1
|
Wang Y, Hong Q, Xia Y, Zhang Z, Wen B. The Lysine Demethylase KDM7A Regulates Immediate Early Genes in Neurons. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2301367. [PMID: 37565374 PMCID: PMC10558696 DOI: 10.1002/advs.202301367] [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: 03/01/2023] [Revised: 07/11/2023] [Indexed: 08/12/2023]
Abstract
Lysine demethylase KDM7A removes histone modifications H3K9me1/2 and H3K27me1/2. KDM7A plays critical roles in gene expression and contribute to biological processes including tumorigenesis, metabolism, and embryonic development. However, the functions of KDM7A in mammalian nervous system are still poorly explored. In this study, functional roles of KDM7A are comprehensively investigated in neuronal cells by applying CUT&Tag-seq, RNA-seq and mice models. Knockdown of Kdm7a in N2A cells result in the alteration of histone modifications near transcription start sites (TSSs) and the expression changes of a large number of genes. In particular, the expression of immediate early genes (IEGs), a series of genes maintaining the function of the nervous system and associating with neurological disorders, are significantly decreased upon Kdm7a knockdown. Furthermore, in vivo knockdown of Kdm7a in dentate gyrus (DG) neuron of mice hippocampus, via Adeno-associated virus (AAV)-based stereotaxic microinjection, led to a significant decrease of the expression of c-Fos, a marker of neuron activity. Behavior assays in mice further revealed that Kdm7a knockdown in hippocampus repress neuron activity, which leading to impairment of emotion and memory. Collectively, the study reveals that KDM7A affects neuron functions by regulating IEGs, which may provide new clues for understanding epigenetic mechanisms in neurological disorders.
Collapse
Affiliation(s)
- Yifan Wang
- Key Laboratory of Metabolism and Molecular Medicine of Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical SciencesFudan University200032130 Dong An RoadShanghaiChina
| | - Qin Hong
- Shengli Clinical Medical College of Fujian Medical University, Center for Experimental Research in Clinical MedicineFujian Provincial Hospital134 East StreetFuzhou350001China
| | - Yueyue Xia
- Key Laboratory of Metabolism and Molecular Medicine of Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical SciencesFudan University200032130 Dong An RoadShanghaiChina
| | - Zhao Zhang
- Key Laboratory of Metabolism and Molecular Medicine of Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical SciencesFudan University200032130 Dong An RoadShanghaiChina
| | - Bo Wen
- Key Laboratory of Metabolism and Molecular Medicine of Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical SciencesFudan University200032130 Dong An RoadShanghaiChina
| |
Collapse
|
2
|
Schiano C, Luongo L, Maione S, Napoli C. Mediator complex in neurological disease. Life Sci 2023; 329:121986. [PMID: 37516429 DOI: 10.1016/j.lfs.2023.121986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 07/18/2023] [Accepted: 07/26/2023] [Indexed: 07/31/2023]
Abstract
Neurological diseases, including traumatic brain injuries, stroke (haemorrhagic and ischemic), and inherent neurodegenerative diseases cause acquired disability in humans, representing a leading cause of death worldwide. The Mediator complex (MED) is a large, evolutionarily conserved multiprotein that facilities the interaction between transcription factors and RNA Polymerase II in eukaryotes. Some MED subunits have been found altered in the brain, although their specific functions in neurodegenerative diseases are not fully understood. Mutations in MED subunits were associated with a wide range of genetic diseases for MED12, MED13, MED13L, MED20, MED23, MED25, and CDK8 genes. In addition, MED12 and MED23 were deregulated in the Alzheimer's Disease. Interestingly, most of the genomic mutations have been found in the subunits of the kinase module. To date, there is only one evidence on MED1 involvement in post-stroke cognitive deficits. Although the underlying neurodegenerative disorders may be different, we are confident that the signal cascades of the biological-cognitive mechanisms of brain adaptation, which begin after brain deterioration, may also differ. Here, we analysed relevant studies in English published up to June 2023. They were identified through a search of electronic databases including PubMed, Medline, EMBASE and Scopus, including search terms such as "Mediator complex", "neurological disease", "brains". Thematic content analysis was conducted to collect and summarize all studies demonstrating MED alteration to understand the role of this central transcriptional regulatory complex in the brain. Improved and deeper knowledge of the regulatory mechanisms in neurological diseases can increase the ability of physicians to predict onset and progression, thereby improving diagnostic care and providing appropriate treatment decisions.
Collapse
Affiliation(s)
- Concetta Schiano
- Department of Advanced Medical and Surgical Sciences (DAMSS), University of Campania "Luigi Vanvitelli", Italy.
| | - Livio Luongo
- Department of Experimental Medicine, University of Campania "Luigi Vanvitelli", Italy; IRCSS, Neuromed, Pozzilli, Italy
| | - Sabatino Maione
- Department of Experimental Medicine, University of Campania "Luigi Vanvitelli", Italy; IRCSS, Neuromed, Pozzilli, Italy
| | - Claudio Napoli
- Department of Advanced Medical and Surgical Sciences (DAMSS), University of Campania "Luigi Vanvitelli", Italy; Clinical Department of Internal Medicine and Specialistic Units, Division of Clinical Immunology and Immunohematology, Transfusion Medicine, and Transplant Immunology (SIMT), Regional Reference Laboratory of Transplant Immunology (LIT), Azienda Universitaria Policlinico (AOU), Italy
| |
Collapse
|
3
|
Ilchuk LA, Kubekina MV, Okulova YD, Silaeva YY, Tatarskiy VV, Filatov MA, Bruter AV. Genetically Engineered Mice Unveil In Vivo Roles of the Mediator Complex. Int J Mol Sci 2023; 24:ijms24119330. [PMID: 37298278 DOI: 10.3390/ijms24119330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 05/16/2023] [Accepted: 05/24/2023] [Indexed: 06/12/2023] Open
Abstract
The Mediator complex is a multi-subunit protein complex which plays a significant role in the regulation of eukaryotic gene transcription. It provides a platform for the interaction of transcriptional factors and RNA polymerase II, thus coupling external and internal stimuli with transcriptional programs. Molecular mechanisms underlying Mediator functioning are intensively studied, although most often using simple models such as tumor cell lines and yeast. Transgenic mouse models are required to study the role of Mediator components in physiological processes, disease, and development. As constitutive knockouts of most of the Mediator protein coding genes are embryonically lethal, conditional knockouts and corresponding activator strains are needed for these studies. Recently, they have become more easily available with the development of modern genetic engineering techniques. Here, we review existing mouse models for studying the Mediator, and data obtained in corresponding experiments.
Collapse
Affiliation(s)
- Leonid A Ilchuk
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Marina V Kubekina
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Yulia D Okulova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Yulia Yu Silaeva
- Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov Street, 119334 Moscow, Russia
| | - Victor V Tatarskiy
- Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov Street, 119334 Moscow, Russia
| | - Maxim A Filatov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Alexandra V Bruter
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia
- Federal State Budgetary Institution "N.N. Blokhin National Medical Research Center of Oncology", Ministry of Health of the Russian Federation, Kashirskoe Sh. 24, 115478 Moscow, Russia
| |
Collapse
|
4
|
Jin M, Fei X, Li T, Lu Z, Chu M, Di R, He X, Wang X, Wang Y, Yuan Z, Quan K, Wang H, Wei C. Oar-miR-432 Regulates Fat Differentiation and Promotes the Expression of BMP2 in Ovine Preadipocytes. Front Genet 2022; 13:844747. [PMID: 35559046 PMCID: PMC9087340 DOI: 10.3389/fgene.2022.844747] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 03/11/2022] [Indexed: 11/13/2022] Open
Abstract
The fat tail is a unique characteristic of sheep that represents energy reserves and is a complex adaptative mechanism of fat-tailed sheep to environmental stress. MicroRNA plays a significant role as regulators at the posttranscriptional level, but no studies have explained the molecular mechanisms of miRNA which regulate fat deposition in sheep tails. In this study, mRNA and miRNA analysis examined tail fat tissue from three Hu fat-tailed and three Tibetan thin-tailed sheep. After aligning to the reference sequences, 2,108 differentially expressed genes and 105 differential expression miRNAs were identified, including 1,247 up- and 861 downregulated genes and 43 up- and 62 downregulated miRNAs. Among these differentially expressed miRNAs, oar-miR-432 was one of the most downregulated miRNAs between Hu sheep and Tibetan sheep, and 712 genes were predicted to be targeted by oar-miR-432, 80 of which overlapped with DEGs. The Gene Ontology analysis on these genes showed that BMP2, LEP, GRK5, BMP7, and RORC were enriched in fat cell differentiation terms. The genes for BMP2 targeted by oar-miR-432 were examined using dual-luciferase assay. The oar-miR-432 mimic transfected into preadipocytes resulted in increased expression of BMP2. The marker gene PPAR-γ of fat differentiation had a lower expression than the negative control on days 0, 2, and 4 after induced differentiation. The decrease in the number of lipids in the oar-miR-432 mimic group detected by oil red O stain was also less than that in the negative control. This is the first study to reveal the fat mechanisms by which oar-miR-432 inhibits fat differentiation and promotes the expression of BMP2 in sheep tails.
Collapse
Affiliation(s)
- Meilin Jin
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.,College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xiaojuan Fei
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Taotao Li
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zengkui Lu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Mingxing Chu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ran Di
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaoyun He
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiangyu Wang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuqing Wang
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
| | - Zehu Yuan
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Kai Quan
- College of Animal Science and Technology, Henan University of Animal Husbandry and Economy, Zhengzhou, China
| | - Huihua Wang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Caihong Wei
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| |
Collapse
|
5
|
Recent advances in nucleotide analogue-based techniques for tracking dividing stem cells: An overview. J Biol Chem 2021; 297:101345. [PMID: 34717955 PMCID: PMC8592869 DOI: 10.1016/j.jbc.2021.101345] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 10/18/2021] [Accepted: 10/19/2021] [Indexed: 01/14/2023] Open
Abstract
Detection of thymidine analogues after their incorporation into replicating DNA represents a powerful tool for the study of cellular DNA synthesis, progression through the cell cycle, cell proliferation kinetics, chronology of cell division, and cell fate determination. Recent advances in the concurrent detection of multiple such analogues offer new avenues for the investigation of unknown features of these vital cellular processes. Combined with quantitative analysis, temporal discrimination of multiple labels enables elucidation of various aspects of stem cell life cycle in situ, such as division modes, differentiation, maintenance, and elimination. Data obtained from such experiments are critically important for creating descriptive models of tissue histogenesis and renewal in embryonic development and adult life. Despite the wide use of thymidine analogues in stem cell research, there are a number of caveats to consider for obtaining valid and reliable labeling results when marking replicating DNA with nucleotide analogues. Therefore, in this review, we describe critical points regarding dosage, delivery, and detection of nucleotide analogues in the context of single and multiple labeling, outline labeling schemes based on pulse-chase, cumulative and multilabel marking of replicating DNA for revealing stem cell proliferative behaviors, and determining cell cycle parameters, and discuss preconditions and pitfalls in conducting such experiments. The information presented in our review is important for rational design of experiments on tracking dividing stem cells by marking replicating DNA with thymidine analogues.
Collapse
|
6
|
Tan C, Zhu S, Chen Z, Liu C, Li YE, Zhu M, Zhang Z, Zhang Z, Zhang L, Gu Y, Liang Z, Boyer TG, Ouyang K, Evans SM, Fang X. Mediator complex proximal Tail subunit MED30 is critical for Mediator core stability and cardiomyocyte transcriptional network. PLoS Genet 2021; 17:e1009785. [PMID: 34506481 PMCID: PMC8432849 DOI: 10.1371/journal.pgen.1009785] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 08/18/2021] [Indexed: 01/28/2023] Open
Abstract
Dysregulation of cardiac transcription programs has been identified in patients and families with heart failure, as well as those with morphological and functional forms of congenital heart defects. Mediator is a multi-subunit complex that plays a central role in transcription initiation by integrating regulatory signals from gene-specific transcriptional activators to RNA polymerase II (Pol II). Recently, Mediator subunit 30 (MED30), a metazoan specific Mediator subunit, has been associated with Langer-Giedion syndrome (LGS) Type II and Cornelia de Lange syndrome-4 (CDLS4), characterized by several abnormalities including congenital heart defects. A point mutation in MED30 has been identified in mouse and is associated with mitochondrial cardiomyopathy. Very recent structural analyses of Mediator revealed that MED30 localizes to the proximal Tail, anchoring Head and Tail modules, thus potentially influencing stability of the Mediator core. However, in vivo cellular and physiological roles of MED30 in maintaining Mediator core integrity remain to be tested. Here, we report that deletion of MED30 in embryonic or adult cardiomyocytes caused rapid development of cardiac defects and lethality. Importantly, cardiomyocyte specific ablation of MED30 destabilized Mediator core subunits, while the kinase module was preserved, demonstrating an essential role of MED30 in stability of the overall Mediator complex. RNAseq analyses of constitutive cardiomyocyte specific Med30 knockout (cKO) embryonic hearts and inducible cardiomyocyte specific Med30 knockout (icKO) adult cardiomyocytes further revealed critical transcription networks in cardiomyocytes controlled by Mediator. Taken together, our results demonstrated that MED30 is essential for Mediator stability and transcriptional networks in both developing and adult cardiomyocytes. Our results affirm the key role of proximal Tail modular subunits in maintaining core Mediator stability in vivo.
Collapse
Affiliation(s)
- Changming Tan
- Department of Medicine, University of California, San Diego, California, United States of America
- Department of Cardiovascular Surgery, the Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Siting Zhu
- Department of Medicine, University of California, San Diego, California, United States of America
- Department of Cardiovascular Surgery, Peking University Shenzhen Hospital, School of Chemical Biology and Biotechnology, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Zee Chen
- Department of Medicine, University of California, San Diego, California, United States of America
- Department of Cardiovascular Surgery, Peking University Shenzhen Hospital, School of Chemical Biology and Biotechnology, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Canzhao Liu
- Department of Medicine, University of California, San Diego, California, United States of America
| | - Yang E. Li
- Department of Medicine, University of California, San Diego, California, United States of America
| | - Mason Zhu
- Department of Medicine, University of California, San Diego, California, United States of America
| | - Zhiyuan Zhang
- Department of Medicine, University of California, San Diego, California, United States of America
- Department of Cardiovascular Surgery, the Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Zhiwei Zhang
- Department of Medicine, University of California, San Diego, California, United States of America
- Department of Cardiovascular Surgery, the Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Lunfeng Zhang
- Department of Medicine, University of California, San Diego, California, United States of America
| | - Yusu Gu
- Department of Medicine, University of California, San Diego, California, United States of America
| | - Zhengyu Liang
- Department of Medicine, University of California, San Diego, California, United States of America
| | - Thomas G. Boyer
- Department of Molecular Medicine, University of Texas Health Science Center, San Antonio, Texas, United States of America
| | - Kunfu Ouyang
- Department of Cardiovascular Surgery, Peking University Shenzhen Hospital, School of Chemical Biology and Biotechnology, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Sylvia M. Evans
- Department of Medicine, University of California, San Diego, California, United States of America
- Department of Pharmacology, University of California, San Diego, California, United States of America
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, California, United States of America
| | - Xi Fang
- Department of Medicine, University of California, San Diego, California, United States of America
| |
Collapse
|
7
|
Yu B, Yao Y, Zhang X, Ruan M, Zhang Z, Xu L, Liang T, Lu J. Synergic Neuroprotection Between Ligusticum Chuanxiong Hort and Borneol Against Ischemic Stroke by Neurogenesis via Modulating Reactive Astrogliosis and Maintaining the Blood-Brain Barrier. Front Pharmacol 2021; 12:666790. [PMID: 34220506 PMCID: PMC8242197 DOI: 10.3389/fphar.2021.666790] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 05/21/2021] [Indexed: 01/26/2023] Open
Abstract
Background:Ligusticum chuanxiong Hort (LCH) is a famous ethnomedicine in Asia known for its excellent output on stroke treatment, and borneol usually acts as an assistant for its reducing permeability of the blood–brain barrier (BBB) after stroke. Although their synergy against brain ischemia was verified in previous studies, the potential mechanism is still unknown. Methods: The research aimed to explore the exact synergic mechanisms between LCH and borneol on neurogenesis within the areas of the dentate gyrus and subventricular zone. After treating middle cerebral artery occlusion rats with LCH (0.1 g/kg) and/or borneol (0.08 g/kg), the neurological severity score, brain infarct ratio, Nissl staining, Evans blue permeability, BBB ultrastructure, and expressions of von Willebrand factor and tight junction–associated proteins were measured. Co-localizations of Nestin+/BrdU+ and doublecortin+/BrdU+, and expressions of neuronal nuclei (NeuN) and glial fibrillary acidic protein (GFAP) were observed under a fluorescence microscope. Moreover, astrocyte polarization markers of complement component 3 and pentraxin 3, and relevant neurotrophins were also detected by immunoblotting. Results: Basically, LCH and borneol had different focuses, although both of them decreased infarct areas, and increased quantity of Nissl bodies and expression of brain-derived neurotrophic factor. LCH increased the neurological severity score, NeuN+ cells, and the ratios of Nestin+/BrdU+ and doublecortin+/BrdU+, and decreased GFAP+ cells and ciliary neurotrophic factor expression. Additionally, it regulated the expressions of complement component 3 and pentraxin 3 to transform astrocyte phenotypes. Borneol improved BBB ultrastructure and increased the expressions of von Willebrand factor, tight junction–associated proteins, vascular endothelial growth factor, and vascular endothelial growth factor receptor 2. Unexpectedly, their combined therapy showed more obvious regulations on the Nissl score, Evans blue permeability, doublecortin+/BrdU+, NeuN+ cells, brain-derived neurotrophic factor, and vascular endothelial growth factor than both of their monotherapies. Conclusions: The results indicated that LCH and borneol were complementary to each other in attenuating brain ischemia by and large. LCH mainly promoted neural stem cell proliferation, neurogenesis, and mature neuron preservation, which was probably related to the transformation of reactive astrocytes from A1 subtype to A2, while borneol preferred to maintain the integrity of the BBB, which provided neurogenesis with a homeostatic environment.
Collapse
Affiliation(s)
- Bin Yu
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yao Yao
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, China
| | - Xiaofeng Zhang
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, China
| | - Ming Ruan
- School of Food Science, Nanjing Xiaozhuang University, Nanjing, China
| | - Zhennian Zhang
- Department of Encephalopathy, Nanjing Hospital of Traditional Chinese Medicine, Nanjing, China
| | - Li Xu
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, China
| | - Tao Liang
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, China
| | - Jinfu Lu
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, China
| |
Collapse
|