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https://www.readbyqxmd.com/read/27885421/role-of-vernalization-mediated-demethylation-in-the-floral-transition-of-brassica-rapa
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
#11
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
#12
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...
July 16, 2016: Oncotarget
https://www.readbyqxmd.com/read/27266718/efficiency-of-methylated-dna-immunoprecipitation-bisulphite-sequencing-for-whole-genome-dna-methylation-analysis
#13
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
#14
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
#15
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
https://www.readbyqxmd.com/read/27144936/contribution-of-heritability-and-epigenetic-factors-to-skeletal-muscle-mass-variation-in-united-kingdom-twins
#16
Gregory Livshits, Fei Gao, Ida Malkin, Maria Needhamsen, Yudong Xia, Wei Yuan, Christopher G Bell, Kirsten Ward, Yuan Liu, Jun Wang, Jordana T Bell, Tim D Spector
CONTEXT: Skeletal muscle mass (SMM) is one of the major components of human body composition, with deviations from normal values often leading to sarcopenia. OBJECTIVE: Our major aim was to conduct a genome-wide DNA methylation study in an attempt to identify potential genomic regions associated with SMM. DESIGN: This was a mixed cross-sectional and longitudinal study. SETTING: Community-based study. PARTICIPANTS: A total of 1550 middle-aged United Kingdom twins (monozygotic [MZ] and dizygotic [DZ]), 297 of which were repeatedly measured participated in the study...
June 2016: Journal of Clinical Endocrinology and Metabolism
https://www.readbyqxmd.com/read/27123440/differential-methylation-of-genomic-regions-associated-with-heteroblasty-detected-by-m-m-algorithm-in-the-nonmodel-species-eucalyptus-globulus-labill
#17
Rodrigo Hasbún, Carolina Iturra, Soraya Bravo, Boris Rebolledo-Jaramillo, Luis Valledor
Epigenetic regulation plays important biological roles in plants, including timing of flowering and endosperm development. Little is known about the mechanisms controlling heterochrony (the change in the timing or rate of developmental events during ontogeny) in Eucalyptus globulus. DNA methylation has been proposed as a potential heterochrony regulatory mechanism in model species, but its role during the vegetative phase in E. globulus has not been explored. In order to investigate the molecular mechanisms governing heterochrony in E...
2016: International Journal of Genomics
https://www.readbyqxmd.com/read/27090932/dynamic-integrated-analysis-of-dna-methylation-and-gene-expression-profiles-in-in-vivo-and-in-vitro-fertilized-mouse-post-implantation-extraembryonic-and-placental-tissues
#18
Kun Tan, Zhenni Zhang, Kai Miao, Yong Yu, Linlin Sui, Jianhui Tian, Lei An
STUDY HYPOTHESIS: How does in vitro fertilization (IVF) alter promoter DNA methylation patterns and its subsequent effects on gene expression profiles during placentation in mice? STUDY FINDING: IVF-induced alterations in promoter DNA methylation might have functional consequences in a number of biological processes and functions during IVF placentation, including actin cytoskeleton organization, hematopoiesis, vasculogenesis, energy metabolism and nutrient transport...
July 2016: Molecular Human Reproduction
https://www.readbyqxmd.com/read/27014907/genomic-and-epigenomic-analysis-of-high-risk-prostate-cancer-reveals-changes-in-hydroxymethylation-and-tet1
#19
Lien Spans, Thomas Van den Broeck, Elien Smeets, Stefan Prekovic, Bernard Thienpont, Diether Lambrechts, R Jeffrey Karnes, Nicholas Erho, Mohammed Alshalalfa, Elai Davicioni, Christine Helsen, Thomas Gevaert, Lorenzo Tosco, Karin Haustermans, Evelyne Lerut, Steven Joniau, Frank Claessens
The clinical heterogeneity of prostate cancer (PCa) makes it difficult to identify those patients that could benefit from more aggressive treatments. As a contribution to a better understanding of the genomic changes in the primary tumor that are associated with the development of high-risk disease, we performed exome sequencing and copy number determination of a clinically homogeneous cohort of 47 high-risk PCas. We confirmed recurrent mutations in SPOP, PTEN and TP53 among the 850 point mutations we detected...
April 26, 2016: Oncotarget
https://www.readbyqxmd.com/read/26980478/hoxa5-undergoes-dynamic-dna-methylation-and-transcriptional-repression-in-the-adipose-tissue-of-mice-exposed-to-high-fat-diet
#20
L Parrillo, V Costa, G A Raciti, M Longo, R Spinelli, R Esposito, C Nigro, V Vastolo, A Desiderio, F Zatterale, A Ciccodicola, P Formisano, C Miele, F Beguinot
BACKGROUND/OBJECTIVES: The genomic bases of the adipose tissue abnormalities induced by chronic positive calorie excess have been only partially elucidated. We adopted a genome-wide approach to directly test whether long-term high-fat diet (HFD) exposure affects the DNA methylation profile of the mouse adipose tissue and to identify the functional consequences of these changes. SUBJECTS/METHODS: We have used epididymal fat of mice fed either high-fat (HFD) or regular chow (STD) diet for 5 months and performed genome-wide DNA methylation analyses by methylated DNA immunoprecipitation sequencing (MeDIP-seq)...
June 2016: International Journal of Obesity: Journal of the International Association for the Study of Obesity
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