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Gardner CC, Abele JA, Winkler TJ, Reckers CN, Anas SA, James PF. Common as well as unique methylation-sensitive DNA regulatory elements in three mammalian SLC9C1 genes. bioRxiv 2023:2023.08.29.555319. [PMID: 37693488 PMCID: PMC10491193 DOI: 10.1101/2023.08.29.555319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
The SLC9C1 gene (which encodes the NHE10 protein) is essential for male fertility in both mice and humans, however the epigenetic mechanisms regulating its testis/sperm-specific gene expression have yet to be studied. Here we identify and characterize DNA regulatory elements of the SLC9C1 gene across three mammalian species: mouse, rat, and human. First, in silico analysis of these mammalian SLC9C1 genes identified a CpG island located upstream of the transcription start site in the same relative position in all three genes. Further analysis reveals that this CpG island behaves differently, with respect to gene regulatory activity, in the mouse SLC9C1 gene than it does in the rat and human SLC9C1 gene. The mouse SLC9C1 CpG island displays strong promoter activity by itself and seems to have a stronger gene regulatory effect than either the rat or human SLC9C1 CpG islands. While the function of the upstream SLC9C1 CpG island may be divergent across the three studied species, it appears that the promoters of these three mammalian SLC9C1 genes share similar DNA methylation-sensitive regulatory mechanisms. All three SLC9C1 promoter regions are differentially methylated in lung and testis, being more hypermethylated in lung relative to the testis, and DNA sequence alignments provide strong evidence of primary sequence conservation. Luciferase assays reveal that in vitro methylation of constructs containing different elements of the three SLC9C1 genes largely exhibit methylation-sensitive promoter activity (reduced promoter activity when methylated) in both HEK 293 and GC-1spg cells. In total, our data suggest that the DNA methylation-sensitive elements of the mouse, rat, and human SLC9C1 promoters are largely conserved, while the upstream SLC9C1 CpG island common to all three species seems to perform a different function in mouse than it does in rat and human. This work provides evidence that while homologous genes can all be regulated by DNA methylation-dependent epigenetic mechanisms, the location of the specific cis-regulatory elements responsible for this regulation can differ across species.
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Fernández A, Astorga J, Bordagaray MJ, Lira MJ, Gebicke-Haerter PJ, Hernández M. Effect of TLR9 methylation on its transcription in apical inflammation. Int Endod J 2022; 55:784-794. [PMID: 35416307 DOI: 10.1111/iej.13745] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 04/05/2022] [Accepted: 04/06/2022] [Indexed: 11/25/2022]
Abstract
AIM to explore the methylation pattern, its role on transcriptional regulation and potential modifiers of methylation of theTLR9 gene in chronic periapical inflammation. METHODOLOGY In this cross-sectional study, apical lesions of endodontic origin (ALEO, n=61) and healthy periodontal ligaments (HPL, n=15) were included. Products from bisulfited and PCR-amplified DNA were analyzed for their methylation profiles in the promoter region and at each CpG island. Additionally, TLR9 mRNA levels were quantified by qPCR and bivariate and multiple modelling were performed to better understand the influence of methylations on gene transcription. RESULTS TLR9 mRNA levels were upregulated in ALEO compared to HPL (p<0.001). TLR9 promoter CpG sites and CpG +2086 in the intragenic island 1 were demethylated in ALEO compared to HPL (p<0.05). Multivariate analysis, adjusted by smoking and gender, revealed that demethylation of TLR9 promoter sites enhanced transcriptional activity, specifically demethylated CpGs at positions -736 and -683, (p=0.02), which are close to CRE binding. Whereas ALEO reduced the global methylation of the gene-promoter and intragenic-island 2 (p<0.05) by -42.5 and -9.5 percentage points, respectively, age reduced the global methylation of intragenic-island 3 within the exon 2. CONCLUSIONS Demethylations of TLR9 promoter CpG sites, along with the intragenic DNA methylation status, were involved in higher transcription in ALEO. Hence, chronic periapical inflammation and aging modify the methylation status both in the gene promoter and in intragenic CpG islands.
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Affiliation(s)
- Alejandra Fernández
- Laboratory of Periodontal Biology, Faculty of Dentistry, Universidad de Chile, Santiago, Chile.,Faculty of Dentistry, Universidad Andres Bello, Santiago, Chile
| | - Jessica Astorga
- Laboratory of Periodontal Biology, Faculty of Dentistry, Universidad de Chile, Santiago, Chile
| | - María José Bordagaray
- Laboratory of Periodontal Biology, Faculty of Dentistry, Universidad de Chile, Santiago, Chile.,Department of Conservative Dentistry, Faculty of Dentistry, Universidad de Chile, Santiago, Chile
| | - María Jesús Lira
- Department of Orthopaedic Surgery, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Peter J Gebicke-Haerter
- Institute of Psychopharmacology, Central Institute of Mental Health, Faculty of Medicine, University of Heidelberg, Mannheim, Germany
| | - Marcela Hernández
- Laboratory of Periodontal Biology, Faculty of Dentistry, Universidad de Chile, Santiago, Chile.,Department of Pathology and Oral Medicine, Faculty of Dentistry, Universidad de Chile, Santiago, Chile
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Faam B, Ghadiri AA, Ghaffari MA, Totonchi M, Amouzegar A, Azizi F, Shahbazian H, Hashemitabar M, Fanaei SA, Khorsandi L. CpG Island Methylation of the Rap1Gap Gene in Medullary Thyroid Cancer. Arch Iran Med 2022; 25:171-177. [PMID: 35429959 DOI: 10.34172/aim.2022.29] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 02/07/2021] [Indexed: 06/14/2023]
Abstract
BACKGROUND Medullary thyroid cancer (MTC) is a rare type of neuroendocrine tumor. This study aimed to investigate the gene and protein expression of RAP1GAP and DNA methylation patterns of its CpG74a , CpG74b , and CpG24 in an Iranian population with MTC. METHODS In this case-control study, we selected 55 individuals who underwent thyroidectomy in Erfan hospital, Tehran, between 2018 and 2020. Samples were divided into normal thyroid tissues (control; n=20), benign nodule (n=20), and MTC (n=15). DNA methylation patterns were investigated using MSP (methylation-specific PCR). The protein level and mRNA expression of RAP1GAP were also evaluated using western blotting and real-time PCR, respectively. RESULTS The hyper-methylation rates of CpG24 and CpG74a in the MTC samples were considerably higher than the controls (83% versus 15% and 74% versus 17%, respectively; P<0.001). The methylation/unmethylation ratio of CpG74a , and CpG24 was considerably higher than the controls (P<0.001). The methylation/unmethylation ratio of CpG24 in the benign nodules was also considerably greater than the controls (P<0.001). The mRNA expression and the protein level of RAP1GAP in the MTC group were considerably lower than the controls (P=0.005 and P=0.035, respectively). In the MTC group, aberrant methylation of CpG74a and CpG24 was significantly correlated with decreasing expression of the Rap1Gap gene (R2 : 0.23; P=0.032 and R2 : 0.56; P=0.001, respectively). CONCLUSION Hyper-methylation in CpG24 and CpG74a and decreasing expression of RAP1GAP can be considered as diagnostic biomarkers for MTC.
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Affiliation(s)
- Bita Faam
- Cellular and Molecular Research Center, Medical Basic Sciences Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Ata A Ghadiri
- Cellular and Molecular Research Center, Medical Basic Sciences Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
- Department of Immunology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Mohammad Ali Ghaffari
- Cellular and Molecular Research Center, Medical Basic Sciences Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Mehdi Totonchi
- Department of Endocrinology and Female Infertility, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran
| | - Atieh Amouzegar
- Endocrine Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Fereidoun Azizi
- Endocrine Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hajiehbibi Shahbazian
- Chronic Disease Care Research Center, School of Nursing and Midwifery, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Mahmoud Hashemitabar
- Department of Anatomical Sciences, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | | | - Layasadat Khorsandi
- Cellular and Molecular Research Center, Medical Basic Sciences Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
- Department of Anatomical Sciences, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
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Zakir U, Siddiqui NN, Naqvi FUH, Khan R. Aberrant STAT1 methylation as a non-invasive biomarker in blood of HCV induced hepatocellular carcinoma. Cancer Biomark 2021; 34:95-103. [PMID: 34657877 DOI: 10.3233/cbm-210216] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is one of the most common types of cancer in the world and a reason behind different oncogenes activation and tumor suppressor genes inactivation. Hyper-methylation of tumor suppressor genes including RASSF1a, GSTP1, p16, and APC cause gene silencing as well as tumor cell invasion. STAT 1 gene is a part of signaling cascade of JAK/STAT and any dysregulation in signaling has been implicated in tumor formation. OBJECTIVE The current investigation focus on the methylation role of STAT1 gene as a non-invasive biomarker in the progression and diagnosis of hepatocellular carcinoma. METHODS STAT1 gene methylation status in 46 HCV induced hepatocellular carcinoma patients and 40 non-HCC controls were examined by methylation specific PCR. STAT1 gene expression was examined by real time PCR and further validated by various bioinformatics tools. RESULTS STAT1 methylation in HCV-induced HCC (67.4%) was significantly higher compared to the non-HCC controls (p< 0.01). However, mRNA expression of STAT1 gene in methylated groups was significantly lower compared to unmethylated groups (p< 0.05). Furthermore, insilco analysis of STAT1 validated our results and shown expression of STAT1 mRNA was lower in liver cancer with the median 24.3 (p= 0.085). CONCLUSION After using peripheral blood samples we observed that STAT1 silencing caused by aberrant methylation could be used as potential non-invasive biomarker for the diagnosis of HCV induced hepatocellular carcinoma. We conclude that blood as a sample source could be used instead of biopsy for early detection of HCC.
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Affiliation(s)
- Umaira Zakir
- Department of Biochemistry, University of Karachi, Karachi, Pakistan
| | - Nadir Naveed Siddiqui
- The Karachi Institute of Biotechnology and Genetic Engineering (KIBGE), University of Karachi, Karachi, Pakistan
| | | | - Rizma Khan
- Department of Molecular Genetics, Dr. Ziauddin Hospital, Karachi, Pakistan
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Fernández A, Veloso P, Astorga J, Rodríguez C, Torres VA, Valdés M, Garrido M, Gebicke-Haerter PJ, Hernández M. Epigenetic regulation of TLR2-mediated periapical inflammation. Int Endod J 2020; 53:1229-1237. [PMID: 32426871 DOI: 10.1111/iej.13329] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 05/12/2020] [Indexed: 12/14/2022]
Abstract
AIM To determine the methylation pattern of TLR2 gene promoter and its association with the transcriptional regulation of periapical inflammatory and angiogenic responses in symptomatic and asymptomatic forms of apical periodontitis. METHODOLOGY In this cross-sectional study, apical lesions were obtained from volunteers with asymptomatic apical periodontitis (AAP) (n = 17) and symptomatic apical periodontitis (SAP) (n = 17) scheduled for tooth extraction, and both total RNA and DNA were extracted. DNA was bisulfite-treated, a region of CpG island within the TLR2 gene was amplified by qPCR and the products were sequenced. Additionally, the mRNA expression of TLR2, TLR4, IL-6, IL-12, TNFalpha, IL-23, IL-10, TGFbeta, VEGFA and CDH5 was analysed by qPCR. The data were analysed with chi-square tests, Mann-Whitney or unpaired t-tests, and Spearman´s correlation; variable adjustments were performed using multiple linear regression (P < 0.05). RESULTS TLR2 depicted a hypomethylated DNA profile at the CpG island in SAP when compared with AAP, along with upregulated expression of TLR2, with pro-inflammatory cytokines IL-6 and IL-23, and the angiogenesis marker CDH5 (P < 0.05). TLR2 methylation percentage negatively correlated with mRNA levels of IL-23 and CDH5 in apical periodontitis. Lower methylation frequencies of single CpG dinucleotides -8 and -10 localized in close proximity to nuclear factor κB (NFκB) binding within the TLR2 promoter were identified in SAP versus AAP (P < 0.05). Finally, unmethylated -10 and -8 single sites demonstrated up-regulation of IL-23, IL-10 and CDH5 transcripts compared to their methylated counterparts (P < 0.05). CONCLUSIONS TLR2 gene promoter hypomethylation was linked to transcriptional activity of pro-inflammatory cytokines and angiogenic markers in exacerbated periapical inflammation. Moreover, unmethylated single sites in close proximity to NFκB binding were involved in active transcription of IL-23, IL-10 and CDH5.
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Affiliation(s)
- A Fernández
- Laboratory of Periodontal Biology, Faculty of Dentistry, Universidad de Chile, Santiago, Chile.,Faculty of Dentistry, Universidad Andres Bello, Santiago, Chile
| | - P Veloso
- Laboratory of Periodontal Biology, Faculty of Dentistry, Universidad de Chile, Santiago, Chile
| | - J Astorga
- Laboratory of Periodontal Biology, Faculty of Dentistry, Universidad de Chile, Santiago, Chile
| | - C Rodríguez
- Faculty of Dentistry, Universidad Andres Bello, Santiago, Chile
| | - V A Torres
- Faculty of Dentistry, Universidad de Chile, Institute for Research in Dental Sciences, Santiago, Chile
| | - M Valdés
- School of Public Health, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - M Garrido
- Laboratory of Periodontal Biology, Faculty of Dentistry, Universidad de Chile, Santiago, Chile
| | - P J Gebicke-Haerter
- Program of Immunology, Faculty of Medicine, Institute of Biomedical Sciences, Universidad de Chile, Santiago, Chile.,Institute of Psychopharmacology, Faculty of Medicine, Central Institute of Mental Health, University of Heidelberg, Mannheim, Germany
| | - M Hernández
- Laboratory of Periodontal Biology, Faculty of Dentistry, Universidad de Chile, Santiago, Chile.,Department of Pathology and Oral Medicine, Faculty of Dentistry, Universidad de Chile, Santiago, Chile
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Dinka H, Milkesa A. Unfolding SARS-CoV-2 viral genome to understand its gene expression regulation. Infect Genet Evol 2020; 84:104386. [PMID: 32473977 PMCID: PMC7256514 DOI: 10.1016/j.meegid.2020.104386] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 05/16/2020] [Accepted: 05/27/2020] [Indexed: 01/07/2023]
Abstract
SARS-CoV-2 is a new virus responsible for an outbreak of respiratory illness known as COVID-19, which has spread to several countries around the world and a global effort is being undertaken to characterize the molecular features and evolutionary origins of this virus. In silico analysis of the transcription start sites, promoter regions, transcription factors and their binding sites, gene ontology, CpG islands for SARS-CoV-2 viral genome are a first step to understand the regulation mechanisms of gene expression and its association with genetic variations in the genomes. For this purpose, we first computationally surveyed all SARS-CoV-2 virus genes with the open reading frames from NCBI database and found eleven sequences to accomplish the mentioned features by using bioinformatics tools. Our analysis revealed that all (100%) of the SARS-CoV-2 virus genes have more than one TSS. By taking all TSSs with the highest predictive score we determined promoter regions and identified five common candidate motifs (MVI, MVII, MVIII, MVIV and MVV) of which MVI was found to be shared by all promoter regions of SARS-CoV-2 virus genes with the least E-value (3.8e-056, statistically highly significant). In our further analysis of MVI we showed MVI serve as binding sites for a single transcription factor (TF) family, EXPREG, involved in the regulatory mode of these genes. From EXPREG family four TFs that belongs to Cyclic AMP (cAMP) receptor protein (CRP) and Catabolite control protein A (CcpA) group mostly serve as transcriptional activator whereas two TFs that belong to LexA group always serve as transcriptional repressor in different kinds of cellular processes and molecular functions. Therefore, we unfolded SARS-CoV-2 viral genome to shed light on its gene expression regulation that could help to design and evaluate diagnostic tests, to track and trace the ongoing outbreak and to identify potential intervention options. Computationally surveyed all SARS-CoV-2 genes with the open reading frames from NCBI database showed eleven gene sequences Our analysis revealed that all (100%) of the SARS-CoV-2 genes have more than one TSS. We determined promoter regions and identified five common candidate motifs of which MVI was found to be shared by all promoter regions of SARS-CoV-2 genes. We showed MVI serve as binding sites for a single transcription factor family, EXPREG, involved in the regulatory mode of these genes.
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Affiliation(s)
- Hunduma Dinka
- Department of Applied Biology, School of Applied Natural Science, Adama Science and Technology University, P.O.Box 1888, Adama, Ethiopia.
| | - Ashenafi Milkesa
- Department of Applied Biology, School of Applied Natural Science, Adama Science and Technology University, P.O.Box 1888, Adama, Ethiopia
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J J, Vanisree AJ, Ravisankar S, K R. Site specific hypermethylation of CpGs in Connexin genes 30, 26 and 43 in different grades of glioma and attenuated levels of their mRNAs. Int J Neurosci 2018; 129:273-282. [PMID: 30280947 DOI: 10.1080/00207454.2018.1526802] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
AIM Gliomas, the intracranial tumours are considered the deadliest malignancies. The gap junctional Connexins (Cxs) that maintain cellular homeostasis perform a unique function in glial tumour suppression. However, the differential methylation patterns of Cxs were not revealed in glioma so far. The current study attempts to categorise promoter methylation of Cx30 and Cx26 and intron methylation of Cx43 in different grades of human glioma. MATERIALS AND METHODS About 85 glioma patients with pathologically confirmed grades and 15 control brain tissues were recruited in the study. Bisulphite-PCR-Single Stranded Conformation analysis(SSCA), Bisulphite sequencing and MeDIP-qPCR were carried out to assess methylation status and Cx mRNA levels were also analysed to evaluate the effect of methylation. RESULTS We found that promoter CpG islands(CpGs) reside in Sp1 and Ap2 sites of Cx30 and 26 were hypermethylated in high grades (HG) of glioma rather than low grades. The input % of both was significantly increased (p < 0.03) in progressive grades. Interestingly, Cx43 could exhibit a significant increase (p < 0.05) in input % only in grade IV. While, Cx30 and 26 mRNAs were downregulated according to their methylation status in progressive fashion with grades, Cx43 was downregulated irrespective of intron methylation. CONCLUSION Thus, we suggest that the sites and extent of methylation of Cxs (30 and 26 but not in 43) are found to be altered. In different grades of glioma can provide better appreciation of the grade of the patient and might help in strategies based on epigenetic approaches.
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Affiliation(s)
- Jayalakshmi J
- a Department of Biochemistry , University of Madras , Chennai , Tamilnadu , India
| | | | - Shantha Ravisankar
- b Department of Neuropathology , Tamilnadu Multispeciality Hospital , Chennai , Tamilnadu , India
| | - Rama K
- c Department of Neuropathology , Madras Medical College and Government General hospital , Chennai , Tamilnadu , India
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Pol Bodetto S, Carouge D, Fonteneau M, Dietrich JB, Zwiller J, Anglard P. Cocaine represses protein phosphatase-1Cβ through DNA methylation and Methyl-CpG Binding Protein-2 recruitment in adult rat brain. Neuropharmacology 2013; 73:31-40. [PMID: 23688924 DOI: 10.1016/j.neuropharm.2013.05.005] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2012] [Revised: 04/28/2013] [Accepted: 05/07/2013] [Indexed: 10/26/2022]
Abstract
Repeated cocaine exposure induces epigenetic factors such as DNA methyl-binding proteins, indicating that resulting changes in gene expression are mediated by alterations in brain DNA methylation. While the activity of protein phosphatase type-1 (PP1) is involved in cocaine effects and in brain plasticity, the expression of the PP1Cβ catalytic subunit gene was identified here as modulated by cocaine. Its expression was induced together with that of PP1Cγ in the brain of Methyl-CpG Binding Protein-2 (Mecp2) mutant mice, whereas PP1Cα expression was not affected, illustrating a different regulation of PP1C isoforms. Repeated cocaine administration was found to increase DNA methylation at the PP1Cβ gene together with its binding to Mecp2 in rat caudate putamen, establishing a link between two genes involved in cocaine-related effects and in learning and memory processes. Cocaine also increased DNMT3 expression, resulting in PP1Cβ repression that did not occur in the presence of DNMT inhibitor. Cocaine-induced PP1Cβ repression was observed in several brain structures, as evaluated by RT-qPCR, immunohistochemistry and Western blot, but did not occur after a single cocaine injection. Our data demonstrate that PP1Cβ is a direct MeCP2-target gene in vivo. They suggest that its repression may participate to behavioral adaptations triggered by the drug.
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Affiliation(s)
- Sarah Pol Bodetto
- Laboratoire de Neurosciences Cognitives et Adaptatives, UMR 7364 CNRS, Université de Strasbourg, 67000 Strasbourg, France
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