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Gitik M, Elberg G, Reichert F, Tal M, Rotshenker S. Deletion of CD47 from Schwann cells and macrophages hastens myelin disruption/dismantling and scavenging in Schwann cells and augments myelin debris phagocytosis in macrophages. J Neuroinflammation 2023; 20:243. [PMID: 37872624 PMCID: PMC10594853 DOI: 10.1186/s12974-023-02929-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 10/10/2023] [Indexed: 10/25/2023] Open
Abstract
BACKGROUND Myelin that surrounds axons breaks in trauma and disease; e.g., peripheral nerve and spinal cord injuries (PNI and SCI) and multiple sclerosis (MS). Resulting myelin debris hinders repair if not effectively scavenged by Schwann cells and macrophages in PNI and by microglia in SCI and MS. We showed previously that myelin debris evades phagocytosis as CD47 on myelin ligates SIRPα (signal regulatory protein-α) on macrophages and microglia, triggering SIRPα to inhibit phagocytosis in phagocytes. Using PNI as a model, we tested the in vivo significance of SIRPα-dependent phagocytosis inhibition in SIRPα null mice, showing that SIRPα deletion leads to accelerated myelin debris clearance, axon regeneration and recovery of function from PNI. Herein, we tested how deletion of CD47, a SIRPα ligand and a cell surface receptor on Schwann cells and phagocytes, affects recovery from PNI. METHODS Using CD47 null (CD47-/-) and wild type mice, we studied myelin disruption/dismantling and debris clearance, axon regeneration and recovery of function from PNI. RESULTS As expected from CD47 on myelin acting as a SIRPα ligand that normally triggers SIRPα-dependent phagocytosis inhibition in phagocytes, myelin debris clearance, axon regeneration and function recovery were all faster in CD47-/- mice than in wild type mice. Unexpectedly compared with wild type mice, myelin debris clearance started sooner and CD47-deleted Schwann cells displayed enhanced disruption/dismantling and scavenging of myelin in CD47-/- mice. Furthermore, CD47-deleted macrophages from CD47-/- mice phagocytosed more myelin debris than CD47-expressing phagocytes from wild type mice. CONCLUSIONS This study reveals two novel normally occurring CD47-dependent mechanisms that impede myelin debris clearance. First, CD47 expressed on Schwann cells inhibits myelin disruption/dismantling and debris scavenging in Schwann cells. Second, CD47 expressed on macrophages inhibits myelin debris phagocytosis in phagocytes. The two add to a third mechanism that we previously documented whereby CD47 on myelin ligates SIRPα on macrophages and microglia, triggering SIRPα-dependent phagocytosis inhibition in phagocytes. Thus, CD47 plays multiple inhibitory roles that combined impede myelin debris clearance, leading to delayed recovery from PNI. Similar inhibitory roles in microglia may hinder recovery from other pathologies in which repair depends on efficient phagocytosis (e.g., SCI and MS).
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Affiliation(s)
- Miri Gitik
- Medical Neurobiology, Faculty of Medicine, IMRIC, Hebrew University, Ein-Kerem Campus, 12272, 91120, Jerusalem, Israel
- Genomic Research Branch, Division of Neuroscience and Basic Behavioral Science (DNBBS), National Institute of Mental Health (NIMH), NIH, Rockville, USA
| | - Gerard Elberg
- Medical Neurobiology, Faculty of Medicine, IMRIC, Hebrew University, Ein-Kerem Campus, 12272, 91120, Jerusalem, Israel
| | - Fanny Reichert
- Medical Neurobiology, Faculty of Medicine, IMRIC, Hebrew University, Ein-Kerem Campus, 12272, 91120, Jerusalem, Israel
| | - Michael Tal
- Medical Neurobiology, Faculties of Medicine and Dentistry, Center for Research on Pain, Hebrew University, Jerusalem, Israel
| | - Shlomo Rotshenker
- Medical Neurobiology, Faculty of Medicine, IMRIC, Hebrew University, Ein-Kerem Campus, 12272, 91120, Jerusalem, Israel.
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2
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Varghese DM, Nussinov R, Ahmad S. Predictive modeling of moonlighting DNA-binding proteins. NAR Genom Bioinform 2022; 4:lqac091. [PMID: 36474806 PMCID: PMC9716651 DOI: 10.1093/nargab/lqac091] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 10/25/2022] [Accepted: 11/11/2022] [Indexed: 09/10/2024] Open
Abstract
Moonlighting proteins are multifunctional, single-polypeptide chains capable of performing multiple autonomous functions. Most moonlighting proteins have been discovered through work unrelated to their multifunctionality. We believe that prediction of moonlighting proteins from first principles, that is, using sequence, predicted structure, evolutionary profiles, and global gene expression profiles, for only one functional class of proteins in a single organism at a time will significantly advance our understanding of multifunctional proteins. In this work, we investigated human moonlighting DNA-binding proteins (mDBPs) in terms of properties that distinguish them from other (non-moonlighting) proteins with the same DNA-binding protein (DBP) function. Following a careful and comprehensive analysis of discriminatory features, a machine learning model was developed to assess the predictability of mDBPs from other DBPs (oDBPs). We observed that mDBPs can be discriminated from oDBPs with high accuracy of 74% AUC of ROC using these first principles features. A number of novel predicted mDBPs were found to have literature support for their being moonlighting and others are proposed as candidates, for which the moonlighting function is currently unknown. We believe that this work will help in deciphering and annotating novel moonlighting DBPs and scale up other functions. The source codes and data sets used for this work are freely available at https://zenodo.org/record/7299265#.Y2pO3ctBxPY.
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Affiliation(s)
- Dana Mary Varghese
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi-110067, India
| | - Ruth Nussinov
- Computational Structural Biology Section, Cancer Innovation Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Israel
| | - Shandar Ahmad
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi-110067, India
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3
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Liu S, Aldinger KA, Cheng CV, Kiyama T, Dave M, McNamara HK, Zhao W, Stafford JM, Descostes N, Lee P, Caraffi SG, Ivanovski I, Errichiello E, Zweier C, Zuffardi O, Schneider M, Papavasiliou AS, Perry MS, Humberson J, Cho MT, Weber A, Swale A, Badea TC, Mao CA, Garavelli L, Dobyns WB, Reinberg D. NRF1 association with AUTS2-Polycomb mediates specific gene activation in the brain. Mol Cell 2021; 81:4663-4676.e8. [PMID: 34637754 PMCID: PMC8604784 DOI: 10.1016/j.molcel.2021.09.020] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 07/21/2021] [Accepted: 09/15/2021] [Indexed: 12/17/2022]
Abstract
The heterogeneous family of complexes comprising Polycomb repressive complex 1 (PRC1) is instrumental for establishing facultative heterochromatin that is repressive to transcription. However, two PRC1 species, ncPRC1.3 and ncPRC1.5, are known to comprise novel components, AUTS2, P300, and CK2, that convert this repressive function to that of transcription activation. Here, we report that individuals harboring mutations in the HX repeat domain of AUTS2 exhibit defects in AUTS2 and P300 interaction as well as a developmental disorder reflective of Rubinstein-Taybi syndrome, which is mainly associated with a heterozygous pathogenic variant in CREBBP/EP300. Moreover, the absence of AUTS2 or mutation in its HX repeat domain gives rise to misregulation of a subset of developmental genes and curtails motor neuron differentiation of mouse embryonic stem cells. The transcription factor nuclear respiratory factor 1 (NRF1) has a novel and integral role in this neurodevelopmental process, being required for ncPRC1.3 recruitment to chromatin.
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Affiliation(s)
- Sanxiong Liu
- Department of Biochemistry and Molecular Pharmacology, New York University Langone School of Medicine, New York, NY 10016, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Kimberly A Aldinger
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Chi Vicky Cheng
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Takae Kiyama
- Ruiz Department of Ophthalmology and Visual Science, McGovern Medical School at The University of Texas Health Science Center at Houston (UTHealth), Houston, TX 77030, USA; National Eye Institute, NIH, Bethesda, MD 20892, USA
| | - Mitali Dave
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Hanna K McNamara
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Wukui Zhao
- Department of Biochemistry and Molecular Pharmacology, New York University Langone School of Medicine, New York, NY 10016, USA
| | - James M Stafford
- Department of Biochemistry and Molecular Pharmacology, New York University Langone School of Medicine, New York, NY 10016, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Nicolas Descostes
- Department of Biochemistry and Molecular Pharmacology, New York University Langone School of Medicine, New York, NY 10016, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Pedro Lee
- Department of Biochemistry and Molecular Pharmacology, New York University Langone School of Medicine, New York, NY 10016, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Stefano G Caraffi
- Struttura Semplice Dipartimentale di Genetica Medica, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Ivan Ivanovski
- Struttura Semplice Dipartimentale di Genetica Medica, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy; Institute of Medical Genetics, University of Zürich, Zürich, Switzerland
| | - Edoardo Errichiello
- Dipartimento di Medicina Molecolare, Università di Pavia, Pavia, Italy; IRCCS Mondino Foundation, Pavia, Italy
| | - Christiane Zweier
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Schwabachanlage 10, 91054 Erlangen, Germany; Department of Human Genetics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Orsetta Zuffardi
- Dipartimento di Medicina Molecolare, Università di Pavia, Pavia, Italy
| | - Michael Schneider
- Carle Physicians Group, Section of Neurology, St. Christopher's Hospital for Children, Urbana, IL, USA
| | | | - M Scott Perry
- Comprehensive Epilepsy Program, Jane and John Justin Neuroscience Center, Cook Children's Medical Center, Fort Worth, TX 76104, USA
| | - Jennifer Humberson
- Division of Genetics, Department of Pediatrics, University of Virginia Children's Hospital, Charlottesville, VA, USA
| | | | | | - Andrew Swale
- Liverpool Women's Hospital, Liverpool, UK; Manchester Centre for Genomic Medicine, Manchester, UK
| | - Tudor C Badea
- National Eye Institute, NIH, Bethesda, MD 20892, USA; Research and Development Institute, Transilvania University of Brasov, School of Medicine, Brasov, Romania
| | - Chai-An Mao
- Ruiz Department of Ophthalmology and Visual Science, McGovern Medical School at The University of Texas Health Science Center at Houston (UTHealth), Houston, TX 77030, USA; National Eye Institute, NIH, Bethesda, MD 20892, USA
| | - Livia Garavelli
- Struttura Semplice Dipartimentale di Genetica Medica, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - William B Dobyns
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA; Department of Pediatrics (Genetic Medicine), University of Washington, Seattle, WA, USA
| | - Danny Reinberg
- Department of Biochemistry and Molecular Pharmacology, New York University Langone School of Medicine, New York, NY 10016, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
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An N-ethyl-N-Nitrosourea Mutagenesis Screen in Mice Reveals a Mutation in Nuclear Respiratory Factor 1 ( Nrf1) Altering the DNA Methylation State and Correct Embryonic Development. Animals (Basel) 2021; 11:ani11072103. [PMID: 34359231 PMCID: PMC8300126 DOI: 10.3390/ani11072103] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/30/2021] [Accepted: 07/12/2021] [Indexed: 12/26/2022] Open
Abstract
Simple Summary In this work, we aimed to discover unknown genes that are important in the regulation of other genes. These genes often play an important role during the development of the embryo. By screening thousands of mice, we found a gene, namely, Nuclear Respiratory Factor 1 (Nrf1), that controls the switching on and off of other genes. Mice with a defective Nrf1 present lesser levels of the gene and embryonic delay. When the mutation is in both chains of the DNA, mice are not born and die in the uterus. Our work unveils a novel, previously unknown functionality of Nrf1 and provides a new mice model for the study of diseases caused by a defective Nrf1. Abstract We have established a genome-wide N-ethyl-N-nitrosourea (ENU) mutagenesis screen to identify novel genes playing a role in epigenetic regulation in mammals. We hypothesize that the ENU mutagenesis screen will lead to the discovery of unknown genes responsible of the maintenance of the epigenetic state as the genes found are modifiers of variegation of the transgene green fluorescent protein (GFP) expression in erythrocytes, which are named MommeD. Here we report the generation of a novel mutant mouse line, MommeD46, that carries a new missense mutation producing an amino acid transversion (L71P) in the dimerization domain of Nuclear Respiratory Factor 1 (Nrf1). The molecular characterization of the mutation reveals a decrease in the Nrf1 mRNA levels and a novel role of Nrf1 in the maintenance of the DNA hypomethylation in vivo. The heritability of the mutation is consistent with paternal imprinting and haploinsufficiency. Homozygous mutants display embryonic lethality at 14.5 days post-coitum and developmental delay. This work adds a new epi-regulatory role to Nrf1 and uncovers unknown phenotypical defects of the Nrf1 hypomorph. The generated mouse line represents a valuable resource for studying NRF1-related diseases.
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5
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Stępniak K, Machnicka MA, Mieczkowski J, Macioszek A, Wojtaś B, Gielniewski B, Poleszak K, Perycz M, Król SK, Guzik R, Dąbrowski MJ, Dramiński M, Jardanowska M, Grabowicz I, Dziedzic A, Kranas H, Sienkiewicz K, Diamanti K, Kotulska K, Grajkowska W, Roszkowski M, Czernicki T, Marchel A, Komorowski J, Kaminska B, Wilczyński B. Mapping chromatin accessibility and active regulatory elements reveals pathological mechanisms in human gliomas. Nat Commun 2021; 12:3621. [PMID: 34131149 PMCID: PMC8206121 DOI: 10.1038/s41467-021-23922-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 05/19/2021] [Indexed: 12/15/2022] Open
Abstract
Chromatin structure and accessibility, and combinatorial binding of transcription factors to regulatory elements in genomic DNA control transcription. Genetic variations in genes encoding histones, epigenetics-related enzymes or modifiers affect chromatin structure/dynamics and result in alterations in gene expression contributing to cancer development or progression. Gliomas are brain tumors frequently associated with epigenetics-related gene deregulation. We perform whole-genome mapping of chromatin accessibility, histone modifications, DNA methylation patterns and transcriptome analysis simultaneously in multiple tumor samples to unravel epigenetic dysfunctions driving gliomagenesis. Based on the results of the integrative analysis of the acquired profiles, we create an atlas of active enhancers and promoters in benign and malignant gliomas. We explore these elements and intersect with Hi-C data to uncover molecular mechanisms instructing gene expression in gliomas.
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Affiliation(s)
- Karolina Stępniak
- Nencki Institute of Experimental Biology of the Polish Academy of Sciences, Warsaw, Poland
| | - Magdalena A Machnicka
- Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Warsaw, Poland
| | - Jakub Mieczkowski
- Nencki Institute of Experimental Biology of the Polish Academy of Sciences, Warsaw, Poland
- Medical University of Gdansk, International Research Agenda 3P Medicine Laboratory, Gdansk, Poland
| | - Anna Macioszek
- Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Warsaw, Poland
| | - Bartosz Wojtaś
- Nencki Institute of Experimental Biology of the Polish Academy of Sciences, Warsaw, Poland
| | - Bartłomiej Gielniewski
- Nencki Institute of Experimental Biology of the Polish Academy of Sciences, Warsaw, Poland
| | - Katarzyna Poleszak
- Nencki Institute of Experimental Biology of the Polish Academy of Sciences, Warsaw, Poland
| | - Malgorzata Perycz
- Nencki Institute of Experimental Biology of the Polish Academy of Sciences, Warsaw, Poland
| | - Sylwia K Król
- Nencki Institute of Experimental Biology of the Polish Academy of Sciences, Warsaw, Poland
| | - Rafał Guzik
- Nencki Institute of Experimental Biology of the Polish Academy of Sciences, Warsaw, Poland
| | - Michał J Dąbrowski
- Institute of Computer Science of the Polish Academy of Sciences, Warsaw, Poland
| | - Michał Dramiński
- Institute of Computer Science of the Polish Academy of Sciences, Warsaw, Poland
| | - Marta Jardanowska
- Institute of Computer Science of the Polish Academy of Sciences, Warsaw, Poland
| | - Ilona Grabowicz
- Institute of Computer Science of the Polish Academy of Sciences, Warsaw, Poland
| | - Agata Dziedzic
- Institute of Computer Science of the Polish Academy of Sciences, Warsaw, Poland
| | - Hanna Kranas
- Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Warsaw, Poland
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Karolina Sienkiewicz
- Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Warsaw, Poland
| | - Klev Diamanti
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Katarzyna Kotulska
- Departments of Neurology, Neurosurgery, Neuropathology, The Children's Memorial Health Institute, Warsaw, Poland
| | - Wiesława Grajkowska
- Departments of Neurology, Neurosurgery, Neuropathology, The Children's Memorial Health Institute, Warsaw, Poland
| | - Marcin Roszkowski
- Departments of Neurology, Neurosurgery, Neuropathology, The Children's Memorial Health Institute, Warsaw, Poland
| | - Tomasz Czernicki
- Department of Neurosurgery, Medical University of Warsaw, Warsaw, Poland
| | - Andrzej Marchel
- Department of Neurosurgery, Medical University of Warsaw, Warsaw, Poland
| | - Jan Komorowski
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Bozena Kaminska
- Nencki Institute of Experimental Biology of the Polish Academy of Sciences, Warsaw, Poland.
| | - Bartek Wilczyński
- Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Warsaw, Poland.
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Harris R, Randle S, Laman H. Analysis of the FBXO7 promoter reveals overlapping Pax5 and c-Myb binding sites functioning in B cells. Biochem Biophys Res Commun 2021; 554:41-48. [PMID: 33774278 PMCID: PMC8082276 DOI: 10.1016/j.bbrc.2021.03.052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 03/10/2021] [Indexed: 02/03/2023]
Abstract
Fbxo7 is a key player in the differentiation and function of numerous blood cell types, and in neurons, oligodendrocytes and spermatocytes. In an effort to gain insight into the physiological and pathological settings where Fbxo7 is likely to play a key role, we sought to define the transcription factors which direct FBXO7 expression. Using sequence alignments across 28 species, we defined the human FBXO7 promoter and found that it contains two conserved regions enriched for multiple transcription factor binding sites. Many of these have roles in either neuronal or haematopoietic development. Using various FBXO7 promoter reporters, we found ELF4, Pax5 and c-Myb have functional binding sites that activate transcription. We find endogenous Pax5 is bound to the FBXO7 promoter in pre-B cells, and that the exogenous expression of Pax5 represses Fbxo7 transcription in early pro-B cells.
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Affiliation(s)
- Rebecca Harris
- University of Cambridge, Department of Pathology, Tennis Court Road, Cambridge, CB2 1QP, United Kingdom
| | - Suzanne Randle
- University of Cambridge, Department of Pathology, Tennis Court Road, Cambridge, CB2 1QP, United Kingdom
| | - Heike Laman
- University of Cambridge, Department of Pathology, Tennis Court Road, Cambridge, CB2 1QP, United Kingdom.
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Decreased Mitochondrial Function, Biogenesis, and Degradation in Peripheral Blood Mononuclear Cells from Amyotrophic Lateral Sclerosis Patients as a Potential Tool for Biomarker Research. Mol Neurobiol 2020; 57:5084-5102. [PMID: 32840822 PMCID: PMC7541388 DOI: 10.1007/s12035-020-02059-1] [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: 05/07/2020] [Accepted: 08/07/2020] [Indexed: 12/11/2022]
Abstract
Amyotrophic lateral sclerosis (ALS) is a multifactorial and progressive neurodegenerative disease of unknown etiology. Due to ALS’s unpredictable onset and progression rate, the search for biomarkers that allow the detection and tracking of its development and therapeutic efficacy would be of significant medical value. Considering that alterations of energy supply are one of ALS’s main hallmarks and that a correlation has been established between gene expression in human brain tissue and peripheral blood mononuclear cells (PBMCs), the present work investigates whether changes in mitochondrial function could be used to monitor ALS. To achieve this goal, PBMCs from ALS patients and control subjects were used; blood sampling is a quite non-invasive method and is cost-effective. Different parameters were evaluated, namely cytosolic calcium levels, mitochondrial membrane potential, oxidative stress, and metabolic compounds levels, as well as mitochondrial dynamics and degradation. Altogether, we observed lower mitochondrial calcium uptake/retention, mitochondria depolarization, and redox homeostasis deregulation, in addition to a decrease in critical metabolic genes, a diminishment in mitochondrial biogenesis, and an augmentation in mitochondrial fission and autophagy-related gene expression. All of these changes can contribute to the decreased ATP and pyruvate levels observed in ALS PBMCs. Our data indicate that PBMCs from ALS patients show a significant mitochondrial dysfunction, resembling several findings from ALS’ neural cells/models, which could be exploited as a powerful tool in ALS research. Our findings can also guide future studies on new pharmacological interventions for ALS since assessments of brain samples are challenging and represent a relevant limited strategy. Graphical abstract ![]()
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E Silva LFS, Brito MD, Yuzawa JMC, Rosenstock TR. Mitochondrial Dysfunction and Changes in High-Energy Compounds in Different Cellular Models Associated to Hypoxia: Implication to Schizophrenia. Sci Rep 2019; 9:18049. [PMID: 31792231 PMCID: PMC6889309 DOI: 10.1038/s41598-019-53605-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 10/24/2019] [Indexed: 02/06/2023] Open
Abstract
Schizophrenia (SZ) is a multifactorial mental disorder, which has been associated with a number of environmental factors, such as hypoxia. Considering that numerous neural mechanisms depends on energetic supply (ATP synthesis), the maintenance of mitochondrial metabolism is essential to keep cellular balance and survival. Therefore, in the present work, we evaluated functional parameters related to mitochondrial function, namely calcium levels, mitochondrial membrane potential, redox homeostasis, high-energy compounds levels and oxygen consumption, in astrocytes from control (Wistar) and Spontaneously Hypertensive Rats (SHR) animals exposed both to chemical and gaseous hypoxia. We show that astrocytes after hypoxia presented depolarized mitochondria, disturbances in Ca2+ handling, destabilization in redox system and alterations in ATP, ADP, Pyruvate and Lactate levels, in addition to modification in NAD+/NADH ratio, and Nfe2l2 and Nrf1 expression. Interestingly, intrauterine hypoxia also induced augmentation in mitochondrial biogenesis and content. Altogether, our data suggest that hypoxia can induce mitochondrial deregulation and a decrease in energy metabolism in the most prevalent cell type in the brain, astrocytes. Since SHR are also considered an animal model of SZ, our results can likewise be related to their phenotypic alterations and, therefore, our work also allow an increase in the knowledge of this burdensome disorder.
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Ashuach T, Fischer DS, Kreimer A, Ahituv N, Theis FJ, Yosef N. MPRAnalyze: statistical framework for massively parallel reporter assays. Genome Biol 2019; 20:183. [PMID: 31477158 PMCID: PMC6717970 DOI: 10.1186/s13059-019-1787-z] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Accepted: 08/09/2019] [Indexed: 11/10/2022] Open
Abstract
Massively parallel reporter assays (MPRAs) can measure the regulatory function of thousands of DNA sequences in a single experiment. Despite growing popularity, MPRA studies are limited by a lack of a unified framework for analyzing the resulting data. Here we present MPRAnalyze: a statistical framework for analyzing MPRA count data. Our model leverages the unique structure of MPRA data to quantify the function of regulatory sequences, compare sequences' activity across different conditions, and provide necessary flexibility in an evolving field. We demonstrate the accuracy and applicability of MPRAnalyze on simulated and published data and compare it with existing methods.
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Affiliation(s)
- Tal Ashuach
- Department of Electrical Engineering and Computer Sciences, University of California Berkeley, Berkeley, California USA
- Center for Computational Biology, University of California Berkeley, Berkeley, California USA
| | - David S. Fischer
- Institute of Computational Biology, Helmholz Zentrum München, Neuherberg, Germany
- TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Anat Kreimer
- Department of Electrical Engineering and Computer Sciences, University of California Berkeley, Berkeley, California USA
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, California USA
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, California USA
| | - Fabian J. Theis
- Institute of Computational Biology, Helmholz Zentrum München, Neuherberg, Germany
| | - Nir Yosef
- Department of Electrical Engineering and Computer Sciences, University of California Berkeley, Berkeley, California USA
- Center for Computational Biology, University of California Berkeley, Berkeley, California USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA USA
- Chan Zuckerberg BioHub, San Francisco, California USA
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Parvalbumin expression in oligodendrocyte-like CG4 cells causes a reduction in mitochondrial volume, attenuation in reactive oxygen species production and a decrease in cell processes' length and branching. Sci Rep 2019; 9:10603. [PMID: 31332265 PMCID: PMC6646370 DOI: 10.1038/s41598-019-47112-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 07/11/2019] [Indexed: 12/11/2022] Open
Abstract
Forebrain glial cells - ependymal cells and astrocytes -acquire upon injury- a "reactive" phenotype associated with parvalbumin (PV) upregulation. Since free radicals, e.g. reactive oxygen species (ROS) play a role in the pathogenesis of multiple sclerosis, and that PV-upregulation in glial cells is inversely correlated with the level of oxidative stress, we hypothesized that PV-upregulation might also protect oligodendrocytes by decreasing ROS production. Lentiviral transduction techniques allowed for PV overexpression in CG4 oligodendrocyte progenitor cells (OPCs). Depending on the growth medium CG4 cells can be maintained in an OPC-like state, or induced to differentiate into an oligodendrocyte (OLG)-like phenotype. While increased levels of PV had no effect on cell proliferation and invasiveness in vitro, PV decreased the mitochondria volume in CG4 cell bodies, as well as the mitochondrial density in CG4 processes in both OPC-like and OLG-like states. In line with the PV-induced global decrease in mitochondrial volume, elevated PV levels reduced transcript levels of mitochondrial transcription factors involved in mitochondria biogenesis. In differentiated PV-overexpressing CG4 cells with a decreased mitochondrial volume, UV-induced ROS production was lower than in control CG4 cells hinting towards a possible role of PV in counteracting oxidative stress. Unexpectedly, PV also decreased the length of processes in undifferentiated CG4 cells and moreover diminished branching of differentiated CG4 cell processes, strongly correlated with the decreased density of mitochondria in CG4 cell processes. Thus besides conferring a protective role against oxidative stress, PV in a cell autonomous fashion additionally affects process' growth and branching in CG4 cells.
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Abstract
Obesity is a medical condition that impacts on all levels of society and causes numerous comorbidities, such as diabetes, cardiovascular disease, and cancer. We assessed the suitability of targeting enolase, a glycolysis pathway enzyme with multiple, secondary functions in cells, to treat obesity. Treating adipocytes with ENOblock, a novel modulator of these secondary ‘moonlighting’ functions of enolase, suppressed the adipogenic program and induced mitochondrial uncoupling. Obese animals treated with ENOblock showed a reduction in body weight and increased core body temperature. Metabolic and inflammatory parameters were improved in the liver, adipose tissue and hippocampus. The mechanism of ENOblock was identified as transcriptional repression of master regulators of lipid homeostasis (Srebp-1a and Srebp-1c), gluconeogenesis (Pck-1) and inflammation (Tnf-α and Il-6). ENOblock treatment also reduced body weight gain, lowered cumulative food intake and increased fecal lipid content in mice fed a high fat diet. Our results support the further drug development of ENOblock as a therapeutic for obesity and suggest enolase as a new target for this disorder.
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AMPK Activation of PGC-1α/NRF-1-Dependent SELENOT Gene Transcription Promotes PACAP-Induced Neuroendocrine Cell Differentiation Through Tolerance to Oxidative Stress. Mol Neurobiol 2018; 56:4086-4101. [DOI: 10.1007/s12035-018-1352-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 09/13/2018] [Indexed: 12/19/2022]
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Ishida K, Aoki K, Takishita T, Miyara M, Sakamoto S, Sanoh S, Kimura T, Kanda Y, Ohta S, Kotake Y. Low-Concentration Tributyltin Decreases GluR2 Expression via Nuclear Respiratory Factor-1 Inhibition. Int J Mol Sci 2017; 18:ijms18081754. [PMID: 28800112 PMCID: PMC5578144 DOI: 10.3390/ijms18081754] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 08/03/2017] [Accepted: 08/09/2017] [Indexed: 12/19/2022] Open
Abstract
Tributyltin (TBT), which has been widely used as an antifouling agent in paints, is a common environmental pollutant. Although the toxicity of high-dose TBT has been extensively reported, the effects of low concentrations of TBT are relatively less well studied. We have previously reported that low-concentration TBT decreases α-amino-3-hydroxy-5-methylisoxazole-4-propionic acid (AMPA)-type glutamate receptor subunit 2 (GluR2) expression in cortical neurons and enhances neuronal vulnerability to glutamate. However, the mechanism of this TBT-induced GluR2 decrease remains unknown. Therefore, we examined the effects of TBT on the activity of transcription factors that control GluR2 expression. Exposure of primary cortical neurons to 20 nM TBT for 3 h to 9 days resulted in a decrease in GluR2 mRNA expression. Moreover, TBT inhibited the DNA binding activity of nuclear respiratory factor-1 (NRF-1), a transcription factor that positively regulates the GluR2. This result indicates that TBT inhibits the activity of NRF-1 and subsequently decreases GluR2 expression. In addition, 20 nM TBT decreased the expression of genes such as cytochrome c, cytochrome c oxidase (COX) 4, and COX 6c, which are downstream of NRF-1. Our results suggest that NRF-1 inhibition is an important molecular action of the neurotoxicity induced by low-concentration TBT.
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Affiliation(s)
- Keishi Ishida
- Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-8553, Japan.
- Research Fellow of the Japan Society for the Promotion of Science, 5-3-1 Kojimachi, Chiyoda-ku, Tokyo 102-0083, Japan.
| | - Kaori Aoki
- Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-8553, Japan.
| | - Tomoko Takishita
- Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-8553, Japan.
| | - Masatsugu Miyara
- Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-8553, Japan.
| | - Shuichiro Sakamoto
- Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-8553, Japan.
| | - Seigo Sanoh
- Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-8553, Japan.
| | - Tomoki Kimura
- Faculty of Science and Engineering, Setsunan University, 17-8 Ikedanakamachi, Neyagawa 572-8508, Japan.
| | - Yasunari Kanda
- Division of Pharmacology, National Institute of Health Sciences, 1-18-1, Kamiyoga, Setagaya-ku, Tokyo 158-8501, Japan.
| | - Shigeru Ohta
- Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-8553, Japan.
| | - Yaichiro Kotake
- Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-8553, Japan.
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Urfer-Buchwalder A, Urfer R. Identification of a Nuclear Respiratory Factor 1 Recognition Motif in the Apolipoprotein E Variant APOE4 linked to Alzheimer's Disease. Sci Rep 2017; 7:40668. [PMID: 28094792 PMCID: PMC5240558 DOI: 10.1038/srep40668] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 12/08/2016] [Indexed: 11/09/2022] Open
Abstract
Alzheimer’s disease affects tens of millions of people worldwide and its prevalence continues to rise. It is caused by a combination of a subject’s heredity, environment, lifestyle, and medical condition. The most significant genetic risk factor for late onset Alzheimer’s disease is a variant of the apolipoprotein E gene, APOE4. Here we show that the single nucleotide polymorphism rs429358 that defines APOE4 is located in a short sequence motif repeated several times within exon 4 of apolipoprotein E, reminiscent of the structure of transcriptional enhancers. A JASPAR database search predicts that the T to C transition in rs429358 generates a binding motif for nuclear respiratory factor NRF1. This site appears to be part of a binding site cluster for this transcription factor on exon 4 of APOE. This de novo NRF1 binding site has therefore the potential to affect the expression of multiple genes in its genomic vicinity. Our in silico analysis, suggesting a novel function for APOE4 at the DNA level, offers a potential mechanism for the observed tissue specific neurodegeneration and the role of environmental factors in Alzheimer’s disease etiology.
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Affiliation(s)
| | - Roman Urfer
- Selonterra LLC, 1025 Alameda de las Pulgas, Suite 126, Belmont CA 94002, USA
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Lithium promotes DNA stability and survival of ischemic retinal neurocytes by upregulating DNA ligase IV. Cell Death Dis 2016; 7:e2473. [PMID: 27853172 PMCID: PMC5260892 DOI: 10.1038/cddis.2016.341] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 09/08/2016] [Accepted: 09/13/2016] [Indexed: 02/01/2023]
Abstract
Neurons display genomic fragility and show fragmented DNA in pathological degeneration. A failure to repair DNA breaks may result in cell death or apoptosis. Lithium protects retinal neurocytes following nutrient deprivation or partial nerve crush, but the underlying mechanisms are not well defined. Here we demonstrate that pretreatment with lithium protects retinal neurocytes from ischemia-induced damage and enhances light response in rat retina following ischemia–reperfusion injury. Moreover, we found that DNA nonhomologous end-joining (NHEJ) repair is implicated in this process because in ischemic retinal neurocytes, lithium significantly reduces the number of γ-H2AX foci (well-characterized markers of DNA double-strand breaks in situ) and increases the DNA ligase IV expression level. Furthermore, we also demonstrate that nuclear respiratory factor 1 (Nrf-1) and phosphorylated cyclic AMP-response element binding protein-1 (P-CREB1) bind to ligase IV promoter to cause upregulation of ligase IV in neurocytes. The ischemic upregulation of Nrf-1 and lithium-induced increase of P-CREB1 cooperate to promote transcription of ligase IV. Short hairpin RNAs against Nrf-1 and CREB1 could significantly inhibit the increase in promoter activity and expression of ligase IV observed in the control oligos following lithium treatment in retinal neurocytes. More importantly, ischemic stimulation triggers the expression of ligase IV. Taken together, our results thus reveal a novel mechanism that lithium offers neuroprotection from ischemia-induced damage by enhancing DNA NHEJ repair.
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Joyce PI, Fratta P, Landman AS, Mcgoldrick P, Wackerhage H, Groves M, Busam BS, Galino J, Corrochano S, Beskina OA, Esapa C, Ryder E, Carter S, Stewart M, Codner G, Hilton H, Teboul L, Tucker J, Lionikas A, Estabel J, Ramirez-Solis R, White JK, Brandner S, Plagnol V, Bennet DLH, Abramov AY, Greensmith L, Fisher EMC, Acevedo-Arozena A. Deficiency of the zinc finger protein ZFP106 causes motor and sensory neurodegeneration. Hum Mol Genet 2015; 25:291-307. [PMID: 26604141 PMCID: PMC4706115 DOI: 10.1093/hmg/ddv471] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 11/11/2015] [Indexed: 12/12/2022] Open
Abstract
Zinc finger motifs are distributed amongst many eukaryotic protein families, directing nucleic acid–protein and protein–protein interactions. Zinc finger protein 106 (ZFP106) has previously been associated with roles in immune response, muscle differentiation, testes development and DNA damage, although little is known about its specific function. To further investigate the function of ZFP106, we performed an in-depth characterization of Zfp106 deficient mice (Zfp106−/−), and we report a novel role for ZFP106 in motor and sensory neuronal maintenance and survival. Zfp106−/− mice develop severe motor abnormalities, major deficits in muscle strength and histopathological changes in muscle. Intriguingly, despite being highly expressed throughout the central nervous system, Zfp106−/− mice undergo selective motor and sensory neuronal and axonal degeneration specific to the spinal cord and peripheral nervous system. Neurodegeneration does not occur during development of Zfp106−/− mice, suggesting that ZFP106 is likely required for the maintenance of mature peripheral motor and sensory neurons. Analysis of embryonic Zfp106−/− motor neurons revealed deficits in mitochondrial function, with an inhibition of Complex I within the mitochondrial electron transport chain. Our results highlight a vital role for ZFP106 in sensory and motor neuron maintenance and reveal a novel player in mitochondrial dysfunction and neurodegeneration.
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Affiliation(s)
- Peter I Joyce
- MRC Mammalian Genetics Unit, Harwell, Oxfordshire OX11 0RD, UK
| | - Pietro Fratta
- UCL Institute of Neurology and MRC Centre for Neuromuscular Disease, Queen Square, London WC1N 3BG, UK
| | | | - Philip Mcgoldrick
- UCL Institute of Neurology and MRC Centre for Neuromuscular Disease, Queen Square, London WC1N 3BG, UK
| | | | - Michael Groves
- UCL Institute of Neurology and MRC Centre for Neuromuscular Disease, Queen Square, London WC1N 3BG, UK
| | | | - Jorge Galino
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford OX3 9DU, UK
| | | | - Olga A Beskina
- UCL Institute of Neurology and MRC Centre for Neuromuscular Disease, Queen Square, London WC1N 3BG, UK
| | | | - Edward Ryder
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford OX3 9DU, UK
| | - Sarah Carter
- MRC Mammalian Genetics Unit, Harwell, Oxfordshire OX11 0RD, UK
| | | | - Gemma Codner
- MRC Mammalian Genetics Unit, Harwell, Oxfordshire OX11 0RD, UK
| | - Helen Hilton
- MRC Mammalian Genetics Unit, Harwell, Oxfordshire OX11 0RD, UK
| | - Lydia Teboul
- MRC Mammalian Genetics Unit, Harwell, Oxfordshire OX11 0RD, UK
| | - Jennifer Tucker
- MRC Mammalian Genetics Unit, Harwell, Oxfordshire OX11 0RD, UK
| | | | - Jeanne Estabel
- Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK and
| | - Ramiro Ramirez-Solis
- Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK and
| | - Jacqueline K White
- Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK and
| | - Sebastian Brandner
- UCL Institute of Neurology and MRC Centre for Neuromuscular Disease, Queen Square, London WC1N 3BG, UK
| | | | - David L H Bennet
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford OX3 9DU, UK
| | - Andrey Y Abramov
- UCL Institute of Neurology and MRC Centre for Neuromuscular Disease, Queen Square, London WC1N 3BG, UK
| | - Linda Greensmith
- UCL Institute of Neurology and MRC Centre for Neuromuscular Disease, Queen Square, London WC1N 3BG, UK,
| | - Elizabeth M C Fisher
- UCL Institute of Neurology and MRC Centre for Neuromuscular Disease, Queen Square, London WC1N 3BG, UK,
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Hsieh CP, Chang WT, Lee YC, Huang AM. Deficits in cerebellar granule cell development and social interactions in CD47 knockout mice. Dev Neurobiol 2014; 75:463-84. [PMID: 25288019 DOI: 10.1002/dneu.22236] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Revised: 09/15/2014] [Accepted: 09/29/2014] [Indexed: 01/18/2023]
Abstract
CD47 is involved in neurite differentiation in cultured neurons, but the function of CD47 in brain development is largely unknown. We determined that CD47 mRNA was robustly expressed in the developing cerebellum, especially in granule cells. CD47 protein was mainly expressed in the inner layer of the external granule layer (EGL), molecular layer, and internal granule layer (IGL), where granule cells individually become postmitotic and migrate, leading to neurite fasciculation. At postnatal day 8 (P8), CD47 knockout mice exhibited an increased number of proliferating granule cells in the EGL, whereas the CD47 agonist peptide 4N1K increased the number of postmitotic cells in primary granule cells. Knocking out the CD47 gene and anti-CD47 antibody impaired the radial migration of granule cells from the EGL to the IGL individually in mice and slice cultures. In primary granule cells, knocking out CD47 reduced the number of axonal collaterals and dendritic branches; by contrast, overexpressing CD47 or 4N1K treatment increased the axonal length and numbers of axonal collaterals and dendritic branches. Furthermore, the length of the fissure between Lobules VI and VII was decreased in CD47 knockout mice at P21 and at 14 wk after birth. Lastly, CD47 knockout mice exhibited increased social interaction at P21 and depressive-like behaviors at 10 wk after birth. Our study revealed that the cell adhesion molecule CD47 participates in multiple phases of granule cell development, including proliferation, migration, and neurite differentiation implying that aberrations of CD47 are risk factors that cause abnormalities in cerebellar development and atypical behaviors.
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Affiliation(s)
- Chung-Pin Hsieh
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan 701
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18
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Satoh JI, Kawana N, Yamamoto Y. Pathway Analysis of ChIP-Seq-Based NRF1 Target Genes Suggests a Logical Hypothesis of their Involvement in the Pathogenesis of Neurodegenerative Diseases. GENE REGULATION AND SYSTEMS BIOLOGY 2013; 7:139-52. [PMID: 24250222 PMCID: PMC3825669 DOI: 10.4137/grsb.s13204] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Nuclear respiratory factor 1 (NRF1) serves as a transcription factor that activates the expression of a wide range of nuclear genes essential for mitochondrial biogenesis and function, including mitochondrial respiratory complex subunits, heme biosynthetic enzymes, and regulatory factors involved in the replication and transcription of mitochondrial DNA. Increasing evidence indicates that mitochondrial function is severely compromised in the brains of aging-related neurodegenerative diseases. To identify the comprehensive set of human NRF1 target genes potentially relevant to the pathogenesis of neurodegenerative diseases, we analyzed the NRF1 chromatin immunoprecipitation followed by deep sequencing (ChIP-Seq) dataset retrieved from the Encyclopedia of DNA Elements (ENCODE) project. Overall, we identified 2,470 highly stringent ChIP-Seq peaks on protein-coding genes in SK-N-SH human neuroblastoma cells. They were accumulated in the proximal promoter regions with an existence of the NRF1-binding consensus sequence. The set of ChIP-Seq-based NRF1 target genes included known NRF1 targets such as EIF2S1, EIF2S2, CYCS, FMR1, FXR2, E2F6, CD47, and TOMM34. By pathway analysis, the molecules located in the core pathways related to mitochondrial respiratory function were determined to be highly enriched in NRF1 target genes. Furthermore, we found that NRF1 target genes play a pivotal role in regulation of extra-mitochondrial biological processes, including RNA metabolism, splicing, cell cycle, DNA damage repair, protein translation initiation, and ubiquitin-mediated protein degradation. We identified a panel of neurodegenerative disease-related genes, such as PARK2 (Parkin), PARK6 (Pink1), PARK7 (DJ-1), and PAELR (GPR37) for Parkinson's disease, as well as PSENEN (Pen2) and MAPT (tau) for Alzheimer's disease, as previously unrecognized NRF1 targets. These results suggest a logical hypothesis that aberrant regulation of NRF1 and its targets might contribute to the pathogenesis of human neurodegenerative diseases via perturbation of diverse mitochondrial and extra-mitochondrial functions.
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Affiliation(s)
- Jun-Ichi Satoh
- Department of Bioinformatics and Molecular Neuropathology, Meiji Pharmaceutical University, Kiyose, Tokyo, Japan
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Wang JL, Tong CW, Chang WT, Huang AM. Novel genes FAM134C, C3orf10 and ENOX1 are regulated by NRF-1 and differentially regulate neurite outgrowth in neuroblastoma cells and hippocampal neurons. Gene 2013; 529:7-15. [DOI: 10.1016/j.gene.2013.08.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Revised: 07/03/2013] [Accepted: 08/02/2013] [Indexed: 01/03/2023]
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Soto-Pantoja DR, Stein EV, Rogers NM, Sharifi-Sanjani M, Isenberg JS, Roberts DD. Therapeutic opportunities for targeting the ubiquitous cell surface receptor CD47. Expert Opin Ther Targets 2013; 17:89-103. [PMID: 23101472 PMCID: PMC3564224 DOI: 10.1517/14728222.2013.733699] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
INTRODUCTION CD47 is a ubiquitously expressed cell surface receptor that serves as a counter-receptor for SIRPα in recognition of self by the innate immune system. Independently, CD47 also functions as an important signaling receptor for regulating cell responses to stress. AREAS COVERED We review the expression, molecular interactions, and pathophysiological functions of CD47 in the cardiovascular and immune systems. CD47 was first identified as a potential tumor marker, and we examine recent evidence that its dysregulation contributes to cancer progression and evasion of anti-tumor immunity. We further discuss therapeutic strategies for enhancing or inhibiting CD47 signaling and applications of such agents in preclinical models of ischemia and ischemia/reperfusion injuries, organ transplantation, pulmonary hypertension, radioprotection, and cancer. EXPERT OPINION Ongoing studies are revealing a central role of CD47 for conveying signals from the extracellular microenvironment that limit cell and tissue survival upon exposure to various types of stress. Based on this key function, therapeutics targeting CD47 or its ligands thrombospondin-1 and SIRPα could have broad applications spanning reconstructive surgery, engineering of tissues and biocompatible surfaces, vascular diseases, diabetes, organ transplantation, radiation injuries, inflammatory diseases, and cancer.
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Affiliation(s)
- David R. Soto-Pantoja
- Cancer Research Training Award Fellow, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-1500
| | - Erica V. Stein
- Predoctoral Cancer Research Training Award Fellow, Laboratoryof Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-1500 and Microbiology and Immunology Program of the Institute for Biomedical Sciences, Departments of Microbiology, Immunology and Tropical Medicine, George Washington University, 2300 Eye St., N.W., Ross Hall, Washington, D.C. 20037
| | - Natasha M. Rogers
- Visiting Research Fellow, Division of Pulmonary Allergy and Critical Care Medicine, Vascular Medicine Institute, University of Pittsburgh School of Medicine, E1240 Biomedical Science Tower, Room E1200, 200 Lothrop Street, Pittsburgh, PA 15261
| | - Maryam Sharifi-Sanjani
- Post-doctoral Fellow, Division of Pulmonary Allergy and Critical Care Medicine, Vascular Medicine Institute, University of Pittsburgh School of Medicine, E1240 Biomedical Science Tower, Room E1200, 200 Lothrop Street, Pittsburgh, PA 15261
| | - Jeffrey S. Isenberg
- Associate Professor of Medicine, Division of Pulmonary Allergy and Critical Care Medicine, Vascular Medicine Institute, University of Pittsburgh School of Medicine, E1240 Biomedical Science Tower, Room E1258, 200 Lothrop Street, Pittsburgh, PA 15261
| | - David D. Roberts
- Chief, Biochemical Pathology Section, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Building 10 Room 2A33, Bethesda, MD 20892-1500
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Tong CW, Wang JL, Jiang MS, Hsu CH, Chang WT, Huang AM. Novel genes that mediate nuclear respiratory factor 1-regualted neurite outgrowth in neuroblastoma IMR-32 cells. Gene 2012; 515:62-70. [PMID: 23219993 DOI: 10.1016/j.gene.2012.11.026] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2012] [Accepted: 11/27/2012] [Indexed: 11/17/2022]
Abstract
Nuclear respiratory factor-1 (NRF-1) is a transcription factor that functions in neurite outgrowth; however, the genes downstream from NRF-1 that mediate this function remain largely unknown. This study employs a genome-wide analysis approach to identify NRF-1-targeted genes in human neuroblastoma IMR-32 cells. A total of 916 human genes containing the putative NRF-1 response element (NRE) in their promoter regions were identified using a cutoff score determined by results from electrophoretic mobility shift assays (EMSA). Seventy-four NRF-1 target genes were listed according to the typical locations and high conservation of NREs. Fifteen genes, MAPRE3, NPDC1, RAB3IP, TRAPPC3, SMAD5, PIP5K1A, USP10, SPRY4, GTF2F2, NR1D1, SUV39H2, SKA3, RHOA, RAPGEF6, and SMAP1 were selected for biological confirmation. EMSA and chromatin immunoprecipitation confirmed that all NREs of these fifteen genes are critical for NRF-1 binding. Quantitative RT-PCR demonstrated that mRNA levels of 12 of these genes are regulated by NRF-1. Overexpression or knockdown of candidate genes demonstrated that MAPRE3, NPDC1, SMAD5, USP10, SPRY4, GTF2F2, SKA3, SMAP1 positively regulated, and RHOA and RAPGEF6 negatively regulated neurite outgrowth. Overall, our data showed that the combination of genome-wide bioinformatic analysis and biological experiments helps to identify the novel NRF-1-regulated genes, which play roles in differentiation of neuroblastoma cells.
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Affiliation(s)
- Chih-Wei Tong
- Department of Physiology, National Cheng Kung University, College of Medicine, Tainan, Taiwan
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22
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Henson BJ, Zhu W, Hardaway K, Wetzel JL, Stefan M, Albers KM, Nicholls RD. Transcriptional and post-transcriptional regulation of SPAST, the gene most frequently mutated in hereditary spastic paraplegia. PLoS One 2012; 7:e36505. [PMID: 22574173 PMCID: PMC3344893 DOI: 10.1371/journal.pone.0036505] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2012] [Accepted: 04/02/2012] [Indexed: 01/01/2023] Open
Abstract
Hereditary spastic paraplegias (HSPs) comprise a group of neurodegenerative disorders that are characterized by progressive spasticity of the lower extremities, due to axonal degeneration in the corticospinal motor tracts. HSPs are genetically heterogeneous and show autosomal dominant inheritance in ∼70–80% of cases, with additional cases being recessive or X-linked. The most common type of HSP is SPG4 with mutations in the SPAST gene, encoding spastin, which occurs in 40% of dominantly inherited cases and in ∼10% of sporadic cases. Both loss-of-function and dominant-negative mutation mechanisms have been described for SPG4, suggesting that precise or stoichiometric levels of spastin are necessary for biological function. Therefore, we hypothesized that regulatory mechanisms controlling expression of SPAST are important determinants of spastin biology, and if altered, could contribute to the development and progression of the disease. To examine the transcriptional and post-transcriptional regulation of SPAST, we used molecular phylogenetic methods to identify conserved sequences for putative transcription factor binding sites and miRNA targeting motifs in the SPAST promoter and 3′-UTR, respectively. By a variety of molecular methods, we demonstrate that SPAST transcription is positively regulated by NRF1 and SOX11. Furthermore, we show that miR-96 and miR-182 negatively regulate SPAST by effects on mRNA stability and protein level. These transcriptional and miRNA regulatory mechanisms provide new functional targets for mutation screening and therapeutic targeting in HSP.
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Affiliation(s)
- Brian J. Henson
- Birth Defects Laboratories, Division of Medical Genetics, Department of Pediatrics, Children’s Hospital of Pittsburgh of UPMC, Pittsburgh, Pennsylvania, United States of America
| | - Wan Zhu
- Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, Pennsylvania, United States of America
| | - Kelsey Hardaway
- Birth Defects Laboratories, Division of Medical Genetics, Department of Pediatrics, Children’s Hospital of Pittsburgh of UPMC, Pittsburgh, Pennsylvania, United States of America
| | - Jaime L. Wetzel
- Birth Defects Laboratories, Division of Medical Genetics, Department of Pediatrics, Children’s Hospital of Pittsburgh of UPMC, Pittsburgh, Pennsylvania, United States of America
| | - Mihaela Stefan
- Birth Defects Laboratories, Division of Medical Genetics, Department of Pediatrics, Children’s Hospital of Pittsburgh of UPMC, Pittsburgh, Pennsylvania, United States of America
| | - Kathryn M. Albers
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Robert D. Nicholls
- Birth Defects Laboratories, Division of Medical Genetics, Department of Pediatrics, Children’s Hospital of Pittsburgh of UPMC, Pittsburgh, Pennsylvania, United States of America
- Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, Pennsylvania, United States of America
- * E-mail:
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Xin N, Benchabane H, Tian A, Nguyen K, Klofas L, Ahmed Y. Erect Wing facilitates context-dependent Wnt/Wingless signaling by recruiting the cell-specific Armadillo-TCF adaptor Earthbound to chromatin. Development 2011; 138:4955-67. [PMID: 22028028 DOI: 10.1242/dev.068890] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
During metazoan development, the Wnt/Wingless signal transduction pathway is activated repetitively to direct cell proliferation, fate specification, differentiation and apoptosis. Distinct outcomes are elicited by Wnt stimulation in different cellular contexts; however, mechanisms that confer context specificity to Wnt signaling responses remain largely unknown. Starting with an unbiased forward genetic screen in Drosophila, we recently uncovered a novel mechanism by which the cell-specific co-factor Earthbound 1 (Ebd1), and its human homolog jerky, promote interaction between the Wnt pathway transcriptional co-activators β-catenin/Armadillo and TCF to facilitate context-dependent Wnt signaling responses. Here, through the same genetic screen, we find an unanticipated requirement for Erect Wing (Ewg), the fly homolog of the human sequence-specific DNA-binding transcriptional activator nuclear respiratory factor 1 (NRF1), in promoting contextual regulation of Wingless signaling. Ewg and Ebd1 functionally interact with the Armadillo-TCF complex and mediate the same context-dependent Wingless signaling responses. In addition, Ewg and Ebd1 have similar cell-specific expression profiles, bind to each other directly and also associate with chromatin at shared genomic sites. Furthermore, recruitment of Ebd1 to chromatin is abolished in the absence of Ewg. Our findings provide in vivo evidence that recruitment of a cell-specific co-factor complex to specific chromatin sites, coupled with its ability to facilitate Armadillo-TCF interaction and transcriptional activity, promotes contextual regulation of Wnt/Wingless signaling responses.
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Affiliation(s)
- Nan Xin
- Department of Genetics and Norris Cotton Cancer Center, Dartmouth Medical School, Hanover, NH 03755, USA
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Mendelev N, Witherspoon S, Li PA. Overexpression of human selenoprotein H in neuronal cells ameliorates ultraviolet irradiation-induced damage by modulating cell signaling pathways. Exp Neurol 2009; 220:328-34. [PMID: 19766117 DOI: 10.1016/j.expneurol.2009.09.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2009] [Revised: 09/04/2009] [Accepted: 09/09/2009] [Indexed: 10/20/2022]
Abstract
Selenoprotein H (SelH) is one of the 25 so far identified selenoproteins. Selenoproteins may function as antioxidants, heavy metal antidotes, and neural survival factors. Previous studies have shown that overexpression of SelH in HT22 cells protected the cells from UVB irradiation-induced death by reducing superoxide formation. The objective of this study was to determine the effects of SelH on cell signaling pathways after UVB irradiation. We exposed both human SelH- and vector-transfected HT22 cells to UVB irradiation and collected samples at 5 and 17 h of recovery. Cell viability was assessed, as well as protein levels of caspase-3, -8, -9, apoptosis-inducing factor (AIF), P53, nuclear respiratory factor-1 (NRF-1) and heat shock protein 40 (HSP40). Mitochondrial membrane potential was determined by flow cytometry. Overexpression of SelH protected cells against UVB-induced injury by blockade of the mitochondria-initiated cell death pathway, prevention of mitochondrial membrane depolarization, and suppression of the increase of p53. Furthermore, overexpression of SelH increased levels of NRF-1, an antioxidant, and HSP40, a protein chaperone that repairs denatured protein. We conclude that SelH protects neurons against UVB-induced damage by inhibiting apoptotic cell death pathways, by preventing mitochondrial depolarization, and by promoting cell survival pathways.
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Affiliation(s)
- Natalia Mendelev
- Department of Pharmaceutical Sciences, Biomanufacturing Research Institute and Technological Enterprise (BRITE), North Carolina Central University, 302 East Lawson Street, Durham, NC 27707, USA
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Wang JL, Chang WT, Tong CW, Kohno K, Huang AM. Human synapsin I mediates the function of nuclear respiratory factor 1 in neurite outgrowth in neuroblastoma IMR-32 cells. J Neurosci Res 2009; 87:2255-63. [DOI: 10.1002/jnr.22059] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Radha V, Rajanna A, Gupta RK, Dayma K, Raman T. The guanine nucleotide exchange factor, C3G regulates differentiation and survival of human neuroblastoma cells. J Neurochem 2008; 107:1424-35. [PMID: 18957052 DOI: 10.1111/j.1471-4159.2008.05710.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Neuronal differentiation involving neurite growth is dependent on environmental cues which are relayed by signalling pathways to actin cytoskeletal remodelling. C3G, the exchange factor for Rap1, functions in pathways leading to actin reorganization and filopodia formation, processes required during neurite growth. In the present study, we have analyzed the function of C3G, in regulating neuronal cell survival and plasticity. Human neuroblastoma cells, IMR-32 induced to differentiate by serum starvation or by treatment with nerve growth factor (NGF) or forskolin showed enhanced C3G protein levels. Transient over-expression of C3G stimulated neurite growth and also increased responsiveness to NGF and serum deprivation induced differentiation. C3G-induced neurite growth was dependent on both its catalytic and N-terminal regulatory domains, and on the functions of Cdc42 and Rap1. Knockdown of C3G using small hairpin RNA inhibited forskolin and NGF-induced morphological differentiation of IMR-32 cells. Forskolin-induced differentiation was dependent on catalytic activity of C3G. Forskolin and NGF treatment resulted in phosphorylation of C3G at Tyr504 predominantly in the Golgi. C3G expression induced the cell cycle inhibitor p21 and C3G knockdown enhanced cell death in response to serum starvation. These findings demonstrate a novel function for C3G in regulating survival and differentiation of human neuroblastoma cells.
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Affiliation(s)
- Vegesna Radha
- Centre for Cellular and Molecular Biology, Council of Scientific & Industrial Research (CSIR), Uppal Road, Hyderabad 500007, India.
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Pennacchio LA, Loots GG, Nobrega MA, Ovcharenko I. Predicting tissue-specific enhancers in the human genome. Genome Res 2007; 17:201-11. [PMID: 17210927 PMCID: PMC1781352 DOI: 10.1101/gr.5972507] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Determining how transcriptional regulatory signals are encoded in vertebrate genomes is essential for understanding the origins of multicellular complexity; yet the genetic code of vertebrate gene regulation remains poorly understood. In an attempt to elucidate this code, we synergistically combined genome-wide gene-expression profiling, vertebrate genome comparisons, and transcription factor binding-site analysis to define sequence signatures characteristic of candidate tissue-specific enhancers in the human genome. We applied this strategy to microarray-based gene expression profiles from 79 human tissues and identified 7187 candidate enhancers that defined their flanking gene expression, the majority of which were located outside of known promoters. We cross-validated this method for its ability to de novo predict tissue-specific gene expression and confirmed its reliability in 57 of the 79 available human tissues, with an average precision in enhancer recognition ranging from 32% to 63% and a sensitivity of 47%. We used the sequence signatures identified by this approach to successfully assign tissue-specific predictions to approximately 328,000 human-mouse conserved noncoding elements in the human genome. By overlapping these genome-wide predictions with a data set of enhancers validated in vivo, in transgenic mice, we were able to confirm our results with a 28% sensitivity and 50% precision. These results indicate the power of combining complementary genomic data sets as an initial computational foray into a global view of tissue-specific gene regulation in vertebrates.
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Affiliation(s)
- Len A. Pennacchio
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, California 94598, USA
| | - Gabriela G. Loots
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, California 94550, USA
| | - Marcelo A. Nobrega
- Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA
| | - Ivan Ovcharenko
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, California 94598, USA
- Computation Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, USA
- Corresponding author.E-mail ; fax (925) 422-2099
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Garber K, Smith KT, Reines D, Warren ST. Transcription, translation and fragile X syndrome. Curr Opin Genet Dev 2006; 16:270-5. [PMID: 16647847 DOI: 10.1016/j.gde.2006.04.010] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2006] [Accepted: 04/18/2006] [Indexed: 10/24/2022]
Abstract
The fragile X mental retardation protein (FMRP) plays a role in the control of local protein synthesis in the dendrites. Loss of its production in fragile X syndrome is associated with transcriptional dysregulation of the gene. Recent work demonstrates that Sp1 and NRF1 transcriptionally control this gene. Other studies reveal how the microRNA pathway and signaling are related to FMRP function through the metabotropic glutamate receptor. These studies provide new insights through which we can better understand the inactivation of the FMR1 gene and, in turn, the consequence of FMRP loss.
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Affiliation(s)
- Kathryn Garber
- Department of Human Genetics, 615 Michael Street, Room 300, Emory University, Atlanta, GA 30322, USA
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