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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
#1
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
https://www.readbyqxmd.com/read/29137437/dna-hypermethyation-and-silencing-of-pitx1-correlated-with-advanced-stage-and-poor-postoperative-prognosis-of-esophageal-squamous-cell-carcinoma
#2
Takeshi Otsubo, Kazuhiko Yamada, Teruki Hagiwara, Kenshiro Oshima, Kei Iida, Koro Nishikata, Tetsuro Toyoda, Toru Igari, Kyoko Nohara, Satoshi Yamashita, Masahira Hattori, Taeko Dohi, Yuki I Kawamura
Esophageal squamous cell carcinoma (ESCC) is associated with the accumulation of genetic and epigenetic changes in the background mucosa. Dysregulated DNA methylation is known to lead to the inactivation of tumor suppressor genes and the activation of oncogenes. To identify the genes whose expression is perturbed by abnormal DNA methylation in ESCC, integrative transcriptomics by serial analysis of gene expression (SAGE) and methylome sequencing by methyl-DNA immunoprecipitation (MeDIP) analysis were performed...
October 13, 2017: Oncotarget
https://www.readbyqxmd.com/read/29115936/analyses-of-methylomes-of-upland-and-lowland-switchgrass-panicum-virgatum-ecotypes-using-medip-seq-and-bs-seq
#3
Mollee Dworkin, Shaojun Xie, Malay Saha, Jyothi Thimmapuram, Venu Kal Kalavacharla
BACKGROUND: Switchgrass is a crop with many desirable traits for bioenergy production. Plant genomes have high DNA methylation levels throughout genes and transposable elements and DNA methylation is known to play a role in silencing transposable elements. Here we analyzed methylomes in two switchgrass genotypes AP13 and VS16. AP13 is derived from a lowland ecotype and VS16, typically considered drought-tolerant, is derived from an upland ecotype, both genotypes are tetraploid (2n = 4× = 36)...
November 7, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29036598/global-dna-methylation-analysis-reveals-mir-214-3p-contributes-to-cisplatin-resistance-in-pediatric-intracranial-nongerminomatous-malignant-germ-cell-tumors
#4
Tsung-Han Hsieh, Yun-Ru Liu, Ting-Yu Chang, Muh-Lii Liang, Hsin-Hung Chen, Hsei-Wei Wang, Yun Yen, Tai-Tong Wong
Background: Pediatric central nervous system germ cell tumors (CNSGCTs) are rare and heterogeneous neoplasms, and they can be divided into germinomas and nongerminomatous GCTs (NGGCTs). NGGCTs are further subdivided into mature teratomas and nongerminomatous malignant GCTs (NGMGCTs). Clinical outcomes suggest that NGMGCTs have poor prognosis and survival, and that they require more extensive radiotherapy and adjuvant chemotherapy. However, the mechanisms underlying this difference are still unclear...
October 3, 2017: Neuro-oncology
https://www.readbyqxmd.com/read/29036558/methrafo-medip-seq-methylation-estimate-using-a-random-forest-regressor
#5
Jun Ding, Ziv Bar-Joseph
Motivation: Profiling of genome wide DNA methylation is now routinely performed when studying development, cancer and several other biological processes. Although Whole genome Bisulfite Sequencing provides high-quality methylation measurements at the resolution of nucleotides, it is relatively costly and so several studies have used alternative methods for such profiling. One of the most widely used low cost alternatives is MeDIP-Seq. However, MeDIP-Seq is biased for CpG enriched regions and thus its results need to be corrected in order to determine accurate methylation levels...
November 1, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29018624/genome-methylation-and-regulatory-functions-for-hypoxic-adaptation-in-tibetan-chicken-embryos
#6
Yawen Zhang, Wenyu Gou, Jun Ma, Hongliang Zhang, Ying Zhang, Hao Zhang
Tibetan chickens have unique adaptations to the extreme high-altitude environment that they inhabit. Epigenetic DNA methylation affects many biological processes, including hypoxic adaptation; however, the regulatory genes for DNA methylation in hypoxic adaptation remain unknown. In this study, methylated DNA immunoprecipitation with high-throughput sequencing (MeDIP-seq) was used to provide an atlas of the DNA methylomes of the heart tissue of hypoxic highland Tibetan and lowland Chahua chicken embryos. A total of 31...
2017: PeerJ
https://www.readbyqxmd.com/read/28948740/-effect-of-baihu-guizhi-decoction-on-characteristic-methylation-genes-expression-of-pyretic-arthralgia-rat-model
#7
Huan Chen, Shao-Hua Ju, Jiang-Ping Wei, Wen-Jun Fu, Hang Zheng, Shi-Jun Xu
To investigate the characteristic methylation genes of pyretic arthralgia model in hot and dampness environment and the regulation effect of Baihu Guizhi decoction on this characteristic methylation genes. Plantar injection of CFA was used in hot and dampness environment to induce the pyretic arthralgia rat models. From 15th day after modeling, Baihu Guizhi decoction was given for 30 days. Foot volume was detected every 4 days after modeling, and HE staining was used to detect the histopathology of all rats' ankle joint at day 45...
January 2017: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
https://www.readbyqxmd.com/read/28853863/nuclear-and-mitochondrial-dna-methylation-patterns-induced-by-valproic-acid-in-human-hepatocytes
#8
Jarno E J Wolters, Simone G J van Breda, Florian Caiment, Sandra M Claessen, Theo M C M de Kok, Jos C S Kleinjans
Valproic acid (VPA) is one of the most widely prescribed antiepileptic drugs in the world. Despite its pharmacological importance, it may cause liver toxicity and steatosis through mitochondrial dysfunction. The aim of this study is to further investigate VPA-induced mechanisms of steatosis by analyzing changes in patterns of methylation in nuclear DNA (nDNA) and mitochondrial DNA (mtDNA). Therefore, primary human hepatocytes (PHHs) were exposed to an incubation concentration of VPA that was shown to cause steatosis without inducing overt cytotoxicity...
October 16, 2017: Chemical Research in Toxicology
https://www.readbyqxmd.com/read/28728367/comparative-analysis-on-genome-wide-dna-methylation-in-longissimus-dorsi-muscle-between-small-tailed-han-and-dorper%C3%A3-small-tailed-han-crossbred-sheep
#9
Yang Cao, Hai-Guo Jin, Hui-Hai Ma, Zhi-Hui Zhao
OBJECTIVE: The objective of this study was to compare the DNA methylation profile in the longissimus dorsi muscle between Small Tailed Han and Dorper×Small Tailed Han crossbred sheep which were known to exhibit significant difference in meat-production. METHODS: Six samples (three in each group) were subjected to the methylated DNA immunoprecipitation sequencing (MeDIP-seq) and subsequent bioinformatics analyses to detect differentially methylated regions (DMRs) between the two groups...
November 2017: Asian-Australasian Journal of Animal Sciences
https://www.readbyqxmd.com/read/28727982/genome-wide-dna-methylation-profile-of-prepubertal-porcine-testis
#10
Xi Chen, Liu-Hong Shen, Li-Xuan Gui, Fang Yang, Jie Li, Sui-Zhong Cao, Zhi-Cai Zuo, Xiao-Ping Ma, Jun-Liang Deng, Zhi-Hua Ren, Zhong-Xu Chen, Shu-Min Yu
The biological structure and function of the mammalian testis undergo important developmental changes during prepuberty and DNA methylation is dynamically regulated during testis development. In this study, we generated the first genome-wide DNA methylation profile of prepubertal porcine testis using methyl-DNA immunoprecipitation (MeDIP) combined with high-throughput sequencing (MeDIP-seq). Over 190 million high-quality reads were generated, containing 43642 CpG islands. There was an overall downtrend of methylation during development, which was clear in promoter regions but less so in gene-body regions...
July 21, 2017: Reproduction, Fertility, and Development
https://www.readbyqxmd.com/read/28715427/global-analysis-of-dna-methylation-in-young-j1-and-senescent-j2-gossypium-hirsutum-l-cotyledons-by-medip-seq
#11
Lingling Dou, Xiaoyun Jia, Hengling Wei, Shuli Fan, Hantao Wang, Yaning Guo, Shan Duan, Chaoyou Pang, Shuxun Yu
DNA methylation is an important epigenetic modification regulating gene expression, genomic imprinting, transposon silencing and chromatin structure in plants and plays an important role in leaf senescence. However, the DNA methylation pattern during Gossypium hirsutum L. cotyledon senescence is poorly understood. In this study, global DNA methylation patterns were compared between two cotyledon development stages, young (J1) and senescence (J2), using methylated DNA immunoprecipitation (MeDIP-Seq). Methylated cytosine occurred mostly in repeat elements, especially LTR/Gypsy in both J1 and J2...
2017: PloS One
https://www.readbyqxmd.com/read/28674382/the-destiny-of-the-resistance-susceptibility-against-gcrv-is-controlled-by-epigenetic-mechanisms-in-cik-cells
#12
Xueying Shang, Chunrong Yang, Quanyuan Wan, Youliang Rao, Jianguo Su
Hemorrhagic disease caused by grass carp reovirus (GCRV) has severely threatened the grass carp (Ctenopharyngodon idella) cultivation industry. It is noteworthy that the resistance against GCRV infection was reported to be inheritable, and identified at both individual and cellular levels. Therefore, this work was inspired and dedicated to unravel the molecular mechanisms of fate decision post GCRV infection in related immune cells. Foremost, the resistant and susceptible CIK (C. idella kidney) monoclonal cells were established by single cell sorting, subculturing and infection screening successively...
July 3, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28619030/integrative-analysis-of-dna-methylation-mrnas-and-small-rnas-during-maize-embryo-dedifferentiation
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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