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Methylation enrichment

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https://www.readbyqxmd.com/read/28339081/hbx-represses-riz1-expression-by-dna-methyltransferase%C3%A2-1-involvement-in-decreased-mir-152-in-hepatocellular-carcinoma
#1
Zhujiang Zhao, Ying Hu, Xiaohui Shen, Yingbin Lao, Lihua Zhang, Xuemei Qiu, Jiaojiao Hu, Pihai Gong, He Cui, Sen Lu, Ying Zheng, Menghan Zhou, Hong Fan
Hepatitis B virus (HBV) is mainly suspected to promote hepatocellular carcinoma (HCC) development by epigenetic alteration. The HBV X protein (HBx) plays a key role in the molecular pathogenesis of HBV-related HCC. However, the mechanism of HBx-mediated hepatocarcinogenesis remains to be elucidated. RIZ1 gene, a candidate HCC suppressor gene, is frequently found to be hypermethylated and downregulated in HCC. In the present study, we show that the expression of RIZ1 was downregulated in 65% HCC tissues. Decreased expression of RIZ1 was restored by 5'-Aza in MHCC-97H HCC cell lines...
March 21, 2017: Oncology Reports
https://www.readbyqxmd.com/read/28335720/widespread-promoter-methylation-of-synaptic-plasticity-genes-in-long-term-potentiation-in-the-adult-brain-in-vivo
#2
Jesper L V Maag, Dominik C Kaczorowski, Debabrata Panja, Timothy J Peters, Clive R Bramham, Karin Wibrand, Marcel E Dinger
BACKGROUND: DNA methylation is a key modulator of gene expression in mammalian development and cellular differentiation, including neurons. To date, the role of DNA modifications in long-term potentiation (LTP) has not been explored. RESULTS: To investigate the occurrence of DNA methylation changes in LTP, we undertook the first detailed study to describe the methylation status of all known LTP-associated genes during LTP induction in the dentate gyrus of live rats...
March 23, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28335437/effect-of-clozapine-on-dna-methylation-in-peripheral-leukocytes-from-patients-with-treatment-resistant-schizophrenia
#3
Makoto Kinoshita, Shusuke Numata, Atsushi Tajima, Hidenaga Yamamori, Yuka Yasuda, Michiko Fujimoto, Shinya Watanabe, Hidehiro Umehara, Shinji Shimodera, Takanobu Nakazawa, Masataka Kikuchi, Akihiro Nakaya, Hitoshi Hashimoto, Issei Imoto, Ryota Hashimoto, Tetsuro Ohmori
Clozapine is an atypical antipsychotic, that is established as the treatment of choice for treatment-resistant schizophrenia (SCZ). To date, no study investigating comprehensive DNA methylation changes in SCZ patients treated with chronic clozapine has been reported. The purpose of the present study is to reveal the effects of clozapine on DNA methylation in treatment-resistant SCZ. We conducted a genome-wide DNA methylation profiling in peripheral leukocytes (485,764 CpG dinucleotides) from treatment-resistant SCZ patients treated with clozapine (n = 21) in a longitudinal study...
March 14, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28334972/enrichment-methods-provide-a-feasible-approach-to-comprehensive-and-adequately-powered-investigations-of-the-brain-methylome
#4
Robin F Chan, Andrey A Shabalin, Lin Y Xie, Daniel E Adkins, Min Zhao, Gustavo Turecki, Shaunna L Clark, Karolina A Aberg, Edwin J C G van den Oord
Methylome-wide association studies are typically performed using microarray technologies that only assay a very small fraction of the CG methylome and entirely miss two forms of methylation that are common in brain and likely of particular relevance for neuroscience and psychiatric disorders. The alternative is to use whole genome bisulfite (WGB) sequencing but this approach is not yet practically feasible with sample sizes required for adequate statistical power. We argue for revisiting methylation enrichment methods that, provided optimal protocols are used, enable comprehensive, adequately powered and cost-effective genome-wide investigations of the brain methylome...
February 25, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334074/genome-wide-analysis-reveals-that-exon-methylation-facilitates-its-selective-usage-in-the-human-transcriptome
#5
Shengli Li, Jiwei Zhang, Shenglin Huang, Xianghuo He
DNA methylation, especially in promoter regions, is a well-characterized epigenetic marker related to gene expression regulation in eukaryotes. However, the role of intragenic DNA methylation in the usage of corresponding exons still remains elusive. In this study, we described the DNA methylome across 10 human tissues. The human genome showed both conserved and varied methylation levels among these tissues. We found that the methylation densities in promoters and first exons were negatively correlated with the corresponding gene expression level...
February 16, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28332741/robust-stimuli-responsive-membranes-prepared-from-a-blend-of-polysulfone-and-a-graft-copolymer-bearing-binary-side-chains-with-thermo-and-ph-responsive-switching-behavior
#6
Lei Miao, Yuanyuan Tu, Yang Yang, Shudong Lin, J W Hu, Min Zhang, Yue Li, Fei Li, Yangmiao Mo
Reported herein is the fabrication of a stimuli-responsive membrane exhibiting independent pH- and temperature-responsive behavior that was prepared from a blend of commercial polysulfone with a functional amphiphilic binary graft copolymer denoted as polysulfone-graft-(poly(isopropylacrylamide-co-acrylic acid)-random-poly(methyl acrylate) (or PSf-g-(P(NIPAAm-co-AA)-r-PMMA)). This series of two graft copolymers with different lengths of P(NIPAAm-co-AA) side-chains were respectively designed and enriched on the membrane surface to serve as thermo- and pH-responsive "on/off" switches...
March 23, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28332084/molecularly-imprinted-membranes-mims-for-selective-removal-of-polychlorinated-biphenyls-pcbs-in-environmental-waters-fabrication-and-characterization
#7
Dennis S Mkhize, Hlengilizwe Nyoni, Laura P Quinn, Bhekie B Mamba, Titus A M Msagati
Molecularly imprinted membranes (MIMs) with selective removal properties for polychlorinated biphenyls (PCBs) were prepared through the phase inversion technique. The MIMs were obtained from casting the viscous solutions of molecularly imprinted polymers (MIPs), polysulfone (PSf), and N-methyl-2-pyrrolidone (NMP) as the casting solvent. Different membranes were prepared at different concentration of MIPs and PSf. The resulting MIMs were characterized by atomic force microscope (AFM), scanning electron microscope (SEM), and Fourier transform infrared spectroscopy (FTIR)...
March 22, 2017: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/28328977/jmjd3-aids-in-reprogramming-of-bone-marrow-progenitor-cells-to-hepatic-phenotype-through-epigenetic-activation-of-hepatic-transcription-factors
#8
Veena Kochat, Zaffar Equbal, Prakash Baligar, Vikash Kumar, Madhulika Srivastava, Asok Mukhopadhyay
The strictly regulated unidirectional differentiation program in some somatic stem/progenitor cells has been found to be modified in the ectopic site (tissue) undergoing regeneration. In these cases, the lineage barrier is crossed by either heterotypic cell fusion or direct differentiation. Though studies have shown the role of coordinated genetic and epigenetic mechanisms in cellular development and differentiation, how the lineage fate of adult bone marrow progenitor cells (BMPCs) is reprogrammed during liver regeneration and whether this lineage switch is stably maintained are not clearly understood...
2017: PloS One
https://www.readbyqxmd.com/read/28323012/extracellular-matrix-alterations-in-the-ketamine-model-of-schizophrenia
#9
Gabriela Matuszko, Sebastiano Curreli, Rahul Kaushik, Axel Becker, Alexander Dityatev
The neural extracellular matrix (ECM) plays an important role in regulation of perisomatic GABAergic inhibition and synaptic plasticity in the hippocampus and cortex. Decreased labeling of perineuronal nets, a form of ECM predominantly associated with parvalbumin-expressing interneurons in the brain, has been observed in post-mortem studies of schizophrenia patients, specifically, in brain areas such as prefrontal cortex, entorhinal cortex, and amygdala. Moreover, glial ECM in the form of dandelion clock-like structures was reported to be altered in schizophrenia patients...
March 16, 2017: Neuroscience
https://www.readbyqxmd.com/read/28322571/age-associated-dna-methylation-changes-in-naive-cd4-t-cells-suggest-an-evolving-autoimmune-epigenotype-in-aging-t-cells
#10
Mikhail G Dozmorov, Patrick Coit, Kathleen Maksimowicz-McKinnon, Amr H Sawalha
AIM: We sought to define age-associated DNA methylation changes in naive CD4(+) T cells. MATERIALS & METHODS: Naive CD4(+) T cells were collected from 74 healthy individuals (age 19-66 years), and age-related DNA methylation changes were characterized. RESULTS: We identified 11,431 age-associated CpG sites, 57% of which were hypermethylated with age. Hypermethylated sites were enriched in CpG islands and repressive transcription factor binding sites, while hypomethylated sites showed T cell specific enrichment in active enhancers marked by H3K27ac and H3K4me1...
March 21, 2017: Epigenomics
https://www.readbyqxmd.com/read/28322272/neuroanatomic-epigenetic-and-genetic-differences-in-monozygotic-twins-discordant-for-attention-deficit-hyperactivity-disorder
#11
Y-C Chen, G Sudre, W Sharp, F Donovan, S C Chandrasekharappa, N Hansen, L Elnitski, P Shaw
The study of monozygotic twins discordant for attention deficit hyperactivity disorder can elucidate mechanisms that contribute to the disorder, which affects ~7% of children. First, using in vivo neuroanatomic imaging on 14 pairs of monozygotic twins (mean age 9.7, s.d. 1.9 years), we found that discordance for the disorder is mirrored by differing dimensions of deep brain structures (the striatum and cerebellum), but not the cerebral cortex. Next, using whole-blood DNA from the same twins, we found a significant enrichment of epigenetic differences in genes expressed in these 'discordant' brain structures...
March 21, 2017: Molecular Psychiatry
https://www.readbyqxmd.com/read/28316770/exaggerated-cph-methylation-in-the-autism-affected-brain
#12
Shannon E Ellis, Simone Gupta, Anna Moes, Andrew B West, Dan E Arking
BACKGROUND: The etiology of autism, a complex, heritable, neurodevelopmental disorder, remains largely unexplained. Given the unexplained risk and recent evidence supporting a role for epigenetic mechanisms in the development of autism, we explored the role of CpG and CpH (H = A, C, or T) methylation within the autism-affected cortical brain tissue. METHODS: Reduced representation bisulfite sequencing (RRBS) was completed, and analysis was carried out in 63 post-mortem cortical brain samples (Brodmann area 19) from 29 autism-affected and 34 control individuals...
2017: Molecular Autism
https://www.readbyqxmd.com/read/28316600/methylation-of-foxp3-tsdr-underlies-the-impaired-suppressive-function-of-tregs-from-long-term-belatacept-treated-kidney-transplant-patients
#13
Evelyn Katy Alvarez Salazar, Arimelek Cortés-Hernández, Germán Rodrigo Alemán-Muench, Josefina Alberú, Jesús R Rodríguez-Aguilera, Félix Recillas-Targa, Victoria Chagoya de Sánchez, Eric Cuevas, Eduardo Mancilla-Urrea, María Pérez García, Guillermo Mondragón-Ramírez, Mario Vilatobá, Ian Bostock, Erick Hernández-Méndez, David De Rungs, Eduardo A García-Zepeda, Gloria Soldevila
Regulatory T cells (Tregs) are considered key players in the prevention of allograft rejection in transplanted patients. Belatacept (BLT) is an effective alternative to calcineurin inhibitors that appears to preserve graft survival and function; however, the impact of this drug in the homeostasis of Tregs in transplanted patients remains controversial. Here, we analyzed the phenotype, function, and the epigenetic status of the Treg-specific demethylated region (TSDR) in FOXP3 of circulating Tregs from long-term kidney transplant patients under BLT or Cyclosporine A treatment...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/28315013/protective-vaccination-and-blood-stage-malaria-modify-dna-methylation-of-gene-promoters-in-the-liver-of-balb-c-mice
#14
Saleh Al-Quraishy, Mohamed A Dkhil, Abdel-Azeem S Abdel-Baki, Foued Ghanjati, Lars Erichsen, Simeon Santourlidis, Frank Wunderlich, Marcos J Araúzo-Bravo
Epigenetic mechanisms such as DNA methylation are increasingly recognized to be critical for vaccination efficacy and outcome of different infectious diseases, but corresponding information is scarcely available for host defense against malaria. In the experimental blood-stage malaria Plasmodium chabaudi, we investigate the possible effects of a blood-stage vaccine on DNA methylation of gene promoters in the liver, known as effector against blood-stage malaria, using DNA methylation microarrays. Naturally susceptible Balb/c mice acquire, by protective vaccination, the potency to survive P...
March 18, 2017: Parasitology Research
https://www.readbyqxmd.com/read/28304185/modulation-of-transcription-factor-binding-and-epigenetic-regulation-of-the-mlh1-cpg-island-and-shore-by-polymorphism-rs1800734-in-colorectal-cancer
#15
Andrea J Savio, Bharati Bapat
The MLH1 promoter polymorphism rs1800734 is associated with MLH1 CpG island hypermethylation and expression loss in colorectal cancer (CRC). Conversely, variant rs1800734 is associated with MLH1 shore, but not island, hypomethylation in peripheral blood mononuclear cell DNA. To explore these distinct patterns, MLH1 CpG island and shore methylation was assessed in CRC cell lines stratified by rs1800734 genotype. Cell lines containing the variant A allele demonstrated MLH1 shore hypomethylation compared to wild type (GG)...
March 17, 2017: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/28303968/sex-differences-in-dna-methylation-of-the-cord-blood-are-related-to-sex-bias-psychiatric-diseases
#16
Mariana Maschietto, Laura Caroline Bastos, Ana Carolina Tahira, Elen Pereira Bastos, Veronica Luiza Vale Euclydes, Alexandra Brentani, Günther Fink, Angelica de Baumont, Aloísio Felipe-Silva, Rossana Pulcineli Vieira Francisco, Gisele Gouveia, Sandra Josefina Ferraz Ellero Grisi, Ana Maria Ulhoa Escobar, Carlos Alberto Moreira-Filho, Guilherme Vanoni Polanczyk, Euripedes Constantino Miguel, Helena Brentani
Sex differences in the prevalence of psychiatric disorders are well documented, with exposure to stress during gestation differentially impacting females and males. We explored sex-specific DNA methylation in the cord blood of 39 females and 32 males born at term and with appropriate weight at birth regarding their potential connection to psychiatric outcomes. Mothers were interviewed to gather information about environmental factors (gestational exposure) that could interfere with the methylation profiles in the newborns...
March 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28302063/epigenetic-and-genetic-alterations-and-their-influence-on-gene-regulation-in-chronic-lymphocytic-leukemia
#17
Di Huang, Ivan Ovcharenko
BACKGROUND: To understand the changes of gene regulation in carcinogenesis, we explored signals of DNA methylation - a stable epigenetic mark of gene regulatory elements - and designed a computational model to profile loss and gain of regulatory elements (REs) during carcinogenesis. We also utilized sequencing data to analyze the allele frequency of single nucleotide polymorphisms (SNPs) and detected the cancer-associated SNPs, i.e., the SNPs displaying the significant allele frequency difference between cancer and normal samples...
March 16, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28301567/integrated-analysis-of-promoter-mutation-methylation-and-expression-of-akt1-gene-in-chinese-breast-cancer-patients
#18
Jianfu Heng, Xinwu Guo, Wenhan Wu, Yue Wang, Guoli Li, Ming Chen, Limin Peng, Shouman Wang, Lizhong Dai, Lili Tang, Jun Wang
BACKGROUND: As downstream mediators of PI3K /PTEN /AKT /mTORC1 pathway, the AKT isoforms play critical roles in tumorgenesis. Although the pleiotropic effects of AKT1 in breast cancer have been reported, the genetic and epigenetic characteristics of AKT1 promoter region in breast cancer remains to be identified. In this study we aimed to investigate the promoter mutation spectrum, methylation and gene expression pattern of AKT1 and their relationship with breast cancer. METHODS: By using PCR target sequence enrichment and next-generation sequencing technology, we sequenced AKT1 promoter region in pairs of breast tumor and normal tissues from 95 unselected Chinese breast cancer patients...
2017: PloS One
https://www.readbyqxmd.com/read/28298692/enrichment-of-maize-and-triticale-bran-with-recombinant-aspergillus-tubingensis-ferulic-acid-esterase
#19
Eunice N Zwane, Petrus J van Zyl, Kwaku G Duodu, Shaunita H Rose, Karl Rumbold, Willem H van Zyl, Marinda Viljoen-Bloom
Ferulic acid is a natural antioxidant found in various plants and serves as a precursor for various fine chemicals, including the flavouring agent vanillin. However, expensive extraction methods have limited the commercial application of ferulic acid, in particular for the enrichment of food substrates. A recombinant Aspergillus tubingensis ferulic acid esterase Type A (FAEA) was expressed in Aspergillus niger D15#26 and purified with anion-exchange chromatography (3487 U/mg, Km  = 0.43 mM, Kcat = 0.48/min on methyl ferulate)...
March 2017: Journal of Food Science and Technology
https://www.readbyqxmd.com/read/28298687/composition-of-volatile-aromatic-compounds-and-minerals-of-tarhana-enriched-with-cherry-laurel-laurocerasus-officinalis
#20
Hasan Temiz, Zekai Tarakçı
Different concentrations of cherry laurel pulp (0, 5, 10, 15 and 20%) were used to produce tarhana samples. Volatile aromatic compounds and minor mineral content were investigated. Volatile aromatic compounds were analyzed by using GC-MS with SPME fiber and minor mineral values were evaluated with inductively coupled plasma optical emission spectrometer. The statistical analysis showed that addition of pulp affected volatile aromatic compounds and minor mineral content significantly. Thirty five volatile aromatic compounds were found in tarhana samples...
March 2017: Journal of Food Science and Technology
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