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https://www.readbyqxmd.com/read/28407838/-effects-of-maternal-folate-deficiency-on-the-methylation-of-insulin-like-growth-factor-system-in-the-offspring-rats
#1
Meng-Meng Wu, Fan Yang, Yi Qu, De-Zhi Mu
OBJECTIVE: To study the effects of maternal folate deficiency on fetal growth and development and the methylation profiles of insulin-like growth factor system in the offspring rats. METHODS: Twenty-two Sprague-Dawley female rats were randomly assigned to two groups: a folate deficient group (n=12) and a control group (n=10). They were fed with folate deficient and normal diet respectively. Dams were mated after 2 weeks of feeding. Eight female rats from each group were pregnant...
April 2017: Zhongguo Dang Dai Er Ke za Zhi, Chinese Journal of Contemporary Pediatrics
https://www.readbyqxmd.com/read/28365388/comparative-analysis-of-mbd-seq-and-medip-seq-and-estimation-of-gene-expression-changes-in-a-rodent-model-of-schizophrenia
#2
Jennifer L Neary, Stephanie M Perez, Kara Peterson, Daniel J Lodge, Melanie A Carless
We conducted a comparative study of multiplexed affinity enrichment sequence methodologies (MBD-seq and MeDIP-seq) in a rodent model of schizophrenia, induced by in utero methylazoxymethanol acetate (MAM) exposure. We also examined related gene expression changes using a pooled sample approach. MBD-seq and MeDIP-seq identified 769 and 1771 differentially methylated regions (DMRs) between F2 offspring of MAM-exposed rats and saline control rats, respectively. The assays showed good concordance, with ~56% of MBD-seq-detected DMRs being identified by or proximal to MeDIP-seq DMRs...
March 29, 2017: Genomics
https://www.readbyqxmd.com/read/28240319/aorta-macrophage-inflammatory-and-epigenetic-changes-in-a-murine-model-of-obstructive-sleep-apnea-potential-role-of-cd36
#3
Rene Cortese, Alex Gileles-Hillel, Abdelnaby Khalyfa, Isaac Almendros, Mahzad Akbarpour, Ahamed A Khalyfa, Zhuanghong Qiao, Tzintzuni Garcia, Jorge Andrade, David Gozal
Obstructive sleep apnea (OSA) affects 8-10% of the population, is characterized by chronic intermittent hypoxia (CIH), and causally associates with cardiovascular morbidities. In CIH-exposed mice, closely mimicking the chronicity of human OSA, increased accumulation and proliferation of pro-inflammatory metabolic M1-like macrophages highly expressing CD36, emerged in aorta. Transcriptomic and MeDIP-seq approaches identified activation of pro-atherogenic pathways involving a complex interplay of histone modifications in functionally-relevant biological pathways, such as inflammation and oxidative stress in aorta macrophages...
February 27, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28129733/medip-seq-reveals-the-features-of-mitochondrial-genomic-methylation-in-immature-testis-of-chinese-mitten-crab-eriocheir-sinensis
#4
Gen-Liang Li, Yi-Jiao Xu, Xiao-Min Huang, Juan Xiao, Song Nong, Chao-Gan Li
In this study, the methylation of mitochondrial genome in the immature testis of Chinese mitten crab Eriocheir sinensis of the Yangtze River system was determined for the first time using MeDIP-seq. Our methylated DNA fragments covered more than 99% of the mitochondrial genome in E. sinensis loaded from GenBank. There were 8 mutated bases and 42 SNPs in the crab mitochondrial genome. The methylation presented in all genes as well as in an A + T region, but less in intergenic regions in the mitochondrial genome...
January 27, 2017: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/27913729/qsea-modelling-of-genome-wide-dna-methylation-from-sequencing-enrichment-experiments
#5
Matthias Lienhard, Sabrina Grasse, Jana Rolff, Steffen Frese, Uwe Schirmer, Michael Becker, Stefan Börno, Bernd Timmermann, Lukas Chavez, Holger Sültmann, Gunda Leschber, Iduna Fichtner, Michal R Schweiger, Ralf Herwig
Genome-wide enrichment of methylated DNA followed by sequencing (MeDIP-seq) offers a reasonable compromise between experimental costs and genomic coverage. However, the computational analysis of these experiments is complex, and quantification of the enrichment signals in terms of absolute levels of methylation requires specific transformation. In this work, we present QSEA, Quantitative Sequence Enrichment Analysis, a comprehensive workflow for the modelling and subsequent quantification of MeDIP-seq data...
April 7, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/27885421/role-of-vernalization-mediated-demethylation-in-the-floral-transition-of-brassica-rapa
#6
Weike Duan, Huijun Zhang, Bei Zhang, Xiaoting Wu, Shuaixu Shao, Ying Li, Xilin Hou, Tongkun Liu
Vernalization-mediated demethylation of BrCKA2 (casein kinase II α-subunit) and BrCKB4 (casein kinase II β-subunit) shorten the period of the clock gene BrCCA1 (circadian clock associated 1) in Brassica rapa. Photoperiod and vernalization are two environmental cues involved in the regulation of floral transition, but the ways in which they interact remain unclear. DNA methylation is one of the main mechanisms involved in controlling the functional state of chromatin and gene expression in response to environmental signals...
November 24, 2016: Planta
https://www.readbyqxmd.com/read/27754176/sy-15-2-endothelial-epigenetics-and-its-role-in-mediating-biomechanical-stress-of-hypertension
#7
Peter F Davies, Elisabetta Manduchi, Christian J Stoeckert, Yi-Zhou Jiang
Hemodynamics creates a constantly changing physical and chemical environment to which the arterial endothelium is exquisitely sensitive. Biomechanical stresses are intrinsic to blood flow characteristics and blood pressure and therefore are important considerations in hypertension. Near branching anatomical sites in arteries, blood flow separates from the main flow to undergo complex multi-directional characteristics for a part of each cardiac cycle (collectively referred to as disturbed flow). Atherosclerosis and aneurysmal pathology develop preferentially at disturbed flow locations, particularly when an additional cardiovascular risk factor such as hypercholesterolemia or high blood pressure are present...
September 2016: Journal of Hypertension
https://www.readbyqxmd.com/read/27706597/epigenetic-mechanism-of-maternal-post-traumatic-stress-disorder-in-delayed-rat-offspring-development-dysregulation-of-methylation-and-gene-expression
#8
X G Zhang, H Zhang, X L Liang, Q Liu, H Y Wang, B Cao, J Cao, S Liu, Y J Long, W Y Xie, D Z Peng
Maternal post-traumatic stress disorder (PTSD) increases the risk of adverse neurodevelopmental outcomes in the child. Epigenetic alternations may play an essential role in the negative effects of PTSD. This study was aimed to investigate the possible epigenetic alterations of maternal PTSD, which underpins the developmental and behavioral impact. 24 pregnant Sprague-Dawley (SD) rats were randomly grouped into PTSD and control groups. Open-field tests (OFTs), elevated pull maze (EPM) assays, gene expression profile chip tests, and methylated DNA immunoprecipitation sequencing (MeDIP-Seq) were performed on the offsprings 30 days after birth...
August 19, 2016: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/27698904/an-integrated-analysis-of-the-genome-wide-profiles-of-dna-methylation-and-mrna-expression-defining-the-side-population-of-a-human-malignant-mesothelioma-cell-line
#9
Myung-Chul Kim, Na-Yon Kim, Yu-Ri Seo, Yongbaek Kim
Intratumoral heterogeneity is a hallmark of all cancers and functions as the major barrier against effective cancer therapy. In contrast to genetic mutations, the role of epigenetic modifications in the generation and maintenance of heterogeneous cancer cells remains largely undetermined. This study was performed to evaluate the epigenetic mechanisms involved in the tumor cell heterogeneity using side population (SP) and non-SP cells isolated from a human malignant mesothelioma (HMM) cell line. The subpopulations of cancer cells were analyzed by methylated DNA immunoprecipitation combined with high-throughput sequencing (MeDIP-seq) and RNA-seq methodology...
2016: Journal of Cancer
https://www.readbyqxmd.com/read/27643133/sy-15-2-endothelial-epigenetics-and-its-role-in-mediating-biomechanical-stress-of-hypertension
#10
Peter F Davies, Elisabetta Manduchi, Christian J Stoeckert, Yi-Zhou Jiang
Hemodynamics creates a constantly changing physical and chemical environment to which the arterial endothelium is exquisitely sensitive. Biomechanical stresses are intrinsic to blood flow characteristics and blood pressure and therefore are important considerations in hypertension. Near branching anatomical sites in arteries, blood flow separates from the main flow to undergo complex multi-directional characteristics for a part of each cardiac cycle (collectively referred to as disturbed flow). Atherosclerosis and aneurysmal pathology develop preferentially at disturbed flow locations, particularly when an additional cardiovascular risk factor such as hypercholesterolemia or high blood pressure are present...
September 2016: Journal of Hypertension
https://www.readbyqxmd.com/read/27627189/screening-of-reproduction-related-single-nucleotide-variations-from-medip-seq-data-in-sheep
#11
Jiaxue Cao, Caihong Wei, Shuzhen Zhang, Terence D Capellini, Li Zhang, Fuping Zhao, Li Li, Tao Zhong, Linjie Wang, Lixin Du, Hongping Zhang
Extensive variation in reproduction has arisen in Chinese Mongolian sheep during recent domestication. Hu and Small-tailed Han sheep, for example, have become non-seasonal breeders and exhibit higher fecundity than Tan and Ujumqin breeds. We therefore scanned reproduction-related single-nucleotide variations from methylated DNA-immunoprecipitation sequencing data generated from each of those four breeds to uncover potential mechanisms underlying this breed variation. We generated a high-quality map of single nucleotide variations (SNVs) in DNA methylation enriched regions, and found that the majority of variants are located within non-coding regions...
November 2016: Molecular Reproduction and Development
https://www.readbyqxmd.com/read/27561685/short-term-calorie-restriction-ameliorates-genomewide-age-related-alterations-in-dna-methylation
#12
Chul H Kim, Eun K Lee, Yoen J Choi, Hye J An, Hyung O Chung, Dae E Park, Byung C Ghim, Byung P Yu, Jong Bhak, Hae Y Chung
DNA methylation plays major roles in many biological processes, including aging, carcinogenesis, and development. Analyses of DNA methylation using next-generation sequencing offer a new way to profile and compare methylomes across the genome in the context of aging. We explored genomewide DNA methylation and the effects of short-term calorie restriction (CR) on the methylome of aged rat kidney. Whole-genome methylation of kidney in young (6 months old), old (25 months old), and OCR (old with 4-week, short-term CR) rats was analyzed by methylated DNA immunoprecipitation and next-generation sequencing (MeDIP-Seq)...
August 25, 2016: Aging Cell
https://www.readbyqxmd.com/read/27494266/variation-of-dna-methylome-of-zebrafish-cells-under-cold-pressure
#13
Bingshe Han, Wenhao Li, Zuozhou Chen, Qiongqiong Xu, Juntao Luo, Yingdi Shi, Xiaoxia Li, Xiaonan Yan, Junfang Zhang
DNA methylation is an essential epigenetic mechanism involved in multiple biological processes. However, the relationship between DNA methylation and cold acclimation remains poorly understood. In this study, Methylated DNA Immunoprecipitation Sequencing (MeDIP-seq) was performed to reveal a genome-wide methylation profile of zebrafish (Danio rerio) embryonic fibroblast cells (ZF4) and its variation under cold pressure. MeDIP-seq assay was conducted with ZF4 cells cultured at appropriate temperature of 28°C and at low temperature of 18°C for 5 (short-term) and 30 (long-term) days, respectively...
2016: PloS One
https://www.readbyqxmd.com/read/27473283/dismiss-detection-of-stranded-methylation-in-medip-seq-data
#14
Umar Niazi, Kathrin K Geyer, Martin J Vickers, Karl F Hoffmann, Martin T Swain
BACKGROUND: DNA methylation is an important regulator of gene expression and chromatin structure. Methylated DNA immunoprecipitation sequencing (MeDIP-Seq) is commonly used to identify regions of DNA methylation in eukaryotic genomes. Within MeDIP-Seq libraries, methylated cytosines can be found in both double-stranded (symmetric) and single-stranded (asymmetric) genomic contexts. While symmetric CG methylation has been relatively well-studied, asymmetric methylation in any dinucleotide context has received less attention...
2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/27462375/genome-wide-dna-methylation-profiling-with-medip-seq-using-archived-dried-blood-spots
#15
Nicklas H Staunstrup, Anna Starnawska, Mette Nyegaard, Lene Christiansen, Anders L Nielsen, Anders Børglum, Ole Mors
BACKGROUND: In utero and early-life experienced environmental exposures are suggested to play an important role in many multifactorial diseases potentially mediated through lasting effects on the epigenome. As the epigenome in addition remains modifiable throughout life, identifying specific disease-relevant biomarkers may prove challenging. This has led to an increased interest in epigenome-wide association studies using dried blood spots (DBS) routinely collected in perinatal screening programs...
2016: Clinical Epigenetics
https://www.readbyqxmd.com/read/27443935/genome-wide-dna-methylation-profiling-in-zebrafish
#16
P J Murphy, B R Cairns
Genomic DNA methylation functions to repress gene expression by interfering with transcription factor binding and/or recruiting repressive chromatin machinery. Recent data support contribution of regulated DNA methylation to embryonic pluripotency, development, and tissue differentiation; this important epigenetic mark is chemically stable yet enzymatically reversible-and heritable through the germline. Importantly, all the major components involved in dynamic DNA methylation are conserved in zebrafish, including the factors that "write, read, and erase" this mark...
2016: Methods in Cell Biology
https://www.readbyqxmd.com/read/27437772/a-cancer-specific-hypermethylation-signature-of-the-tert-promoter-predicts-biochemical-relapse-in-prostate-cancer-a-retrospective-cohort-study
#17
Pedro Castelo-Branco, Ricardo Leão, Tatiana Lipman, Brittany Campbell, Donghyun Lee, Aryeh Price, Cindy Zhang, Abolfazl Heidari, Derek Stephens, Stefan Boerno, Hugo Coelho, Ana Gomes, Celia Domingos, Joana D Apolonio, Georg Schäfer, Robert G Bristow, Michal R Schweiger, Robert Hamilton, Alexandre Zlotta, Arnaldo Figueiredo, Helmut Klocker, Holger Sültmann, Uri Tabori
The identification of new biomarkers to differentiate between indolent and aggressive prostate tumors is an important unmet need. We examined the role of THOR (TERT Hypermethylated Oncological Region) as a diagnostic and prognostic biomarker in prostate cancer (PCa).We analyzed THOR in common cancers using genome-wide methylation arrays. Methylation status of the whole TERT gene in benign and malignant prostate samples was determined by MeDIP-Seq. The prognostic role of THOR in PCa was assessed by pyrosequencing on discovery and validation cohorts from patients who underwent radical prostatectomy with long-term follow-up data...
September 6, 2016: Oncotarget
https://www.readbyqxmd.com/read/27266718/efficiency-of-methylated-dna-immunoprecipitation-bisulphite-sequencing-for-whole-genome-dna-methylation-analysis
#18
Hae Min Jeong, Sangseon Lee, Heejoon Chae, RyongNam Kim, Mi Jeong Kwon, Ensel Oh, Yoon-La Choi, Sun Kim, Young Kee Shin
AIMS: We compared four common methods for measuring DNA methylation levels and recommended the most efficient method in terms of cost and coverage. MATERIALS & METHODS: The DNA methylation status of liver and stomach tissues was profiled using four different methods, whole-genome bisulphite sequencing (WG-BS), targeted bisulphite sequencing (Targeted-BS), methylated DNA immunoprecipitation sequencing (MeDIP-seq) and methylated DNA immunoprecipitation bisulphite sequencing (MeDIP-BS)...
August 2016: Epigenomics
https://www.readbyqxmd.com/read/27221337/whole-genome-dna-methylation-and-hydroxymethylation-profiling-for-hbv-related-hepatocellular-carcinoma
#19
Chao Ye, Ran Tao, Qingyi Cao, Danhua Zhu, Yini Wang, Jie Wang, Juan Lu, Ermei Chen, Lanjuan Li
Hepatocellular carcinoma (HCC) is a common solid tumor worldwide with a poor prognosis. Accumulating evidence has implicated important regulatory roles of epigenetic modifications in the occurrence and progression of HCC. In the present study, we analyzed 5-methylcytosine (5-mC) and 5-hydroxymethylcytosine (5-hmC) levels in the tumor tissues and paired adjacent peritumor tissues (APTs) from four individual HCC patients using a (hydroxy)methylated DNA immunoprecipitation approach combined with deep sequencing [(h)MeDIP-Seq]...
August 2016: International Journal of Oncology
https://www.readbyqxmd.com/read/27199997/analyses-of-methylomes-derived-from-meso-american-common-bean-phaseolus-vulgaris-l-using-medip-seq-and-whole-genome-sodium-bisulfite-sequencing
#20
Mollee Crampton, Venkateswara R Sripathi, Khwaja Hossain, Venu Kalavacharla
Common bean (Phaseolus vulgaris L.) is economically important for its high protein, fiber, and micronutrient contents, with a relatively small genome size of ∼587 Mb. Common bean is genetically diverse with two major gene pools, Meso-American and Andean. The phenotypic variability within common bean is partly attributed to the genetic diversity and epigenetic changes that are largely influenced by environmental factors. It is well established that an important epigenetic regulator of gene expression is DNA methylation...
2016: Frontiers in Plant Science
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