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Methylation enrichment

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https://www.readbyqxmd.com/read/28735484/microsphere-based-assessment-of-dna-methylation-for-aml-prognosis
#1
Gerald B W Wertheim, Marlise R Luskin, Martin Carroll, Stephen R Master
Epigenetic dysregulation, including aberrant methylation of cytosine residues in DNA, is a hallmark of cancer and clearly results in oncogenic cellular alterations such as transcriptional attenuation of tumor suppressors and genomic instability. A number of studies have examined DNA methylation alterations in patients with acute myeloid leukemia (AML) and have shown that analysis of multilocus methylation patterns can identify biologically distinct AML subclasses and can predict patient prognosis. In order to utilize the prognostic capability of methylation analysis in a clinical setting, we have developed a microsphere-based HpaII tiny fragment enrichment by ligation-mediated PCR (xMELP) assay to interrogate the methylation state of genomic multiple loci along with a random forest-based classification algorithm that correlates DNA methylation status with patient prognosis...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28735351/multiple-correlation-analyses-revealed-complex-relationship-between-dna-methylation-and-mrna-expression-in-human-peripheral-blood-mononuclear-cells
#2
Fang-Fei Xie, Fei-Yan Deng, Long-Fei Wu, Xing-Bo Mo, Hong Zhu, Jian Wu, Yu-Fan Guo, Ke-Qin Zeng, Ming-Jun Wang, Xiao-Wei Zhu, Wei Xia, Lan Wang, Pei He, Peng-Fei Bing, Xin Lu, Yong-Hong Zhang, Shu-Feng Lei
DNA methylation is an important regulator on the mRNA expression. However, a genome-wide correlation pattern between DNA methylation and mRNA expression in human peripheral blood mononuclear cells (PBMCs) is largely unknown. The comprehensive relationship between mRNA and DNA methylation was explored by using four types of correlation analyses and a genome-wide methylation-mRNA expression quantitative trait locus (eQTL) analysis in PBMCs in 46 unrelated female subjects. An enrichment analysis was performed to detect biological function for the detected genes...
July 22, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28734214/effects-of-damming-on-the-distribution-and-methylation-of-mercury-in-wujiang-river-southwest-china
#3
Lei Zhao, Yanna Guo, Bo Meng, Heng Yao, Xinbin Feng
Newly built reservoirs are regarded as sensitive ecosystem for mercury (Hg) methylation. A comprehensive study was conducted to understand the influence of damming on the distribution and methylation of Hg within a river-reservoir ecosystem in Wujiang River Basin (WRB), Southwest China. Hg species in inflow-outflow rivers of six cascade reservoirs were analyzed each month during 2006. Mean concentrations of total Hg (THg) and methylmercury (MeHg) in river water in WRB were 3.41 ± 1.98 ng L(-1) and 0.15 ± 0...
July 17, 2017: Chemosphere
https://www.readbyqxmd.com/read/28733112/distinctions-in-gene-specific-changes-in-dna-methylation-in-response-to-folic-acid-supplementation-between-women-with-normal-weight-and-obesity
#4
Hea Jin Park, Lynn B Bailey, Deanna C Shade, Dorothy B Hausman, Natalie M Hohos, Richard B Meagher, Gail Pa Kauwell, Richard D Lewis, Alicia K Smith
BACKGROUND/OBJECTIVES: Obesity and maternal folate deficiency are associated with increased risk for neural tube defects (NTDs). Limited knowledge exists on the impact of folate status or obesity on DNA methylation of genes related to NTD risk and folate metabolism. SUBJECTS/METHODS: Women (18-35y) with normal weight (NW; BMI 18.5-24.9kg/m(2); n=12) and obesity (OB; BMI >30kg/m(2); n=6) were provided FA (800μg/d) for 8-weeks. Serum folate concentration and changes in DNA methylation across 2098 CpG sites in 91 genes related to NTD risk and folate metabolism were examined...
July 18, 2017: Obesity Research & Clinical Practice
https://www.readbyqxmd.com/read/28731140/integrated-analysis-of-genome%C3%A2-wide-gene-expression-and-dna-methylation-microarray-of-diffuse-large-b%C3%A2-cell-lymphoma-with-tet-mutations
#5
Pengfei Liu, Wenhua Jiang, Jinkun Zhao, Huilai Zhang
Diffuse large B-cell lymphoma (DLBCL), the most frequently occurring type of lymphoid malignancy, has been demonstrated to be associated with mutations of Ten‑Eleven Translocation (TET). In order to explore the association between DLBCL and TET mutations, the present study analyzed the gene expression and methylation profiles in human DLBCL biopsy tissues with wildtype and mutated TET2. The microarray dataset GSE37365, containing two subseries: the genome‑wide gene expression dataset GSE37362 and the DNA methylation microarray dataset GSE37363, was downloaded from the Gene Expression Omnibus database...
July 21, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28730638/plasma-pharmacokinetics-of-quinocetone-in-ducks-after-oral-and-intravenous-administration
#6
M Qiu, Z Hao, R Zhang, L Cui, C Wang, S Qu, S Yuan, Y Bai
Quinocetone (QCT), an antimicrobial growth promoter, is widely used in food-producing animals. However, information about pharmacokinetics (PK) of QCT in ducks still remains unavailable up to now. In this study, QCT and its major metabolites (1-desoxyquinocetone, di-desoxyquinocetone and 3-methyl-quinoxaline-2-carboxylic) in ducks were studied using a simple and sensitive UHPLC-MS/MS assay. Twenty ducks were divided into two groups. (n = 10/group). One group received QCT by oral administration at dose of 40 mg/kg while another group received QCT intravenously at 10 mg/kg...
July 20, 2017: Journal of Veterinary Pharmacology and Therapeutics
https://www.readbyqxmd.com/read/28730284/a-novel-interplay-between-hotair-and-dna-methylation-in-osteosarcoma-cells-indicates-a-new-therapeutic-strategy
#7
Xingang Li, Hongming Lu, Guilian Fan, Miao He, Yu Sun, Kai Xu, Fengjun Shi
PURPOSE: Osteosarcoma (OS) is one of the most prevalent primary malignant bone tumors in adolescent. HOTAIR is highly expressed and associated with the epigenetic modifications, especially DNA methylation, in cancer. However, the regulation mechanism between HOTAIR and DNA methylation and the biological effects of them in the pathogenesis of osteosarcoma remains elusive. METHOD: Through RNA-sequencing and computational analysis, followed by a variety of experimental validations, we report a novel interplay between HOTAIR, miR-126, and DNA methylation in OS...
July 20, 2017: Journal of Cancer Research and Clinical Oncology
https://www.readbyqxmd.com/read/28729527/comparative-transcriptome-analysis-of-the-floral-transition-in-rosa-chinensis-old-blush-and-r-odorata-var-gigantea
#8
Xuelian Guo, Chao Yu, Le Luo, Huihua Wan, Yushu Li, Jia Wang, Tangren Cheng, Huitang Pan, Qixiang Zhang
The floral transition is a crucial developmental event, but little is known about the underlying regulatory networks in seasonally and continuously flowering roses. In this study, we compared the genetic basis of flowering in two rose species, Rosa chinensis 'Old Blush', which flowers continuously, and R. odorata var. gigantea, which blooms in early spring. Gene ontology (GO) terms related to methylation, light reaction, and starch metabolism were enriched in R. odorata var. gigantea and terms associated with sugar metabolism were enriched in R...
July 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28729092/annexin-a2-modulated-proliferation-of-pulmonary-arterial-smooth-muscle-cells-depends-on-caveolae-and-caveolin-1-in-hepatopulmonary-syndrome
#9
Lin Liao, Binwu Zheng, Bin Yi, Chang Liu, Lin Chen, Ziyang Zeng, Jing Gao
We have established that annexin A2 (ANXA2) is an important factor in the experimental hepatopulmonary syndrome (HPS) serum-induced proliferation of pulmonary arterial smooth muscle cells (PASMCs). However, the detailed mechanism remains unclear. ANXA2 translocated to the caveolin-enriched microdomains (caveolae) in PASMCs upon HPS serum stimulation. The disruption of caveolae by Methyl-β-cyclodextrin (MβCD) alleviated the caveolae recruitment of ANXA2 and the ANXA2-mediated activation of ERK1/2 and NF-κB, so that ANXA2-modulated PASMC proliferation was suppressed...
July 17, 2017: Experimental Cell Research
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
#10
Yang Cao, Hai-Guo Jin, Hui-Hai Ma, Zhihui Zhao
Objective: The objective of this study was to compare the DNA methylation profile in the longissimus dorsi muscle (LDM) between Small Tailed Han and Dorper × Small Tailed Han crossbred sheep which were known to exhibit significant difference in meat-production. Methods: Six samples were subjected to MeDIP-seq and subsequent bioinformatics analyses to detect differentially methylated regions (DMRs) between the two groups. Results: 23.08 Gb clean data from six samples were generated and 808 DMRs were identified in gene body or their neighboring up/downstream regions...
June 27, 2017: Asian-Australasian Journal of Animal Sciences
https://www.readbyqxmd.com/read/28728275/-changes-and-differences-of-dna-methylation-in-human-macrophages-infected-with-virulent-and-avirulent-mycobacterium-tuberculosis
#11
L N Lyu, H Y Jia, Z H Li, Z Q Liu, Z D Zhang
Objective: To profile DNA methylation and compare differentially methylated region (DMR) of macrophages infected with virulent and avirulent strains of Mycobacterium tuberculosis (MTB). Methods: PMA(50 ng/ml) treated THP-1 macrophages were left uninfected or infected with the virulent H37Rv(THP-1/Rv) or avirulent H37Ra(THP-1/Ra). The genomic DNA was then extracted and DNA methylation was profiled via Reduced Representation Bisulfite Sequencing (RRBS). The DNA methylation pattern and DMRs between the tested samples were indentified...
July 12, 2017: Chinese Journal of Tuberculosis and Respiratory Diseases
https://www.readbyqxmd.com/read/28726847/mapping-genome-wide-transcription-factor-binding-sites-using-dap-seq
#12
Anna Bartlett, Ronan C O'Malley, Shao-Shan Carol Huang, Mary Galli, Joseph R Nery, Andrea Gallavotti, Joseph R Ecker
To enable low-cost, high-throughput generation of cistrome and epicistrome maps for any organism, we developed DNA affinity purification sequencing (DAP-seq), a transcription factor (TF)-binding site (TFBS) discovery assay that couples affinity-purified TFs with next-generation sequencing of a genomic DNA library. The method is fast, inexpensive, and more easily scaled than chromatin immunoprecipitation sequencing (ChIP-seq). DNA libraries are constructed using native genomic DNA from any source of interest, preserving cell- and tissue-specific chemical modifications that are known to affect TF binding (such as DNA methylation) and providing increased specificity as compared with in silico predictions based on motifs from methods such as protein-binding microarrays (PBMs) and systematic evolution of ligands by exponential enrichment (SELEX)...
August 2017: Nature Protocols
https://www.readbyqxmd.com/read/28725180/endothelial-nitric-oxide-synthase-is-present-in-dendritic-spines-of-neurons-in-primary-cultures
#13
Ariel Caviedes, Manuel Varas-Godoy, Carlos Lafourcade, Soledad Sandoval, Javiera Bravo-Alegria, Thilo Kaehne, Angela Massmann, Jorge P Figueroa, Francisco Nualart, Ursula Wyneken
Nitric oxide exerts important regulatory functions in various brain processes. Its synthesis in neurons has been most commonly ascribed to the neuronal nitric oxide synthase (nNOS) isoform. However, the endothelial isoform (eNOS), which is significantly associated with caveolae in different cell types, has been implicated in synaptic plasticity and is enriched in the dendrites of CA1 hippocampal neurons. Using high resolution microscopy and co-distribution analysis of eNOS with synaptic and raft proteins, we now show for the first time in primary cortical and hippocampal neuronal cultures, virtually devoid of endothelial cells, that eNOS is present in neurons and is localized in dendritic spines...
2017: Frontiers in Cellular Neuroscience
https://www.readbyqxmd.com/read/28723632/potential-link-between-fusobacterium-enrichment-and-dna-methylation-accumulation-in-the-inflammatory-colonic-mucosa-in-ulcerative-colitis
#14
Tomomitsu Tahara, Ichiro Hirata, Naoko Nakano, Sayumi Tahara, Noriyuki Horiguchi, Tomohiko Kawamura, Masaaki Okubo, Takamitsu Ishizuka, Hyuga Yamada, Dai Yoshida, Takafumi Ohmori, Kohei Maeda, Naruomi Komura, Hirokazu Ikuno, Yasutaka Jodai, Toshiaki Kamano, Mitsuo Nagasaka, Yoshihito Nakagawa, Tetsuya Tuskamoto, Makoto Urano, Tomoyuki Shibata, Makoto Kuroda, Naoki Ohmiya
BACKGROUND AND AIM: Fusobacterium enrichment has been associated with colorectal cancer development. Ulcerative colitis (UC) associated tumorigenesis is characterized as high degree of methylation accumulation through continuous colonic inflammation. The aim of this study was to investigate a potential link between Fusobacterium enrichment and DNA methylation accumulation in the inflammatory colonic mucosa in UC. METHODS: In the candidate analysis, inflamed colonic mucosa from 86 UC patients were characterized the methylation status of colorectal a panel of cancer related 24 genes...
June 27, 2017: Oncotarget
https://www.readbyqxmd.com/read/28722229/a-transposon-directed-epigenetic-change-in-zmcct-underlies-quantitative-resistance-to-gibberella-stalk-rot-in-maize
#15
Chao Wang, Qin Yang, Weixiang Wang, Yipu Li, Yanling Guo, Dongfeng Zhang, Xuena Ma, Wei Song, Jiuran Zhao, Mingliang Xu
A major resistance quantitative trait locus, qRfg1, significantly enhances maize resistance to Gibberella stalk rot, a devastating disease caused by Fusarium graminearum. However, the underlying molecular mechanism remains unknown. We adopted a map-based cloning approach to identify the resistance gene at qRfg1 and examined the dynamic epigenetic changes during qRfg1-mediated maize resistance to the disease. A CCT domain-containing gene, ZmCCT, is the causal gene at the qRfg1 locus and a polymorphic CACTA-like transposable element (TE1) c...
July 19, 2017: New Phytologist
https://www.readbyqxmd.com/read/28719192/precise-molecular-design-of-high-tc-3d-organic-inorganic-perovskite-ferroelectric-mehdabco-rbi3-mehdabco-n-methyl-1-4-diazabi-cyclo-2-2-2-octane
#16
Wan-Ying Zhang, Yuan-Yuan Tang, Peng-Fei Li, Ping-Ping Shi, Wei-Qiang Liao, Da-Wei Fu, Heng-Yun Ye, Yi Zhang, Ren-Gen Xiong
With the flourishing development of (CH3NH3)PbI3, three-dimensional (3D) organic-inorganic perovskites with unique structure-property flexibility have become a worldwide focus. However, they still face great challenges in effec-tively inducing ferroelectricity. Despite the typical 3D perovskite structure and the ability of dabco to trigger phase transition, unfortunately [H2dabco]RbCl3 (dabco = 1,4-diazabicyclo[2.2.2]octane) adopts a nonpolar crystal structure without ferroelectricity. Within larger RbI3 framework, we assemble N-methyl-dabco gained by reducing the molecular symmetry of dabco into a new 3D organic-inorganic perovskite...
July 18, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28716088/loss-of-dip2c-in-rko-cells-stimulates-changes-in-dna-methylation-and-epithelial-mesenchymal-transition
#17
Chatarina Larsson, Muhammad Akhtar Ali, Tatjana Pandzic, Anders M Lindroth, Liqun He, Tobias Sjöblom
BACKGROUND: The disco-interacting protein 2 homolog C (DIP2C) gene is an uncharacterized gene found mutated in a subset of breast and lung cancers. To understand the role of DIP2C in tumour development we studied the gene in human cancer cells. METHODS: We engineered human DIP2C knockout cells by genome editing in cancer cells. The growth properties of the engineered cells were characterised and transcriptome and methylation analyses were carried out to identify pathways deregulated by inactivation of DIP2C...
July 17, 2017: BMC Cancer
https://www.readbyqxmd.com/read/28715427/global-analysis-of-dna-methylation-in-young-j1-and-senescent-j2-gossypium-hirsutum-l-cotyledons-by-medip-seq
#18
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/28711544/concordance-of-dna-methylation-profiles-between-breast-core-biopsy-and-surgical-excision-specimens-containing-ductal-carcinoma-in-situ-dcis
#19
Youdinghuan Chen, Jonathan D Marotti, Erik G Jenson, Tracy L Onega, Kevin C Johnson, Brock C Christensen
The utility and reliability of assessing molecular biomarkers for translational applications on pre-operative core biopsy specimens assume consistency of molecular profiles with larger surgical specimens. Whether DNA methylation in ductal carcinoma in situ (DCIS), measured in core biopsy and surgical specimens are similar, remains unclear. Here, we compared genome-scale DNA methylation measured in matched core biopsy and surgical specimens from DCIS, including specific DNA methylation biomarkers of subsequent invasive cancer...
July 12, 2017: Experimental and Molecular Pathology
https://www.readbyqxmd.com/read/28709003/3d-chromatin-structures-of-mature-gametes-and-structural-reprogramming-during-mammalian-embryogenesis
#20
Yuwen Ke, Yanan Xu, Xuepeng Chen, Songjie Feng, Zhenbo Liu, Yaoyu Sun, Xuelong Yao, Fangzhen Li, Wei Zhu, Lei Gao, Haojie Chen, Zhenhai Du, Wei Xie, Xiaocui Xu, Xingxu Huang, Jiang Liu
High-order chromatin structure plays important roles in gene expression regulation. Knowledge of the dynamics of 3D chromatin structures during mammalian embryo development remains limited. We report the 3D chromatin architecture of mouse gametes and early embryos using an optimized Hi-C method with low-cell samples. We find that mature oocytes at the metaphase II stage do not have topologically associated domains (TADs). In sperm, extra-long-range interactions (>4 Mb) and interchromosomal interactions occur frequently...
July 13, 2017: Cell
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