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Methylation of sites CpG in promoter

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https://www.readbyqxmd.com/read/29030974/dopamine-transporter-gene-methylation-is-associated-with-nucleus-accumbens-activation-during-reward-processing-in-healthy-but-not-alcohol-dependent-individuals
#1
Christine Muench, Corinde E Wiers, Carlos R Cortes, Reza Momenan, Falk W Lohoff
BACKGROUND: Alcohol's reinforcement is mediated by dopamine signaling in the ventral striatum, which is modulated by the dopamine transporter (DAT). We hypothesized that methylomic variation in the DAT gene (SLC6A3) affects DAT expression thus contributing to differences in brain reward circuitry in individuals with alcohol dependence (ALC). METHODS: Blood from 45 recently detoxified ALC and 45 healthy control (HC) individuals was used to assess DNA methylation across 5 functional regions of SLC6A3...
October 14, 2017: Alcoholism, Clinical and Experimental Research
https://www.readbyqxmd.com/read/29029492/gata2-regulates-the-erythropoietin-receptor-in-t-12-21-all
#2
Marie E Gaine, Daniel J Sharpe, James S Smith, Hilary A A Colyer, Vivien M Hodges, Terry R Lappin, Ken I Mills
The t(12;21) (p13;q22) chromosomal translocation resulting in the ETV6/RUNX1 fusion gene is the most frequent structural cytogenetic abnormality in children with acute lymphoblastic leukemia (ALL). The erythropoietin receptor (EPOR), usually associated with erythroid progenitor cells, is highly expressed in ETV6/RUNX1 positive cases compared to other B-lineage ALL subtypes. Gene expression analysis of a microarray database and direct quantitative analysis of patient samples revealed strong correlation between EPOR and GATA2 expression in ALL, and higher expression of GATA2 in t(12;21) patients...
September 12, 2017: Oncotarget
https://www.readbyqxmd.com/read/29028809/nasal-dna-methylation-differentiates-corticosteroid-treatment-response-in-pediatric-asthma-a-pilot-study
#3
Xue Zhang, Jocelyn M Biagini Myers, Veda K Yadagiri, Ashley Ulm, Xiaoting Chen, Matthew T Weirauch, Gurjit K Khurana Hershey, Hong Ji
BACKGROUND: Treatment response to systemic corticosteroid in asthmatic children is heterogeneous and may be mediated by epigenetic mechanism(s). We aim to identify DNA methylation (DNAm) changes responsive to steroid, and DNAm biomarkers that distinguish treatment response. MATERIALS AND METHODS: We followed 33 children (ages 5-18) presenting to the Emergency Department (ED) for asthma exacerbation. Based on whether they met discharge criteria in ≤24 hours, participants were grouped into good and poor responders to steroid treatment...
2017: PloS One
https://www.readbyqxmd.com/read/29019275/identification-of-dna-methylation-and-transcriptional-regulatory-regions-in-the-promoter-of-duck-retinoic-acid-inducible-gene-i-rig-i
#4
Y U Zhang, Yang Chen, Qi Xu, Ran Liu, Ningzhao Wu, Guohong Chen
1. The aim of this study was to identify the active control area of the duck RIG-I core promoter, to predict the binding sites of transcription factors, and to provide a theoretical basis for the study of duck RIG-I function and mechanism of regulation. 2. The promoter region of duRIG-I was obtained from Ensembl; the CpG island in the duRIG-I promoter was predicted online; and the methylation status of the duRIG-I promoter was detected by the bisulphite sequencing PCR (BSP) method. 3. There was an obvious CpG island in the duRIG-I promoter, with a total of 44 CG dinucleotides...
October 11, 2017: British Poultry Science
https://www.readbyqxmd.com/read/28985495/mendelian-randomization-analysis-identifies-cpg-sites-as-putative-mediators-for-genetic-influences-on-cardiovascular-disease-risk
#5
Tom G Richardson, Jie Zheng, George Davey Smith, Nicholas J Timpson, Tom R Gaunt, Caroline L Relton, Gibran Hemani
The extent to which genetic influences on cardiovascular disease risk are mediated by changes in DNA methylation levels has not been systematically explored. We developed an analytical framework that integrates genetic fine mapping and Mendelian randomization with epigenome-wide association studies to evaluate the causal relationships between methylation levels and 14 cardiovascular disease traits. We identified ten genetic loci known to influence proximal DNA methylation which were also associated with cardiovascular traits after multiple-testing correction...
October 5, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28979808/analysis-of-bladder-cancer-tumor-cpg-methylation-and-gene-expression-within-the-cancer-genome-atlas-identifies-gria1-as-a-prognostic-biomarker-for-basal-like-bladder-cancer
#6
Sloane K Tilley, William Y Kim, Rebecca C Fry
Increased methylation levels at cytosines proximal to guanines (CpG) in the promoter regions of tumor suppressor genes have been reported to play an important role in the development and progression of bladder cancer. In this study, we conducted a genome-wide analysis using data from The Cancer Genome Atlas to better characterize CpG methylation and mRNA expression patterns in urothelial carcinomas and to identify new epigenetic biomarkers of survival. Across 408 tumors, we identified 223 genes that displayed significant relationships between CpG methylation and mRNA expression levels...
2017: American Journal of Cancer Research
https://www.readbyqxmd.com/read/28977914/potential-link-between-fusobacterium-enrichment-and-dna-methylation-accumulation-in-the-inflammatory-colonic-mucosa-in-ulcerative-colitis
#7
Tomomitsu Tahara, Ichiro Hirata, Naoko Nakano, Sayumi Tahara, Noriyuki Horiguchi, Tomohiko Kawamura, Masaaki Okubo, Takamitsu Ishizuka, Hyuga Yamada, Dai Yoshida, Takafumi Ohmori, Kohei Maeda, Naruomi Komura, Hirokazu Ikuno, Yasutaka Jodai, Toshiaki Kamano, Mitsuo Nagasaka, Yoshihito Nakagawa, Tetsuya Tuskamoto, Makoto Urano, Tomoyuki Shibata, Makoto Kuroda, Naoki Ohmiya
BACKGROUND AND AIM: Fusobacterium enrichment has been associated with colorectal cancer development. Ulcerative colitis (UC) associated tumorigenesis is characterized as high degree of methylation accumulation through continuous colonic inflammation. The aim of this study was to investigate a potential link between Fusobacterium enrichment and DNA methylation accumulation in the inflammatory colonic mucosa in UC. METHODS: In the candidate analysis, inflamed colonic mucosa from 86 UC patients were characterized the methylation status of colorectal a panel of cancer related 24 genes...
September 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/28968778/neuronal-expression-of-opioid-gene-is-controlled-by-dual-epigenetic-and-transcriptional-mechanism-in-human-brain
#8
Igor Bazov, Daniil Sarkisyan, Olga Kononenko, Hiroyuki Watanabe, Mumtaz Malik Taqi, Lada Stålhandske, Dineke S Verbeek, Jan Mulder, Grazyna Rajkowska, Donna Sheedy, Jillian Kril, Xueguang Sun, Ann-Christine Syvänen, Tatiana Yakovleva, Georgy Bakalkin
Molecular mechanisms that define patterns of neuropeptide expression are essential for the formation and rewiring of neural circuits. The prodynorphin gene (PDYN) gives rise to dynorphin opioid peptides mediating depression and substance dependence. We here demonstrated that PDYN is expressed in neurons in human dorsolateral prefrontal cortex (dlPFC), and identified neuronal differentially methylated region in PDYN locus framed by CCCTC-binding factor binding sites. A short, nucleosome size human-specific promoter CpG island (CGI), a core of this region may serve as a regulatory module, which is hypomethylated in neurons, enriched in 5-hydroxymethylcytosine, and targeted by USF2, a methylation-sensitive E-box transcription factor (TF)...
July 28, 2017: Cerebral Cortex
https://www.readbyqxmd.com/read/28967952/real-time-methylation-specific-polymerase-chain-reaction-for-mgmt-promoter-methylation-clinical-testing-in-glioblastoma-an-alternative-detection-method-for-a-heterogeneous-process
#9
Cristiane M Ida, Malinda L Butz, Robert B Jenkins, Jann N Sarkaria, Gaspar J Kitange, Caterina Giannini, Benjamin R Kipp
Objectives: To develop and evaluate a real-time methylation-specific polymerase chain reaction (RT-MSP) MGMT assay, with a particular focus on small biopsies and indeterminate testing results. Methods: We assessed formalin-fixed paraffin-embedded glioblastoma or gliosarcoma specimens (n = 641). A test-validation group (n = 51) with previously obtained reference laboratory (RL) results was used to determine performance characteristics of the RT-MSP assay. An indeterminate (equivocal) category was established for cases that could not be clearly classified as positive or negative...
October 1, 2017: American Journal of Clinical Pathology
https://www.readbyqxmd.com/read/28959253/methylation-of-the-vitamin-d-receptor-vdr-gene-together-with-genetic-variation-race-and-environment-influence-the-signaling-efficacy-of-the-toll-like-receptor-2-1-vdr-pathway
#10
Vanessa Meyer, Donovan Sean Saccone, Fidele Tugizimana, Furaha Florence Asani, Tamsyn Jacki Jeffery, Liza Bornman
BACKGROUND: The disparity in prevalence of infectious diseases across the globe is common knowledge. Vitamin D receptor (VDR)-mediated toll-like receptor (TLR) 2/1 signaling produces antimicrobial peptides, which is critical as a first line of defense in innate immunity. Numerous studies disclosed the independent role of genetic polymorphisms in this pathway, vitamin D status or season and more recently epigenetics, as factors contributing to infectious disease predisposition. Few studies address the interaction between environment, genetics, and epigenetics...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/28958754/kiaa0319-promoter-dna-methylation-predicts-dichotic-listening-performance-in-forced-attention-conditions
#11
Judith Schmitz, Robert Kumsta, Dirk Moser, Onur Güntürkün, Sebastian Ocklenburg
Language lateralization is one of the most prominent examples of functional hemispheric asymmetries. Previous studies indicate a significant contribution of factors not related to DNA sequence variation on the development of language lateralization, but the molecular processes underlying this relation are unclear. The Brandler-Paracchini model of hemispheric asymmetries assumes that genes involved in the establishment of ciliogenesis and bodily asymmetries also affect functional hemispheric asymmetries. Thus, genes implicated in this model represent a key target for epigenetic modulation of language lateralization...
September 25, 2017: Behavioural Brain Research
https://www.readbyqxmd.com/read/28957329/uncovering-the-dna-methylation-landscape-in-key-regulatory-regions-within-the-fads-cluster
#12
Elaheh Rahbar, Hannah C Ainsworth, Timothy D Howard, Gregory A Hawkins, Ingo Ruczinski, Rasika Mathias, Michael C Seeds, Susan Sergeant, James E Hixson, David M Herrington, Carl D Langefeld, Floyd H Chilton
Genetic variants near and within the fatty acid desaturase (FADS) cluster are associated with polyunsaturated fatty acid (PUFA) biosynthesis, levels of several disease biomarkers and risk of human disease. However, determining the functional mechanisms by which these genetic variants impact PUFA levels remains a challenge. Utilizing an Illumina 450K array, we previously reported strong allele-specific methylation (ASM) associations (p = 2.69×10-29) between a single nucleotide polymorphism (SNP) rs174537 and DNA methylation of CpG sites located in the putative enhancer region between FADS1 and FADS2, in human liver tissue...
2017: PloS One
https://www.readbyqxmd.com/read/28954414/alpha-lipoic-acid-downregulates-il-1%C3%AE-and-il-6-by-dna-hypermethylation-in-sk-n-be-neuroblastoma-cells
#13
Simona Dinicola, Sara Proietti, Alessandra Cucina, Mariano Bizzarri, Andrea Fuso
Alpha-lipoic acid (ALA) is a pleiotropic molecule with antioxidant and anti-inflammatory properties, of which the effects are exerted through the modulation of NF-kB. This nuclear factor, in fact, modulates different inflammatory cytokines, including IL-1b and IL-6, in different tissues and cell types. We recently showed that IL-1b and IL-6 DNA methylation is modulated in the brain of Alzheimer's disease patients, and that IL-1b expression is associated to DNA methylation in the brain of patients with tuberous sclerosis complex...
September 26, 2017: Antioxidants (Basel, Switzerland)
https://www.readbyqxmd.com/read/28952189/irf7-gene-expression-profile-and-methylation-of-its-promoter-region-in-patients-with-systemic-sclerosis
#14
Ramazan Rezaei, Mahdi Mahmoudi, Farhad Gharibdoost, Hoda Kavosi, Navid Dashti, Vahideh Imeni, Ahmadreza Jamshidi, Saeed Aslani, Shayan Mostafaei, Mohammad Vodjgani
OBJECTIVE: The aim of the current study was to evaluate if methylation status of CpG sites of interferon regulatory factor 7 (IRF7) promoter in peripheral blood mononuclear cells (PBMCs) of systemic sclerosis (SSc) patients is involved in pathogenesis of the disease. METHODS: PBMCs were isolated from whole blood of 50 SSc patients and 30 controls. After the extraction of total RNA and DNA contents from PBMCs, complementary DNA (cDNA) was synthesized. Afterwards, quantitative analysis of IRF7 messenger RNA (mRNA) was conducted by real-time polymerase chain reaction (PCR)...
September 26, 2017: International Journal of Rheumatic Diseases
https://www.readbyqxmd.com/read/28951969/quantitative-evaluation-of-the-relationship-between-comp-promoter-methylation-and-the-susceptibility-and-curve-progression-of-adolescent-idiopathic-scoliosis
#15
Sai-Hu Mao, Bang-Ping Qian, Benlong Shi, Ze-Zhang Zhu, Yong Qiu
PURPOSE: The cartilage oligomeric matrix protein (COMP) was reported to be down-regulated in adolescent idiopathic scoliosis (AIS). The purposes of the study were to evaluate the roles of COMP promoter methylation on the abnormal gene expression and the epigenetic phenotype in AIS. METHODS: DNA samples of 50 AIS patients and 50 healthy controls were analyzed. Five CpG sites of COMP gene were amplified and sequenced using the polymerase chain reaction (PCR) and the pyrophosphate sequencing technology, while the COMP gene expression was evaluated using real-time PCR...
September 26, 2017: European Spine Journal
https://www.readbyqxmd.com/read/28943934/l-securinine-inhibits-the-proliferation-of-a549-lung-cancer-cells-and-promotes-dkk1-promoter-methylation
#16
Shuwen Han, Xi Yang, Yuefen Pan, Quan Qi, Junjun Shen, Huifen Fang, Zhaoning Ji
L-securinine is a natural product extracted and isolated from the leaf of dried Securinega suffruticosa. The aim of the present study was to explore the effects of L-securinine on proliferation, and the methylation profile of the dickkopf-related protein 1 (DKK1) gene in human lung cancer cells and fibroblasts. L-securinine was extracted, isolated and the structure was identified. The cytotoxicity of L-securinine in A549 cells was evaluated by Cell Counting Kit-8 assays. The expression and DNA methylation profile of DKK genes was analyzed by reverse transcription-quantitative polymerase chain reaction and bisulfite sequencing polymerase chain reaction, respectively...
October 2017: Oncology Letters
https://www.readbyqxmd.com/read/28938548/promoter-dna-methylation-analysis-reveals-a-combined-diagnosis-of-cpg-based-biomarker-for-prostate-cancer
#17
Yuanyuan Tang, Shusuan Jiang, Yinmin Gu, Weidong Li, Zengnan Mo, Yuanjie Huang, Tianyu Li, Yanling Hu
BACKGROUND: Prostate cancer (PCa) is the most common tumor in elderly men. However, the specificity and sensitivity of serum prostate-specific antigen levels in PCa diagnosis are controversial. This study aims to reveal a novel diagnosis biomarker in PCa. MATERIALS AND METHODS: The differential methylated CpG sites between 423 primary PCa and 39 adjacent samples from The Cancer Genome Atlas (TCGA) on Illumina HumanMethylation 450 platform were analyzed. The diagnostic methylation markers were mined using the Prediction Analysis of Microarrays package in Bioconductor...
August 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/28924038/passive-dna-demethylation-preferentially-up-regulates-pluripotency-related-genes-and-facilitates-the-generation-of-induced-pluripotent-stem-cells
#18
Songwei He, Hao Sun, Lilong Lin, Yixin Zhang, Jinlong Chen, Lining Liang, Yuan Li, Mengdan Zhang, Xiao Yang, Xiaoshan Wang, Fuhui Wang, Feiyan Zhu, Jiekai Chen, Duanqing Pei, Hui Zheng
A high proliferation rate has been observed to facilitate somatic cell reprogramming, but the pathways that connect proliferation and reprogramming have not been reported. DNA methyltransferase 1 (DNMT1) methylates hemimethylated CpG sites produced during S phase and maintains stable inheritance of DNA methylation. Impairing this process results in passive DNA demethylation. In this study, we show that the cell proliferation rate positively correlated with the expression of Dnmt1 in G1 phase. In addition, as determined by whole genome bisulfate sequencing and high-performance liquid chromatography, global DNA methylation of mouse embryonic fibroblasts (MEFs) was significantly higher in G1 phase than in G2/M phase...
September 18, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28898397/genome-wide-dna-methylation-analysis-of-senescence-in-repetitively-infected-memory-ctls-dna-methylation-analysis-of-repetitively-infected-memory-ctls
#19
Jumpei Shosaku
The immune system including antigen-specific CD8 T cells, which are cytotoxic T lymphocytes (CTLs), can acquire the potential of more effective elimination of the pathogen for reinfection. Since memory CTLs could exert protective immunity after the next response, we aimed to elucidate the substantial change of repetitively infected memory CTLs. Currently, DNA methylation status in repetitively infected memory CTLs is still unknown. Therefore, we performed next generation sequencing (NGS) to evaluate methylation status and transcriptional regulation of naive, primary and secondary memory CD8 T cells on the basis of transcription start sites (TSS)...
September 12, 2017: Immunology
https://www.readbyqxmd.com/read/28890397/regulated-expression-of-the-tp%C3%AE-isoform-of-the-human-t-prostanoid-receptor-by-the-tumour-suppressors-foxp1-and-nkx3-1-implications-for-the-role-of-thromboxane-in-prostate-cancer
#20
Aine G O'Sullivan, Sarah B Eivers, Eamon P Mulvaney, B Therese Kinsella
The prostanoid thromboxane (TX)A2 signals through the TPα and TPβ isoforms of T Prostanoid receptor (TP) that are transcriptionally regulated by distinct promoters termed Prm1 and Prm3, respectively, within the TBXA2R gene. We recently demonstrated that expression of TPα and TPβ is increased in PCa, differentially correlating with Gleason grade and with altered CpG methylation of the individual Prm1/Prm3 regions within the TBXA2R. The current study sought to localise the sites of CpG methylation within Prm1 and Prm3, and to identify the main transcription factors regulating TPβ expression through Prm3 in the prostate adenocarcinoma PC-3 and LNCaP cell lines...
September 8, 2017: Biochimica et Biophysica Acta
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