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CpG Islands

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https://www.readbyqxmd.com/read/29352321/inflammatory-linked-changes-in-cpg-island-methylation-of-three-opioid-peptide-genes-in-a-rat-model-for-pain
#1
Charlotte Louise Justine Jacobi, Christoph Stein
Expression of the opioid peptide genes proopiomelanocortin (Pomc), proenkephalin (Penk), and prodynorphin (Pdyn), in immune cells plays a key role in endogenous pain control. In a rat model of painful unilateral paw inflammation, we isolated cells from popliteal lymph nodes and evaluated the role of CpG island C5-methylation on the transcriptional activation of those genes. Using methylated DNA immunoprecipitation, we sorted gDNA into methylated (me) and non-me fractions and then determined the CpG island methylation status of each fraction via quantitative Real Time-PCR (qRT-PCR)...
2018: PloS One
https://www.readbyqxmd.com/read/29350455/a-novel-prognostic-six-cpg-signature-in-glioblastomas
#2
An-An Yin, Nan Lu, Amandine Etcheverry, Marc Aubry, Jill Barnholtz-Sloan, Lu-Hua Zhang, Jean Mosser, Wei Zhang, Xiang Zhang, Yu-He Liu, Ya-Long He
AIMS: We aimed to identify a clinically useful biomarker using DNA methylation-based information to optimize individual treatment of patients with glioblastoma (GBM). METHODS: A six-CpG panel was identified by incorporating genome-wide DNA methylation data and clinical information of three distinct discovery sets and was combined using a risk-score model. Different validation sets of GBMs and lower-grade gliomas and different statistical methods were implemented for prognostic evaluation...
January 19, 2018: CNS Neuroscience & Therapeutics
https://www.readbyqxmd.com/read/29344148/identification-of-potentially-critical-differentially-methylated-genes-in-nasopharyngeal-carcinoma-a-comprehensive-analysis-of-methylation-profiling-and-gene-expression-profiling
#3
Lian Hui, Jingru Zhang, Xiaoxu Ding, Xing Guo, Xuejun Jang
The present study aimed to identify potentially critical differentially methylated genes associated with the progression of nasopharyngeal carcinoma (NPC). Methylation profiling data of GSE62336 deposited in the Gene Expression Omnibus database were used to identify differentially methylated regions (DMRs) and differentially methylated CpG islands (DMIs). Concurrently, differentially expressed genes (DEGs) were identified using a meta-analysis of three gene expression datasets (GSE53819, GSE13597 and GSE12452)...
December 2017: Oncology Letters
https://www.readbyqxmd.com/read/29342962/functional-analyses-of-runx3-and-camkiin%C3%AE-in-ovarian-cancer-cell-lines-reveal-tumor-suppressive-functions-for-camkiin%C3%AE-and-dichotomous-roles-for-runx3-transcript-variants
#4
Karolin Heinze, Daniel Kritsch, Alexander S Mosig, Matthias Dürst, Norman Häfner, Ingo B Runnebaum
(1) Background: Epithelial ovarian cancer (EOC) is the most lethal cancer of the female reproductive system. In an earlier study, we identified multiple genes as hypermethylated in tumors of patients with poor prognosis. The most promising combination of markers to predict a patient's outcome was CaMKIINα and RUNX3. Aim of this study was to functionally validate the importance of both genes. (2) Methods: IC50 measurements, cell cycle distribution-, proliferation, and migration experiments were conducted after transgene overexpression in two EOC cell lines...
January 15, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29341861/genome-wide-survey-reveals-dynamic-effects-of-folate-supplement-on-dna-methylation-and-gene-expression-during-c2c12-differentiation
#5
Yi Li, Qiang Feng, Miao Guo, Yuding Wang, Yunliang Jiang, Jinyi Xing
Folic acid supplements during pregnancy can prevent neural tube defects and other developmental abnormalities. Here, we explored the effects of folate supplement on gene expression and DNA methylation during C2C12 differentiation. Based on the folic acid concentration, this study comprised three groups: low folate (L), normal folate (N), and high-folate supplement (H). Our analyses revealed that differentiation and the mRNA expression of myogenin in C2C12 cell were enhanced by folic acid, however, the overall methylation percentage in myogenin promoter between different treatment groups was not significantly different (P>0...
January 12, 2018: Physiological Genomics
https://www.readbyqxmd.com/read/29341152/meta-analysis-of-the-prognostic-value-of-cpg-island-methylator-phenotype-in-gastric-cancer
#6
REVIEW
A G M T Powell, S Soul, A Christian, W G Lewis
BACKGROUND: CpG island methylator phenotype (CIMP) has been identified as a distinct molecular subtype of gastric cancer, yet associations with survival are conflicting. A meta-analysis was performed to estimate the prognostic significance of CIMP. METHODS: Embase, MEDLINE, PubMed, PubMed Central and Cochrane databases were searched systematically for studies related to the association between CIMP and survival in patients undergoing potentially curative resection for gastric cancer...
January 2018: British Journal of Surgery
https://www.readbyqxmd.com/read/29339976/detection-of-dioxin-induced-demethylation-of-mouse-cyp1a1-gene-promoter-by-a-new-labeling-method-for-short-dna-fragments-possessing-5-methylcytosine-at-the-end
#7
Hisaka Kurita, Toshiki Aiba, Toshiyuki Saito, Seiichiroh Ohsako
Environmental factors stimulate alteration of DNA methylation level. Investigation of the genome-wide DNA methylation status is important for environmental health studies. We here designed a genomic DNA amplification and labeling protocol using a methylation-sensitive restriction enzyme HinP1 I. This method can specifically amplify genomic DNA fragments possessing methyl-CpG at the end. The fragments are a relatively short size and dominantly located on CpG-islands. By using the samples prepared by this method, a dioxin-induced change in the methylation level of the mouse Cyp1a1 promoter was successfully evaluated using oligonucleotide probes covalently bound onto a glass plate...
2018: Genes and Environment: the Official Journal of the Japanese Environmental Mutagen Society
https://www.readbyqxmd.com/read/29339652/smoking-and-promoter-specific-deoxyribonucleic-acid-methylation-of-the-atrial-natriuretic-peptide-gene-methylation-of-smokers-and-non-smokers-differs-significantly-during-withdrawal
#8
Alexander Glahn, Mathias Rhein, Helge Frieling, Rilana Schuster, Alain El Aissami, Stefan Bleich, Thomas Hillemacher, Marc Muschler
BACKGROUND: Atrial natriuretic peptide (ANP) is well known in psychiatric disorders to modulate hypothalamic-pituitary-adrenal axis activity. Disturbances of ANP have been described in early abstinent alcohol-dependent patients. This is the first longitudinal investigation on cytosine-phosphatidyl-guanine (CpG)-island promoter methylation of the ANP gene in the blood of tobacco-dependent patients. METHODS: In a longitudinal approach, we investigated whether changes in ANP serum levels correlated to CpG methylation of the respective gene promoters on days 1, 7, and 14 of tobacco withdrawal...
January 16, 2018: European Addiction Research
https://www.readbyqxmd.com/read/29339171/dna-methylation-level-of-the-neprilysin-promoter-in-alzheimer-s-disease-brains
#9
Kenichi Nagata, Tatsuo Mano, Shigeo Murayama, Takaomi C Saido, Atsushi Iwata
Neprilysin (NEP), a membrane-bound metalloprotease, has been shown to play an essential role in the clearance of amyloid beta (Aβ) peptides. Previous studies have reported that NEP expression is downregulated in the normal aging brain as well as in the Alzheimer's disease (AD) brain, providing evidence that the downregulation of NEP expression contributes to the age-dependent deposition of Aβ-containing plaques, a pathological hallmark of AD. However, the mechanisms underlying the downregulation remain unclear...
January 12, 2018: Neuroscience Letters
https://www.readbyqxmd.com/read/29337882/functional-analysis-of-promoters-from-three-subtypes-of-the-pi3k-family-and-their-roles-in-the-regulation-of-lipid-metabolism-by-insulin-in-yellow-catfish-pelteobagrus-fulvidraco
#10
Mei-Qin Zhuo, Zhi Luo, Yi-Huan Xu, Dan-Dan Li, Ya-Xiong Pan, Kun Wu
In the present study, the length of 360, 1848 and 367 bp sequences of promoters from three subtypes of PI3K family (PI3KCa, PI3KC2b and PI3KC3) of yellow catfish Pelteobagrus fulvidraco were cloned and characterized. Bioinformatics analysis revealed that PI3KCa, PI3KC2b and PI3KC3 had different structures in their core promoter regions. The promoter regions of PI3KCa and PI3KC2b had CpG islands but no CAAT and TATA box. In contrast, the promoter of PI3KC3 had the canonical TATA and CAAT box but no CpG island...
January 16, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29334402/noninvasive-reconstruction-of-placental-methylome-from-maternal-plasma-dna-potential-for-prenatal-testing-and-monitoring
#11
Kun Sun, Fiona M F Lun, Tak Y Leung, Rossa W K Chiu, Y M Dennis Lo, Hao Sun
OBJECTIVE: During human pregnancy, the DNA methylation of placental tissue is highly relevant to the normal growth and development of the fetus, therefore methylomic analysis of the placental tissue possesses high research and clinical value in prenatal testing and monitoring. Thus our aim is to develop an approach for reconstruction of the placental methylome, which should be completely noninvasive and achieve high accuracy and resolution. RESULTS: We propose a novel size-based algorithm, FEMER, to noninvasively reconstruct the placental methylome by genomewide bisulfite sequencing and size-based analysis of maternal plasma DNA...
January 15, 2018: Prenatal Diagnosis
https://www.readbyqxmd.com/read/29333422/epigenetic-inactivation-of-runx3-in-colorectal-cancer
#12
Eung Jin Shin, Han Jo Kim, Myoung Won Son, Tae Sung Ahn, Hyun Yong Lee, Dae Ro Lim, Sang Byung Bae, Seob Jeon, Hyungjoo Kim, Dongjun Jeong, Moon Soo Lee, Dong-Sun Kim, Jeong Se Noh, Moo-Jun Baek
Purpose: Emerging evidence indicates that runt-related transcription factor 3 (RUNX3) is an important tumor suppressor gene in several cancer types, including colorectal cancer (CRC). However, the clinical significance of RUNX3 inactivation in CRC remains unclear. The aim of this study was to examine the correlation between clinicopathologic factors and RUNX3 hypermethylation/expression in CRC. Methods: Sixty-two CRC patients who were treated at the Soonchunhyang University College of Medicine were recruited in this study...
January 2018: Annals of Surgical Treatment and Research
https://www.readbyqxmd.com/read/29325057/tumor-purity-quantification-by-clonal-dna-methylation-signatures
#13
Matteo Benelli, Dario Romagnoli, Francesca Demichelis
Motivation: Controlling for tumor purity in molecular analyses is essential to allow for reliable genomic aberration calls, for inter-sample comparison and to monitor heterogeneity of cancer cell populations. In genome wide screening studies, the assessment of tumor purity is typically performed by means of computational methods that exploit somatic copy number aberrations (SCNAs). Results: We present a strategy, called PAMES (Purity Assessment from clonal MEthylation Sites), which uses the methylation level of a few dozen, highly clonal, tumor type specific CpG sites to estimate the purity of tumor samples, without the need of a matched benign control...
January 8, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29322419/analysis-of-dna-methylation-in-tissues-exposed-to-inflammation
#14
Naoko Hattori, Toshikazu Ushijima
Induction of aberrant DNA methylation is one of the most important mechanisms mediating the effect of inflammation on cancer development. Aberrant methylation of promoter CpG islands of tumor suppressor genes can silence their downstream genes, and that in cancer tissues is associated with prognosis or therapeutic effects. In addition, aberrant methylation can occur in tissues exposed to specific types of inflammation, producing a so-called "epigenetic field for cancerization," and its accumulation is correlated with cancer risk...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29321608/the-effect-of-maternal-vitamin-d-deficiency-during-pregnancy-on-body-fat-and-adipogenesis-in-rat-offspring
#15
Juan Wen, Qin Hong, Xingyun Wang, Lijun Zhu, Tianqi Wu, Pengfei Xu, Ziyi Fu, Lianghui You, Xing Wang, Chenbo Ji, Xirong Guo
To evaluate the effects of maternal vitamin D deficiency on body fat and adipogenesis in offspring rats, and explore the potential mechanism, we constructed a vitamin D deficient rat model and performed metabolic activity evaluation, body fat monitoring, biochemical analysis, adipogenesis assay, methylation microarray and RNA-seq for their offspring rats. We found the weight of vitamin D deficient (VDD) offspring was gradually higher than that of control (CLT) offspring, and the difference was significant since 10 weeks old...
January 10, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29317594/polymorphism-in-tmem132d-regulates-expression-and-anxiety-related-behavior-through-binding-of-rna-polymerase-ii-complex
#16
Roshan R Naik, Sergey V Sotnikov, Rebekka P Diepold, Stella Iurato, Patrick O Markt, Andrea Bultmann, Nadine Brehm, Tobias Mattheus, Beat Lutz, Angelika Erhardt, Elisabeth B Binder, Ulrike Schmidt, Florian Holsboer, Rainer Landgraf, Ludwig Czibere
TMEM132D is a candidate gene, where risk genotypes have been associated with anxiety severity along with higher mRNA expression in the frontal cortex of panic disorder patients. Concurrently, in a high (HAB) and low (LAB) trait anxiety mouse model, Tmem132d was found to show increased expression in the anterior cingulate cortex (aCC) of HAB as compared to LAB mice. To understand the molecular underpinnings underlying the differential expression, we sequenced the gene and found two single-nucleotide polymorphisms (SNPs) in the promoter differing between both lines which could explain the observed mRNA expression profiles using gene reporter assays...
January 10, 2018: Translational Psychiatry
https://www.readbyqxmd.com/read/29313708/human-lung-dna-methylation-quantitative-trait-loci-colocalize-with-copd-genome-wide-association-loci
#17
Jarrett D Morrow, Kimberly Glass, Michael H Cho, Craig P Hersh, Victor Pinto-Plata, Bartolome Celli, Nathaniel Marchetti, Gerard Criner, Raphael Bueno, George Washko, Augustine M K Choi, John Quackenbush, Edwin K Silverman, Dawn L DeMeo
RATIONALE: As the third leading cause of death in the United States, the impact of chronic obstructive pulmonary disease (COPD) makes identification of its molecular mechanisms of great importance. Genome-wide association studies have identified multiple genomic regions associated with COPD. However, genetic variation only explains a small fraction of the susceptibility to COPD and sub-genome-wide significant loci may play a role in pathogenesis. OBJECTIVES: Regulatory annotation with epigenetic evidence may give priority for further investigation, particularly for GWAS associations in non-coding regions...
January 9, 2018: American Journal of Respiratory and Critical Care Medicine
https://www.readbyqxmd.com/read/29310712/genome-wide-screening-of-dna-methylation-in-bovine-blastocysts-with-different-kinetics-of-development
#18
Jessica Ispada, Camila Bruna de Lima, Marc-André Sirard, Patrícia Kubo Fontes, Marcelo Fábio Gouveia Nogueira, Kelly Annes, Marcella Pecora Milazzotto
BACKGROUND: The timing of the first cell divisions may predict the developmental potential of an embryo, including its ability to establish pregnancy. Besides differences related to metabolism, stress, and survival, embryos with different speeds of development present distinct patterns of gene expression, mainly related to energy and lipid metabolism. As gene expression is regulated by epigenetic factors, and that includes DNA methylation patterns, in this study we compared the global DNA methylation profile of embryos with different kinetics of development in order to identify general pathways and regions that are most influenced by this phenotype...
January 8, 2018: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/29298087/quantitative-evaluation-of-mmp-9-and-timp-1-promoter-methylation-in-chronic-periodontitis
#19
Xiting Li, Jiaxuan Lu, Wei Teng, Chuanjiang Zhao, Xiaolei Ye
In this study, we investigated the promoter DNA methylation (DNAm) status of the MMP-9 and TIMP-1 genes in patients with chronic periodontitis to evaluate disease progression. Using pyrosequencing technology, DNAm levels of MMP-9 and TIMP-1 CpG islands were measured in 88 chronic periodontitis patients and 15 healthy controls. We found a positive correlation between methylation levels of MMP-9 CpG islands and the severity of chronic periodontitis. Methylated CpG islands were also closely associated with the duration of chronic periodontitis...
January 3, 2018: DNA and Cell Biology
https://www.readbyqxmd.com/read/29296220/sequencing-of-lynch-syndrome-tumors-reveals-the-importance-of-epigenetic-alterations
#20
Noora Porkka, Satu Valo, Taina T Nieminen, Alisa Olkinuora, Satu Mäki-Nevala, Samuli Eldfors, Päivi Peltomäki
Genomic instability and epigenetic aberrations are important classifiers of human tumors, yet, their interrelations are poorly understood. We used Lynch syndrome (LS) to address such relationships. Forty-five tumors (11 colorectal adenomas, 18 colorectal carcinomas, and 16 ovarian carcinomas) were profiled for CpG Island Methylator Phenotype (CIMP) and somatic mutations. All tumors showed high-degree microsatellite instability. Panel sequencing of 578 cancer-relevant genes revealed the average number of 1433, 1124, and 657 non-synonymous somatic mutations per colorectal adenoma, colorectal carcinoma, and ovarian carcinoma, respectively...
December 8, 2017: Oncotarget
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