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Methylation of sites CpG in promoter

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https://www.readbyqxmd.com/read/29456678/association-between-dscr4-gene-methylation-in-plasma-in-early-pregnancy-and-down-s-syndrome
#1
Lingyu Hu, Changju Zhou
Down's syndrome (DS), a chromosomal abnormal genetic disease caused by a local or total copy of chromosome 21, leads to patients suffering from delayed body growth, special facies, mild to moderate mental retardation and other symptoms, seriously affecting the life of patients. The aim of the present study was to examine the association between Down's syndrome critical region 4 ( DSCR4 ) gene methylation in plasma in high-risk pregnant women with DS in early pregnancy (hereinafter referred to as pregnant women in early pregnancy) and DS, in order to screen new epigenetic markers for the clinical diagnosis of DS...
March 2018: Experimental and Therapeutic Medicine
https://www.readbyqxmd.com/read/29456534/critical-role-of-tgf-%C3%AE-and-il-2-receptor-signaling-in-foxp3-induction-by-an-inhibitor-of-dna-methylation
#2
Kristin Freudenberg, Nadja Lindner, Sebastian Dohnke, Annette I Garbe, Sonja Schallenberg, Karsten Kretschmer
Under physiological conditions, CD4+ regulatory T (Treg) cells expressing the transcription factor Foxp3 are generated in the thymus [thymus-derived Foxp3+ Treg (tTregs) cells] and extrathymically at peripheral sites [peripherally induced Foxp3+ Treg (pTreg) cell], and both developmental subsets play non-redundant roles in maintaining self-tolerance throughout life. In addition, a variety of experimental in vitro and in vivo modalities can extrathymically elicit a Foxp3+ Treg cell phenotype in peripheral CD4+ Foxp3- T cells, which has attracted much interest as an approach toward cell-based therapy in clinical settings of undesired immune responses...
2018: Frontiers in Immunology
https://www.readbyqxmd.com/read/29445424/promoter-methylation-of-dna-damage-repair-ddr-genes-in-human-tumor-entities-rbbp8-ctip-is-almost-exclusively-methylated-in-bladder-cancer
#3
Jolein Mijnes, Jürgen Veeck, Nadine T Gaisa, Eduard Burghardt, Tim C de Ruijter, Sonja Gostek, Edgar Dahl, David Pfister, Sebastian C Schmid, Ruth Knüchel, Michael Rose
Background: Genome-wide studies identified pan-cancer genes and shared biological networks affected by epigenetic dysregulation among diverse tumor entities. Here, we systematically screened for hypermethylation of DNA damage repair (DDR) genes in a comprehensive candidate-approach and exemplarily identify and validate candidate DDR genes as targets of epigenetic inactivation unique to bladder cancer (BLCA), which may serve as non-invasive biomarkers. Methods: Genome-wide DNA methylation datasets (2755 CpG probes of n = 7819 tumor and n = 659 normal samples) of the TCGA network covering 32 tumor entities were analyzed in silico for 177 DDR genes...
2018: Clinical Epigenetics
https://www.readbyqxmd.com/read/29445184/parental-micronutrient-deficiency-distorts-liver-dna-methylation-and-expression-of-lipid-genes-associated-with-a-fatty-liver-like-phenotype-in-offspring
#4
Kaja H Skjærven, Lars Martin Jakt, Jorge M O Fernandes, John Arne Dahl, Anne-Catrin Adam, Johanna Klughammer, Christoph Bock, Marit Espe
Micronutrient status of parents can affect long term health of their progeny. Around 2 billion humans are affected by chronic micronutrient deficiency. In this study we use zebrafish as a model system to examine morphological, molecular and epigenetic changes in mature offspring of parents that experienced a one-carbon (1-C) micronutrient deficiency. Zebrafish were fed a diet sufficient, or marginally deficient in 1-C nutrients (folate, vitamin B12, vitamin B6, methionine, choline), and then mated. Offspring livers underwent histological examination, RNA sequencing and genome-wide DNA methylation analysis...
February 14, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29429487/dynamic-changes-in-dna-methylation-patterns-in-canine-lymphoma-cell-lines-demonstrated-by-genome-wide-quantitative-dna-methylation-analysis
#5
J Yamazaki, J Jelinek, S Hisamoto, A Tsukamoto, M Inaba
DNA methylation is the conversion of cytosine to 5-methylcytosine, leading to changes in the interactions between DNA and proteins. Methylation of cytosine-guanine (CpG) islands (CGIs) is associated with gene expression silencing of the involved promoter. Although studies focussing on global changes or a few single loci in DNA methylation have been performed in dogs with certain diseases, genome-wide analysis of DNA methylation is required to prospectively identify specific regions with DNA methylation change...
January 2018: Veterinary Journal
https://www.readbyqxmd.com/read/29426343/differences-in-mwcnt-and-swcnt-induced-dna-methylation-alterations-in-association-with-the-nuclear-deposition
#6
Deniz Öner, Manosij Ghosh, Hannelore Bové, Matthieu Moisse, Bram Boeckx, Radu C Duca, Katrien Poels, Katrien Luyts, Eveline Putzeys, Kirsten Van Landuydt, Jeroen Aj Vanoirbeek, Marcel Ameloot, Diether Lambrechts, Lode Godderis, Peter Hm Hoet
BACKGROUND: Subtle DNA methylation alterations mediated by carbon nanotubes (CNTs) exposure might contribute to pathogenesis and disease susceptibility. It is known that both multi-walled carbon nanotubes (MWCNTs) and single-walled carbon nanotubes (SWCNTs) interact with nucleus. Such, nuclear-CNT interaction may affect the DNA methylation effects. In order to understand the epigenetic toxicity, in particular DNA methylation alterations, of SWCNTs and short MWCNTs, we performed global/genome-wide, gene-specific DNA methylation and RNA-expression analyses after exposing human bronchial epithelial cells (16HBE14o- cell line)...
February 9, 2018: Particle and Fibre Toxicology
https://www.readbyqxmd.com/read/29423052/mage-a11-is-activated-through-tfcp2-zeb1-binding-sites-de-methylation-as-well-as-histone-modification-and-facilitates-escc-tumor-growth
#7
Shina Liu, Fei Liu, Weina Huang, Lina Gu, Lingjiao Meng, Yingchao Ju, Yunyan Wu, Juan Li, Lihua Liu, Meixiang Sang
Recently, we have reported that the product of Melanoma Antigens Genes (MAGE) family member MAGE-A11 is an independent poor prognostic marker for esophageal squamous cell carcinoma (ESCC). However, the reason how MAGE-A11 is activated in ESCC progression still remains unclear. In the current study, we demonstrated that DNA methylation and the subsequent histone posttranslational modifications play crucial roles in the regulation of MAGE-A11 in ESCC progression. We found that the methylation rate of TFCP2/ZEB1 binding site on MAGE-A11 promoter in ESCC tissues and cells is higher than the normal esophageal epithelial tissues and cells...
January 9, 2018: Oncotarget
https://www.readbyqxmd.com/read/29416641/-pd-l1-cd274-and-pd-l2-pdcd1lg2-promoter-methylation-is-associated-with-hpv-infection-and-transcriptional-repression-in-head-and-neck-squamous-cell-carcinomas
#8
Alina Franzen, Timo J Vogt, Tim Müller, Jörn Dietrich, Andreas Schröck, Carsten Golletz, Peter Brossart, Friedrich Bootz, Jennifer Landsberg, Glen Kristiansen, Dimo Dietrich
Background: DNA methylation of the immune checkpoint gene PD-L1 has recently been shown to be associated with PD-L1 mRNA expression in various malignancies. This study aimed to investigate the association of PD-L1 and PD-L2 methylation with mRNA expression, immune cell infitration, protein expression and human papilloma virus (HPV) infection in head and neck squamous cell carcinoma (HNSCC) patients. Results: DNA methylation of PD-L1 and PD-L2 correlates inversely with mRNA expression ( PD-L1 : p ≤ 0...
January 2, 2018: Oncotarget
https://www.readbyqxmd.com/read/29414941/structural-basis-for-dnmt3a-mediated-de-novo-dna-methylation
#9
Zhi-Min Zhang, Rui Lu, Pengcheng Wang, Yang Yu, Dongliang Chen, Linfeng Gao, Shuo Liu, Debin Ji, Scott B Rothbart, Yinsheng Wang, Gang Greg Wang, Jikui Song
DNA methylation by de novo DNA methyltransferases 3A (DNMT3A) and 3B (DNMT3B) at cytosines is essential for genome regulation and development. Dysregulation of this process is implicated in various diseases, notably cancer. However, the mechanisms underlying DNMT3 substrate recognition and enzymatic specificity remain elusive. Here we report a 2.65-ångström crystal structure of the DNMT3A-DNMT3L-DNA complex in which two DNMT3A monomers simultaneously attack two cytosine-phosphate-guanine (CpG) dinucleotides, with the target sites separated by 14 base pairs within the same DNA duplex...
February 7, 2018: Nature
https://www.readbyqxmd.com/read/29409936/epigenetic-regulation-by-cpg-methylation-splits-strong-from-retarded-ifn%C3%AE-induced-il-18bp-in-epithelial-versus-monocytic-cells
#10
Malte Bachmann, Josef Pfeilschifter, Heiko Mühl
Interferon (IFN)-γ-inducing interleukin (IL)-18 is a crucial inflammatory cytokine systemically provided by monocytes. It is counteracted by IL-18 binding protein (IL-18BP), a decoy receptor that displays IFNγ-inducibility thus curbing inflammation by negative feedback. Since IL18BP inducibility is pronounced in human epithelial cells but diminished in monocytes, differential IL18BP regulation was investigated herein in both types of cells. Interestingly, DNA-demethylating 5-aza-2'-deoxycytidine enhanced IFNγ-induced IL-18BP only in monocytic but not in epithelial cells...
January 30, 2018: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29409498/dna-methylome-profiling-at-single-base-resolution-through-bisulfite-sequencing-of-5mc-immunoprecipitated-dna
#11
Zhen Jia, Yueyi Shi, Lei Zhang, Yipeng Ren, Tong Wang, Lejun Xing, Baorong Zhang, Guolan Gao, Rongfa Bu
BACKGROUND: Detection of DNA methylome at single-base resolution is a significant challenge but promises to shed considerable light on human disease etiology. Current technologies could not detect DNA methylation genome-wide at single-base resolution with small amount of sequencing data and could not avoid detecting the methylation of repetitive elements which are considered as "junk DNA". METHODS: In this study, we have developed a novel DNA methylome profiling technology named MB-seq with its ability to identify genome-wide 5mC and quantify DNA methylation levels by introduced an assistant adapter AluI-linker This linker can be ligated to sonicated DNA and then be digested after the bisulfite treatment and amplification, which has no effect of MeDIP enrichment...
February 6, 2018: BMC Biotechnology
https://www.readbyqxmd.com/read/29405013/region-specific-methylation-profiling-in-acute-myeloid-leukemia
#12
Agnieszka Cecotka, Joanna Polanska
Alteration of DNA methylation level in cancer diseases leads to deregulation of gene expression-silencing of tumor suppressor genes and enhancing of protooncogenes. There are several tools devoted to the problem of identification of CpG sites' demethylation but majority of them focuses on single site level and does not allow for quantification of region methylation changes. The aim was to create an adaptive algorithm supporting detection of differentially methylated CpG sites and genomic regions specific for acute myeloid leukemia...
February 5, 2018: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/29404838/germline-promoter-hypermethylation-in-brca1-and-brca2-genes-is-not-present-in-hereditary-breast-cancer-patients
#13
M Rodríguez-Balada, B Roig, M Melé, M Salvat, L Martorell, J Borràs, J Gumà
PURPOSE: Germline promoter hypermethylation of BRCA1 and BRCA2 genes is an alternative event of gene silencing that has not been widely investigated in hereditary breast and ovarian cancer (HBOC) syndrome. METHODS: We analyzed germline BRCA promoter hypermethylation in HBOC patients with and without BRCA mutations and control subjects, using a recently developed BRCA methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA) assay. RESULTS: Neither the patients tested nor the control subjects showed germline hypermethylation of the BRCA1 and BRCA2 promoter regions analyzed...
February 5, 2018: Clinical & Translational Oncology
https://www.readbyqxmd.com/read/29393154/long-interspersed-element-1-methylation-level-as-a-prognostic-biomarker-in-gastrointestinal-cancers
#14
Yoshifumi Baba, Taisuke Yagi, Hiroshi Sawayama, Yukiharu Hiyoshi, Takatsugu Ishimoto, Masaaki Iwatsuki, Yuji Miyamoto, Naoya Yoshida, Hideo Baba
Epigenetic changes play a crucial role in human cancer development. DNA methylation is a central epigenetic process that regulates levels of gene expression. Changes in DNA methylation that occur in human tumors include global DNA hypomethylation and site-specific CpG island promoter hypermethylation. Long interspersed element-1 (LINE-1) is a repetitive DNA retrotransposon that duplicates via a copy-and-paste genetic mechanism. As LINE-1 constitutes approximately 17% of the human genome, the extent of LINE-1 methylation is regarded as a surrogate marker of global DNA methylation...
February 1, 2018: Digestion
https://www.readbyqxmd.com/read/29382254/methymer-design-of-combinations-of-specific-primers-for-bisulfite-sequencing-of-complete-cpg-islands
#15
George S Krasnov, Nataliya V Melnikova, Valentina A Lakunina, Anastasiya V Snezhkina, Anna V Kudryavtseva, Alexey A Dmitriev
We present MethyMer, a Python-based tool aimed at selecting primers for amplification of complete CpG islands. These regions are difficult in terms of selecting appropriate primers because of their low-complexity, high GC content. Moreover, bisulfite treatment, in fact, leads to the reduction of the 4-letter alphabet (ATGC) to 3-letter one (ATG, except for methylated cytosines), and this also reduces region complexity and increases mispriming potential. MethyMer has a flexible scoring system, which optimizes the balance between various characteristics such as nucleotide composition, thermodynamic features (melting temperature, dimers [Formula: see text]G, etc...
January 30, 2018: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/29374520/evaluation-of-cpg-snps-in-mirna-promoters-and-risk-of-breast-cancer
#16
Jiaping Chen, Yue Jiang, Jing Zhou, Sijun Liu, Na Qin, Jiangbo Du, Guangfu Jin, Zhibin Hu, Hongxia Ma, Hongbing Shen, Juncheng Dai
CpG-SNPs in gene promoter regions are proposed to be associated with multiple diseases. To date, few studies have focused on the associations between CpG-SNPs in miRNA promoters and the risk of breast cancer. In this study, 138 miRNAs differentially expressed between breast cancer and non-cancer tissues (fold change >2, P < 0.05) were identified using The Cancer Genome Atlas (TCGA) Research database. In total, 13 SNPs were selected in the promoters of the miRNAs and were evaluated in a case-control study of Chinese women including 1486 cases and 1519 controls...
January 24, 2018: Gene
https://www.readbyqxmd.com/read/29374078/locus-specific-reversible-dna-methylation-regulates-transient-il-10-expression-in-th1-cells
#17
Won Hwang, Choong-Gu Lee, Changhon Lee, Ravi Verma, Dipayan Rudra, Zee Yong Park, Sin-Hyeog Im
IL-10 is a pleiotropic cytokine with multifaceted functions in establishing immune homeostasis. Although expressed by Th1 and Th2 cells, conventional Th1 cells produce marginal levels of IL-10 compared with their Th2 counterparts. In this study, we investigated the epigenetic mechanisms of Il-10 gene expression in Th1 cells. Bioinformatics EMBOSS CpG plot analysis and bisulfite pyrosequencing revealed three CpG DNA methylation sites in the Il-10 gene locus. Progressive DNA methylation at all of the CpG regions of interest (ROIs) established a repressive program of Il-10 gene expression in Th1 cells...
January 26, 2018: Journal of Immunology: Official Journal of the American Association of Immunologists
https://www.readbyqxmd.com/read/29368212/the-dna-methylome-of-ddr-genes-and-benefit-from-rt-or-tmz-in-idh-mutant-low-grade-glioma-treated-in-eortc-22033
#18
Pierre Bady, Sebastian Kurscheid, Mauro Delorenzi, Thierry Gorlia, Martin J van den Bent, Khê Hoang-Xuan, Élodie Vauléon, Anja Gijtenbeek, Roelien Enting, Brian Thiessen, Olivier Chinot, Frédéric Dhermain, Alba A Brandes, Jaap C Reijneveld, Christine Marosi, Martin J B Taphoorn, Wolfgang Wick, Andreas von Deimling, Pim French, Roger Stupp, Brigitta G Baumert, Monika E Hegi
The optimal treatment for patients with low-grade glioma (LGG) WHO grade II remains controversial. Overall survival ranges from 2 to over 15 years depending on molecular and clinical factors. Hence, risk-adjusted treatments are required for optimizing outcome and quality of life. We aim at identifying mechanisms and associated molecular markers predictive for benefit from radiotherapy (RT) or temozolomide (TMZ) in LGG patients treated in the randomized phase III trial EORTC 22033. As candidate biomarkers for these genotoxic treatments, we considered the DNA methylome of 410 DNA damage response (DDR) genes...
January 24, 2018: Acta Neuropathologica
https://www.readbyqxmd.com/read/29356883/evaluation-of-itgb2-cd18-and-sell-cd62l-genes-expression-and-methylation-of-itgb2-promoter-region-in-patients-with-systemic-sclerosis
#19
Navid Dashti, Mahdi Mahmoudi, Farhad Gharibdoost, Hoda Kavosi, Ramazan Rezaei, Vahideh Imeni, Ahmadreza Jamshidi, Saeed Aslani, Shayan Mostafaei, Mohammad Vodjgani
Systemic sclerosis (SSc), an autoimmune disease of connective tissue, is characterized by inflammation, fibrosis, and vessel endothelial damage. Products of Integrin subunit beta 2 (ITGB2) and selectin L (SELL) genes participate in several functional pathways of immune system. The aim of this investigation was to survey the transcript level of ITGB2 and SELL genes as well as methylation status of CpG sites in promoter region of differently expressed gene in PBMCs of SSc patients. PBMCs were isolated from whole blood of 50 SSc patients and 30 healthy controls...
January 22, 2018: Rheumatology International
https://www.readbyqxmd.com/read/29353016/pyrosequencing-analysis-of-methylation-levels-of-clock-genes-in-leukocytes-from-parkinson-s-disease-patients
#20
Wei Mao, Chunsong Zhao, Hui Ding, Kuo Liang, Jinhua Xue, Piu Chan, Yanning Cai
DNA methylation of neuronal PAS domain protein 2 (NPAS2) and cryptochrome circadian clock 1 (CRY1) promoters may be associated with Parkinson's disease (PD). However, there is no simple and cost-effective method to quantify DNA methylation in these regions. Additionally, it is not clear whether DNA methylation of NPAS2 and CRY1 promoters is altered in peripheral blood of PD patients, especially newly diagnosed drug-naïve PD patients, and thus can be used as a PD biomarker. In the present study, we utilized bisulfite pyrosequencing assays to examine DNA methylation levels of six CpG sites in the NPAS2 promoter and five CpG sites in the CRY1 promoter...
January 17, 2018: Neuroscience Letters
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