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https://www.readbyqxmd.com/read/28619030/integrative-analysis-of-dna-methylation-mrnas-and-small-rnas-during-maize-embryo-dedifferentiation
#1
Hongjun Liu, Langlang Ma, Xuerong Yang, Lin Zhang, Xing Zeng, Shupeng Xie, Huanwei Peng, Shibin Gao, Haijian Lin, Guangtang Pan, Yongrui Wu, Yaou Shen
BACKGROUND: Maize (Zea mays) is an important model crop for transgenic studies. However, genetic transformation of maize requires embryonic calli derived from immature embryo, and the impact of utilizing tissue culture methods on the maize epigenome is poorly understood. Here, we generated whole-genome MeDIP-seq data examining DNA methylation in dedifferentiated and normal immature maize embryos. RESULTS: We observed that most of the dedifferentiated embryos exhibited a methylation increase compared to normal embryos...
June 15, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28606200/exomic-and-epigenomic-analyses-in-a-pair-of-monozygotic-twins-discordant-for-cryptorchidism
#2
Peng Lu, Pengyun Wang, Lianbing Li, Chengqi Xu, Jing Crystal Liu, Xiangqian Guo, Dawei He, Huizhe Huang, Zhi Cheng
Cryptorchidism represents one of the most common human congenital anomalies. In most cases, its etiology remains unclear and seems to be multifactorial. In the present study, a pair of monozygotic twins discordant for cryptorchidism was identified. Twin zygosity was confirmed by microsatellite genotyping. Whole exome sequencing and methylated DNA immunoprecipitation sequencing (MeDIP-Seq) of DNA extract from leucocytes were performed to, respectively, evaluate their exomes and epigenomes. No differences in exome sequencing data were found between the twins after validation...
June 13, 2017: Twin Research and Human Genetics: the Official Journal of the International Society for Twin Studies
https://www.readbyqxmd.com/read/28589689/genetic-variation-in-the-developmental-regulation-of-cortical-avpr1a-among-prairie-voles
#3
M Okhovat, I C Chen, Z Dehghani, D J Zheng, J E Ikpatt, H Momoh, S M Phelps
Early experiences can have enduring impacts on brain and behavior, but the strength of these effects can be influenced by genetic variation. In principle, polymorphic CpGs (polyCpGs) may contribute to gene-by-environment interactions (GxE) by altering DNA methylation. In this study, we investigate the influence of polyCpGs on the development of vasopressin receptor 1a abundance in the retrosplenial cortex (RSC-V1aR) of prairie voles (Microtus ochrogaster). Two alternative alleles (HI/LO) predict RSC avpr1a expression, V1aR abundance and sexual fidelity in adulthood; these alleles differ in the frequency of CpG sites and in methylation at a putative intron enhancer...
June 7, 2017: Genes, Brain, and Behavior
https://www.readbyqxmd.com/read/28536466/fipronil-induced-enantioselective-developmental-toxicity-to-zebrafish-embryo-larvae-involves-changes-in-dna-methylation
#4
Yi Qian, Cui Wang, Jinghua Wang, Xiaofeng Zhang, Zhiqiang Zhou, Meirong Zhao, Chensheng Lu
Enantioselectivity in the aquatic toxicity of chiral pesticides has been widely investigated, while the molecular mechanisms remain unclear. Thus far, few studies has focused on genomic expression related to selective toxicity in chiral pesticide, nor on epigenetic changes, such as DNA methylation. Here, we used fipronil, a broad-spectrum insecticide, as a model chemical to probe its enantioselective toxicity in embryo development. Our results showed that S-(+)-fipronil caused severer developmental toxicity in embryos...
May 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28533820/medip-seq-and-ncpg-analyses-illuminate-sexually-dimorphic-methylation-of-gonadal-development-genes-with-high-historic-methylation-in-turtle-hatchlings-with-temperature-dependent-sex-determination
#5
Srihari Radhakrishnan, Robert Literman, Beatriz Mizoguchi, Nicole Valenzuela
BACKGROUND: DNA methylation alters gene expression but not DNA sequence and mediates some cases of phenotypic plasticity. Temperature-dependent sex determination (TSD) epitomizes phenotypic plasticity where environmental temperature drives embryonic sexual fate, as occurs commonly in turtles. Importantly, the temperature-specific transcription of two genes underlying gonadal differentiation is known to be induced by differential methylation in TSD fish, turtle and alligator. Yet, how extensive is the link between DNA methylation and TSD remains unclear...
2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/28499430/genome-wide-dna-methylation-analysis-in-lung-fibroblasts-co-cultured-with-silica-exposed-alveolar-macrophages
#6
Juan Li, Wu Yao, Lin Zhang, Lei Bao, Huiting Chen, Di Wang, Zhongzheng Yue, Yiping Li, Miao Zhang, Changfu Hao
BACKGROUND: Exposure to crystalline silica is considered to increase the risk of lung fibrosis. The primary effector cell, the myofibroblast, plays an important role in the deposition of extracellular matrix (ECM). DNA methylation change is considered to have a potential effect on myofibroblast differentiation. Therefore, the present study was designed to investigate the genome-wide DNA methylation profiles of lung fibroblasts co-cultured with alveolar macrophages exposed to crystalline silica in vitro...
May 12, 2017: Respiratory Research
https://www.readbyqxmd.com/read/28459064/comparison-of-dna-methylation-in-schwann-cells-before-and-after-peripheral-nerve-injury-in-rats
#7
Xian-Hu Zhou, Wei Lin, Yi-Ming Ren, Shen Liu, Bao-You Fan, Zhi-Jian Wei, Gui-Dong Shi, Xin Cheng, Yan Hao, Shi-Qing Feng
This study aims to find the difference of genomewide DNA methylation in Schwann cells (SCs) before and after peripheral nerve system (PNS) injury by Methylated DNA Immunoprecipitation Sequencing (MeDIP-Seq) and seek meaningful differentially methylated genes related to repairment of injured PNS. SCs harvested from sciatic nerve were named as activated Schwann cells (ASCs), and the ones harvested from brachial plexus were named as normal Schwann cells (NSCs). Genomic DNA of ASCs and NSCs were isolated and MeDIP-Seq was conducted...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28407838/-effects-of-maternal-folate-deficiency-on-the-methylation-of-insulin-like-growth-factor-system-in-the-offspring-rats
#8
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
#9
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
#10
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
#11
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
#12
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
#13
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...
January 2017: Planta
https://www.readbyqxmd.com/read/27754176/sy-15-2-endothelial-epigenetics-and-its-role-in-mediating-biomechanical-stress-of-hypertension
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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