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https://www.readbyqxmd.com/read/30208958/modulation-of-mitochondrial-dna-copy-number-in-a-model-of-glioblastoma-induces-changes-to-dna-methylation-and-gene-expression-of-the-nuclear-genome-in-tumours
#1
Xin Sun, Justin C St John
BACKGROUND: There are multiple copies of mitochondrial DNA (mtDNA) present in each cell type, and they are strictly regulated in a cell-specific manner by a group of nuclear-encoded mtDNA-specific replication factors. This strict regulation of mtDNA copy number is mediated by cell-specific DNA methylation of these replication factors. Glioblastoma multiforme, HSR-GBM1, cells are hyper-methylated and maintain low mtDNA copy number to support their tumorigenic status. We have previously shown that when HSR-GBM1 cells with 50% of their original mtDNA content were inoculated into mice, tumours grew more aggressively than non-depleted cells...
September 12, 2018: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/30135512/alterations-of-63-hub-genes-during-lingual-carcinogenesis-in-c57bl-6j-mice
#2
Hua Liu, Jianjiao Li, Ying Yang, Liu Liu, Lifu Yu, Minsong Tu, Ruihong Yuan, Wanyuan Yue, Qi Luo, Yonghua Ruan, Xiaoming Dai
To identify potential biomarkers of lingual cancer, 75 female C57BL/6J mice were subjected to 16-week oral delivery of 4-nitroquinoline-1-oxide (4NQO; 50 mg/L), with 10 mice used as controls. Lingual mucosa samples representative of normal tissue (week 0) and early (week 12) and advanced (week 28) tumorigenesis were harvested for microarray and methylated DNA immunoprecipitation sequencing (MeDIP-Seq). Combined analysis with Short Time-series Expression Miner (STEM), the Cytoscape plugin cytoHubba, and screening of differentially expressed genes enabled identification of 63 hub genes predominantly altered in the early stage rather than the advanced stage...
August 22, 2018: Scientific Reports
https://www.readbyqxmd.com/read/30086146/methylation-level-inferences-and-detection-of-differential-methylation-with-medip-seq-data
#3
Yan Zhou, Jiadi Zhu, Mingtao Zhao, Baoxue Zhang, Chunfu Jiang, Xiyan Yang
DNA methylation is an essential epigenetic modification involved in regulating the expression of mammalian genomes. A variety of experimental approaches to generate genome-wide or whole-genome DNA methylation data have emerged in recent years. Methylated DNA immunoprecipitation followed by sequencing (MeDIP-seq) is one of the major tools used in whole-genome epigenetic studies. However, analyzing this data in terms of accuracy, sensitivity, and speed still remains an important challenge. Existing methods, such as BATMAN and MEDIPS, analyze MeDIP-seq data by dividing the whole genome into equal length windows and assume that each CpG of the same window has the same methylation level...
2018: PloS One
https://www.readbyqxmd.com/read/30086113/multi-omics-analyses-of-frailty-and-common-widespread-pain-suggest-involvement-of-shared-neurological-pathways
#4
Gregory Livshits, Ida Malkin, Ruth C E Bowyer, Serena Verdi, Jordana Bell, Cristina Menni, Frances M K Williams, Claire J Steves
Common widespread pain (CWP) and frailty are prevalent conditions in older people. We have shown previously that interindividual variation in frailty and CWP is genetically determined. We also reported an association of frailty and CWP caused by shared genetic and common environmental factors. The aim of the present study was to use omic approaches to identify molecular genetic factors underlying the heritability of frailty and its genetic correlation with CWP.Frailty was quantified through the Rockwood Frailty Index (FI) as a proportion of deficits from 33 binary health deficit questions in 3626 female twins...
August 6, 2018: Pain
https://www.readbyqxmd.com/read/30029672/epigenomic-profiling-of-non-small-cell-lung-cancer-xenografts-uncover-lrp12-dna-methylation-as-predictive-biomarker-for-carboplatin-resistance
#5
Sabrina Grasse, Matthias Lienhard, Steffen Frese, Martin Kerick, Anne Steinbach, Christina Grimm, Michelle Hussong, Jana Rolff, Michael Becker, Felix Dreher, Uwe Schirmer, Stefan Boerno, Anna Ramisch, Gunda Leschber, Bernd Timmermann, Christian Grohé, Heike Lüders, Martin Vingron, Iduna Fichtner, Sebastian Klein, Margarete Odenthal, Reinhard Büttner, Hans Lehrach, Holger Sültmann, Ralf Herwig, Michal R Schweiger
BACKGROUND: Non-small cell lung cancer (NSCLC) is the most common cause of cancer-related deaths worldwide and is primarily treated with radiation, surgery, and platinum-based drugs like cisplatin and carboplatin. The major challenge in the treatment of NSCLC patients is intrinsic or acquired resistance to chemotherapy. Molecular markers predicting the outcome of the patients are urgently needed. METHODS: Here, we employed patient-derived xenografts (PDXs) to detect predictive methylation biomarkers for platin-based therapies...
July 20, 2018: Genome Medicine
https://www.readbyqxmd.com/read/29986310/folic-acid-supplementation-alters-the-dna-methylation-profile-and-improves-insulin-resistance-in-high-fat-diet-fed-mice
#6
Wei Li, Renqiao Tang, Feifei Ma, Shengrong Ouyang, Zhuo Liu, Jianxin Wu
Folic acid (FA) supplementation may protect from obesity and insulin resistance, the effects and mechanism of FA on chronic high-fat-diet-induced obesity-related metabolic disorders are not well elucidated. We adopted a genome-wide approach to directly examine whether FA supplementation affects the DNA methylation profile of mouse adipose tissue and identify the functional consequences of these changes. Mice were fed a high-fat diet (HFD), normal diet (ND) or an HFD supplemented with folic acid (20 μg/ml in drinking water) for 10 weeks, epididymal fat was harvested, and genome-wide DNA methylation analyses were performed using methylated DNA immunoprecipitation sequencing (MeDIP-seq)...
September 2018: Journal of Nutritional Biochemistry
https://www.readbyqxmd.com/read/29899524/microrna-30-modulates-metabolic-inflammation-by-regulating-notch-signaling-in-adipose-tissue-macrophages
#7
Kathryn Miranda, Xiaoming Yang, Marpe Bam, E Angela Murphy, Prakash S Nagarkatti, Mitzi Nagarkatti
BACKGROUND/OBJECTIVES: Obesity is a pandemic disorder that is characterized by accumulation of adipose tissue and chronic low-grade inflammation that is driven primarily by adipose tissue macrophages (ATMs). While ATM polarization from pro-(M1) to anti-(M2) inflammatory phenotype influences insulin sensitivity and energy expenditure, the mechanisms of such a switch are unclear. In the current study, we identified epigenetic pathways including microRNAs (miR) in ATMs that regulate obesity-induced inflammation...
June 13, 2018: International Journal of Obesity: Journal of the International Association for the Study of Obesity
https://www.readbyqxmd.com/read/29775429/genome-wide-dna-methylation-profiles-of-porcine-ovaries-in-estrus-and-proestrus
#8
Xiaolong Zhou, Songbai Yang, Feifei Yan, Ke He, Ayong Zhao
DNA methylation is an important epigenetic modification involved in the estrous cycle and the regulation of reproduction. Here, we investigated the genome-wide profiles of DNA methylation in porcine ovaries in proestrus and estrus using methylated DNA immunoprecipitation sequencing. The results showed that DNA methylation was enriched in intergenic and intron regions. The methylation levels of coding regions were higher than those of the 5'- and 3'-flanking regions of genes. There were 4,813 differentially methylated regions (DMRs) of CpG islands in the estrus vs...
September 1, 2018: Physiological Genomics
https://www.readbyqxmd.com/read/29752693/effects-of-zhizi-chuanxiong-capsule-on-the-abnormal-methylation-in-rabbits-with-atherosclerosis
#9
Qing-Bing Zhou, Li-Qi Wu, Yin Zhang, Zhi-Fang Zhang, Feng-Qin Xu
OBJECTIVE: To investigate the effects of Zhizi Chuanxiong Capsule (ZCC, ) on abnormal DNA methylation in a rabbit model of atherosclerosis (AS). METHODS: After 1 week of adaptive feeding, 48 New Zealand white rabbits were randomly divided into 4 groups: a control group (n=12) fed with normal diet for 22 weeks; a model group (n=12) fed with high fat diet for 14 weeks followed by 8 weeks of normal diet feeding; a low-dose ZCC group (n=12) fed with high fat diet and low-dose ZCC for 14 weeks, followed by 8 weeks of normal diet and low-dose drug; a high-dose ZCC group (n=12) fed with high fat diet and high-dose drug for 14 weeks, followed by 8 weeks of normal diet and high-dose drug...
May 11, 2018: Chinese Journal of Integrative Medicine
https://www.readbyqxmd.com/read/29733394/sin3a-tet1-interaction-activates-gene-transcription-and-is-required-for-embryonic-stem-cell-pluripotency
#10
Fugui Zhu, Qianshu Zhu, Dan Ye, Qingquan Zhang, Yiwei Yang, Xudong Guo, Zhenping Liu, Zeyidan Jiapaer, Xiaoping Wan, Guiying Wang, Wen Chen, Songcheng Zhu, Cizhong Jiang, Weiyang Shi, Jiuhong Kang
Sin3a is a core component of histone-deacetylation-activity-associated transcriptional repressor complex, playing important roles in early embryo development. Here, we reported that down-regulation of Sin3a led to the loss of embryonic stem cell (ESC) self-renewal and skewed differentiation into mesendoderm lineage. We found that Sin3a functioned as a transcriptional coactivator of the critical Nodal antagonist Lefty1 through interacting with Tet1 to de-methylate the Lefty1 promoter. Further studies showed that two amino acid residues (Phe147, Phe182) in the PAH1 domain of Sin3a are essential for Sin3a-Tet1 interaction and its activity in regulating pluripotency...
July 6, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29722878/global-dna-methylation-synergistically-regulates-the-nuclear-and-mitochondrial-genomes-in-glioblastoma-cells
#11
Xin Sun, Jacqueline Johnson, Justin C St John
Replication of mitochondrial DNA is strictly regulated during differentiation and development allowing each cell type to acquire its required mtDNA copy number to meet its specific needs for energy. Undifferentiated cells establish the mtDNA set point, which provides low numbers of mtDNA copy but sufficient template for replication once cells commit to specific lineages. However, cancer cells, such as those from the human glioblastoma multiforme cell line, HSR-GBM1, cannot complete differentiation as they fail to enforce the mtDNA set point and are trapped in a 'pseudo-differentiated' state...
July 6, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29514460/altered-dna-methylation-patterns-associated-with-clinically-relevant-increases-in-ptsd-symptoms-and-ptsd-symptom-profiles-in-military-personnel
#12
Christiana Martin, Young-Eun Cho, Hyungsuk Kim, Sijung Yun, Rebekah Kanefsky, Hyunhwa Lee, Vincent Mysliwiec, Ann Cashion, Jessica Gill
Military personnel experience posttraumatic stress disorder (PTSD), which is associated with differential DNA methylation across the whole genome. However, the relationship between these DNA methylation patterns and clinically relevant increases in PTSD severity is not yet clearly understood. The purpose of this study was to identify differences in DNA methylation associated with PTSD symptoms and investigate DNA methylation changes related to increases in the severity of PTSD in military personnel. In this pilot study, a cross-sectional comparison was made between military personnel with PTSD (n = 8) and combat-matched controls without PTSD (n = 6)...
May 2018: Biological Research for Nursing
https://www.readbyqxmd.com/read/29420797/octopus-toolkit-a-workflow-to-automate-mining-of-public-epigenomic-and-transcriptomic-next-generation-sequencing-data
#13
Taemook Kim, Hogyu David Seo, Lothar Hennighausen, Daeyoup Lee, Keunsoo Kang
Octopus-toolkit is a stand-alone application for retrieving and processing large sets of next-generation sequencing (NGS) data with a single step. Octopus-toolkit is an automated set-up-and-analysis pipeline utilizing the Aspera, SRA Toolkit, FastQC, Trimmomatic, HISAT2, STAR, Samtools, and HOMER applications. All the applications are installed on the user's computer when the program starts. Upon the installation, it can automatically retrieve original files of various epigenomic and transcriptomic data sets, including ChIP-seq, ATAC-seq, DNase-seq, MeDIP-seq, MNase-seq and RNA-seq, from the gene expression omnibus data repository...
May 18, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29409498/dna-methylome-profiling-at-single-base-resolution-through-bisulfite-sequencing-of-5mc-immunoprecipitated-dna
#14
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/29358109/deepaligner-deep-encoding-of-pathways-to-align-epigenetic-signatures
#15
R Visakh, K A Abdul Nazeer
BACKGROUND AND OBJECTIVE: Recently, differential DNA Methylation is known to affect the regulatory mechanism of biological pathways. A pathway encompasses a set of interacting genes or gene products that altogether perform a given biological function. Pathways often encode strong methylation signatures that are capable of distinguishing biologically distinct subtypes. Even though Next Generation Sequencing techniques such as MeDIP-seq and MBD-isolated genome sequencing (MiGS) allow for genome-wide identification of clinical and biological subtypes, there is a pressing need for computational methods to compare epigenetic signatures across pathways...
February 2018: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/29344347/epigenetic-alterations-in-tramp-mice-epigenome-dna-methylation-profiling-using-medip-seq
#16
Wenji Li, Ying Huang, Davit Sargsyan, Tin Oo Khor, Yue Guo, Limin Shu, Anne Yuqing Yang, Chengyue Zhang, Ximena Paredes-Gonzalez, Michael Verzi, Ronald P Hart, Ah-Ng Kong
Purpose: We investigated the genomic DNA methylation profile of prostate cancer in transgenic adenocarcinoma of the mouse prostate (TRAMP) cancer model and to analyze the crosstalk among targeted genes and the related functional pathways. Methods: Prostate DNA samples from 24-week-old TRAMP and C57BL/6 male mice were isolated. The DNA methylation profiles were analyzed by methylated DNA immunoprecipitation (MeDIP) followed by next-generation sequencing (MeDIP-seq)...
2018: Cell & Bioscience
https://www.readbyqxmd.com/read/29295990/obligatory-and-facilitative-allelic-variation-in-the-dna-methylome-within-common-disease-associated-loci
#17
Christopher G Bell, Fei Gao, Wei Yuan, Leonie Roos, Richard J Acton, Yudong Xia, Jordana Bell, Kirsten Ward, Massimo Mangino, Pirro G Hysi, Jun Wang, Timothy D Spector
Integrating epigenetic data with genome-wide association study (GWAS) results can reveal disease mechanisms. The genome sequence itself also shapes the epigenome, with CpG density and transcription factor binding sites (TFBSs) strongly encoding the DNA methylome. Therefore, genetic polymorphism impacts on the observed epigenome. Furthermore, large genetic variants alter epigenetic signal dosage. Here, we identify DNA methylation variability between GWAS-SNP risk and non-risk haplotypes. In three subsets comprising 3128 MeDIP-seq peripheral-blood DNA methylomes, we find 7173 consistent and functionally enriched Differentially Methylated Regions...
January 2, 2018: Nature Communications
https://www.readbyqxmd.com/read/29224147/comprehensive-whole-dna-methylome-analysis-by-integrating-medip-seq-and-mre-seq
#18
Xiaoyun Xing, Bo Zhang, Daofeng Li, Ting Wang
Understanding the role of DNA methylation often requires accurate assessment and comparison of these modifications in a genome-wide fashion. Sequencing-based DNA methylation profiling provides an unprecedented opportunity to map and compare complete DNA CpG methylomes. These include whole genome bisulfite sequencing (WGBS), Reduced-Representation Bisulfite-Sequencing (RRBS), and enrichment-based methods such as MeDIP-seq, MBD-seq, and MRE-seq. An investigator needs a method that is flexible with the quantity of input DNA, provides the appropriate balance among genomic CpG coverage, resolution, quantitative accuracy, and cost, and comes with robust bioinformatics software for analyzing the data...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29201983/data-on-novel-dna-methylation-changes-induced-by-valproic-acid-in-human-hepatocytes
#19
JarnoEJ Wolters, SimoneGJ van Breda, SandraM Claessen, TheoMCM de Kok, JosCS Kleinjans
Valproic acid (VPA) is a widely prescribed antiepileptic drug in the world. Despite its pharmacological importance, it may cause liver toxicity and steatosis. However the exact mechanism of the steatosis formation is unknown. The data presented in this DIB publication is used to further investigate the VPA-induced mechanisms of steatosis by analyzing changes in patterns of methylation. Therefore, primary human hepatocytes (PHHs) were exposed to VPA at a concentration which was shown to cause steatosis without inducing overt cytotoxicity...
February 2018: Data in Brief
https://www.readbyqxmd.com/read/29147574/generational-comparisons-f1-versus-f3-of-vinclozolin-induced-epigenetic-transgenerational-inheritance-of-sperm-differential-dna-methylation-regions-epimutations-using-medip-seq
#20
Daniel Beck, Ingrid Sadler-Riggleman, Michael K Skinner
Environmentally induced epigenetic transgenerational inheritance of disease and phenotypic variation has been shown to involve DNA methylation alterations in the germline (e.g. sperm). These differential DNA methylation regions (DMRs) are termed epimutations and in part transmit the transgenerational phenotypes. The agricultural fungicide vinclozolin exposure of a gestating female rat has previously been shown to promote transgenerational disease and epimutations in F3 generation (great-grand-offspring) animals...
July 2017: Environmental Epigenetics
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