOC cell phenotype and metastatic potential, as LY75 depletion directed mesenchymal-epithelial transition (MET) in EOC cell lines with mesenchymal phenotype. We used the LY75-mediated modulation of EMT as a model to investigate for DNA methylation changes during EMT in EOC cells, by applying the reduced representation bisulfite sequencing (RRBS) methodology. Numerous genes have displayed EMT-related DNA methylation patterns alterations in their promoter/exon regions. Ten selected genes, whose DNA methylation alterations were further confirmed by alternative methods, were further identified, some of which could represent new EOC biomarkers/therapeutic targets. Moreover, our methylation data were strongly indicative for the predominant implication of the Wnt/β-catenin pathway in the EMT-induced DNA methylation variations in EOC cells. Consecutive experiments, including alterations in the Wnt/β-catenin pathway activity in EOC cells with a specific inhibitor and the identification of LY75-interacting partners by a proteomic approach, were strongly indicative for the direct implication of the LY75 receptor in modulating the Wnt/β-catenin signaling in EOC cells.
Collapse
|
36
|
Inflammation-induced JMJD2D promotes colitis recovery and colon tumorigenesis by activating Hedgehog signaling. Oncogene 2020; 39:3336-3353. [PMID: 32094404 DOI: 10.1038/s41388-020-1219-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 02/10/2020] [Accepted: 02/11/2020] [Indexed: 12/11/2022]
Abstract
Histone demethylase JMJD2D can promote gene expression by specifically demethylating H3K9me2/3. The role of JMJD2D in colitis and colitis-associated colorectal cancer (CRC) progression remains unclear. Here, we show that colonic JMJD2D is induced by TNFα during dextran sulfate sodium-induced colitis. JMJD2D-deficient mice exhibit more severe colon damage and defective colon regeneration due to impaired Hedgehog signaling activation after colitis. JMJD2D knockdown in CRC cells suppresses Hedgehog signaling, resulting in reduced CRC growth and metastasis. Mechanistically, JMJD2D promotes Hedgehog target gene expression through interacting with Gli2 to reduce H3K9me3 levels at the promoter. Clinically, JMJD2D expression is upregulated and positively correlated with Gli2 expression in human inflammatory bowel disease specimens and CRC specimens. The JMJD2D inhibitor 5-c-8HQ or aspirin synergizes with Hedgehog inhibitor vismodegib to inhibit CRC cell proliferation and tumorigenesis. Collectively, our findings unveil an essential role of JMJD2D in activating the processes of colonic protection, regeneration, and tumorigenesis.
Collapse
|
37
|
Stein EM, DiNardo CD, Pollyea DA, Schuh AC. Response Kinetics and Clinical Benefits of Nonintensive AML Therapies in the Absence of Morphologic Response. CLINICAL LYMPHOMA MYELOMA & LEUKEMIA 2020; 20:e66-e75. [DOI: 10.1016/j.clml.2019.11.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 11/05/2019] [Accepted: 11/19/2019] [Indexed: 02/06/2023]
|
38
|
Lavery WJ, Barski A, Wiley S, Schorry EK, Lindsley AW. KMT2C/D COMPASS complex-associated diseases [K CDCOM-ADs]: an emerging class of congenital regulopathies. Clin Epigenetics 2020; 12:10. [PMID: 31924266 PMCID: PMC6954584 DOI: 10.1186/s13148-019-0802-2] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 12/23/2019] [Indexed: 12/15/2022] Open
Abstract
The type 2 lysine methyltransferases KMT2C and KMT2D are large, enzymatically active scaffold proteins that form the core of nuclear regulatory structures known as KMT2C/D COMPASS complexes (complex of proteins associating with Set1). These evolutionarily conserved proteins regulate DNA promoter and enhancer elements, modulating the activity of diverse cell types critical for embryonic morphogenesis, central nervous system development, and post-natal survival. KMT2C/D COMPASS complexes and their binding partners enhance active gene expression of specific loci via the targeted modification of histone-3 tail residues, in general promoting active euchromatic conformations. Over the last 20 years, mutations in five key COMPASS complex genes have been linked to three human congenital syndromes: Kabuki syndrome (type 1 [KMT2D] and 2 [KDM6A]), Rubinstein-Taybi syndrome (type 1 [CBP] and 2 [EP300]), and Kleefstra syndrome type 2 (KMT2C). Here, we review the composition and biochemical function of the KMT2 complexes. The specific cellular and embryonic roles of the KMT2C/D COMPASS complex are highlight with a focus on clinically relevant mechanisms sensitive to haploinsufficiency. The phenotypic similarities and differences between the members of this new family of disorders are outlined and emerging therapeutic strategies are detailed.
Collapse
Affiliation(s)
- William J Lavery
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center (CCHMC), 3333 Burnet Avenue, Cincinnati, OH, 45229-3026, USA
| | - Artem Barski
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center (CCHMC), 3333 Burnet Avenue, Cincinnati, OH, 45229-3026, USA
- Division of Human Genetics, CCHMC, Cincinnati, OH, USA
| | - Susan Wiley
- Division of Developmental and Behavioral Pediatrics, CCHMC, Cincinnati, OH, USA
| | | | - Andrew W Lindsley
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center (CCHMC), 3333 Burnet Avenue, Cincinnati, OH, 45229-3026, USA.
| |
Collapse
|
39
|
Sarno F, Nebbioso A, Altucci L. DOT1L: a key target in normal chromatin remodelling and in mixed-lineage leukaemia treatment. Epigenetics 2019; 15:439-453. [PMID: 31790636 PMCID: PMC7188393 DOI: 10.1080/15592294.2019.1699991] [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] [Indexed: 02/06/2023] Open
Abstract
Methylation of histone 3 at lysine 79 (H3K79) is one of the principal mechanisms involved in gene expression. The histone methyltransferase DOT1L, which mono-, di- and trimethylates H3K79 using S-adenosyl-L-methionine as a co-factor, is involved in cell development, cell cycle progression, and DNA damage repair. However, changes in normal expression levels of this enzyme are found in prostate, breast, and ovarian cancer. High levels of H3K79me are also detected in acute myeloid leukaemia patients bearing MLL rearrangements (MLL-r). MLL translocations are found in approximately 80% of paediatric patients, leading to poor prognosis. DOT1L is recruited on DNA and induces hyperexpression of HOXA9 and MEIS1. Based on these findings, selective drugs have been developed to induce apoptosis in MLL-r leukaemia cells by specifically inhibiting DOT1L. The most potent DOT1L inhibitor pinometostat has been investigated in Phase I clinical trials for treatment of paediatric and adult patients with MLL-driven leukaemia, showing promising results.
Collapse
Affiliation(s)
- Federica Sarno
- Dipartimento di Medicina di Precisione, Università degli Studi della Campania "Luigi Vanvitelli" Napoli, Napoli, Italy
| | - Angela Nebbioso
- Dipartimento di Medicina di Precisione, Università degli Studi della Campania "Luigi Vanvitelli" Napoli, Napoli, Italy
| | - Lucia Altucci
- Dipartimento di Medicina di Precisione, Università degli Studi della Campania "Luigi Vanvitelli" Napoli, Napoli, Italy
| |
Collapse
|
40
|
Drelon C, Rogers MF, Belalcazar HM, Secombe J. The histone demethylase KDM5 controls developmental timing in Drosophila by promoting prothoracic gland endocycles. Development 2019; 146:dev.182568. [PMID: 31862793 PMCID: PMC6955219 DOI: 10.1242/dev.182568] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 12/03/2019] [Indexed: 12/14/2022]
Abstract
In Drosophila, the larval prothoracic gland integrates nutritional status with developmental signals to regulate growth and maturation through the secretion of the steroid hormone ecdysone. While the nutritional signals and cellular pathways that regulate prothoracic gland function are relatively well studied, the transcriptional regulators that orchestrate the activity of this tissue remain less characterized. Here, we show that lysine demethylase 5 (KDM5) is essential for prothoracic gland function. Indeed, restoring kdm5 expression only in the prothoracic gland in an otherwise kdm5 null mutant animal is sufficient to rescue both the larval developmental delay and the pupal lethality caused by loss of KDM5. Our studies show that KDM5 functions by promoting the endoreplication of prothoracic gland cells, a process that increases ploidy and is rate limiting for the expression of ecdysone biosynthetic genes. Molecularly, we show that KDM5 activates the expression of the receptor tyrosine kinase torso, which then promotes polyploidization and growth through activation of the MAPK signaling pathway. Taken together, our studies provide key insights into the biological processes regulated by KDM5 and expand our understanding of the transcriptional regulators that coordinate animal development. Summary: Identification of KDM5 as a new transcriptional regulator of the MAPK signaling cascade provides insights into the molecular mechanisms governing the regulation of ecdysone production and developmental growth control.
Collapse
Affiliation(s)
- Coralie Drelon
- Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | - Michael F Rogers
- Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | - Helen M Belalcazar
- Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | - Julie Secombe
- Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA .,Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, 1410 Pelham Parkway South, Bronx, NY 10461, USA
| |
Collapse
|
41
|
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.
Collapse
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
| |
Collapse
|
42
|
Bachleitner S, Sørensen JL, Gacek-Matthews A, Sulyok M, Studt L, Strauss J. Evidence of a Demethylase-Independent Role for the H3K4-Specific Histone Demethylases in Aspergillus nidulans and Fusarium graminearum Secondary Metabolism. Front Microbiol 2019; 10:1759. [PMID: 31456754 PMCID: PMC6700381 DOI: 10.3389/fmicb.2019.01759] [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] [Received: 05/08/2019] [Accepted: 07/16/2019] [Indexed: 12/11/2022] Open
Abstract
Fungi produce a plethora of secondary metabolites (SMs) involved in cellular protection, defense, and signaling. Like other metabolic processes, transcription of SM biosynthesis genes is tightly regulated to prevent an unnecessary use of resources. Genes involved in SM biosynthesis are usually physically linked, arranged in secondary metabolite gene clusters (SMGCs). Research over the last decades has shown that chromatin structure and posttranslational modifications (PTMs) of histones represent important layers of SMGC regulation. For instance, trimethylation of histone H3 lysine 4 (H3K4me3) is a PTM typically associated with promoter regions of actively transcribed genes. Previously, we have shown that the H3K4me3-specific, JmjC domain-containing histone demethylase KdmB functions not only in repression but also in activation of secondary metabolism in Aspergillus nidulans, suggesting that KdmB has additional functions apart from histone demethylation. In this study, we identified demethylase-independent functions of KdmB in transcriptional regulation of SM gene clusters. Furthermore, we show that this activating and demethylase-independent role of the H3K4 demethylase is also conserved in the phytopathogenic fungus Fusarium graminearum. Lack of FgKdm5 resulted in significant downregulation of five of seven analyzed SMs, whereby only one SMGC depends on a functional JmjC-domain. In A. nidulans strains deficient in H3K4 methylation, i.e., cclA∆, largely phenocopied kdmB∆, while this is not the case for most of the SMs analyzed in Fusarium spp. Notably, KdmB could not rescue the demethylase function in ∆fgkdm5 but restored all demethylase-independent phenotypes.
Collapse
Affiliation(s)
- Simone Bachleitner
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna (BOKU), Vienna, Austria
| | - Jens Laurids Sørensen
- Department of Biotechnology, Chemistry and Environmental Engineering, Aalborg University, Aalborg, Denmark
| | - Agnieszka Gacek-Matthews
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna (BOKU), Vienna, Austria
| | - Michael Sulyok
- Department for Agrobiotechnology (IFA-Tulln), Institute of Bioanalytics and Agro-Metabolomics, University of Natural Resources and Life Sciences, Vienna (BOKU), Vienna, Austria
| | - Lena Studt
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna (BOKU), Vienna, Austria
| | - Joseph Strauss
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna (BOKU), Vienna, Austria
| |
Collapse
|
43
|
Metabolic Plasticity and Epithelial-Mesenchymal Transition. J Clin Med 2019; 8:jcm8070967. [PMID: 31277295 PMCID: PMC6678349 DOI: 10.3390/jcm8070967] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 06/26/2019] [Accepted: 06/28/2019] [Indexed: 01/13/2023] Open
Abstract
A major transcriptional and phenotypic reprogramming event during development is the establishment of the mesodermal layer from the ectoderm through epithelial-mesenchymal transition (EMT). EMT is employed in subsequent developmental events, and also in many physiological and pathological processes, such as the dissemination of cancer cells through metastasis, as a reversible transition between epithelial and mesenchymal states. The remarkable phenotypic remodeling accompanying these transitions is driven by characteristic transcription factors whose activities and/or activation depend upon signaling cues and co-factors, including intermediary metabolites. In this review, we summarize salient metabolic features that enable or instigate these transitions, as well as adaptations undergone by cells to meet the metabolic requirements of their new states, with an emphasis on the roles played by the metabolic regulation of epigenetic modifications, notably methylation and acetylation.
Collapse
|
44
|
Decreased Nuclear Ascorbate Accumulation Accompanied with Altered Genomic Methylation Pattern in Fibroblasts from Arterial Tortuosity Syndrome Patients. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2019; 2019:8156592. [PMID: 30800210 PMCID: PMC6360052 DOI: 10.1155/2019/8156592] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 11/28/2018] [Indexed: 12/12/2022]
Abstract
Ascorbate requiring Fe2+/2-oxoglutarate-dependent dioxygenases located in the nucleoplasm have been shown to participate in epigenetic regulation of gene expression via histone and DNA demethylation. Transport of dehydroascorbic acid is impaired in the endomembranes of fibroblasts from arterial tortuosity syndrome (ATS) patients, due to the mutation in the gene coding for glucose transporter GLUT10. We hypothesized that altered nuclear ascorbate concentration might be present in ATS fibroblasts, affecting dioxygenase activity and DNA demethylation. Therefore, our aim was to characterize the subcellular distribution of vitamin C, the global and site-specific changes in 5-methylcytosine and 5-hydroxymethylcytosine levels, and the effect of ascorbate supplementation in control and ATS fibroblast cultures. Diminished nuclear accumulation of ascorbate was found in ATS fibroblasts upon ascorbate or dehydroascorbic acid addition. Analyzing DNA samples of cultured fibroblasts from controls and ATS patients, a lower global 5-hydroxymethylcytosine level was found in ATS fibroblasts, which could not be significantly modified by ascorbate addition. Investigation of the (hydroxy)methylation status of specific regions in six candidate genes related to ascorbate metabolism and function showed that ascorbate addition could stimulate hydroxymethylation and active DNA demethylation at the PPAR-γ gene region in control fibroblasts only. The altered DNA hydroxymethylation patterns in patient cells both at the global level and at specific gene regions accompanied with decreased nuclear accumulation of ascorbate suggests the epigenetic role of vitamin C in the pathomechanism of ATS. The present findings represent the first example for the role of vitamin C transport in epigenetic regulation suggesting that ATS is a compartmentalization disease.
Collapse
|
45
|
Leon KE, Aird KM. Jumonji C Demethylases in Cellular Senescence. Genes (Basel) 2019; 10:genes10010033. [PMID: 30634491 PMCID: PMC6356615 DOI: 10.3390/genes10010033] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 12/20/2018] [Accepted: 01/03/2019] [Indexed: 12/17/2022] Open
Abstract
Senescence is a stable cell cycle arrest that is either tumor suppressive or tumor promoting depending on context. Epigenetic changes such as histone methylation are known to affect both the induction and suppression of senescence by altering expression of genes that regulate the cell cycle and the senescence-associated secretory phenotype. A conserved group of proteins containing a Jumonji C (JmjC) domain alter chromatin state, and therefore gene expression, by demethylating histones. Here, we will discuss what is currently known about JmjC demethylases in the induction of senescence, and how these enzymes suppress senescence to contribute to tumorigenesis.
Collapse
Affiliation(s)
- Kelly E Leon
- Department of Cellular & Molecular Physiology, Penn Stage College of Medicine, Hershey, PA 17033, USA.
| | - Katherine M Aird
- Department of Cellular & Molecular Physiology, Penn Stage College of Medicine, Hershey, PA 17033, USA.
| |
Collapse
|
46
|
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.
Collapse
|
47
|
Xu W, Zhou B, Zhao X, Zhu L, Xu J, Jiang Z, Chen D, Wei Q, Han M, Feng L, Wang S, Wang X, Zhou J, Jin H. KDM5B demethylates H3K4 to recruit XRCC1 and promote chemoresistance. Int J Biol Sci 2018; 14:1122-1132. [PMID: 29989047 PMCID: PMC6036731 DOI: 10.7150/ijbs.25881] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 06/03/2018] [Indexed: 12/15/2022] Open
Abstract
Chemotherapy is the main treatment for human cancers including gastric cancer. However, in response to chemotherapeutic drugs, tumor cells can develop drug resistance by reprogramming intracellular metabolic and epigenetic networks to maintain their intrinsic homeostasis. Previously, we have established cisplatin-resistant gastric cancer cells as a drug resistant model, and elucidated the XRCC1 as the core DNA repair mechanism of drug resistance. This study investigated the regulation of XRCC1 by lysine demethylase 5B (KDM5B) in drug resistance. We found that the methylation level of H3K4 decreased significantly in drug-resistant cells. The chemical inhibitor of H3K4 demethylases, JIB-04, restored the methylation of H3K4 and blocked the co-localization of XRCC1 and γH2AX, eventually improved drug sensitivity. We further found that the expression level of KDM5B increased significantly in drug-resistant cells. Knockdown of KDM5B increased the methylation level of H3K4 and blocked the localization of XRCC1 to the DNA damage site, leads to increased drug sensitivity. In the sensitive cells, overexpression of KDM5B suppressed H3K4 methylation levels, which resulted to resistance to cisplatin. Moreover, we found that the posttranslational modification of KDM5B is responsible for its high expression in drug-resistant cells. Through mass spectrometry screening and co-immunoprecipitation validation, we found that the molecular chaperone HSP90 forms a complex with KDM5B in drug resistance cells. Interestingly, HSP90 inhibitor 17-AAG induced KDM5B degradation in a time-and-dose-dependent manner, indicating that HSP90 protected KDM5B from protein degradation. Targeting inhibition of HSP90 and KDM5B reversed drug resistance both in vitro and in vivo. Taken together, molecular chaperon HSP90 interacted with KDM5B to protect it from ubiquitin-dependent proteasomal degradation. Increased KDM5B demethylated H3K4 and facilitated the recruitment of XRCC1 to repair damaged DNA. Therefore, inhibition of HSP90 or KDM5B represented a novel approach to reverse chemoresistance in human cancers.
Collapse
Affiliation(s)
- Wenxia Xu
- Laboratory of Cancer Biology, Key Laboratory of Biotherapy in Zhejiang, Sir Run Run Shaw hospital, Medical School of Zhejiang University, China
| | - Bingluo Zhou
- Department of Medical Oncology, Sir Run Run Shaw hospital, Medical School of Zhejiang University, China
| | - Xiaoya Zhao
- Department of Medical Oncology, Sir Run Run Shaw hospital, Medical School of Zhejiang University, China
| | - Liyuan Zhu
- Laboratory of Cancer Biology, Key Laboratory of Biotherapy in Zhejiang, Sir Run Run Shaw hospital, Medical School of Zhejiang University, China
| | - Jinye Xu
- Department of Medical Oncology, Sir Run Run Shaw hospital, Medical School of Zhejiang University, China
| | - Zhinong Jiang
- Department of Pathology, Sir Run Run Shaw hospital, Medical School of Zhejiang University, China
| | - Dingwei Chen
- Department of general surgery, Sir Run Run Shaw hospital, Medical School of Zhejiang University, China
| | - Qi Wei
- Laboratory of Cancer Biology, Key Laboratory of Biotherapy in Zhejiang, Sir Run Run Shaw hospital, Medical School of Zhejiang University, China
| | - Mengjiao Han
- Department of Medical Oncology, Sir Run Run Shaw hospital, Medical School of Zhejiang University, China
| | - Lifeng Feng
- Laboratory of Cancer Biology, Key Laboratory of Biotherapy in Zhejiang, Sir Run Run Shaw hospital, Medical School of Zhejiang University, China
| | - Shouyu Wang
- Department of Molecular Cell Biology and Toxicology, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Xian Wang
- Department of Medical Oncology, Sir Run Run Shaw hospital, Medical School of Zhejiang University, China
| | - Jianwei Zhou
- Department of Molecular Cell Biology and Toxicology, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Hongchuan Jin
- Laboratory of Cancer Biology, Key Laboratory of Biotherapy in Zhejiang, Sir Run Run Shaw hospital, Medical School of Zhejiang University, China
| |
Collapse
|
48
|
Abstract
Protein lysine methylation is a distinct posttranslational modification that causes minimal changes in the size and electrostatic status of lysine residues. Lysine methylation plays essential roles in regulating fates and functions of target proteins in an epigenetic manner. As a result, substrates and degrees (free versus mono/di/tri) of protein lysine methylation are orchestrated within cells by balanced activities of protein lysine methyltransferases (PKMTs) and demethylases (KDMs). Their dysregulation is often associated with neurological disorders, developmental abnormalities, or cancer. Methyllysine-containing proteins can be recognized by downstream effector proteins, which contain methyllysine reader domains, to relay their biological functions. While numerous efforts have been made to annotate biological roles of protein lysine methylation, limited work has been done to uncover mechanisms associated with this modification at a molecular or atomic level. Given distinct biophysical and biochemical properties of methyllysine, this review will focus on chemical and biochemical aspects in addition, recognition, and removal of this posttranslational mark. Chemical and biophysical methods to profile PKMT substrates will be discussed along with classification of PKMT inhibitors for accurate perturbation of methyltransferase activities. Semisynthesis of methyllysine-containing proteins will also be covered given the critical need for these reagents to unambiguously define functional roles of protein lysine methylation.
Collapse
Affiliation(s)
- Minkui Luo
- Chemical Biology Program , Memorial Sloan Kettering Cancer Center , New York , New York 10065 , United States.,Program of Pharmacology, Weill Graduate School of Medical Science , Cornell University , New York , New York 10021 , United States
| |
Collapse
|
49
|
Bargiela D, Burr SP, Chinnery PF. Mitochondria and Hypoxia: Metabolic Crosstalk in Cell-Fate Decisions. Trends Endocrinol Metab 2018; 29:249-259. [PMID: 29501229 DOI: 10.1016/j.tem.2018.02.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 01/31/2018] [Accepted: 02/02/2018] [Indexed: 01/07/2023]
Abstract
Alterations in mitochondrial metabolism influence cell differentiation and growth. This process is regulated by the activity of 2-oxoglutarate (2OG)-dependent dioxygenases (2OGDDs) - a diverse superfamily of oxygen-consuming enzymes - through modulation of the epigenetic landscape and transcriptional responses. Recent reports have described the role of mitochondrial metabolites in directing 2OGDD-driven cell-fate switches in stem cells (SCs), immune cells, and cancer cells. An understanding of the metabolic mechanisms underlying 2OGDD autoregulation is required for therapeutic targeting of this system. We propose a model dependent on oxygen and metabolite availability and discuss how this integrates 2OGDD metabolic signalling, the hypoxic transcriptional response, and fate-determining epigenetic changes.
Collapse
Affiliation(s)
- David Bargiela
- MRC Mitochondrial Biology Unit, Cambridge Biomedical Campus, Cambridge CB2 0XY, UK; Department of Clinical Neurosciences, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Stephen P Burr
- MRC Mitochondrial Biology Unit, Cambridge Biomedical Campus, Cambridge CB2 0XY, UK; Department of Clinical Neurosciences, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Patrick F Chinnery
- MRC Mitochondrial Biology Unit, Cambridge Biomedical Campus, Cambridge CB2 0XY, UK; Department of Clinical Neurosciences, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0QQ, UK.
| |
Collapse
|
50
|
Levin M, Stark M, Assaraf YG. The JmjN domain as a dimerization interface and a targeted inhibitor of KDM4 demethylase activity. Oncotarget 2018; 9:16861-16882. [PMID: 29682190 PMCID: PMC5908291 DOI: 10.18632/oncotarget.24717] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Accepted: 02/25/2018] [Indexed: 12/14/2022] Open
Abstract
Histone methylation is regulated to shape the epigenome by modulating DNA compaction, thus playing central roles in fundamental chromatin-based processes including transcriptional regulation, DNA repair and cell proliferation. Histone methylation is erased by demethylases including the well-established KDM4 subfamily members, however, little is known about their dimerization capacity and its impact on their demethylase activity. Using the powerful bimolecular fluorescence complementation technique, we herein show the in situ formation of human KDM4A and KDM4C homodimers and heterodimers in nuclei of live transfectant cells and evaluate their H3K9me3 demethylation activity. Using size exclusion HPLC as well as Western blot analysis, we show that endogenous KDM4C undergoes dimerization under physiological conditions. Importantly, we identify the JmjN domain as the KDM4C dimerization interface and pin-point specific charged residues therein to be essential for this dimerization. We further demonstrate that KDM4A/C dimerization is absolutely required for their demethylase activity which was abolished by the expression of free JmjN peptides. In contrast, KDM4B does not dimerize and functions as a monomer, and hence was not affected by free JmjN expression. KDM4 proteins are overexpressed in numerous malignancies and their pharmacological inhibition or depletion in cancer cells was shown to impair tumor cell proliferation, invasion and metastasis. Thus, the KDM4 dimer-interactome emerging from the present study bears potential implications for cancer therapeutics via selective inhibition of KDM4A/C demethylase activity using JmjN-based peptidomimetics.
Collapse
Affiliation(s)
- May Levin
- The Fred Wyszkowski Cancer Research Laboratory, Department of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Michal Stark
- The Fred Wyszkowski Cancer Research Laboratory, Department of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Yehuda G Assaraf
- The Fred Wyszkowski Cancer Research Laboratory, Department of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| |
Collapse
|