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      Tumor Necrosis Factor α Influences Phenotypic Plasticity and Promotes Epigenetic Changes in Human Basal Forebrain Cholinergic Neuroblasts

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          Abstract

          TNFα is the main proinflammatory cytokine implicated in the pathogenesis of neurodegenerative disorders, but it also modulates physiological functions in both the developing and adult brain. In this study, we investigated a potential direct role of TNFα in determining phenotypic changes of a recently established cellular model of human basal forebrain cholinergic neuroblasts isolated from the nucleus basalis of Meynert (hfNBMs). Exposing hfNBMs to TNFα reduced the expression of immature markers, such as nestin and β-tubulin III, and inhibited primary cilium formation. On the contrary, TNFα increased the expression of TNFα receptor TNFR2 and the mature neuron marker MAP2, also promoting neurite elongation. Moreover, TNFα affected nerve growth factor receptor expression. We also found that TNFα induced the expression of DNA-methylation enzymes and, accordingly, downregulated genes involved in neuronal development through epigenetic mechanisms, as demonstrated by methylome analysis. In summary, TNFα showed a dual role on hfNBMs phenotypic plasticity, exerting a negative influence on neurogenesis despite a positive effect on differentiation, through mechanisms that remain to be elucidated. Our results help to clarify the complexity of TNFα effects in human neurons and suggest that manipulation of TNFα signaling could provide a potential therapeutic approach against neurodegenerative disorders.

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          Genome-wide mapping of DNA methylation: a quantitative technology comparison

          DNA methylation is a key component of mammalian gene regulation and the most classical example of an epigenetic mark. DNA methylation patterns are mitotically heritable and stable over time, but they undergo considerable changes in response to cell differentiation, diseases and environmental influences. Several methods have been developed for DNA methylation profiling on a genomic scale. Here, we benchmark four of these methods on two sample pairs, comparing their accuracy and power to detect DNA methylation differences. The results show that all evaluated methods (MeDIP-seq: methylated DNA immunoprecipitation, MethylCap-seq: methylated DNA capture by affinity purification, RRBS: reduced representation bisulfite sequencing, and the Infinium HumanMethylation27 assay) produce accurate DNA methylation data. However, these methods differ in their ability to detect differentially methylated regions between pairs of samples. We highlight strengths and weaknesses of the four methods and give practical recommendations for the design of epigenomic case-control studies.
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            New concepts in DNA methylation.

            The widely-cited model of maintenance of DNA methylation at CpG sites implies that DNA methylation is introduced by the Dnmt3 de novo DNA methyltransferases during early development, and methylation at hemimethylated CpG sites is specifically maintained by the Dnmt1 maintenance methyltransferase. However, substantial experimental evidence from the past decade indicates that this simple model needs to be revised. DNA methylation can be described by a dynamic stochastic model, in which DNA methylation at each site is determined by the local activity of DNA methyltransferases (Dnmts), DNA demethylases, and the DNA replication rate. Through the targeting and regulation of these enzymes, DNA methylation is controlled by the network of chromatin marks. Copyright © 2014 Elsevier Ltd. All rights reserved.
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              CpG and Non-CpG Methylation in Epigenetic Gene Regulation and Brain Function

              DNA methylation is a major epigenetic mark with important roles in genetic regulation. Methylated cytosines are found primarily at CpG dinucleotides, but are also found at non-CpG sites (CpA, CpT, and CpC). The general functions of CpG and non-CpG methylation include gene silencing or activation depending on the methylated regions. CpG and non-CpG methylation are found throughout the whole genome, including repetitive sequences, enhancers, promoters, and gene bodies. Interestingly, however, non-CpG methylation is restricted to specific cell types, such as pluripotent stem cells, oocytes, neurons, and glial cells. Thus, accumulation of methylation at non-CpG sites and CpG sites in neurons seems to be involved in development and disease etiology. Here, we provide an overview of CpG and non-CpG methylation and their roles in neurological diseases.
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                Author and article information

                Journal
                Int J Mol Sci
                Int J Mol Sci
                ijms
                International Journal of Molecular Sciences
                MDPI
                1422-0067
                25 August 2020
                September 2020
                : 21
                : 17
                : 6128
                Affiliations
                [1 ]Section of Human Anatomy and Histology, Department of Experimental and Clinical Medicine, University of Florence, 50134 Florence, Italy; erica.sarchielli@ 123456unifi.it (E.S.); vannelli@ 123456unifi.it (G.B.V.)
                [2 ]Sexual Medicine and Andrology Unit, Department of Experimental and Clinical Biomedical Sciences “Mario Serio”, University of Florence, 50134 Florence, Italy; paolo.comeglio@ 123456unifi.it
                [3 ]Biology Group CES-EIA, CES University, Medellín 050021, Colombia; yamile.herrera@ 123456gmail.com
                [4 ]Department of Neuroscience, Psychology, Drug Research and Child Health, University of Florence, 50134 Florence, Italy; irene.piaceri@ 123456gmail.com (I.P.); benedetta.nacmias@ 123456unifi.it (B.N.)
                [5 ]Bioinformatics Unit, Hospital of Prato, Azienda USL Toscana Centro, 50122 Prato, Italy; matteo.benelli@ 123456uslcentro.toscana.it
                [6 ]Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, UK; gavin.kelsey@ 123456babraham.ac.uk
                [7 ]Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 1TN, UK
                [8 ]Endocrinology Unit, Department of Experimental and Clinical Biomedical Sciences “Mario Serio”, University of Florence, 50134 Florence, Italy; mario.maggi@ 123456unifi.it
                [9 ]Neurosurgical Unit, Department of Neurosciences, Psychology, Drug Research and Child Health, University of Florence, 50134 Florence, Italy; pgallina@ 123456unifi.it
                Author notes
                [* ]Correspondence: giulia.guarnieri@ 123456unifi.it (G.G.); a.morelli@ 123456unifi.it (A.M.); Tel.: +39-3203843280 (G.G.); +39-0552758058 (A.M.)
                Author information
                https://orcid.org/0000-0001-9338-9040
                https://orcid.org/0000-0002-9762-5634
                Article
                ijms-21-06128
                10.3390/ijms21176128
                7504606
                32854421
                6f968c3a-d47f-4cfb-8eff-f01b94cdcf64
                © 2020 by the authors.

                Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license ( http://creativecommons.org/licenses/by/4.0/).

                History
                : 17 July 2020
                : 18 August 2020
                Categories
                Article

                Molecular biology
                neuroinflammation,alzheimer’s disease,neurogenesis,human fetal neurons,dna methylation,nucleus basalis of meynert,ciliogenesis,ngf,tnfα receptors

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