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Location of ChIP PCR primer sets relative to the transcription start site (TSS) of Bdnf exon 1. The genomic region defined by each primer set (designated ‘pm’) is shown above their position on the reference sequence relative to the TSS. Potential transcription factor and cofactor-binding sites are indicated on the map. PCR primer sequences can be found in Supporting information.
Source publication
To determine the epigenetic events associated with NMDA receptor-mediated activation of brain-derived neurotrophic factor gene (Bdnf) promoter 1 by hippocampal neurons in culture, we screened 12 loci across 4.5 kb of genomic DNA 5' of the transcription start site (TSS) of rat Bdnf for specific changes in histone modification and transcription facto...
Contexts in source publication
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... modifications and other DNA-binding proteins being involved in remodeling of chromatin at some, but not all sites, within the promoter ( Tian et al. 2009). Therefore, we expanded the region profiled, analyzing 12 loci within a 4.5 kb segment of promoter 1. This segment contained potential transcription factor-binding sites and multiple CpGs (Fig. 5). We used ChIP assays (Materials and methods) to profile H3K4me2 and H3K9me2 changes prior to and 45 min or 3 h following NMDA receptor stimulation. Methylation at K4 is associated with transcriptional activation while methylation at K9 is associated with repression of gene expression ( Sims et al. 2003;Martin and Zhang 2005). It should ...
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... modification was not seen in the promoter 4 region defined by the pmS4 PCR primers (Fig. S2). By contrast, in the same cells, there was a time-dependent decrease in H3K9me2 levels at these same five loci and others across promoter 1, with the exception of two regions, located )1640 to )1776 and )4037 to )4178 (defined by PCR primers pm8 and pm11, Fig. 5) which did not differ from vehicle-treated control neurons (Fig. 6b, Fig. S3). There was a decrease in H3K9me2 at the promoter 4 region (Fig. S3). Taken together, these results support the idea that selective sites in promoter 1 have increased H3K4me2, while H3K9me2 levels are decreased across promoter ...
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... ( Tao et al. 1998;West et al. 2001;Marini et al. 2004;Jiang et al. 2008). To determine if endogenous CREB and NF-jB transcription factors occupy sites within promoter 1 in response to NMDA receptor stimulation, we performed additional ChIP assays. In silico analysis pre- dicted CREB binding at sites defined by the pm51 and pm2 PCR amplicons (Fig. 5, CRE Sites 1 and 2), while NF-jB- 8) were treated with 0.5 lM or 1 lM 5-aza-dC or vehicle for 1-3 days. The medium was replaced daily during treatment. The final RNA extracted from the plates without DNA contamination was reverse transcribed by cloned AMV using a first-strand cDNA synthesis kit. Q-RT-PCR was performed on ABI PRISM 7700 ...
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... system with the sequence detection primer and probe designed by ABI primer express software and synthesized by Applied Biosystems (ABI). The data are expressed relative to the vehicle-treated control, normalized for18 S RNA, for five samples at each time point. binding sites were predicted within sites from pm1, pm3, pm52, and pm6 amplicons (Fig. 5, NF-jB Sites1, 2, 3, and 4, proximal to distal orientation). A negative control ChIP primer pair from promoter 1 was also incorporated (pmnc amplicon, Fig. 5) into the experiment. Cross-linked chroma- tin from hippocampal neuron cultures treated with NMDA (50 lM) or vehicle-treated neurons was sonicated and subsequently incubated with ...
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... relative to the vehicle-treated control, normalized for18 S RNA, for five samples at each time point. binding sites were predicted within sites from pm1, pm3, pm52, and pm6 amplicons (Fig. 5, NF-jB Sites1, 2, 3, and 4, proximal to distal orientation). A negative control ChIP primer pair from promoter 1 was also incorporated (pmnc amplicon, Fig. 5) into the experiment. Cross-linked chroma- tin from hippocampal neuron cultures treated with NMDA (50 lM) or vehicle-treated neurons was sonicated and subsequently incubated with antibodies specific to the p65 subunit of NF-jB, CREB, CBP, or RNA polymerase II (RNA pol II) to immunoprecipitate proteins bound to the chromatin. ...
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... on the protein's ability to regulate Bdnf promoter 4 activity ( Yasuda et al. 2009), but in response to NMDA receptor stimulation. Three regions, including the TSS proximal region, pm51, displayed rapid, time-dependent, decreases in HDAC1 binding following NMDA receptor activation (Fig. 9a). The other two loci included pm6, located 3¢ of the TSS (Fig. 5) and pm7, located 5¢ of the TSS. HDAC1 was released from the pm1 locus with slower kinetics than any of the other regions. HDAC1 was not associated with the distal promoter 1 site (pm9) or the proximal site 3¢ of the TSS (pm52) (Fig. 9a). For the same neuronal cultures, the Bdnf promoter 4 site, defined by the pmS4 amplicon, displayed ...
Citations
... could promote the histone acetylation of brain-derived neurotrophic factor (BDNF), which modulates the strength of existing synaptic connections and acts in the formation of new synaptic contacts [19,20]. Moreover, there were some derivatives of memantine (e.g. ...
The multitarget-directed ligands approach represents a potential strategy to provide effective treatments for Alzheimer's disease (AD) given its multifactorial pathology. Herein, a series of N-benzyl piperidine derivatives were designed, synthesized, and biologically characterized for dual inhibitions of histone deacetylase (HDAC) and acetylcholinesterase (AChE). Among the compounds tested, d5 and d10 exhibited dual enzyme inhibitions (d5: HDACIC50 = 0.17 μM, AChEIC50 = 6.89 μM, d10: HDACIC50 = 0.45 μM, AChEIC50 = 3.22 μM), and both compounds showed activities on scavenging free radical, metal chelating, and inhibiting Aβ aggregations. More importantly, both compounds exhibited promising neuroprotective activities in PC-12 cells and good AChE selectivity. Collectively, the multifunctional profiles of compound d5 and d10 encourage further optimization and exploration to develop more potent analogues as potential treatments for AD.
... It is currently involved in several clinical trials as an anticancer compound. Conversely, systemic (Zhong et al., 2020), hippocampal (Sales et al., 2011) or into the ventrolateral orbital cortex (Xing et al., 2014) treatment with DNMT inhibitors (e.g., decitabine) elicited antidepressant-like effects, at least by increasing hippocampal BDNF levels (Tian et al., 2009). The DNMT inhibitor 5-aza-deoxycytidine restored striatal synaptic plasticity and improved behavioral phenotype via reducing the binding of DNMT1 to D2R promoter in adult stressed mice (Li et al., 2021a). ...
Although the etiopathogenesis of mental disorders is not fully understood, accumulating evidence support that clinical symptomatology cannot be assigned to a single gene mutation, but it involves several genetic factors. More specifically, a tight association between genes and environmental risk factors, which could be mediated by epigenetic mechanisms, may play a role in the development of mental disorders. Several data suggest that epigenetic modifications such as DNA methylation, post-translational histone modification and interference of microRNA (miRNA) or long non-coding RNA (lncRNA) may modify the severity of the disease and the outcome of the therapy. Indeed, these changes may help to identify patients particularly vulnerable to mental disorders and may have potential utility as biomarkers to facilitate diagnosis and treatment of psychiatric disorders. This article summarizes the most relevant preclinical and human data showing how epigenetic modifications can be central to the therapeutic efficacy of antidepressant and/or antipsychotic agents, as possible predictor of drugs response.
... Another study also indicated that DNMT regulates dendritic spine density and chronic stress-induced depression-like behaviors (LaPlant et al., 2010). Sales et al. (2011) showed that treatment with DNMT inhibitors exhibited antidepressant-like effects mediated via the inhibition of DNA methylation in the hippocampus and rescued stress-induced reduction of Bdnf expression (Tian et al., 2009). Taken together, these observations suggest that there may be an association between DNMT activity and depression. ...
Major depressive disorder (MDD) is a leading cause of disability worldwide. Although the etiology and pathophysiology of MDD remain poorly understood, aberrant neuroplasticity mediated by the epigenetic dysregulation of gene expression within the brain, which may occur due to genetic and environmental factors, may increase the risk of this disorder. Evidence has also been reported for sex-related differences in the pathophysiology of MDD, with female patients showing a greater severity of symptoms, higher degree of functional impairment, and more atypical depressive symptoms. Males and females also differ in their responsiveness to antidepressants. These clinical findings suggest that sex-dependent molecular and neural mechanisms may underlie the development of depression and the actions of antidepressant medications. This review discusses recent advances regarding the role of epigenetics in stress and depression. The first section presents a brief introduction of the basic mechanisms of epigenetic regulation, including histone modifications, DNA methylation, and non-coding RNAs. The second section reviews their contributions to neural plasticity, the risk of depression, and resilience against depression, with a particular focus on epigenetic modulators that have causal relationships with stress and depression in both clinical and animal studies. The third section highlights studies exploring sex-dependent epigenetic alterations associated with susceptibility to stress and depression. Finally, we discuss future directions to understand the etiology and pathophysiology of MDD, which would contribute to optimized and personalized therapy.
... Therefore, future studies are required to examine the long-term treatment of curcumin on central sensitization in rodent chronic neuropathic pain model. In addition, NMDAR-mediated activation of brain-derived neurotrophic factor (BDNF) is associated with the enrichment of p300/CREBbinding protein (CBP) at the BDNF gene promoter I [143]. Curcumin exerted its therapeutic activity by downregulating the recruitment of p300/CBP and histone acetyltransferase (HAT) (acetyl-Histone H3/acetyl-Histone H4) to the BDNF promoter [135]. ...
Lesion or disease of the somatosensory system leads to the development of neuropathic pain. Peripheral neuropathic pain encompasses damage or injury of the peripheral nervous system. On the other hand, 10–15% of individuals suffer from acute postoperative pain followed by persistent pain after undergoing surgeries. Antidepressants, anticonvulsants, baclofen, and clonidine are used to treat peripheral neuropathy, whereas opioids are used to treat postoperative pain. The negative effects associated with these drugs emphasize the search for alternative therapeutics with better efficacy and fewer side effects. Curcumin, a polyphenol isolated from the roots of Curcuma longa, possesses antibacterial, antioxidant, and anti-inflammatory properties. Furthermore, the low bioavailability and fast metabolism of curcumin have led to the advent of various curcumin formulations. The present review provides a comprehensive analysis on the effects of curcumin and its formulations in preclinical and clinical studies of neuropathic and postoperative pain. Based on the positive outcomes from both preclinical and clinical studies, curcumin holds the promise of mitigating or preventing neuropathic and postoperative pain conditions. However, more clinical studies with improved curcumin formulations are required to involve its use as adjuvant to neuropathic and postoperative drugs.
... 188,189 In addition, findings from in vitro experiments showed the transcript expression of these two Bdnf exons were effectively modulated by neuronal activity. 35,190 It is therefore possible that certain activity-dependent cellular components, such as Dnmt3a2 and MeCP2 involved in the aforementioned pathways, overlap, as they have previously been found to have roles in memory extinction. 191,192 The IL could also be a potential electrical stimulation target for depression and memory extinction, which could bridge these two aspects. ...
Advances in characterizing molecular profiles provide valuable insights and opportunities for deciphering the neuropathology of depression. Although abnormal brain‐derived neurotrophic factor (BDNF) expression in depression has gained much support from preclinical and clinical research, how it mediates behavioral alterations in the depressed state remains largely obscure. Environmental factors contribute significantly to the onset of depression and produce robust epigenetic changes. Epigenetic regulation of BDNF, as one of the most characterized gene loci in epigenetics, has recently emerged as a target in research on memory and psychiatric disorders. Specifically, epigenetic alterations of BDNF exons are heavily involved in mediating memory functions and antidepressant effects. In this review, we discuss key research on stress‐induced depression from both preclinical and clinical studies, which revealed that differential epigenetic regulation of specific BDNF exons is associated with depression pathophysiology. Considering that BDNF has a central role in depression, we argue that memory extinction, an adaptive response to fear exposure, is dependent on BDNF modulation and holds promise as a prospective target for alleviating or treating depression and anxiety disorders.
... could promote the histone acetylation of brain-derived neurotrophic factor (BDNF), which modulates the strength of existing synaptic connections and acts in the formation of new synaptic contacts [19,20]. Moreover, there were some derivatives of memantine (e.g. ...
Histone deacetylases (HDACs) have been indicated important roles in neurodegenerative disorders including Alzheimer’s disease (AD). Herein, a series of novel compounds that contain a memantine moiety were designed to target HDACs and N-methyl-D-aspartate receptor (NMDAR) which are related to the treatment of AD. Biological characterization established that compound 9d exhibited a balanced inhibitory activity on NMDAR and HDACs. This compound is relatively selective to HDAC6 with IC50 of 0.18 μM and also maintains comparable activity on NMDAR (Ki = 0.59 μM) as memantine. Functionally, treatment with 9d increased the level of AcTubulin in MV4-11 cells and rescued PC-12 cells from H2O2-induced cytotoxicity with EC50 of 0.94 μM. Studies in mice also demonstrated that compound 9d efficiently penetrates the blood brain barrier to reach the brain tissue. Collectively, the results strongly encourage further development of 9d as a potential therapeutic agent for AD.
... The association of MeCP2 with H3K9 methylation has been reported in the region of IL-6 gene [32]. A direct correlation between the binding of MeCP2 and the presence of H3K9me in promoter of the IκBα gene and the BDNF gene also has been described [52,53]. Our ChIP results showed, for the first time, that MeCP2 represses expression of miR-200c by regulating H3K9 methylation of miR-200c promoter. ...
Background:
The epithelial-to-mesenchymal transition (EMT) has been linked to the regulation of glioma progression. However, the underlying signaling mechanisms that regulate EMT are poorly understood.
Methods:
Quantitative real-time PCR (RT-qPCR) and western blot were performed to detect the expression of MeCP2 in glioma tissues and cell lines. MeCP2 functions were tested with cell immunofluorescence staining and western blot. For in vivo experiments, mouse xenograft model was used to investigate the effects of MeCP2 on glioma. ChIP and Co-IP were used to detect the relationships among MeCP2, miR-200c and Suv39H1.
Results:
In this study, we found that MeCP2 was frequently up-regulated in human glioma tissues and cell lines. MeCP2 knockdown remarkably induced cell epithelial phenotype and inhibited mesenchymal marker ZEB1 and ZEB2 in vitro and in vivo. In addition, MeCP2 in glioma tissues was negatively correlated with miR-200c expression, and miR-200c overexpression partially abrogated mesenchymal phenotype induced by MeCP2. More importantly, we showed that MeCP2 recruited H3K9 to the promoter of miR-200c by interacting with SUV39H1, resulting in EMT of glioma cells.
Conclusions:
This study for the first time reveals MeCP2 as a novel regulator of EMT in glioma and suggest that MeCP2 inhibition may represent a promising therapeutic option for suppressing EMT in glioma.
... Despite this evidence, the dowregulation BDNF acts and drives the phosphorylations of TrkB and CREB in depressive etiology [38]. The binding between BDNF and TrkB protects hippocampal neurons against glutamate-mediated toxicity [39]. Furthermore, the bioactive ingredient of Radix glycyrrhizae promoted the BDNF protein levels [40,41]. ...
Depression is a highly debilitating and life-threatening psychiatric disorder. The classical antidepressants are still not adequate due to undesirable side effects. Therefore, the development of new drugs for depression treatment is an urgent strategic to achieving clinical needs. Licorisoflavan A is a bioactive ingredient isolated from Glycyrrhizae Radix and has been recently reported for neuroprotective effects. In this study, the antidepressant-like effect and neural mechanism of licorisoflavan A were explored. In the mice behavioral despair test, we observed that licorisoflavan A exhibited powerful antidepressant-like effect in forced swimming test (FST), tail suspension test (TST), without affecting locomotor activity in open field test (OFT). Additionally, licorisoflavan A administration significantly restored Chronic mild stress (CMS)-induced changes in sucrose preference test (SPT), FST, and TST, without altering the locomotion in OFT. In chronical-stimulated mice, the licorisoflavan A treatment effectively attenuated the expressions of Brain-derived neurotrophic factor (BDNF), tyrosine kinase B (TrkB), the phosphorylations of cAMP response element binding protein (CREB), extracellular signal-regulated kinase (ERK)-1/2, eukaryotic elongation factor 2 (eEF2), mammalian target of rapamycin (mTOR), initiation factor 4E-binding protein 1 (4E-BP-1), and p70 ribosomal protein S6 kinase (p70S6K) in hippocampus of CMS-induced mice. Additionally, licorisoflavan A could reverse the decreases in synaptic proteins post-synaptic density protein 95 (PSD-95) and α-amino-3-hydroxy-5-methyl-4-isoxazole-propionic acid (AMPA) receptor subunit glutamate receptor 1 (GluR1) caused by CMS, and its antidepressant-like effect was blocked by the AMPA receptor antagonist NBQX. These findings served as preclinical evidence that licorisoflavan A exerted potent antidepressant-like effects involving BDNF-TrkB pathway and AMPA receptors. Licorisoflavan A might be used as a potential medicine against depression-like disorder.
... The regulation of Bdnf is complex and involves multiple splice variants [37,51]. REST, EZH2, JMJD3, and CBP have all been reported to regulate the transcription of Bdnf [36,37,52]. Using our simplified culture model, there is impaired transcription of Bdnf exon 1 in the Tspyl2 mutant neurons which can be rescued by inhibiting EZH2. ...
Testis-specific protein, Y-encoded-like 2 (TSPYL2) is an X-linked gene in the locus for several neurodevelopmental disorders. We have previously shown that Tspyl2 knockout mice had impaired learning and sensorimotor gating, and TSPYL2 facilitates the expression of Grin2a and Grin2b through interaction with CREB-binding protein. To identify other genes regulated by TSPYL2, here, we showed that Tspyl2 knockout mice had an increased level of H3K27 trimethylation (H3K27me3) in the hippocampus, and TSPYL2 interacted with the H3K27 methyltransferase enhancer of zeste 2 (EZH2). We performed chromatin immunoprecipitation (ChIP)-sequencing in primary hippocampal neurons and divided all Refseq genes by k-mean clustering into four clusters from highest level of H3K27me3 to unmarked. We confirmed that mutant neurons had an increased level of H3K27me3 in cluster 1 genes, which consist of known EZH2 target genes important in development. We detected significantly reduced expression of genes including Gbx2 and Prss16 from cluster 1 and Acvrl1, Bdnf, Egr3, Grin2c, and Igf1 from cluster 2 in the mutant. In support of a dynamic role of EZH2 in repressing marked synaptic genes, the specific EZH2 inhibitor GSK126 significantly upregulated, while the demethylase inhibitor GSKJ4 downregulated the expression of Egr3 and Grin2c. GSK126 also upregulated the expression of Bdnf in mutant primary neurons. Finally, ChIP showed that hemagglutinin-tagged TSPYL2 co-existed with EZH2 in target promoters in neuroblastoma cells. Taken together, our data suggest that TSPYL2 is recruited to promoters of specific EZH2 target genes in neurons, and enhances their expression for proper neuronal maturation and function.
Electronic supplementary material
The online version of this article (10.1007/s12035-018-1238-y) contains supplementary material, which is available to authorized users.
... In hippocampal cultures, NMDA stimulation and resulting calcium influx, increased phosphorylation of MeCp2 leading to increased BDNF mRNA levels (Zhou et al., 2006). Work by Lipsky's group expanded these findings with CHIP to show that NMDA activation results in multiple epigenetic changes to the BDNF promoter, including a decrease in histone H3 at lysine 9 dimethylation (H3K9me2) and increases in H3K4me2 and H3K9/14 acetylation (H3AcK9/14) (Tian et al., 2009). Furthermore, Lau et al. show that BDNFinduced neuroprotection is mediated by synaptic NMDA-receptor-dependent nuclear calcium signals activating transcription of inhibin b-A (activin A). ...
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.
