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Tang Y, Jia Z, Xu H, Da LT, Wu Q. Mechanism of REST/NRSF regulation of clustered protocadherin α genes. Nucleic Acids Res 2021; 49:4506-4521. [PMID: 33849071 PMCID: PMC8096226 DOI: 10.1093/nar/gkab248] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/23/2021] [Accepted: 03/26/2021] [Indexed: 12/16/2022] Open
Abstract
Repressor element-1 silencing transcription factor (REST) or neuron-restrictive silencer factor (NRSF) is a zinc-finger (ZF) containing transcriptional repressor that recognizes thousands of neuron-restrictive silencer elements (NRSEs) in mammalian genomes. How REST/NRSF regulates gene expression remains incompletely understood. Here, we investigate the binding pattern and regulation mechanism of REST/NRSF in the clustered protocadherin (PCDH) genes. We find that REST/NRSF directionally forms base-specific interactions with NRSEs via tandem ZFs in an anti-parallel manner but with striking conformational changes. In addition, REST/NRSF recruitment to the HS5-1 enhancer leads to the decrease of long-range enhancer-promoter interactions and downregulation of the clustered PCDHα genes. Thus, REST/NRSF represses PCDHα gene expression through directional binding to a repertoire of NRSEs within the distal enhancer and variable target genes.
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Affiliation(s)
- Yuanxiao Tang
- Center for Comparative Biomedicine, MOE Key Laboratory of Systems Biomedicine, State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Institute of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zhilian Jia
- Center for Comparative Biomedicine, MOE Key Laboratory of Systems Biomedicine, State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Institute of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Honglin Xu
- Center for Comparative Biomedicine, MOE Key Laboratory of Systems Biomedicine, State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Institute of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lin-tai Da
- Center for Comparative Biomedicine, MOE Key Laboratory of Systems Biomedicine, State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Institute of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qiang Wu
- Center for Comparative Biomedicine, MOE Key Laboratory of Systems Biomedicine, State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Institute of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
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52
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Wang YC, Liu P, Yue LY, Huang F, Xu YX, Zhu CQ. NRSF deficiency leads to abnormal postnatal development of dentate gyrus and impairment of progenitors in subgranular zone of hippocampus. Hippocampus 2021; 31:935-956. [PMID: 33960056 DOI: 10.1002/hipo.23336] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 04/19/2021] [Accepted: 04/25/2021] [Indexed: 02/05/2023]
Abstract
Neuron-restrictive silencing factor (NRSF) is a zinc-finger transcription factor that regulates expression of a diverse set of genes. However, NRSF function in brain development still remains elusive. In the present study, we generated NRSF-conditional knockout (NRSF-cKO) mice by hGFAP-Cre/loxp system to study the effect of NRSF deficiency on brain development. Results showed that NRSF conditional knockout caused a smaller hippocampus and a thinner granule cell layer (GCL) in mice. Moreover, the reduction and disarrangement of GFAP+ cells in subgranular zone (SGZ) of NRSF-cKO mice was accompanied with the decreased number of premature neurons, neural stem cells (NSCs) and neural progenitor cells (NPCs), as well as compromising the majority of mitotically active cells. The analysis of postnatal development of hippocampus indicated the existence of an abnormality at postnatal day (P) 8, rather than at P1, in NRSF-cKO mice, although the densities of Ki67+ cells with mitotic ability in dentate gyrus were relatively unaffected at P1 and P8. Meanwhile, NRSF deficiency led to abnormal organization of SGZ at P8 during postnatal development. RNA-Seq analysis revealed 79 deregulated genes in hippocampus of NRSF-cKO mice at P8, which were involved in p53 signal transduction, neuron migration and negative regulation of cell proliferation, etc. The deregulation of p53 pathway in NRSF-cKO mice at P1 and P8 was evidenced, of which p21/Cdkn1a was accumulated in a portion of NSCs and NPCs in hippocampus during postnatal development. Together, these results, for the first time, revealed that NRSF could significantly influence the postnatal development of hippocampus, especially the formation of SGZ.
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Affiliation(s)
- Yan-Cong Wang
- Department of Translational Neuroscience, Jing'an District Center Hospital of Shanghai, State Key Laboratory of Medical Neurobiology and MOE Frontier Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai, China
| | - Pu Liu
- Department of Translational Neuroscience, Jing'an District Center Hospital of Shanghai, State Key Laboratory of Medical Neurobiology and MOE Frontier Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai, China
| | - Ling-Yun Yue
- Department of Translational Neuroscience, Jing'an District Center Hospital of Shanghai, State Key Laboratory of Medical Neurobiology and MOE Frontier Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai, China
| | - Fang Huang
- Department of Translational Neuroscience, Jing'an District Center Hospital of Shanghai, State Key Laboratory of Medical Neurobiology and MOE Frontier Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai, China
| | - Yu-Xia Xu
- Department of Translational Neuroscience, Jing'an District Center Hospital of Shanghai, State Key Laboratory of Medical Neurobiology and MOE Frontier Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai, China
| | - Cui-Qing Zhu
- Department of Translational Neuroscience, Jing'an District Center Hospital of Shanghai, State Key Laboratory of Medical Neurobiology and MOE Frontier Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai, China
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53
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Dolatshahi M, Ranjbar Hameghavandi MH, Sabahi M, Rostamkhani S. Nuclear factor-kappa B (NF-κB) in pathophysiology of Parkinson disease: Diverse patterns and mechanisms contributing to neurodegeneration. Eur J Neurosci 2021; 54:4101-4123. [PMID: 33884689 DOI: 10.1111/ejn.15242] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 03/25/2021] [Accepted: 04/07/2021] [Indexed: 01/02/2023]
Abstract
Parkinson's disease (PD), the most common movement disorder, comprises several pathophysiologic mechanisms including misfolded alpha-synuclein aggregation, inflammation, mitochondrial dysfunction, and synaptic loss. Nuclear Factor-Kappa B (NF-κB), as a key regulator of a myriad of cellular reactions, is shown to be involved in such mechanisms associated with PD, and the changes in NF-κB expression is implicated in PD. Alpha-synuclein accumulation, the characteristic feature of PD pathology, is known to trigger NF-κB activation in neurons, thereby propagating apoptosis through several mechanisms. Furthermore, misfolded alpha-synuclein released from degenerated neurons, activates several signaling pathways in glial cells which culminate in activation of NF-κB and production of pro-inflammatory cytokines, thereby aggravating neurodegenerative processes. On the other hand, NF-κB activation, acting as a double-edged sword, can be necessary for survival of neurons. For instance, NF-κB activation is necessary for competent mitochondrial function and deficiency in c-Rel, one of the NF-κB proteins, is known to propagate DA neuron loss via several mechanisms. Despite the dual role of NF-κB in PD, several agents by selectively modifying the mechanisms and pathways associated with NF-κB, can be effective in attenuating DA neuron loss and PD, as reviewed in this paper.
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Affiliation(s)
- Mahsa Dolatshahi
- Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran
- NeuroImaging Network (NIN), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | | | - Mohammadmahdi Sabahi
- NeuroImaging Network (NIN), Universal Scientific Education and Research Network (USERN), Tehran, Iran
- Neurosurgery Research Group (NRG), Student Research Committee, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Sabra Rostamkhani
- Sina Trauma and Surgery Research Center, Tehran University of Medical Sciences, Tehran, Iran
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54
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Song Y, Dagil L, Fairall L, Robertson N, Wu M, Ragan TJ, Savva CG, Saleh A, Morone N, Kunze MBA, Jamieson AG, Cole PA, Hansen DF, Schwabe JWR. Mechanism of Crosstalk between the LSD1 Demethylase and HDAC1 Deacetylase in the CoREST Complex. Cell Rep 2021; 30:2699-2711.e8. [PMID: 32101746 PMCID: PMC7043024 DOI: 10.1016/j.celrep.2020.01.091] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 12/31/2019] [Accepted: 01/24/2020] [Indexed: 01/08/2023] Open
Abstract
The transcriptional corepressor complex CoREST is one of seven histone deacetylase complexes that regulate the genome through controlling chromatin acetylation. The CoREST complex is unique in containing both histone demethylase and deacetylase enzymes, LSD1 and HDAC1, held together by the RCOR1 scaffold protein. To date, it has been assumed that the enzymes function independently within the complex. Now, we report the assembly of the ternary complex. Using both structural and functional studies, we show that the activity of the two enzymes is closely coupled and that the complex can exist in at least two distinct states with different kinetics. Electron microscopy of the complex reveals a bi-lobed structure with LSD1 and HDAC1 enzymes at opposite ends of the complex. The structure of CoREST in complex with a nucleosome reveals a mode of chromatin engagement that contrasts with previous models. The activities of LSD1 and HDAC1 are closely coupled in the CoREST complex Both LSD1 and HDAC1 exist in two different kinetic states CoREST has a bi-lobed, flexible structure with the two enzymes located at opposite ends CoREST interacts with methylated nucleosomes via LSD1, but not HDAC1 or RCOR1
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Affiliation(s)
- Yun Song
- Leicester Institute of Chemical and Molecular Biology, Department of Molecular and Cell Biology, University of Leicester, Lancaster Road, Leicester LE1 7RH, UK
| | - Lisbeth Dagil
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London WC1E 6BT, UK
| | - Louise Fairall
- Leicester Institute of Chemical and Molecular Biology, Department of Molecular and Cell Biology, University of Leicester, Lancaster Road, Leicester LE1 7RH, UK
| | - Naomi Robertson
- Department of Chemistry, University of Leicester, University Road, Leicester LE1 7RH, UK
| | - Mingxuan Wu
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - T J Ragan
- Leicester Institute of Chemical and Molecular Biology, Department of Molecular and Cell Biology, University of Leicester, Lancaster Road, Leicester LE1 7RH, UK
| | - Christos G Savva
- Leicester Institute of Chemical and Molecular Biology, Department of Molecular and Cell Biology, University of Leicester, Lancaster Road, Leicester LE1 7RH, UK
| | - Almutasem Saleh
- Leicester Institute of Chemical and Molecular Biology, Department of Molecular and Cell Biology, University of Leicester, Lancaster Road, Leicester LE1 7RH, UK
| | - Nobuhiro Morone
- MRC-Toxicology Unit, University of Cambridge, University Road, Leicester LE1 7RH, UK
| | - Micha B A Kunze
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London WC1E 6BT, UK
| | - Andrew G Jamieson
- Department of Chemistry, University of Leicester, University Road, Leicester LE1 7RH, UK
| | - Philip A Cole
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - D Flemming Hansen
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London WC1E 6BT, UK.
| | - John W R Schwabe
- Leicester Institute of Chemical and Molecular Biology, Department of Molecular and Cell Biology, University of Leicester, Lancaster Road, Leicester LE1 7RH, UK.
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55
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Harada M, Nagai J, Kurata R, Cui X, Isagawa T, Semba H, Yoshida Y, Takeda N, Maemura K, Yonezawa T. Establishment of Novel Protein Interaction Assays between Sin3 and REST Using Surface Plasmon Resonance and Time-Resolved Fluorescence Energy Transfer. Int J Mol Sci 2021; 22:ijms22052323. [PMID: 33652591 PMCID: PMC7956749 DOI: 10.3390/ijms22052323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 02/12/2021] [Accepted: 02/22/2021] [Indexed: 11/16/2022] Open
Abstract
Repressor element-1 (RE-1) or neural restrictive silencer element (NRSE) bound with a zinc finger transcription repressor, RE-1 silencing transcription factor (REST, also known as neural restrictive silencer factor, NRSF) has been identified as a fundamental repressor element in many genes, including neuronal genes. Genes regulated by REST/NRSF regulate multifaceted neuronal phenotypes, and their defects in the machinery cause neuropathies, disorders of neuron activity), autism and so on. In REST repressions, the N-terminal repressor domain recruits Sin3B via its paired amphipathic helix 1 (PAH1) domain, which plays an important role as a scaffold for histone deacetylase 1 and 2. This machinery has a critical role in maintaining neuronal robustness. In this study, in order to establish protein–protein interaction assays mimicking a binding surface between Sin3B and REST, we selected important amino acids from structural information of the PAH1/REST complex and then tried to reconstitute it using recombinant short peptides derived from PAH1/REST. Initially, we validated whether biotinylated REST interacts with glutathione S-transferase (GST)-tagged PAH1 and whether another PAH1 peptide (PAH1-FLAG) competitively binds with biotinylated REST using surface plasmon resonance (SPR). We observed a direct interaction and competitive binding of two PAH1 peptides. Secondly, in order to establish a high-throughput and high-dynamic-range assay, we utilized an easily performed novel time-resolved fluorescence energy transfer (TR-FRET) assay, and closely monitored this interaction. Finally, we succeeded in establishing a novel high-quality TR-FRET assay and a novel interaction assay based on SPR.
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Affiliation(s)
- Masamitsu Harada
- Center for Therapeutic Innovation, Gene Research Center for Frontiers Life Sciences, Nagasaki University, Graduate School of Biomedical Sciences, 1-12-14 Sakamoto, Nagasaki 852-8523, Japan; (M.H.); (J.N.)
| | - Jun Nagai
- Center for Therapeutic Innovation, Gene Research Center for Frontiers Life Sciences, Nagasaki University, Graduate School of Biomedical Sciences, 1-12-14 Sakamoto, Nagasaki 852-8523, Japan; (M.H.); (J.N.)
| | - Riho Kurata
- Education and Research Center for Pharmaceutical Sciences, Osaka University of Pharmaceutical Sciences, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan;
| | - Xiaofeng Cui
- School of Chemistry, Chemical Engineering and Life Sciences, School of Materials and Engineering, Wuhan University of Technology, 122 Loushi Rd, Wuhan 430070, China;
| | - Takayuki Isagawa
- Data Science Center, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke 329-0498, Japan;
| | - Hiroaki Semba
- Department of Cardiovascular Medicine, The Cardiovascular Institute, Nishiazabu 3-2-19, Minato-ku, Tokyo 106-0031, Japan;
| | - Yasuhiro Yoshida
- Department of Immunology and Parasitology, University of Occupational and Environmental Health, 1-1 Iseigaoka, Yahatanishi-ku, Kitakyushu 807-8555, Japan;
| | - Norihiko Takeda
- Division of Cardiology and Metabolism, Center for Molecular Medicine, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke 329-0498, Japan;
| | - Koji Maemura
- Department of Cardiovascular Medicine, Graduate School of Biomedical Sciences, Nagasaki University Hospital, 1-7-1 Sakamoto, Nagasaki 852-8501, Japan;
| | - Tomo Yonezawa
- Center for Therapeutic Innovation, Gene Research Center for Frontiers Life Sciences, Nagasaki University, Graduate School of Biomedical Sciences, 1-12-14 Sakamoto, Nagasaki 852-8523, Japan; (M.H.); (J.N.)
- Correspondence: or ; Tel.: +81-95-819-8525
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56
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Stelman CR, Smith BM, Chandra B, Roberts-Galbraith RH. CBP/p300 homologs CBP2 and CBP3 play distinct roles in planarian stem cell function. Dev Biol 2021; 473:130-143. [PMID: 33607113 DOI: 10.1016/j.ydbio.2021.02.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 02/08/2021] [Accepted: 02/09/2021] [Indexed: 11/19/2022]
Abstract
Chromatin modifications function as critical regulators of gene expression and cellular identity, especially in the regulation and maintenance of the pluripotent state. However, many studies of chromatin modification in stem cells-and pluripotent stem cells in particular-are performed in mammalian stem cell culture, an in vitro condition mimicking a very transient state during mammalian development. Thus, new models for studying pluripotent stem cells in vivo could be helpful for understanding the roles of chromatin modification, for confirming prior in vitro studies, and for exploring evolution of the pluripotent state. The freshwater flatworm, Schmidtea mediterranea, is an excellent model for studying adult pluripotent stem cells, particularly in the context of robust, whole-body regeneration. To identify chromatin modifying and remodeling enzymes critical for planarian regeneration and stem cell maintenance, we took a candidate approach and screened planarian homologs of 25 genes known to regulate chromatin biology in other organisms. Through our study, we identified six genes with novel functions in planarian homeostasis, regeneration, and behavior. Of the list of genes characterized, we identified five planarian homologs of the mammalian CREB-Binding Protein (CBP) and p300 family of histone acetyltransferases, representing an expansion of this family in planarians. We find that two planarian CBP family members are required for planarian survival, with knockdown of Smed-CBP2 and Smed-CBP3 causing distinct defects in stem cell maintenance or function. Loss of CBP2 causes a quick, dramatic loss of stem cells, while knockdown of CBP3 affects stem cells more narrowly, influencing differentiation of several cell types that include neuronal subtypes and cells of the eye. Further, we find that Smed-CBP1 is required for planarian fissioning behavior. We propose that the division of labor among a diversified CBP family in planarians presents an opportunity to dissect specific functions of a broadly important histone acetyltransferase family.
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Affiliation(s)
- Clara R Stelman
- Department of Molecular and Cellular Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Britessia M Smith
- Department of Cellular Biology, University of Georgia, Athens, GA, USA
| | - Bidushi Chandra
- Department of Cellular Biology, University of Georgia, Athens, GA, USA
| | - Rachel H Roberts-Galbraith
- Department of Molecular and Cellular Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Department of Cellular Biology, University of Georgia, Athens, GA, USA.
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57
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Xiong Y, Wang L, Di Giorgio E, Akimova T, Beier UH, Han R, Trevisanut M, Kalin JH, Cole PA, Hancock WW. Inhibiting the coregulator CoREST impairs Foxp3+ Treg function and promotes antitumor immunity. J Clin Invest 2020; 130:1830-1842. [PMID: 31917688 DOI: 10.1172/jci131375] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 01/03/2020] [Indexed: 12/15/2022] Open
Abstract
Foxp3+ Tregs are key to immune homeostasis, but the contributions of various large, multiprotein complexes that regulate gene expression remain unexplored. We analyzed the role in Tregs of the evolutionarily conserved CoREST complex, consisting of a scaffolding protein, Rcor1 or Rcor2, plus Hdac1 or Hdac2 and Lsd1 enzymes. Rcor1, Rcor2, and Lsd1 were physically associated with Foxp3, and mice with conditional deletion of Rcor1 in Foxp3+ Tregs had decreased proportions of Tregs in peripheral lymphoid tissues and increased Treg expression of IL-2 and IFN-γ compared with what was found in WT cells. Mice with conditional deletion of the gene encoding Rcor1 in their Tregs had reduced suppression of homeostatic proliferation, inability to maintain long-term allograft survival despite costimulation blockade, and enhanced antitumor immunity in syngeneic models. Comparable findings were seen in WT mice treated with CoREST complex bivalent inhibitors, which also altered the phenotype of human Tregs and impaired their suppressive function. Our data point to the potential for therapeutic modulation of Treg functions by pharmacologic targeting of enzymatic components of the CoREST complex and contribute to an understanding of the biochemical and molecular mechanisms by which Foxp3 represses large gene sets and maintains the unique properties of this key immune cell.
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Affiliation(s)
- Yan Xiong
- Institute of Hepatobiliary Diseases of Wuhan University, Transplant Center of Wuhan University, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China.,Division of Transplant Immunology, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia and Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Liqing Wang
- Division of Transplant Immunology, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia and Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Eros Di Giorgio
- Division of Transplant Immunology, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia and Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Department of Medicine, Università degli Studi di Udine, Udine, Italy
| | - Tatiana Akimova
- Division of Transplant Immunology, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia and Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Ulf H Beier
- Division of Nephrology, Department of Pediatrics, Children's Hospital of Philadelphia and Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Rongxiang Han
- Division of Transplant Immunology, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia and Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Matteo Trevisanut
- Division of Transplant Immunology, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia and Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Department of Medicine, Università degli Studi di Udine, Udine, Italy
| | - Jay H Kalin
- Departments of Medicine and Biological Chemistry and Molecular Pharmacology, Harvard Medical School and Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Philip A Cole
- Departments of Medicine and Biological Chemistry and Molecular Pharmacology, Harvard Medical School and Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Wayne W Hancock
- Division of Transplant Immunology, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia and Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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58
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Herpes simplex virus 1 targets IRF7 via ICP0 to limit type I IFN induction. Sci Rep 2020; 10:22216. [PMID: 33335135 PMCID: PMC7747705 DOI: 10.1038/s41598-020-77725-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 11/10/2020] [Indexed: 12/18/2022] Open
Abstract
Herpes simplex keratitis (HSK), caused by herpes simplex virus type 1 (HSV-1) infection, is the commonest cause of infectious blindness in the developed world. Following infection the virus is initially suspended in the tear film, where it encounters a multi-pronged immune response comprising enzymes, complement, immunoglobulins and crucially, a range of anti-viral and pro-inflammatory cytokines. However, given that HSV-1 can overcome innate immune responses to establish lifelong latency throughout a susceptible individual's lifetime, there is significant interest in understanding the mechanisms employed by HSV-1 to downregulate the anti-viral type I interferon (IFN) mediated immune responses. This study aimed to investigate the interactions between infected cell protein (ICP)0 and key elements of the IFN pathway to identify possible novel targets that contribute to viral immune evasion. Reporter gene assays demonstrated the ability of ICP0 to inhibit type I IFN activity downstream of pathogen recognition receptors (PRRs) which are known to be involved in host antiviral defences. Further experiments identified interferon regulatory factor (IRF)7, a driver of type I IFN, as a potential target for ICP0. These findings increase our understanding of the pathogenesis of HSK and suggest IRF7 as a potential therapeutic target.
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59
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Perillo B, Tramontano A, Pezone A, Migliaccio A. LSD1: more than demethylation of histone lysine residues. Exp Mol Med 2020; 52:1936-1947. [PMID: 33318631 PMCID: PMC8080763 DOI: 10.1038/s12276-020-00542-2] [Citation(s) in RCA: 90] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 10/21/2020] [Accepted: 11/03/2020] [Indexed: 12/19/2022] Open
Abstract
Lysine-specific histone demethylase 1 (LSD1) represents the first example of an identified nuclear protein with histone demethylase activity. In particular, it plays a special role in the epigenetic regulation of gene expression, as it removes methyl groups from mono- and dimethylated lysine 4 and/or lysine 9 on histone H3 (H3K4me1/2 and H3K9me1/2), behaving as a repressor or activator of gene expression, respectively. Moreover, it has been recently found to demethylate monomethylated and dimethylated lysine 20 in histone H4 and to contribute to the balance of several other methylated lysine residues in histone H3 (i.e., H3K27, H3K36, and H3K79). Furthermore, in recent years, a plethora of nonhistone proteins have been detected as targets of LSD1 activity, suggesting that this demethylase is a fundamental player in the regulation of multiple pathways triggered in several cellular processes, including cancer progression. In this review, we analyze the molecular mechanism by which LSD1 displays its dual effect on gene expression (related to the specific lysine target), placing final emphasis on the use of pharmacological inhibitors of its activity in future clinical studies to fight cancer. Further research into the complex structure and behavior of an enzyme involved in gene regulation could improve future cancer therapies. The modification of chromosomal proteins known as histones can fundamentally change gene expression and influence the progression of diseases such as cancer. Bruno Perillo at the Italian National Research Council, Naples, Italy, and co-workers reviewed understanding of the structurally complex enzyme lysine-specific histone demethylase 1 A (LSD1), which interacts with multiple targets including histones. LSD1 removes methyl groups from histones, fine-tuning gene expression and influencing protein activity. The overexpression of LSD1 is linked to cancer development, particularly in aggressive cancers, and inhibiting LSD1 has shown promise in slowing progression and cancer spread. The researchers call for further research into the complexities of LSD1 activity, both in cancers and normal cell function.
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Affiliation(s)
- Bruno Perillo
- Istituto per l'Endocrinologia e l'Oncologia Sperimentale "G. Salvatore" C.N.R, 80131, Naples, Italy.
| | - Alfonso Tramontano
- Dipartimento di Medicina di Precisione Università della Campania "L. Vanvitelli", 80138, Naples, Italy
| | - Antonio Pezone
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche Università Federico II, 80131, Naples, Italy.
| | - Antimo Migliaccio
- Dipartimento di Medicina di Precisione Università della Campania "L. Vanvitelli", 80138, Naples, Italy
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60
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Knaupp AS, Mohenska M, Larcombe MR, Ford E, Lim SM, Wong K, Chen J, Firas J, Huang C, Liu X, Nguyen T, Sun YBY, Holmes ML, Tripathi P, Pflueger J, Rossello FJ, Schröder J, Davidson KC, Nefzger CM, Das PP, Haigh JJ, Lister R, Schittenhelm RB, Polo JM. TINC- A Method to Dissect Regulatory Complexes at Single-Locus Resolution- Reveals an Extensive Protein Complex at the Nanog Promoter. Stem Cell Reports 2020; 15:1246-1259. [PMID: 33296673 PMCID: PMC7724517 DOI: 10.1016/j.stemcr.2020.11.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 11/08/2020] [Accepted: 11/09/2020] [Indexed: 12/16/2022] Open
Abstract
Cellular identity is ultimately dictated by the interaction of transcription factors with regulatory elements (REs) to control gene expression. Advances in epigenome profiling techniques have significantly increased our understanding of cell-specific utilization of REs. However, it remains difficult to dissect the majority of factors that interact with these REs due to the lack of appropriate techniques. Therefore, we developed TINC: TALE-mediated isolation of nuclear chromatin. Using this new method, we interrogated the protein complex formed at the Nanog promoter in embryonic stem cells (ESCs) and identified many known and previously unknown interactors, including RCOR2. Further interrogation of the role of RCOR2 in ESCs revealed its involvement in the repression of lineage genes and the fine-tuning of pluripotency genes. Consequently, using the Nanog promoter as a paradigm, we demonstrated the power of TINC to provide insight into the molecular makeup of specific transcriptional complexes at individual REs as well as into cellular identity control in general. TINC allows the isolation of a specific locus for molecular analyses TINC identified hundreds of proteins at the Nanog promoter RCOR2 is a component of the pluripotency network in embryonic stem cells RCOR2 is required for efficient differentiation
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Affiliation(s)
- Anja S Knaupp
- Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC 3800, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Clayton, VIC 3800, Australia; Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia
| | - Monika Mohenska
- Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC 3800, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Clayton, VIC 3800, Australia; Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia
| | - Michael R Larcombe
- Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC 3800, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Clayton, VIC 3800, Australia; Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia
| | - Ethan Ford
- Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, WA 6009, Australia; Harry Perkins Institute of Medical Research, Nedlands, WA 6009, Australia
| | - Sue Mei Lim
- Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC 3800, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Clayton, VIC 3800, Australia; Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia
| | - Kayla Wong
- Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC 3800, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Clayton, VIC 3800, Australia; Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia
| | - Joseph Chen
- Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC 3800, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Clayton, VIC 3800, Australia; Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia
| | - Jaber Firas
- Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC 3800, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Clayton, VIC 3800, Australia; Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia
| | - Cheng Huang
- Monash Proteomics and Metabolomics Facility, Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia
| | - Xiaodong Liu
- Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC 3800, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Clayton, VIC 3800, Australia; Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia
| | - Trung Nguyen
- Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, WA 6009, Australia; Harry Perkins Institute of Medical Research, Nedlands, WA 6009, Australia
| | - Yu B Y Sun
- Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC 3800, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Clayton, VIC 3800, Australia; Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia
| | - Melissa L Holmes
- Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC 3800, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Clayton, VIC 3800, Australia; Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia
| | - Pratibha Tripathi
- Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC 3800, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Clayton, VIC 3800, Australia
| | - Jahnvi Pflueger
- Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, WA 6009, Australia; Harry Perkins Institute of Medical Research, Nedlands, WA 6009, Australia
| | - Fernando J Rossello
- Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC 3800, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Clayton, VIC 3800, Australia; Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia
| | - Jan Schröder
- Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC 3800, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Clayton, VIC 3800, Australia; Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia
| | - Kathryn C Davidson
- Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC 3800, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Clayton, VIC 3800, Australia; Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia
| | - Christian M Nefzger
- Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC 3800, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Clayton, VIC 3800, Australia; Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia
| | - Partha P Das
- Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC 3800, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Clayton, VIC 3800, Australia
| | - Jody J Haigh
- Australian Centre for Blood Diseases, Monash University, Clayton, VIC 3004, Australia; Department of Pharmacology and Therapeutics, University of Manitoba, Winnipeg, MB, Canada; Research Institute in Oncology and Hematology, CancerCare Manitoba, Winnipeg, MB, Canada
| | - Ryan Lister
- Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, WA 6009, Australia; Harry Perkins Institute of Medical Research, Nedlands, WA 6009, Australia
| | - Ralf B Schittenhelm
- Monash Proteomics and Metabolomics Facility, Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia.
| | - Jose M Polo
- Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC 3800, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Clayton, VIC 3800, Australia; Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia.
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61
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Luo Y, Li H. Structure-Based Inhibitor Discovery of Class I Histone Deacetylases (HDACs). Int J Mol Sci 2020; 21:E8828. [PMID: 33266366 PMCID: PMC7700698 DOI: 10.3390/ijms21228828] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 11/13/2020] [Accepted: 11/16/2020] [Indexed: 12/17/2022] Open
Abstract
Class I histone deacetylases (HDACs) are promising targets for epigenetic therapies for a range of diseases such as cancers, inflammations, infections and neurological diseases. Although six HDAC inhibitors are now licensed for clinical treatments, they are all pan-inhibitors with little or no HDAC isoform selectivity, exhibiting undesirable side effects. A major issue with the currently available HDAC inhibitors is that they have limited specificity and target multiple deacetylases. Except for HDAC8, Class I HDACs (1, 2 and 3) are recruited to large multiprotein complexes to function. Therefore, there are rising needs to develop new, hopefully, therapeutically efficacious HDAC inhibitors with isoform or complex selectivity. Here, upon the introduction of the structures of Class I HDACs and their complexes, we provide an up-to-date overview of the structure-based discovery of Class I HDAC inhibitors, including pan-, isoform-selective and complex-specific inhibitors, aiming to provide an insight into the discovery of additional HDAC inhibitors with greater selectivity, specificity and therapeutic utility.
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Affiliation(s)
- Yuxiang Luo
- School of Pharmaceutical Sciences, Sun Yat-sen University, No.132 Wai Huan Dong lu, Guangzhou Higher Education Mega Center, Guangzhou 510006, Guangdong, China;
| | - Huilin Li
- School of Pharmaceutical Sciences, Sun Yat-sen University, No.132 Wai Huan Dong lu, Guangzhou Higher Education Mega Center, Guangzhou 510006, Guangdong, China;
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, Guangdong, China
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62
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Leiendecker L, Jung PS, Krecioch I, Neumann T, Schleiffer A, Mechtler K, Wiesner T, Obenauf AC. LSD1 inhibition induces differentiation and cell death in Merkel cell carcinoma. EMBO Mol Med 2020; 12:e12525. [PMID: 33026191 PMCID: PMC7645387 DOI: 10.15252/emmm.202012525] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 09/07/2020] [Accepted: 09/08/2020] [Indexed: 01/05/2023] Open
Abstract
Merkel cell carcinoma (MCC) is a highly aggressive, neuroendocrine skin cancer that lacks actionable mutations, which could be utilized for targeted therapies. Epigenetic regulators governing cell identity may represent unexplored therapeutic entry points. Here, we targeted epigenetic regulators in a pharmacological screen and discovered that the lysine‐specific histone demethylase 1A (LSD1/KDM1A) is required for MCC growth in vitro and in vivo. We show that LSD1 inhibition in MCC disrupts the LSD1‐CoREST complex leading to displacement and degradation of HMG20B (BRAF35), a poorly characterized complex member that is essential for MCC proliferation. Inhibition of LSD1 causes derepression of transcriptional master regulators of the neuronal lineage, activates a gene expression signature resembling normal Merkel cells, and induces cell cycle arrest and cell death. Our study unveils the importance of LSD1 for maintaining cellular plasticity and proliferation in MCC. There is also growing evidence that cancer cells exploit cellular plasticity and dedifferentiation programs to evade destruction by the immune system. The combination of LSD1 inhibitors with checkpoint inhibitors may thus represent a promising treatment strategy for MCC patients.
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Affiliation(s)
- Lukas Leiendecker
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Pauline S Jung
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria.,Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Izabela Krecioch
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Tobias Neumann
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Alexander Schleiffer
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Karl Mechtler
- Institute of Molecular Biotechnology (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Thomas Wiesner
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Anna C Obenauf
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
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63
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Liu Y, Zhang Y. ETV5 is Essential for Neuronal Differentiation of Human Neural Progenitor Cells by Repressing NEUROG2 Expression. Stem Cell Rev Rep 2020; 15:703-716. [PMID: 31273540 DOI: 10.1007/s12015-019-09904-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Neural progenitor cells (NPCs) are multipotent cells that have the potential to produce neurons and glial cells in the neural system. NPCs undergo identity maintenance or differentiation regulated by different kinds of transcription factors. Here we present evidence that ETV5, which is an ETS transcription factor, promotes the generation of glial cells and drives the neuronal subtype-specific genes in newly differentiated neurons from the human embryonic stem cells-derived NPCs. Next, we find a new role for ETV5 in the repression of NEUROG2 expression in NPCs. ETV5 represses NEUROG2 transcription via NEUROG2 promoter and requires the ETS domain. We identify ETV5 has the binding sites and is implicated in silent chromatin in NEUROG2 promoter by chromatin immunoprecipitation (ChIP) assays. Further, NEUROG2 transcription repression by ETV5 was shown to be dependent on a transcriptional corepressor (CoREST). During NPC differentiation toward neurons, ETV5 represses NEUROG2 expression and blocks the appearance of glutamatergic neurons. This finding suggests that ETV5 negatively regulates NEUROG2 expression and increases the number of GABAergic subtype neurons derived from NPCs. Thus, ETV5 represents a potent new candidate protein with benefits for the generation of GABAergic neurons.
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Affiliation(s)
- Yang Liu
- School of Medicine, Tongji University, No.1239, Siping Road, Shanghai, 200092, People's Republic of China.
| | - Yuanyuan Zhang
- School of Medicine, Tongji University, No.1239, Siping Road, Shanghai, 200092, People's Republic of China
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64
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Bucholc K, Skrajna A, Adamska K, Yang XC, Krajewski K, Poznański J, Dadlez M, Domiński Z, Zhukov I. Structural Analysis of the SANT/Myb Domain of FLASH and YARP Proteins and Their Complex with the C-Terminal Fragment of NPAT by NMR Spectroscopy and Computer Simulations. Int J Mol Sci 2020; 21:ijms21155268. [PMID: 32722282 PMCID: PMC7432317 DOI: 10.3390/ijms21155268] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 07/15/2020] [Accepted: 07/20/2020] [Indexed: 11/16/2022] Open
Abstract
FLICE-associated huge protein (FLASH), Yin Yang 1-Associated Protein-Related Protein (YARP) and Nuclear Protein, Ataxia-Telangiectasia Locus (NPAT) localize to discrete nuclear structures called histone locus bodies (HLBs) where they control various steps in histone gene expression. Near the C-terminus, FLASH and YARP contain a highly homologous domain that interacts with the C-terminal region of NPAT. Structural aspects of the FLASH-NPAT and YARP-NPAT complexes and their role in histone gene expression remain largely unknown. In this study, we used multidimensional NMR spectroscopy and in silico modeling to analyze the C-terminal domain in FLASH and YARP in an unbound form and in a complex with the last 31 amino acids of NPAT. Our results demonstrate that FLASH and YARP domains share the same fold of a triple α -helical bundle that resembles the DNA binding domain of Myb transcriptional factors and the SANT domain found in chromatin-modifying and remodeling complexes. The NPAT peptide contains a single α -helix that makes multiple contacts with α -helices I and III of the FLASH and YARP domains. Surprisingly, in spite of sharing a significant amino acid similarity, each domain likely binds NPAT using a unique network of interactions, yielding two distinct complexes. In silico modeling suggests that both complexes are structurally compatible with DNA binding, raising the possibility that they may function in identifying specific sequences within histone gene clusters, hence initiating the assembly of HLBs and regulating histone gene expression during cell cycle progression.
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Affiliation(s)
- Katarzyna Bucholc
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, ul. Pawińskiego 5a, 02-106 Warsaw, Poland; (K.B.); (A.S.); (K.A.); (J.P.); (M.D.)
| | - Aleksandra Skrajna
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, ul. Pawińskiego 5a, 02-106 Warsaw, Poland; (K.B.); (A.S.); (K.A.); (J.P.); (M.D.)
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA;
| | - Kinga Adamska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, ul. Pawińskiego 5a, 02-106 Warsaw, Poland; (K.B.); (A.S.); (K.A.); (J.P.); (M.D.)
| | - Xiao-Cui Yang
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA;
| | - Krzysztof Krajewski
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA;
| | - Jarosław Poznański
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, ul. Pawińskiego 5a, 02-106 Warsaw, Poland; (K.B.); (A.S.); (K.A.); (J.P.); (M.D.)
| | - Michał Dadlez
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, ul. Pawińskiego 5a, 02-106 Warsaw, Poland; (K.B.); (A.S.); (K.A.); (J.P.); (M.D.)
| | - Zbigniew Domiński
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA;
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA;
- Correspondence: (Z.D.); (I.Z.); Tel.: +48-22-592-2038 (I.Z.)
| | - Igor Zhukov
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, ul. Pawińskiego 5a, 02-106 Warsaw, Poland; (K.B.); (A.S.); (K.A.); (J.P.); (M.D.)
- NanoBioMedical Centre, Adam Mickiewicz University, ul. Wszechnicy Piastowskiej 3, 61-614 Poznań, Poland
- Correspondence: (Z.D.); (I.Z.); Tel.: +48-22-592-2038 (I.Z.)
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65
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Xiao-Die X, Xiao-Hong W, Cheng-Feng H, Zhong-Yu Y, Jian-Tao W, Hou-Guang Z, Jing-Chun G. Increased NRSF/REST in anterior cingulate cortex contributes to diabetes-related neuropathic pain. Biochem Biophys Res Commun 2020; 527:785-790. [PMID: 32423826 DOI: 10.1016/j.bbrc.2020.04.106] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 04/16/2020] [Indexed: 02/07/2023]
Abstract
Diabetic neuropathic pain is one of the most common complications of diabetes. Mechanisms underlying the central modulation are still unclear. Here, we investigated the role of the neuron-restricted silencing factor (NRSF/REST) in diabetic-related neuropathic pain. Mechanical allodynia and thermal hyperalgesia were assessed to evaluate painful behaviors. Our results found that in the anterior cingulate cortex (ACC) of db/db mice, NRSF/REST levels increased significantly. Reduction of NRSF/REST improved the painful sensation. Meanwhile, in vitro study found that high glucose and high palmitic acid treatment induced elevation of NRSF/REST and its cofactors (mSin3A, CoREST and HDAC1), whereas downregulation of GluR2 and NMDAR2B. Knockdown of NRSF/REST could attenuate the LDH release and partially reversed the expression changes of HDAC1 and NMDAR2B. Our results suggested that the elevation of NRSF/REST in the ACC area of db/db mice is one of the key mediators of diabetic neuropathic pain.
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Affiliation(s)
- Xu Xiao-Die
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Department of Translational Neuroscience Jing'an District Centre Hospital of Shanghai, Fudan University, Shanghai, China
| | - Wen Xiao-Hong
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Department of Translational Neuroscience Jing'an District Centre Hospital of Shanghai, Fudan University, Shanghai, China
| | - He Cheng-Feng
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Department of Translational Neuroscience Jing'an District Centre Hospital of Shanghai, Fudan University, Shanghai, China
| | - Yu Zhong-Yu
- Department of Geriatric Neurology, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Wang Jian-Tao
- Department of Geriatric Neurology, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Zhou Hou-Guang
- Department of Geriatric Neurology, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Guo Jing-Chun
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Department of Translational Neuroscience Jing'an District Centre Hospital of Shanghai, Fudan University, Shanghai, China.
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66
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Mondal B, Jin H, Kallappagoudar S, Sedkov Y, Martinez T, Sentmanat MF, Poet GJ, Li C, Fan Y, Pruett-Miller SM, Herz HM. The histone deacetylase complex MiDAC regulates a neurodevelopmental gene expression program to control neurite outgrowth. eLife 2020; 9:57519. [PMID: 32297854 PMCID: PMC7192582 DOI: 10.7554/elife.57519] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 04/07/2020] [Indexed: 12/14/2022] Open
Abstract
The mitotic deacetylase complex (MiDAC) is a recently identified histone deacetylase (HDAC) complex. While other HDAC complexes have been implicated in neurogenesis, the physiological role of MiDAC remains unknown. Here, we show that MiDAC constitutes an important regulator of neural differentiation. We demonstrate that MiDAC functions as a modulator of a neurodevelopmental gene expression program and binds to important regulators of neurite outgrowth. MiDAC upregulates gene expression of pro-neural genes such as those encoding the secreted ligands SLIT3 and NETRIN1 (NTN1) by a mechanism suggestive of H4K20ac removal on promoters and enhancers. Conversely, MiDAC inhibits gene expression by reducing H3K27ac on promoter-proximal and -distal elements of negative regulators of neurogenesis. Furthermore, loss of MiDAC results in neurite outgrowth defects that can be rescued by supplementation with SLIT3 and/or NTN1. These findings indicate a crucial role for MiDAC in regulating the ligands of the SLIT3 and NTN1 signaling axes to ensure the proper integrity of neurite development.
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Affiliation(s)
- Baisakhi Mondal
- Department of Cell & Molecular Biology, St. Jude Children's Research Hospital, Memphis, United States
| | - Hongjian Jin
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, United States
| | - Satish Kallappagoudar
- Department of Cell & Molecular Biology, St. Jude Children's Research Hospital, Memphis, United States
| | - Yurii Sedkov
- Department of Cell & Molecular Biology, St. Jude Children's Research Hospital, Memphis, United States
| | - Tanner Martinez
- Department of Cell & Molecular Biology, St. Jude Children's Research Hospital, Memphis, United States
| | - Monica F Sentmanat
- Genome Engineering & iPS Center, Department of Genetics, Washington University, St. Louis, United States
| | - Greg J Poet
- Department of Tumor Cell Biology, St. Jude Children's Research Hospital, Memphis, United States
| | - Chunliang Li
- Department of Tumor Cell Biology, St. Jude Children's Research Hospital, Memphis, United States
| | - Yiping Fan
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, United States
| | - Shondra M Pruett-Miller
- Department of Cell & Molecular Biology, St. Jude Children's Research Hospital, Memphis, United States
| | - Hans-Martin Herz
- Department of Cell & Molecular Biology, St. Jude Children's Research Hospital, Memphis, United States
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MYT1 attenuates neuroblastoma cell differentiation by interacting with the LSD1/CoREST complex. Oncogene 2020; 39:4212-4226. [PMID: 32251364 DOI: 10.1038/s41388-020-1268-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 03/07/2020] [Accepted: 03/11/2020] [Indexed: 02/08/2023]
Abstract
Impaired neuronal differentiation is a feature of neuroblastoma tumorigenesis, and the differentiation grade of neuroblastoma tumors is associated with patient prognosis. Detailed understanding of the molecular mechanisms underlying neuroblastoma differentiation will facilitate the development of effective treatment strategies. Recent studies have shown that myelin transcription factor 1 (MYT1) promotes vertebrate neurogenesis by regulating gene expression. We performed quantitative analysis of neuroblastoma samples, which revealed that MYT1 was differentially expressed among neuroblastoma patients with different pathological diagnoses. Analysis of clinical data showed that MYT1 overexpression was associated with a significantly shorter 3-year overall survival rate and poor differentiation in neuroblastoma specimens. MYT1 knockdown inhibited proliferation and promoted the expression of multiple differentiation-associated proteins. Integrated omics data indicated that many genes involved in neuro-differentiation were regulated by MYT1. Interestingly, many of these genes are targets of the REST complex; therefore, we further identified the physical interaction of MYT1 with LSD1/CoREST. Depletion of LSD1 or inhibition of LSD1 by ORY-1001 decreased MYT1 expression, providing an alternative approach to target MYT1. Taken together, our results indicate that MYT1 significantly attenuates cell differentiation by interacting with the LSD1/CoREST complex. MYT1 is, therefore, a promising therapeutic target for enhancing the neurite-inducing effect of retinoic acid and for inhibiting the growth of neuroblastoma.
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68
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Roopra A. MAGIC: A tool for predicting transcription factors and cofactors driving gene sets using ENCODE data. PLoS Comput Biol 2020; 16:e1007800. [PMID: 32251445 PMCID: PMC7162552 DOI: 10.1371/journal.pcbi.1007800] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 04/16/2020] [Accepted: 03/19/2020] [Indexed: 01/26/2023] Open
Abstract
Transcriptomic profiling is an immensely powerful hypothesis generating tool. However, accurately predicting the transcription factors (TFs) and cofactors that drive transcriptomic differences between samples is challenging. A number of algorithms draw on ChIP-seq tracks to define TFs and cofactors behind gene changes. These approaches assign TFs and cofactors to genes via a binary designation of 'target', or 'non-target' followed by Fisher Exact Tests to assess enrichment of TFs and cofactors. ENCODE archives 2314 ChIP-seq tracks of 684 TFs and cofactors assayed across a 117 human cell lines under a multitude of growth and maintenance conditions. The algorithm presented herein, Mining Algorithm for GenetIc Controllers (MAGIC), uses ENCODE ChIP-seq data to look for statistical enrichment of TFs and cofactors in gene bodies and flanking regions in gene lists without an a priori binary classification of genes as targets or non-targets. When compared to other TF mining resources, MAGIC displayed favourable performance in predicting TFs and cofactors that drive gene changes in 4 settings: 1) A cell line expressing or lacking single TF, 2) Breast tumors divided along PAM50 designations 3) Whole brain samples from WT mice or mice lacking a single TF in a particular neuronal subtype 4) Single cell RNAseq analysis of neurons divided by Immediate Early Gene expression levels. In summary, MAGIC is a standalone application that produces meaningful predictions of TFs and cofactors in transcriptomic experiments.
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Affiliation(s)
- Avtar Roopra
- Dept. of Neuroscience, 5507 WIMR, University of Wisconsin-Madison, Madison, United States of America
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69
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More than a Corepressor: The Role of CoREST Proteins in Neurodevelopment. eNeuro 2020; 7:ENEURO.0337-19.2020. [PMID: 32075869 PMCID: PMC7070449 DOI: 10.1523/eneuro.0337-19.2020] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 01/19/2020] [Accepted: 02/05/2020] [Indexed: 12/22/2022] Open
Abstract
The molecular mechanisms governing normal neurodevelopment are tightly regulated by the action of transcription factors. Repressor element 1 (RE1) silencing transcription factor (REST) is widely documented as a regulator of neurogenesis that acts by recruiting corepressor proteins and repressing neuronal gene expression in non-neuronal cells. The REST corepressor 1 (CoREST1), CoREST2, and CoREST3 are best described for their role as part of the REST complex. However, recent evidence has shown the proteins have the ability to repress expression of distinct target genes in a REST-independent manner. These findings indicate that each CoREST paralogue may have distinct and critical roles in regulating neurodevelopment and are more than simply “REST corepressors,” whereby they act as independent repressors orchestrating biological processes during neurodevelopment.
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70
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Snyder MA, Gao WJ. NMDA receptor hypofunction for schizophrenia revisited: Perspectives from epigenetic mechanisms. Schizophr Res 2020; 217:60-70. [PMID: 30979669 PMCID: PMC7258307 DOI: 10.1016/j.schres.2019.03.010] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 03/08/2019] [Accepted: 03/11/2019] [Indexed: 02/06/2023]
Abstract
Schizophrenia (SZ) is a neurodevelopmental disorder with cognitive deficits manifesting during early stages of the disease. Evidence suggests that genetic factors in combination with environmental insults lead to complex changes to glutamatergic, GABAergic, and dopaminergic systems. In particular, the N-methyl-d-aspartate receptor (NMDAR), a major glutamate receptor subtype, is implicated in both the disease progression and symptoms of SZ. NMDARs are critical for synaptic plasticity and cortical maturation, as well as learning and memory processes. In fact, any deviation from normal NMDAR expression and function can have devastating consequences. Surprisingly, there is little evidence from human patients that direct mutations of NMDAR genes contribute to SZ. One intriguing hypothesis is that epigenetic changes, which could result from early insults, alter protein expression and contribute to the NMDAR hypofunction found in SZ. Epigenetics is referred to as modifications that alter gene transcription without changing the DNA sequence itself. In this review, we first discuss how epigenetic changes to NMDAR genes could contribute to NMDAR hypofunction. We then explore how NMDAR hypofunction may contribute to epigenetic changes in other proteins or genes that lead to synaptic dysfunction and symptoms in SZ. We argue that NMDAR hypofunction occurs in early stage of the disease, and it may consequentially initiate GABA and dopamine deficits. Therefore, targeting NMDAR dysfunction during the early stages would be a promising avenue for prevention and therapeutic intervention of cognitive and social deficits that remain untreatable. Finally, we discuss potential questions regarding the epigenetic of SZ and future directions for research.
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Affiliation(s)
- Melissa A. Snyder
- Ottawa Hospital Research Institute, Ottawa, Ontario, Canada, K1H 8M5,Correspondence: Wen-Jun Gao, M.D., Ph.D., Department of Neurobiology and Anatomy, Drexel University College of Medicine, 2900 Queen Lane, Philadelphia, PA 19129, Phone: (215) 991-8907, Fax: (215) 843-9802, ; Melissa A. Snyder, Ph.D.,
| | - Wen-Jun Gao
- Department of Neurobiology and Anatomy, Drexel University College of Medicine, Philadelphia, PA 19129, United States of America.
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71
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Pray-Grant MG, Grant PA. Ant-icipating Change: An Epigenetic Switch in Reprogramming the Social Lives of Ants. Mol Cell 2020; 77:205-206. [PMID: 31951544 DOI: 10.1016/j.molcel.2019.12.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Glastad et al. (2019) describe a role for the neuronal CoREST corepressor and changes in juvenile hormone (JH) and ecdysone signaling during the reprogramming of social behavioral phenotypes in ants that are reflective of a natural mechanism differentiating "Major" and "Minor" worker ants.
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Affiliation(s)
- Marilyn G Pray-Grant
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Patrick A Grant
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA.
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72
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Carminati E, Buffolo F, Rocchi A, Michetti C, Cesca F, Benfenati F. Mild Inactivation of RE-1 Silencing Transcription Factor (REST) Reduces Susceptibility to Kainic Acid-Induced Seizures. Front Cell Neurosci 2020; 13:580. [PMID: 31998079 PMCID: PMC6965066 DOI: 10.3389/fncel.2019.00580] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Accepted: 12/18/2019] [Indexed: 11/13/2022] Open
Abstract
RE-1 Silencing Transcription factor (REST) controls several steps in neural development by modulating the expression of a wide range of neural genes. Alterations in REST expression have been associated with the onset of epilepsy; however, whether such alterations are deleterious or represent a protective homeostatic response remains elusive. To study the impact of REST modulation on seizure propensity, we developed a tool for its negative modulation in vivo. The tool is composed of the paired-amphipathic helix 1 (PAH1) domain, a competitive inhibitor of REST activation by mSin3, fused to the light-oxygen-voltage sensing 2 (LOV2) domain of Avena sativa phototropin 1, a molecular switch to alternatively hide or expose the PAH1 inhibitor. We employed the C450A and I539E light-independent AsLOV2 variants to mimic the closed (inactive) and open (active) states of LOV2-PAH1, respectively. Recombinant AAV1/2 viral particles (rAAVs) allowed LOV2-PAH1 expression in HEK293T cells and primary neurons, and efficiently transduced hippocampal neurons in vivo. mRNA expression analysis revealed an increased expression of several neuronal genes in the hippocampi of mice expressing the open probe. AAV-transduced mice received a single dose of kainic acid (KA), a treatment known to induce a transient increase of REST levels in the hippocampus. Remarkably, mice expressing the active variant displayed a reduced number of KA-induced seizures, which were less severe compared to mice carrying the inactive probe. These data support the validity of our tool to modulate REST activity in vivo and the potential impact of REST modulation on epileptogenesis.
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Affiliation(s)
- Emanuele Carminati
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Genova, Italy
| | - Federica Buffolo
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Genova, Italy
| | - Anna Rocchi
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Genova, Italy.,IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | - Caterina Michetti
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Genova, Italy.,IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | - Fabrizia Cesca
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Genova, Italy.,Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Fabio Benfenati
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Genova, Italy.,IRCCS Ospedale Policlinico San Martino, Genova, Italy
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73
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Li H, Liu Z, Wu Y, Chen Y, Wang J, Wang Z, Huang D, Wang M, Yu M, Fei J, Huang F. The deficiency of NRSF/REST enhances the pro-inflammatory function of astrocytes in a model of Parkinson's disease. Biochim Biophys Acta Mol Basis Dis 2020; 1866:165590. [DOI: 10.1016/j.bbadis.2019.165590] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 09/11/2019] [Accepted: 09/30/2019] [Indexed: 12/15/2022]
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74
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Poiana G, Gioia R, Sineri S, Cardarelli S, Lupo G, Cacci E. Transcriptional regulation of adult neural stem/progenitor cells: tales from the subventricular zone. Neural Regen Res 2020; 15:1773-1783. [PMID: 32246617 PMCID: PMC7513981 DOI: 10.4103/1673-5374.280301] [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] [Indexed: 01/06/2023] Open
Abstract
In rodents, well characterized neurogenic niches of the adult brain, such as the subventricular zone of the lateral ventricles and the subgranular zone of the hippocampus, support the maintenance of neural/stem progenitor cells (NSPCs) and the production of new neurons throughout the lifespan. The adult neurogenic process is dependent on the intrinsic gene expression signatures of NSPCs that make them competent for self-renewal and neuronal differentiation. At the same time, it is receptive to regulation by various extracellular signals that allow the modulation of neuronal production and integration into brain circuitries by various physiological stimuli. A drawback of this plasticity is the sensitivity of adult neurogenesis to alterations of the niche environment that can occur due to aging, injury or disease. At the core of the molecular mechanisms regulating neurogenesis, several transcription factors have been identified that maintain NSPC identity and mediate NSPC response to extrinsic cues. Here, we focus on REST, Egr1 and Dbx2 and their roles in adult neurogenesis, especially in the subventricular zone. We review recent work from our and other laboratories implicating these transcription factors in the control of NSPC proliferation and differentiation and in the response of NSPCs to extrinsic influences from the niche. We also discuss how their altered regulation may affect the neurogenic process in the aged and in the diseased brain. Finally, we highlight key open questions that need to be addressed to foster our understanding of the transcriptional mechanisms controlling adult neurogenesis.
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Affiliation(s)
- Giancarlo Poiana
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Rome, Italy
| | - Roberta Gioia
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Rome, Italy
| | - Serena Sineri
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Rome, Italy
| | - Silvia Cardarelli
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Rome, Italy
| | - Giuseppe Lupo
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Rome, Italy
| | - Emanuele Cacci
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Rome, Italy
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75
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Mačinković I, Theofel I, Hundertmark T, Kovač K, Awe S, Lenz J, Forné I, Lamp B, Nist A, Imhof A, Stiewe T, Renkawitz-Pohl R, Rathke C, Brehm A. Distinct CoREST complexes act in a cell-type-specific manner. Nucleic Acids Res 2019; 47:11649-11666. [PMID: 31701127 PMCID: PMC7145674 DOI: 10.1093/nar/gkz1050] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 10/16/2019] [Accepted: 10/23/2019] [Indexed: 01/10/2023] Open
Abstract
CoREST has been identified as a subunit of several protein complexes that generate transcriptionally repressive chromatin structures during development. However, a comprehensive analysis of the CoREST interactome has not been carried out. We use proteomic approaches to define the interactomes of two dCoREST isoforms, dCoREST-L and dCoREST-M, in Drosophila. We identify three distinct histone deacetylase complexes built around a common dCoREST/dRPD3 core: A dLSD1/dCoREST complex, the LINT complex and a dG9a/dCoREST complex. The latter two complexes can incorporate both dCoREST isoforms. By contrast, the dLSD1/dCoREST complex exclusively assembles with the dCoREST-L isoform. Genome-wide studies show that the three dCoREST complexes associate with chromatin predominantly at promoters. Transcriptome analyses in S2 cells and testes reveal that different cell lineages utilize distinct dCoREST complexes to maintain cell-type-specific gene expression programmes: In macrophage-like S2 cells, LINT represses germ line-related genes whereas other dCoREST complexes are largely dispensable. By contrast, in testes, the dLSD1/dCoREST complex prevents transcription of germ line-inappropriate genes and is essential for spermatogenesis and fertility, whereas depletion of other dCoREST complexes has no effect. Our study uncovers three distinct dCoREST complexes that function in a lineage-restricted fashion to repress specific sets of genes thereby maintaining cell-type-specific gene expression programmes.
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Affiliation(s)
- Igor Mačinković
- Institute of Molecular Biology and Tumor Research, Biomedical Research Center, Philipps-University, Hans-Meerwein-Strasse 2, 35043, Marburg, Germany
| | - Ina Theofel
- Department of Biology, Philipps-University, Karl-von-Frisch-Strasse 8, 35043, Marburg, Germany
| | - Tim Hundertmark
- Department of Biology, Philipps-University, Karl-von-Frisch-Strasse 8, 35043, Marburg, Germany
| | - Kristina Kovač
- Institute of Molecular Biology and Tumor Research, Biomedical Research Center, Philipps-University, Hans-Meerwein-Strasse 2, 35043, Marburg, Germany
| | - Stephan Awe
- Institute of Molecular Biology and Tumor Research, Biomedical Research Center, Philipps-University, Hans-Meerwein-Strasse 2, 35043, Marburg, Germany
| | - Jonathan Lenz
- Institute of Molecular Biology and Tumor Research, Biomedical Research Center, Philipps-University, Hans-Meerwein-Strasse 2, 35043, Marburg, Germany
| | - Ignasi Forné
- Protein Analysis Unit, BioMedical Center, Faculty of Medicine, Ludwig-Maximilians-University Munich, Großhadernerstrasse 9, 82152 Martinsried, Germany
| | - Boris Lamp
- Genomics Core Facility, Institute of Molecular Oncology, Philipps-University, Hans-Meerwein-Strasse 3, 35043 Marburg, Germany
| | - Andrea Nist
- Genomics Core Facility, Institute of Molecular Oncology, Philipps-University, Hans-Meerwein-Strasse 3, 35043 Marburg, Germany
| | - Axel Imhof
- Protein Analysis Unit, BioMedical Center, Faculty of Medicine, Ludwig-Maximilians-University Munich, Großhadernerstrasse 9, 82152 Martinsried, Germany
| | - Thorsten Stiewe
- Genomics Core Facility, Institute of Molecular Oncology, Philipps-University, Hans-Meerwein-Strasse 3, 35043 Marburg, Germany
| | - Renate Renkawitz-Pohl
- Department of Biology, Philipps-University, Karl-von-Frisch-Strasse 8, 35043, Marburg, Germany
| | - Christina Rathke
- Department of Biology, Philipps-University, Karl-von-Frisch-Strasse 8, 35043, Marburg, Germany
| | - Alexander Brehm
- Institute of Molecular Biology and Tumor Research, Biomedical Research Center, Philipps-University, Hans-Meerwein-Strasse 2, 35043, Marburg, Germany
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76
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Miller SA, Policastro RA, Savant SS, Sriramkumar S, Ding N, Lu X, Mohammad HP, Cao S, Kalin JH, Cole PA, Zentner GE, O'Hagan HM. Lysine-Specific Demethylase 1 Mediates AKT Activity and Promotes Epithelial-to-Mesenchymal Transition in PIK3CA-Mutant Colorectal Cancer. Mol Cancer Res 2019; 18:264-277. [PMID: 31704733 DOI: 10.1158/1541-7786.mcr-19-0748] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Revised: 09/24/2019] [Accepted: 11/05/2019] [Indexed: 12/23/2022]
Abstract
Activation of the epithelial-to-mesenchymal transition (EMT) program is a critical mechanism for initiating cancer progression and migration. Colorectal cancers contain many genetic and epigenetic alterations that can contribute to EMT. Mutations activating the PI3K/AKT signaling pathway are observed in >40% of patients with colorectal cancer contributing to increased invasion and metastasis. Little is known about how oncogenic signaling pathways such as PI3K/AKT synergize with chromatin modifiers to activate the EMT program. Lysine-specific demethylase 1 (LSD1) is a chromatin-modifying enzyme that is overexpressed in colorectal cancer and enhances cell migration. In this study, we determine that LSD1 expression is significantly elevated in patients with colorectal cancer with mutation of the catalytic subunit of PI3K, PIK3CA, compared with patients with colorectal cancer with WT PIK3CA. LSD1 enhances activation of the AKT kinase in colorectal cancer cells through a noncatalytic mechanism, acting as a scaffolding protein for the transcription-repressing CoREST complex. In addition, growth of PIK3CA-mutant colorectal cancer cells is uniquely dependent on LSD1. Knockdown or CRISPR knockout of LSD1 blocks AKT-mediated stabilization of the EMT-promoting transcription factor Snail and effectively blocks AKT-mediated EMT and migration. Overall, we uniquely demonstrate that LSD1 mediates AKT activation in response to growth factors and oxidative stress, and LSD1-regulated AKT activity promotes EMT-like characteristics in a subset of PIK3CA-mutant cells. IMPLICATIONS: Our data support the hypothesis that inhibitors targeting the CoREST complex may be clinically effective in patients with colorectal cancer harboring PIK3CA mutations.
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Affiliation(s)
- Samuel A Miller
- Genome, Cell, and Developmental Biology, Department of Biology, Indiana University Bloomington, Bloomington, Indiana.,Medical Sciences Program, Indiana University School of Medicine, Bloomington, Indiana
| | - Robert A Policastro
- Genome, Cell, and Developmental Biology, Department of Biology, Indiana University Bloomington, Bloomington, Indiana
| | - Sudha S Savant
- Medical Sciences Program, Indiana University School of Medicine, Bloomington, Indiana
| | - Shruthi Sriramkumar
- Medical Sciences Program, Indiana University School of Medicine, Bloomington, Indiana
| | - Ning Ding
- Medical Sciences Program, Indiana University School of Medicine, Bloomington, Indiana
| | - Xiaoyu Lu
- Center for Computational Biology and Bioinformatics, Department of Biostatistics, Indiana University School of Medicine, Indianapolis, Indiana.,Department of Biohealth Informatics, Indiana University-Purdue University, Indianapolis, Indiana
| | - Helai P Mohammad
- Epigenetics Research Unit, Oncology, GlaxoSmithKline, Collegeville, Pennsylvania
| | - Sha Cao
- Department of Biohealth Informatics, Indiana University-Purdue University, Indianapolis, Indiana
| | - Jay H Kalin
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts
| | - Philip A Cole
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts
| | - Gabriel E Zentner
- Genome, Cell, and Developmental Biology, Department of Biology, Indiana University Bloomington, Bloomington, Indiana.,Indiana University Melvin and Bren Simon Cancer Center, Indianapolis, Indiana
| | - Heather M O'Hagan
- Medical Sciences Program, Indiana University School of Medicine, Bloomington, Indiana. .,Indiana University Melvin and Bren Simon Cancer Center, Indianapolis, Indiana
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77
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Zwinderman MRH, de Weerd S, Dekker FJ. Targeting HDAC Complexes in Asthma and COPD. EPIGENOMES 2019; 3:19. [PMID: 34968229 PMCID: PMC8594684 DOI: 10.3390/epigenomes3030019] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 09/02/2019] [Accepted: 09/04/2019] [Indexed: 01/08/2023] Open
Abstract
Around three million patients die due to airway inflammatory diseases each year. The most notable of these diseases are asthma and chronic obstructive pulmonary disease (COPD). Therefore, new therapies are urgently needed. Promising targets are histone deacetylases (HDACs), since they regulate posttranslational protein acetylation. Over a thousand proteins are reversibly acetylated, and acetylation critically influences aberrant intracellular signaling pathways in asthma and COPD. The diverse set of selective and non-selective HDAC inhibitors used in pre-clinical models of airway inflammation show promising results, but several challenges still need to be overcome. One such challenge is the design of HDAC inhibitors with unique selectivity profiles, such as selectivity towards specific HDAC complexes. Novel strategies to disrupt HDAC complexes should be developed to validate HDACs further as targets for new anti-inflammatory pulmonary treatments.
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Affiliation(s)
| | | | - Frank J. Dekker
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, 9713 AV Groningen, The Netherlands (M.R.H.Z.) (S.d.W.)
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78
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Wohl SG, Hooper MJ, Reh TA. MicroRNAs miR-25, let-7 and miR-124 regulate the neurogenic potential of Müller glia in mice. Development 2019; 146:dev179556. [PMID: 31383796 PMCID: PMC6765125 DOI: 10.1242/dev.179556] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 07/24/2019] [Indexed: 12/21/2022]
Abstract
Müller glial cells (MG) generate retinal progenitor (RPC)-like cells after injury in non-mammalian species, although this does not occur in the mammalian retina. Studies have profiled gene expression in these cells to define genes that may be relevant to their differences in neurogenic potential. However, less is known about differences in micro-RNA (miRNA) expression. In this study, we compared miRNAs from RPCs and MG to identify miRNAs more highly expressed in RPCs, and others more highly expressed in MG. To determine whether these miRNAs are relevant to the difference in neurogenic potential between these two cell types, we tested them in dissociated cultures of MG using either mimics or antagomiRs to increase or reduce expression, respectively. Among the miRNAs tested, miR-25 and miR-124 overexpression, or let-7 antagonism, induced Ascl1 expression and conversion of ∼40% of mature MG into a neuronal/RPC phenotype. Our results suggest that the differences in miRNA expression between MG and RPCs contribute to their difference in neurogenic potential, and that manipulations in miRNAs provide a new tool with which to reprogram MG for retinal regeneration.
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Affiliation(s)
- Stefanie G Wohl
- Department of Biological Structure, University of Washington, School of Medicine, Seattle, WA 98195, USA
- Department of Biological and Vision Sciences, The State University of New York, College of Optometry, New York, NY 10036, USA
| | - Marcus J Hooper
- Department of Biological Structure, University of Washington, School of Medicine, Seattle, WA 98195, USA
| | - Thomas A Reh
- Department of Biological Structure, University of Washington, School of Medicine, Seattle, WA 98195, USA
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79
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Lambert MP, Terrone S, Giraud G, Benoit-Pilven C, Cluet D, Combaret V, Mortreux F, Auboeuf D, Bourgeois CF. The RNA helicase DDX17 controls the transcriptional activity of REST and the expression of proneural microRNAs in neuronal differentiation. Nucleic Acids Res 2019; 46:7686-7700. [PMID: 29931089 PMCID: PMC6125624 DOI: 10.1093/nar/gky545] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 06/04/2018] [Indexed: 12/22/2022] Open
Abstract
The Repressor Element 1-silencing transcription factor (REST) represses a number of neuronal genes in non-neuronal cells or in undifferentiated neural progenitors. Here, we report that the DEAD box RNA helicase DDX17 controls important REST-related processes that are critical during the early phases of neuronal differentiation. First, DDX17 associates with REST, promotes its binding to the promoter of a subset of REST-targeted genes and co-regulates REST transcriptional repression activity. During neuronal differentiation, we observed a downregulation of DDX17 along with that of the REST complex that contributes to the activation of neuronal genes. Second, DDX17 and its paralog DDX5 regulate the expression of several proneural microRNAs that are known to target the REST complex during neurogenesis, including miR-26a/b that are also direct regulators of DDX17 expression. In this context, we propose a new mechanism by which RNA helicases can control the biogenesis of intronic miRNAs. We show that the processing of the miR-26a2 precursor is dependent on RNA helicases, owing to an intronic regulatory region that negatively impacts on both miRNA processing and splicing of its host intron. Our work places DDX17 in the heart of a pathway involving REST and miRNAs that allows neuronal gene repression.
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Affiliation(s)
- Marie-Pierre Lambert
- Laboratoire de Biologie et Modelisation de la Cellule, Universite de Lyon, INSERM U1210, CNRS UMR 5239, Ecole Normale Superieure de Lyon, Universite Claude Bernard Lyon 1, F-69007 Lyon, France
| | - Sophie Terrone
- Laboratoire de Biologie et Modelisation de la Cellule, Universite de Lyon, INSERM U1210, CNRS UMR 5239, Ecole Normale Superieure de Lyon, Universite Claude Bernard Lyon 1, F-69007 Lyon, France
| | - Guillaume Giraud
- Laboratoire de Biologie et Modelisation de la Cellule, Universite de Lyon, INSERM U1210, CNRS UMR 5239, Ecole Normale Superieure de Lyon, Universite Claude Bernard Lyon 1, F-69007 Lyon, France
| | - Clara Benoit-Pilven
- Laboratoire de Biologie et Modelisation de la Cellule, Universite de Lyon, INSERM U1210, CNRS UMR 5239, Ecole Normale Superieure de Lyon, Universite Claude Bernard Lyon 1, F-69007 Lyon, France
| | - David Cluet
- Laboratoire de Biologie et Modelisation de la Cellule, Universite de Lyon, INSERM U1210, CNRS UMR 5239, Ecole Normale Superieure de Lyon, Universite Claude Bernard Lyon 1, F-69007 Lyon, France
| | - Valérie Combaret
- Laboratoire de Recherche Translationnelle, Centre Léon Bérard, F-69008 Lyon, France
| | - Franck Mortreux
- Laboratoire de Biologie et Modelisation de la Cellule, Universite de Lyon, INSERM U1210, CNRS UMR 5239, Ecole Normale Superieure de Lyon, Universite Claude Bernard Lyon 1, F-69007 Lyon, France
| | - Didier Auboeuf
- Laboratoire de Biologie et Modelisation de la Cellule, Universite de Lyon, INSERM U1210, CNRS UMR 5239, Ecole Normale Superieure de Lyon, Universite Claude Bernard Lyon 1, F-69007 Lyon, France
| | - Cyril F Bourgeois
- Laboratoire de Biologie et Modelisation de la Cellule, Universite de Lyon, INSERM U1210, CNRS UMR 5239, Ecole Normale Superieure de Lyon, Universite Claude Bernard Lyon 1, F-69007 Lyon, France
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80
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Jayaprakash S, Drakulic S, Zhao Z, Sander B, Golas MM. The ATPase BRG1/SMARCA4 is a protein interaction platform that recruits BAF subunits and the transcriptional repressor REST/NRSF in neural progenitor cells. Mol Cell Biochem 2019; 461:171-182. [DOI: 10.1007/s11010-019-03600-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 08/08/2019] [Indexed: 10/26/2022]
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81
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Monestime CM, Taibi A, Gates KP, Jiang K, Sirotkin HI. CoRest1 regulates neurogenesis in a stage‐dependent manner. Dev Dyn 2019; 248:918-930. [DOI: 10.1002/dvdy.86] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 07/01/2019] [Accepted: 07/04/2019] [Indexed: 12/31/2022] Open
Affiliation(s)
| | - Andrew Taibi
- Department of Neurobiology and BehaviorStony Brook University Stony Brook New York
| | - Keith P. Gates
- Department of Neurobiology and BehaviorStony Brook University Stony Brook New York
| | - Karen Jiang
- Department of Neurobiology and BehaviorStony Brook University Stony Brook New York
| | - Howard I. Sirotkin
- Department of Neurobiology and BehaviorStony Brook University Stony Brook New York
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82
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Kuehner JN, Bruggeman EC, Wen Z, Yao B. Epigenetic Regulations in Neuropsychiatric Disorders. Front Genet 2019; 10:268. [PMID: 31019524 PMCID: PMC6458251 DOI: 10.3389/fgene.2019.00268] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 03/11/2019] [Indexed: 12/14/2022] Open
Abstract
Precise genetic and epigenetic spatiotemporal regulation of gene expression is critical for proper brain development, function and circuitry formation in the mammalian central nervous system. Neuronal differentiation processes are tightly regulated by epigenetic mechanisms including DNA methylation, histone modifications, chromatin remodelers and non-coding RNAs. Dysregulation of any of these pathways is detrimental to normal neuronal development and functions, which can result in devastating neuropsychiatric disorders, such as depression, schizophrenia and autism spectrum disorders. In this review, we focus on the current understanding of epigenetic regulations in brain development and functions, as well as their implications in neuropsychiatric disorders.
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Affiliation(s)
- Janise N Kuehner
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, United States
| | - Emily C Bruggeman
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, United States
| | - Zhexing Wen
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, United States.,Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, United States.,Department of Neurology, Emory University School of Medicine, Atlanta, GA, United States
| | - Bing Yao
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, United States
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83
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Mampay M, Sheridan GK. REST: An epigenetic regulator of neuronal stress responses in the young and ageing brain. Front Neuroendocrinol 2019; 53:100744. [PMID: 31004616 DOI: 10.1016/j.yfrne.2019.04.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 04/03/2019] [Accepted: 04/11/2019] [Indexed: 12/27/2022]
Abstract
The transcriptional repressor REST (Repressor Element-1 Silencing Transcription factor) is a key modulator of the neuronal epigenome and targets genes involved in neuronal differentiation, axonal growth, vesicular transport, ion channel conductance and synaptic plasticity. Whilst its gene expression-modifying properties have been examined extensively in neuronal development, REST's response towards stress-induced neuronal insults has only recently been explored. Overall, REST appears to be an ideal candidate to fine-tune neuronal gene expression following different forms of cellular, neuropathological, psychological and physical stressors. Upregulation of REST is reportedly protective against premature neural stem cell depletion, neuronal hyperexcitability, oxidative stress, neuroendocrine system dysfunction and neuropathology. In contrast, neuronal REST activation has also been linked to neuronal dysfunction and neurodegeneration. Here, we highlight key findings and discrepancies surrounding our current understanding of REST's function in neuronal adaptation to stress and explore its potential role in neuronal stress resilience in the young and ageing brain.
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Affiliation(s)
- Myrthe Mampay
- Neuroimmunology & Neurotherapeutics Laboratory, School of Pharmacy and Biomolecular Sciences, University of Brighton, Brighton BN2 4GJ, UK
| | - Graham K Sheridan
- Neuroimmunology & Neurotherapeutics Laboratory, School of Pharmacy and Biomolecular Sciences, University of Brighton, Brighton BN2 4GJ, UK.
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84
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Shapson-Coe A, Valeiras B, Wall C, Rada C. Aicardi-Goutières Syndrome associated mutations of RNase H2B impair its interaction with ZMYM3 and the CoREST histone-modifying complex. PLoS One 2019; 14:e0213553. [PMID: 30889214 PMCID: PMC6424451 DOI: 10.1371/journal.pone.0213553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 02/24/2019] [Indexed: 11/18/2022] Open
Abstract
DNA-RNA hybrids arise in all cell types, and are removed by multiple enzymes, including the trimeric ribonuclease, RNase H2. Mutations in human RNase H2 result in Aicardi–Goutières syndrome (AGS), an inflammatory brain disorder notable for being a Mendelian mimic of congenital viral infection. Previous studies have shown that several AGS-associated mutations of the RNase H2B subunit do not affect trimer stability or catalytic activity and are clustered on the surface of the complex, leading us to speculate that these mutations might impair important interactions of RNase H2 with so far unidentified proteins. In this study, we show that AGS mutations in this cluster impair the interaction of RNase H2 with several members of the CoREST chromatin-silencing complex that include the histone deacetylase HDAC2 and the demethylase KDM1A, the transcriptional regulators RCOR1 and GTFII-I as well as ZMYM3, an MYM-type zinc finger protein. We also show that the interaction is mediated by the zinc finger protein ZMYM3, suggesting that ZMYM3 acts as a novel type of scaffold protein coordinating interactions between deacetylase, demethylase and RNase H type enzymes, raising the question of whether coordination between histone modifications and the degradation of RNA-DNA hybrids may be required to prevent inflammation in humans.
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Affiliation(s)
- Alexander Shapson-Coe
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, United Kingdom
- * E-mail: (ASC); (CR)
| | - Brenda Valeiras
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, United Kingdom
| | - Christopher Wall
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, United Kingdom
| | - Cristina Rada
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, United Kingdom
- * E-mail: (ASC); (CR)
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85
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NRSF and Its Epigenetic Effectors: New Treatments for Neurological Disease. Brain Sci 2018; 8:brainsci8120226. [PMID: 30572571 PMCID: PMC6316267 DOI: 10.3390/brainsci8120226] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 12/13/2018] [Accepted: 12/14/2018] [Indexed: 12/02/2022] Open
Abstract
The Neuron Restrictive Silencer Factor (NRSF) is the well-known master transcriptional repressor of the neuronal phenotype. Research to date has shown that it is an important player in the growth and development of the nervous system. Its role in the maturation of neural precursor cells to adult neurons has been well characterized in stem cell models. While much has been characterized from a developmental perspective, research is revealing that NRSF plays a role in various neurological diseases, ranging from neurodegenerative, neuropsychiatric, to cancer. Dysregulation of NRSF activity disrupts downstream gene expression that is responsible for neuronal cell homeostasis in several models that contribute to pathologic states. Interestingly, it is now becoming apparent that the dysregulation of NRSF contributes to neurological disease through epigenetic mechanisms. Although NRSF itself is a transcription factor, its major effectors are chromatin modifiers. At the level of epigenetics, changes in NRSF activity have been well characterized in models of neuropathic pain and epilepsy. Better understanding of the epigenetic basis of brain diseases has led to design and use of small molecules that can prevent NRSF from repressing gene expression by neutralizing its interactions with its chromatin remodelers. This review will address the basic function of NRSF and its cofactors, investigate their mechanisms, then explore how their dysfunction can cause disease states. This review will also address research on NRSF as a therapeutic target and delve into new therapeutic strategies that focus on disrupting NRSF’s ability to recruit chromatin remodelers.
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86
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Zhang J, Chen SR, Chen H, Pan HL. RE1-silencing transcription factor controls the acute-to-chronic neuropathic pain transition and Chrm2 receptor gene expression in primary sensory neurons. J Biol Chem 2018; 293:19078-19091. [PMID: 30327427 DOI: 10.1074/jbc.ra118.005846] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 10/12/2018] [Indexed: 12/15/2022] Open
Abstract
Neuropathic pain is associated with persistent changes in gene expression in primary sensory neurons, but the underlying epigenetic mechanisms that cause these changes remain unclear. The muscarinic cholinergic receptors (mAChRs), particularly the M2 subtype (encoded by the cholinergic receptor muscarinic 2 (Chrm2) gene), are critically involved in the regulation of spinal nociceptive transmission. However, little is known about how Chrm2 expression is transcriptionally regulated. Here we show that nerve injury persistently increased the expression of RE1-silencing transcription factor (REST, also known as neuron-restrictive silencing factor [NRSF]), a gene-silencing transcription factor, in the dorsal root ganglion (DRG). Remarkably, nerve injury-induced chronic but not acute pain hypersensitivity was attenuated in mice with Rest knockout in DRG neurons. Also, siRNA-mediated Rest knockdown reversed nerve injury-induced chronic pain hypersensitivity in rats. Nerve injury persistently reduced Chrm2 expression in the DRG and diminished the analgesic effect of muscarine. The RE1 binding site on the Chrm2 promoter is required for REST-mediated Chrm2 repression, and nerve injury increased the enrichment of REST in the Chrm2 promoter in the DRG. Furthermore, Rest knockdown or genetic ablation in DRG neurons normalized Chrm2 expression and augmented muscarine's analgesic effect on neuropathic pain and fully reversed the nerve injury-induced reduction in the inhibitory effect of muscarine on glutamatergic input to spinal dorsal horn neurons. Our findings indicate that nerve injury-induced REST up-regulation in DRG neurons plays an important role in the acute-to-chronic pain transition and is essential for the transcriptional repression of Chrm2 in neuropathic pain.
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Affiliation(s)
- Jixiang Zhang
- From the Center for Neuroscience and Pain Research, Department of Anesthesiology and Perioperative Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas 77030
| | - Shao-Rui Chen
- From the Center for Neuroscience and Pain Research, Department of Anesthesiology and Perioperative Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas 77030
| | - Hong Chen
- From the Center for Neuroscience and Pain Research, Department of Anesthesiology and Perioperative Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas 77030
| | - Hui-Lin Pan
- From the Center for Neuroscience and Pain Research, Department of Anesthesiology and Perioperative Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas 77030
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87
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Anderson EM, Penrod RD, Barry SM, Hughes BW, Taniguchi M, Cowan CW. It is a complex issue: emerging connections between epigenetic regulators in drug addiction. Eur J Neurosci 2018; 50:2477-2491. [PMID: 30251397 DOI: 10.1111/ejn.14170] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 09/04/2018] [Accepted: 09/11/2018] [Indexed: 02/06/2023]
Abstract
Drug use leads to addiction in some individuals, but the underlying brain mechanisms that control the transition from casual drug use to an intractable substance use disorder (SUD) are not well understood. Gene x environment interactions such as the frequency of drug use and the type of substance used likely to promote maladaptive plastic changes in brain regions that are critical for controlling addiction-related behavior. Epigenetics encompasses a broad spectrum of mechanisms important for regulating gene transcription that are not dependent on changes in DNA base pair sequences. This review focuses on the proteins and complexes contributing to epigenetic modifications in the nucleus accumbens (NAc) following drug experience. We discuss in detail the three major mechanisms: histone acetylation and deacetylation, histone methylation, and DNA methylation. We discuss how drug use alters the regulation of the associated proteins regulating these processes and highlight how experimental manipulations of these proteins in the NAc can alter drug-related behaviors. Finally, we discuss the ways that histone modifications and DNA methylation coordinate actions by recruiting large epigenetic enzyme complexes to aid in transcriptional repression. Targeting these multiprotein epigenetic enzyme complexes - and the individual proteins that comprise them - might lead to effective therapeutics to reverse or treat SUDs in patients.
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Affiliation(s)
- Ethan M Anderson
- Departments of Neuroscience and Psychiatry and Behavioral Sciences, Medical University of South Carolina, 173 Ashley Ave, MSC 510, Charleston, SC, 29425-2030, USA
| | - Rachel D Penrod
- Departments of Neuroscience and Psychiatry and Behavioral Sciences, Medical University of South Carolina, 173 Ashley Ave, MSC 510, Charleston, SC, 29425-2030, USA
| | - Sarah M Barry
- Departments of Neuroscience and Psychiatry and Behavioral Sciences, Medical University of South Carolina, 173 Ashley Ave, MSC 510, Charleston, SC, 29425-2030, USA
| | - Brandon W Hughes
- Departments of Neuroscience and Psychiatry and Behavioral Sciences, Medical University of South Carolina, 173 Ashley Ave, MSC 510, Charleston, SC, 29425-2030, USA
| | - Makoto Taniguchi
- Departments of Neuroscience and Psychiatry and Behavioral Sciences, Medical University of South Carolina, 173 Ashley Ave, MSC 510, Charleston, SC, 29425-2030, USA
| | - Christopher W Cowan
- Departments of Neuroscience and Psychiatry and Behavioral Sciences, Medical University of South Carolina, 173 Ashley Ave, MSC 510, Charleston, SC, 29425-2030, USA
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88
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Ciuculete DM, Boström AE, Tuunainen AK, Sohrabi F, Kular L, Jagodic M, Voisin S, Mwinyi J, Schiöth HB. Changes in methylation within the STK32B promoter are associated with an increased risk for generalized anxiety disorder in adolescents. J Psychiatr Res 2018; 102:44-51. [PMID: 29604450 DOI: 10.1016/j.jpsychires.2018.03.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 03/20/2018] [Accepted: 03/21/2018] [Indexed: 12/20/2022]
Abstract
Generalized anxiety disorder (GAD) is highly prevalent among adolescents. An early detection of individuals at risk may prevent later psychiatric condition. Genome-wide studies investigating single nucleotide polymorphisms (SNPs) concluded that a focus on epigenetic mechanisms, which mediate the impact of environmental factors, could more efficiently help the understanding of GAD pathogenesis. We investigated the relationship between epigenetic shifts in blood and the risk to develop GAD, evaluated by the Development and Well-Being Assessment (DAWBA) score, in 221 otherwise healthy adolescents. Our analysis focused specifically on methylation sites showing high inter-individual variation but low tissue-specific variation, in order to infer a potential correlation between results obtained in blood and brain. Two statistical methods were applied, 1) a linear model with limma and 2) a likelihood test followed by Bonferroni correction. Methylation findings were validated in a cohort of 160 adults applying logistic models against the outcome variable "anxiety treatment obtained in the past" and studied in a third cohort with regards to associated expression changes measured in monocytes. One CpG site showed 1% increased methylation in adolescents at high risk of GAD (cg16333992, padj. = 0.028, estimate = 3.22), as confirmed in the second cohort (p = 0.031, estimate = 1.32). The identified and validated CpG site is located within the STK32B promoter region and its methylation level was positively associated with gene expression. Gene ontology analysis revealed that STK32B is involved in stress response and defense response. Our results provide evidence that shifts in DNA methylation are associated with a modulated risk profile for GAD in adolescence.
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Affiliation(s)
- Diana M Ciuculete
- Department of Neuroscience, Functional Pharmacology, Uppsala University, BMC, Box 593, 751 24 Uppsala, Sweden.
| | - Adrian E Boström
- Department of Neuroscience, Functional Pharmacology, Uppsala University, BMC, Box 593, 751 24 Uppsala, Sweden
| | - Anna-Kaisa Tuunainen
- Department of Neuroscience, Functional Pharmacology, Uppsala University, BMC, Box 593, 751 24 Uppsala, Sweden
| | - Farah Sohrabi
- Department of Neuroscience, Functional Pharmacology, Uppsala University, BMC, Box 593, 751 24 Uppsala, Sweden
| | - Lara Kular
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, 171 76 Stockholm, Sweden
| | - Maja Jagodic
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, 171 76 Stockholm, Sweden
| | - Sarah Voisin
- Institute of Sport, Exercise and Active Living, Victoria University, Functional Pharmacology, Uppsala University, BMC, Box 593, 751 24 Uppsala, Sweden
| | - Jessica Mwinyi
- Department of Neuroscience, Functional Pharmacology, Uppsala University, BMC, Box 593, 751 24 Uppsala, Sweden
| | - Helgi B Schiöth
- Department of Neuroscience, Functional Pharmacology, Uppsala University, BMC, Box 593, 751 24 Uppsala, Sweden
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89
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PIASγ controls stability and facilitates SUMO-2 conjugation to CoREST family of transcriptional co-repressors. Biochem J 2018; 475:1441-1454. [PMID: 29555846 DOI: 10.1042/bcj20170983] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 03/14/2018] [Accepted: 03/16/2018] [Indexed: 02/05/2023]
Abstract
CoREST family of transcriptional co-repressors regulates gene expression and cell fate determination during development. CoREST co-repressors recruit with different affinity the histone demethylase LSD1 (KDM1A) and the deacetylases HDAC1/2 to repress with variable strength the expression of target genes. CoREST protein levels are differentially regulated during cell fate determination and in mature tissues. However, regulatory mechanisms of CoREST co-repressors at the protein level have not been studied. Here, we report that CoREST (CoREST1, RCOR1) and its homologs CoREST2 (RCOR2) and CoREST3 (RCOR3) interact with PIASγ (protein inhibitor of activated STAT), a SUMO (small ubiquitin-like modifier)-E3-ligase. PIASγ increases the stability of CoREST proteins and facilitates their SUMOylation by SUMO-2. Interestingly, the SUMO-conjugating enzyme, Ubc9 also facilitates the SUMOylation of CoREST proteins. However, it does not change their protein levels. Specificity was shown using the null enzymatic form of PIASγ (PIASγ-C342A) and the SUMO protease SENP-1, which reversed SUMOylation and the increment of CoREST protein levels induced by PIASγ. The major SUMO acceptor lysines are different and are localized in nonconserved sequences among CoREST proteins. SUMOylation-deficient CoREST1 and CoREST3 mutants maintain a similar interaction profile with LSD1 and HDAC1/2, and consequently maintain similar repressor capacity compared with wild-type counterparts. In conclusion, CoREST co-repressors form protein complexes with PIASγ, which acts both as SUMO E3-ligase and as a protein stabilizer for CoREST proteins. This novel regulation of CoREST by PIASγ interaction and SUMOylation may serve to control cell fate determination during development.
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90
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91
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Negative regulation of REST on NR2B in spinal cord contributes to the development of bone cancer pain in mice. Oncotarget 2018; 7:85564-85572. [PMID: 27732941 PMCID: PMC5356758 DOI: 10.18632/oncotarget.9447] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 07/15/2016] [Indexed: 11/25/2022] Open
Abstract
In this study, C3H/HeNCrlVr mice are implanted with sarcoma NCTC 2472 cells into the intramedullary space of the femur to induce ongoing bone cancer-related pain behaviors. During the progress of the bone cancer pain, the down-regulation in spinal REST (Neuron-restrictive silencer factor, NRSF/REST) with concomitant up-regulation in spinal NR2B (2B subunit of N-methyl-D-aspartate receptor, NR2B) protein expression are observed at days 5, 7, 10 and 14 post-inoculation. Immunofluorescence assay shows that almost all of REST and NR2B-positive signals encompass NeuN (neuron-specific nuclear protein, a neuronal marker)-positive signals in spinal cord of sham and tumor-bearing mice. Different from previous researches involved in the main distribution of REST in neural progenitors, the expression of REST in mature neurons in spinal cord of adult mice is observed. Intrathecal administration of AS-ODN of REST at days 0, 2, 4 and 6 post-inoculation further enhances expression of spinal NR2B at day 7 post-inoculation, which suggests the reduced suppression of spinal REST on NR2B during the development of bone cancer pain. In summary, our study provides the evidence that the negative regulation of REST on NR2B in spinal cord takes part in the exacerbation of bone cancer pain.
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92
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Hwang JY, Zukin RS. REST, a master transcriptional regulator in neurodegenerative disease. Curr Opin Neurobiol 2018; 48:193-200. [PMID: 29351877 DOI: 10.1016/j.conb.2017.12.008] [Citation(s) in RCA: 136] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 12/04/2017] [Accepted: 12/17/2017] [Indexed: 12/19/2022]
Abstract
The restrictive element-1 silencing transcription factor)/NRSF (neuron-restrictive silencing factor (NRSF) is a transcriptional repressor which acts via epigenetic remodeling to silence target genes. Emerging evidence indicates that REST is a master transcriptional regulator of neuron-specific genes not only in neurogenesis and neuronal differentiation, but also in differentiated neurons during the critical period in postnatal brain development, where it plays a role in fine-tuning of genes involved in synaptic plasticity, and in normal aging, where it promotes neuroprotection by repressing genes involved in oxidative stress and β-amyloid toxicity. This review focuses on recent findings that dysregulation of REST and REST-dependent epigenetic remodeling provide a central mechanism critical to the progressive neurodegeneration associated with neurologic disorders and diseases including global ischemia, stroke, epilepsy, Alzheimer's and Huntington's disease.
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Affiliation(s)
- Jee-Yeon Hwang
- Dominick P. Purpura Department of Neuroscience, Rose F. Kennedy Center, Room 610, Albert Einstein College of Medicine, 1300 Morris Park Avenue, New York, NY 10461, USA
| | - R Suzanne Zukin
- Dominick P. Purpura Department of Neuroscience, Rose F. Kennedy Center, Room 610, Albert Einstein College of Medicine, 1300 Morris Park Avenue, New York, NY 10461, USA.
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93
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Hirano K, Namihira M. FAD influx enhances neuronal differentiation of human neural stem cells by facilitating nuclear localization of LSD1. FEBS Open Bio 2017; 7:1932-1942. [PMID: 29226080 PMCID: PMC5715241 DOI: 10.1002/2211-5463.12331] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 09/07/2017] [Accepted: 09/30/2017] [Indexed: 01/09/2023] Open
Abstract
Flavin adenine dinucleotide (FAD), synthesized from riboflavin, is redox cofactor in energy production and plays an important role in cell survival. More recently, riboflavin deficiency has been linked to developmental disorders, but its role in stem cell differentiation remains unclear. Here, we show that FAD treatment, using DMSO as a solvent, enabled an increase in the amount of intracellular FAD and promoted neuronal differentiation of human neural stem cells (NSCs) derived not only from fetal brain, but also from induced pluripotent stem cells. Depression of FAD‐dependent histone demethylase, lysine‐specific demethylase‐1 (LSD1), prevented FAD‐induced neuronal differentiation. Furthermore, FAD influx facilitated nuclear localization of LSD1 and its enzymatic activity. Together, these findings led us to propose that FAD contributes to proper neuronal production from NSCs in the human fetal brain during development.
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Affiliation(s)
- Kazumi Hirano
- Molecular Neurophysiology Research Group Biomedical Research Institute The National Institute of Advanced Industrial Science and Technology (AIST) Tsukuba Japan
| | - Masakazu Namihira
- Molecular Neurophysiology Research Group Biomedical Research Institute The National Institute of Advanced Industrial Science and Technology (AIST) Tsukuba Japan
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94
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Figueroa J, Phillips LM, Shahar T, Hossain A, Gumin J, Kim H, Bean AJ, Calin GA, Fueyo J, Walters ET, Kalluri R, Verhaak RG, Lang FF. Exosomes from Glioma-Associated Mesenchymal Stem Cells Increase the Tumorigenicity of Glioma Stem-like Cells via Transfer of miR-1587. Cancer Res 2017; 77:5808-5819. [PMID: 28855213 DOI: 10.1158/0008-5472.can-16-2524] [Citation(s) in RCA: 157] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2016] [Revised: 07/07/2017] [Accepted: 08/21/2017] [Indexed: 12/21/2022]
Abstract
Tumor-stromal communications impact tumorigenesis in ways that are incompletely understood. Here, we show that glioma-associated human mesenchymal stem cells (GA-hMSC), a newly identified stromal component of glioblastoma, release exosomes that increase the proliferation and clonogenicity of tumor-initiating glioma stem-like cells (GSC). This event leads to a significantly greater tumor burden and decreased host survival compared with untreated GSCs in orthotopic xenografts. Analysis of the exosomal content identified miR-1587 as a mediator of the exosomal effects on GSCs, in part via downregulation of the tumor-suppressive nuclear receptor corepressor NCOR1. Our results illuminate the tumor-supporting role for GA-hMSCs by identifying GA-hMSC-derived exosomes in the intercellular transfer of specific miRNA that enhance the aggressiveness of glioblastoma. Cancer Res; 77(21); 5808-19. ©2017 AACR.
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Affiliation(s)
- Javier Figueroa
- Department of Neurosurgery, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Lynette M Phillips
- Department of Neurosurgery, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Tal Shahar
- Department of Neurosurgery, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Anwar Hossain
- Department of Neurosurgery, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Joy Gumin
- Department of Neurosurgery, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Hoon Kim
- Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Andrew J Bean
- Department of Neurobiology and Anatomy, University of Texas Health Science Center at Houston, Houston, Texas
| | - George A Calin
- Department of Experimental Therapeutics, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Juan Fueyo
- Department of Neuro-Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Edgar T Walters
- Department of Integrated Biology and Pharmacology, University of Texas Health Science Center at Houston, Houston, Texas
| | - Raghu Kalluri
- Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Roel G Verhaak
- Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Frederick F Lang
- Department of Neurosurgery, University of Texas MD Anderson Cancer Center, Houston, Texas.
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95
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Mozzi A, Guerini FR, Forni D, Costa AS, Nemni R, Baglio F, Cabinio M, Riva S, Pontremoli C, Clerici M, Sironi M, Cagliani R. REST, a master regulator of neurogenesis, evolved under strong positive selection in humans and in non human primates. Sci Rep 2017; 7:9530. [PMID: 28842657 PMCID: PMC5573535 DOI: 10.1038/s41598-017-10245-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 08/07/2017] [Indexed: 12/03/2022] Open
Abstract
The transcriptional repressor REST regulates many neuronal genes by binding RE1 motifs. About one third of human RE1s are recently evolved and specific to primates. As changes in the activity of a transcription factor reverberate on its downstream targets, we assessed whether REST displays fast evolutionary rates in primates. We show that REST was targeted by very strong positive selection during primate evolution. Positive selection was also evident in the human lineage, with six selected sites located in a region that surrounds a VNTR in exon 4. Analysis of expression data indicated that REST brain expression peaks during aging in humans but not in other primates. Because a REST coding variant (rs3796529) was previously associated with protection from hippocampal atrophy in elderly subjects with mild cognitive impairment (MCI), we analyzed a cohort of Alzheimer disease (AD) continuum patients. Genotyping of two coding variants (rs3796529 and rs2227902) located in the region surrounding the VNTR indicated a role for rs2227902 in modulation of hippocampal volume loss, indirectly confirming a role for REST in neuroprotection. Experimental studies will be instrumental to determine the functional effect of positively selected sites in REST and the role of REST variants in neuropreservation/neurodegeneration.
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Affiliation(s)
- Alessandra Mozzi
- Bioinformatics, Scientific Institute IRCCS E. MEDEA, 23842, Bosisio Parini, Italy
| | | | - Diego Forni
- Bioinformatics, Scientific Institute IRCCS E. MEDEA, 23842, Bosisio Parini, Italy
| | | | | | | | - Monia Cabinio
- Don C. Gnocchi Foundation ONLUS, IRCCS, 20148, Milan, Italy
| | - Stefania Riva
- Bioinformatics, Scientific Institute IRCCS E. MEDEA, 23842, Bosisio Parini, Italy
| | - Chiara Pontremoli
- Bioinformatics, Scientific Institute IRCCS E. MEDEA, 23842, Bosisio Parini, Italy
| | - Mario Clerici
- Don C. Gnocchi Foundation ONLUS, IRCCS, 20148, Milan, Italy.,Department of Physiopathology and Transplantation, University of Milan, 20090, Milan, Italy
| | - Manuela Sironi
- Bioinformatics, Scientific Institute IRCCS E. MEDEA, 23842, Bosisio Parini, Italy
| | - Rachele Cagliani
- Bioinformatics, Scientific Institute IRCCS E. MEDEA, 23842, Bosisio Parini, Italy.
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Nawa Y, Kaneko H, Oda M, Tsubonoya M, Hiroi T, Gentile MT, Colucci-D'Amato L, Takahashi R, Matsui H. Functional characterization of the neuron-restrictive silencer element in the human tryptophan hydroxylase 2 gene expression. J Neurochem 2017; 142:827-840. [PMID: 28464229 DOI: 10.1111/jnc.14060] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 04/20/2017] [Accepted: 04/21/2017] [Indexed: 12/24/2022]
Abstract
Tryptophan hydroxylase 2 (TPH2) is the key enzyme in the synthesis of neuronal serotonin. Although previous studies suggest that TPH2 neuron-restrictive silencer element (NRSE) functions as a negative regulator dependent on neuron-restrictive silencer factor (NRSF) activity, the underlying mechanisms are yet to be fully elucidated. Here, we show a detailed analysis of the NRSE-mediated repression of the human TPH2 (hTPH2) promoter activity in RN46A cells, a cell line derived from rat raphe neurons. Quantitative real-time RT-PCR analysis revealed the expression of serotonergic marker genes (Mash1, Nkx2.2, Gata2, Gata3, Lmx1b, Pet-1, 5-Htt, and Vmat2) and Nrsf gene in RN46A cells. Tph1 mRNA is the prevalent form expressed in RN46A cells; Tph2 mRNA is also expressed but at a lower level. Electrophoretic mobility shift assays and reporter assays showed that hTPH2 NRSE is necessary for the efficient DNA binding of NRSF and for the NRSF-dependent repression of the hTPH2 promoter activity. The hTPH2 promoter activity was increased by knockdown of NRSF, or over-expression of the engineered NRSF (a dominant-negative mutant or a DNA-binding domain and activation domain fusion protein). MS-275, a class I histone deacetylase (HDAC) inhibitor, was found to be more potent than MC-1568, a class II HDAC inhibitor, in enhancing the hTPH2 promoter activity. Furthermore, treatment with the ubiquitin-specific protease 7 deubiquitinase inhibitors, P-22077 or HBX 41108, increased the hTPH2 promoter activity. Collectively, our data demonstrate that the hTPH2 NRSE-mediated promoter repression via NRSF involves class I HDACs and is modulated by the ubiquitin-specific protease 7-mediated deubiquitination and stabilization of NRSF.
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Affiliation(s)
- Yukino Nawa
- Institute of Radioisotope Research, St. Marianna University Graduate School of Medicine, Kawasaki, Japan
| | - Hanae Kaneko
- Institute of Radioisotope Research, St. Marianna University Graduate School of Medicine, Kawasaki, Japan
| | - Masayuki Oda
- Department of Pharmacogenomics, St. Marianna University Graduate School of Medicine, Kawasaki, Japan
| | - Masaaki Tsubonoya
- Institute of Radioisotope Research, St. Marianna University Graduate School of Medicine, Kawasaki, Japan
| | - Tomoko Hiroi
- Institute of Radioisotope Research, St. Marianna University Graduate School of Medicine, Kawasaki, Japan
| | - Maria Teresa Gentile
- Laboratory of Molecular and Cellular Pathology, Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, Caserta, Italy
| | - Luca Colucci-D'Amato
- Laboratory of Molecular and Cellular Pathology, Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, Caserta, Italy
| | - Ryoya Takahashi
- Department of Biochemistry, Faculty of Pharmaceutical Sciences, Toho University, Funabashi, Japan
| | - Hiroaki Matsui
- Institute of Radioisotope Research, St. Marianna University Graduate School of Medicine, Kawasaki, Japan.,Department of Molecular and Behavioral Neuroscience, St. Marianna University Graduate School of Medicine, Kawasaki, Japan
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97
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Lempiäinen JK, Niskanen EA, Vuoti KM, Lampinen RE, Göös H, Varjosalo M, Palvimo JJ. Agonist-specific Protein Interactomes of Glucocorticoid and Androgen Receptor as Revealed by Proximity Mapping. Mol Cell Proteomics 2017; 16:1462-1474. [PMID: 28611094 DOI: 10.1074/mcp.m117.067488] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 06/02/2017] [Indexed: 11/06/2022] Open
Abstract
Glucocorticoid receptor (GR) and androgen receptor (AR) are steroid-inducible transcription factors (TFs). The GR and the AR are central regulators of various metabolic, homeostatic and differentiation processes and hence important therapeutic targets, especially in inflammation and prostate cancer, respectively. Hormone binding to these steroid receptors (SRs) leads to DNA binding and activation or repression of their target genes with the aid of interacting proteins, coregulators. However, protein interactomes of these important drug targets have remained poorly defined. We used proximity-dependent biotin identification to map the protein interaction landscapes of GR and AR in the presence and absence of their cognate agonist (dexamethasone, 5α-dihydrotestosterone) and antagonist (RU486, enzalutamide) in intact human cells. We reproducibly identified more than 30 proteins that interacted with the GR in an agonist-specific manner and whose interactions were significantly influenced by the DNA-binding function of the receptor. Interestingly, the agonist-dependent interactome of the GR overlapped considerably with that of the AR. In addition to known coactivators, corepressors and components of BAF (SWI/SNF) chromatin-remodeling complex, we identified a number of proteins, including lysine methyltransferases and demethylases that have not been previously linked to glucocorticoid or androgen signaling. A substantial number of these novel agonist-dependent GR/AR-interacting proteins, e.g. BCOR, IRF2BP2, RCOR1, and TLE3, have previously been implicated in transcription repression. This together with our data on the effect of BCOR, IRF2BP2, and RCOR1 on GR target gene expression suggests multifaceted functions and roles for SR coregulators. These first high confidence SR interactomes will aid in therapeutic targeting of the GR and the AR.
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Affiliation(s)
- Joanna K Lempiäinen
- From the ‡Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Einari A Niskanen
- From the ‡Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Kaisa-Mari Vuoti
- From the ‡Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Riikka E Lampinen
- From the ‡Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Helka Göös
- §Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Markku Varjosalo
- §Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Jorma J Palvimo
- From the ‡Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland;
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98
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Gavin DP, Grayson DR, Varghese SP, Guizzetti M. Chromatin Switches during Neural Cell Differentiation and Their Dysregulation by Prenatal Alcohol Exposure. Genes (Basel) 2017; 8:E137. [PMID: 28492482 PMCID: PMC5448011 DOI: 10.3390/genes8050137] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 05/01/2017] [Accepted: 05/06/2017] [Indexed: 02/07/2023] Open
Abstract
Prenatal alcohol exposure causes persistent neuropsychiatric deficits included under the term fetal alcohol spectrum disorders (FASD). Cellular identity emerges from a cascade of intrinsic and extrinsic (involving cell-cell interactions and signaling) processes that are partially initiated and maintained through changes in chromatin structure. Prenatal alcohol exposure influences neuronal and astrocyte development, permanently altering brain connectivity. Prenatal alcohol exposure also alters chromatin structure through histone and DNA modifications. However, the data linking alcohol-induced differentiation changes with developmental alterations in chromatin structure remain to be elucidated. In the first part of this review, we discuss the sequence of chromatin structural changes involved in neural cell differentiation during normal development. We then discuss the effects of prenatal alcohol on developmental histone modifications and DNA methylation in the context of neurogenesis and astrogliogenesis. We attempt to synthesize the developmental literature with the FASD literature, proposing that alcohol-induced changes to chromatin structure account for altered neurogenesis and astrogliogenesis as well as altered neuron and astrocyte differentiation. Together these changes may contribute to the cognitive and behavioral abnormalities in FASD. Future studies using standardized alcohol exposure paradigms at specific developmental stages will advance the understanding of how chromatin structural changes impact neural cell fate and maturation in FASD.
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Affiliation(s)
- David P Gavin
- Jesse Brown Veterans Affairs Medical Center, 820 South Damen Avenue (M/C 151), Chicago, IL 60612, USA.
- Center for Alcohol Research in Epigenetics, Department of Psychiatry, University of Illinois at Chicago, 1601 W. Taylor St., Chicago, IL 60612, USA.
| | - Dennis R Grayson
- Center for Alcohol Research in Epigenetics, Department of Psychiatry, University of Illinois at Chicago, 1601 W. Taylor St., Chicago, IL 60612, USA.
| | - Sajoy P Varghese
- Jesse Brown Veterans Affairs Medical Center, 820 South Damen Avenue (M/C 151), Chicago, IL 60612, USA.
| | - Marina Guizzetti
- Department of Behavioral Neuroscience, Oregon Health & Science University, 3181 SW Sam Jackson Park Road L470, Portland, OR 97239, USA.
- Veterans Affairs Portland Health Care System, 3710 Southwest US Veterans Hospital Road, Portland, OR 97239, USA.
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99
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Lee WS, McColl B, Maksimovic J, Vadolas J. Epigenetic interplay at the β-globin locus. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2017; 1860:393-404. [DOI: 10.1016/j.bbagrm.2017.01.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 01/28/2017] [Accepted: 01/30/2017] [Indexed: 02/02/2023]
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100
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Sagner A, Briscoe J. Morphogen interpretation: concentration, time, competence, and signaling dynamics. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2017; 6. [PMID: 28319331 PMCID: PMC5516147 DOI: 10.1002/wdev.271] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 01/22/2017] [Accepted: 02/10/2017] [Indexed: 12/14/2022]
Abstract
Tissue patterning during animal development is orchestrated by a handful of inductive signals. Most of these developmental cues act as morphogens, meaning they are locally produced secreted molecules that act at a distance to govern tissue patterning. The iterative use of the same signaling molecules in different developmental contexts demands that signal interpretation occurs in a highly context‐dependent manner. Hence the interpretation of signal depends on the specific competence of the receiving cells. Moreover, it has become clear that the differential interpretation of morphogens depends not only on the level of signaling but also the signaling dynamics, particularly the duration of signaling. In this review, we outline molecular mechanisms proposed in recent studies that explain how the response to morphogens is determined by differential competence, pathway intrinsic feedback, and the interpretation of signaling dynamics by gene regulatory networks. WIREs Dev Biol 2017, 6:e271. doi: 10.1002/wdev.271 For further resources related to this article, please visit the WIREs website.
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