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Methylation enrichment

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https://www.readbyqxmd.com/read/28550290/differential-methylation-is-associated-with-non-syndromic-cleft-lip-and-palate-and-contributes-to-penetrance-effects
#1
Lucas Alvizi, Xiayi Ke, Luciano Abreu Brito, Rimante Seselgyte, Gudrun E Moore, Philip Stanier, Maria Rita Passos-Bueno
Non-syndromic cleft lip and/or palate (NSCLP) is a common congenital malformation with a multifactorial model of inheritance. Although several at-risk alleles have been identified, they do not completely explain the high heritability. We postulate that epigenetic factors as DNA methylation might contribute to this missing heritability. Using a Methylome-wide association study in a Brazilian cohort (67 NSCLP, 59 controls), we found 578 methylation variable positions (MVPs) that were significantly associated with NSCLP...
May 26, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28545453/genome-wide-methylation-analysis-reveals-differentially-methylated-loci-that-are-associated-with-an-age-dependent-increase-in-bovine-fibroblast-response-to-lps
#2
Filiz T Korkmaz, David E Kerr
BACKGROUND: Differences in DNA methylation are known to contribute to the development of immune-related disorders in humans but relatively little is known about how methylation regulates immune function in cattle. Utilizing whole-transcriptome analyses of bovine dermal fibroblasts, we have previously identified an age and breed-dependent up-regulation of genes within the toll-like receptor 4 (TLR4) pathway that correlates with enhanced fibroblast production of IL-8 in response to lipopolysaccharide (LPS)...
May 25, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28537885/identifying-cpg-sites-with-different-differential-methylation-frequencies-in-colorectal-cancer-tissues-based-on-individualized-differential-methylation-analysis
#3
Haidan Yan, Jun He, Qingzhou Guan, Hao Cai, Lin Zhang, Weicheng Zheng, Lishuang Qi, Suyun Zhang, Huaping Liu, Hongdong Li, Wenyuan Zhao, Sheng Yang, Zheng Guo
A big challenge to clinical diagnosis and therapy of colorectal cancer (CRC) is its extreme heterogeneity, and thus it would be of special importance if we could find common biomarkers besides subtype-specific biomarkers for CRC. Here, with DNA methylation data produced by different laboratories, we firstly revealed that the relative methylation-level orderings (RMOs) of CpG sites within colorectal normal tissues are highly stable but widely disrupted in the CRC tissues. This finding provides the basis for using the RankComp algorithm to identify differentially methylated (DM) CpG sites in every individual CRC sample through comparing the RMOs within the individual sample with the stable RMOs predetermined in normal tissues...
May 7, 2017: Oncotarget
https://www.readbyqxmd.com/read/28537673/comprehensive-analysis-of-microrna-mrna-signature-in-colon-adenocarcinoma
#4
J-Y Wang, C-L Wang, X-M Wang, F-J Liu
OBJECTIVE: The goal of our study was to identify the regulatory mechanisms of gene expression mediated by miRNAs and DNA methylation in colon adenocarcinoma (COAD). MATERIALS AND METHODS:   The miRNAs and mRNAs expression and DNA methylation data of COAD and adjacent normal tissues were obtained from The Cancer Genome Atlas (TCGA) database. Based on the differentially expressed miRNAs and mRNAs, miRNA-mRNA pairs were obtained by correlation analysis and prediction algorithms...
May 2017: European Review for Medical and Pharmacological Sciences
https://www.readbyqxmd.com/read/28537268/global-mapping-of-carm1-substrates-defines-enzyme-specificity-and-substrate-recognition
#5
Evgenia Shishkova, Hao Zeng, Fabao Liu, Nicholas W Kwiecien, Alexander S Hebert, Joshua J Coon, Wei Xu
Protein arginine methyltransferases (PRMTs) introduce arginine methylation, a post-translational modification with the increasingly eminent role in normal physiology and disease. PRMT4 or coactivator-associated arginine methyltransferase 1 (CARM1) is a propitious target for cancer therapy; however, few CARM1 substrates are known, and its mechanism of substrate recognition is poorly understood. Here we employed a quantitative mass spectrometry approach to globally profile CARM1 substrates in breast cancer cell lines...
May 24, 2017: Nature Communications
https://www.readbyqxmd.com/read/28533479/the-landscape-of-dna-methylation-mediated-regulation-of-long-non-coding-rnas-in-breast-cancer
#6
Chunlong Zhang, Xinyu Wang, Xuecang Li, Ning Zhao, Yihan Wang, Xiaole Han, Ce Ci, Jian Zhang, Meng Li, Yan Zhang
Although systematic studies have identified a host of long non-coding RNAs (lncRNAs) which are involved in breast cancer, the knowledge about the methyla-tion-mediated dysregulation of those lncRNAs remains limited. Here, we integrated multi-omics data to analyze the methylated alteration of lncRNAs in breast invasive carcinoma (BRCA). We found that lncRNAs showed diverse methylation patterns on promoter regions in BRCA. LncRNAs were divided into two categories and four subcategories based on their promoter methylation patterns and expression levels be-tween tumor and normal samples...
May 8, 2017: Oncotarget
https://www.readbyqxmd.com/read/28530603/modelling-of-the-effect-of-selenium-fertilization-on-the-content-of-bioactive-compounds-in-broccoli-heads
#7
Andrea Mahn
Selenium (Se) exerts many effects beneficial to health. Broccoli is a Se-hyperaccumulator plant, with Se-fertilization increasing its potential as a functional food. We studied the effect of dose, and the developmental stage at the beginning of Se-fortification, on antioxidant capacity, phenolics, glucosinolates, sulphoraphane, Se-methyl selenocysteine and myrosinase in broccoli. Se-fortification decreased the antioxidant properties and sulphur-containing compounds, but increased Se-methyl-selenocysteine content...
October 15, 2017: Food Chemistry
https://www.readbyqxmd.com/read/28529454/characterization-of-cytosine-methylation-and-the-dna-methyltransferases-of-toxoplasma-gondii
#8
Haixia Wei, Shichen Jiang, Longfei Chen, Cheng He, Shuizhen Wu, Hongjuan Peng
DNA methylation is a key epigenetic modification which confers phenotypic plasticity and adaptation. Cyst-forming strains of Toxoplasma gondii undergo tachyzoite to bradyzoite conversion after initial acute infection of a host, and the reverse conversion may occur in immune-suppressed hosts. The formation of m(5)C is catalyzed by DNA methyltransferase (DNMT). We identified two functional DNA methyltransferases, TgDNMTa and TgDNMTb, in T. gondii that may mediate DNA methylation. The recombinant proteins showed intrinsic methyltransferase activity; both have higher transcription levels in bradyzoites than that in tachyzoites...
2017: International Journal of Biological Sciences
https://www.readbyqxmd.com/read/28522752/mismatch-repair-proteins-initiate-epigenetic-alterations-during-inflammation-driven-tumorigenesis
#9
Ashley R Maiuri, Michael Peng, Shruthi Sriramkumar, Caitlin M Kamplain, Christina DeStefano Shields, Cynthia L Sears, Heather M O'Hagan
Aberrant silencing of genes by DNA methylation contributes to cancer, yet how this process is initiated remains unclear. Using a murine model of inflammation-induced tumorigenesis, we tested the hypothesis that inflammation promotes recruitment of epigenetic proteins to chromatin, initiating methylation and gene silencing in tumors. Compared to normal epithelium and non-inflammation-induced tumors, inflammation-induced tumors gained DNA methylation at CpG islands, some of which are associated with putative tumor suppressor genes...
May 18, 2017: Cancer Research
https://www.readbyqxmd.com/read/28521766/the-histone-h3-variant-h3-3-regulates-gene-body-dna-methylation-in-arabidopsis-thaliana
#10
Heike Wollmann, Hume Stroud, Ramesh Yelagandula, Yoshiaki Tarutani, Danhua Jiang, Li Jing, Bhagyshree Jamge, Hidenori Takeuchi, Sarah Holec, Xin Nie, Tetsuji Kakutani, Steven E Jacobsen, Frédéric Berger
BACKGROUND: Gene bodies of vertebrates and flowering plants are occupied by the histone variant H3.3 and DNA methylation. The origin and significance of these profiles remain largely unknown. DNA methylation and H3.3 enrichment profiles over gene bodies are correlated and both have a similar dependence on gene transcription levels. This suggests a mechanistic link between H3.3 and gene body methylation. RESULTS: We engineered an H3.3 knockdown in Arabidopsis thaliana and observed transcription reduction that predominantly affects genes responsive to environmental cues...
May 18, 2017: Genome Biology
https://www.readbyqxmd.com/read/28521446/candidate-mirnas-and-pathogenesis-investigation-for-hepatocellular-carcinoma-based-on-bioinformatics-analysis
#11
Wenbin Ding, Haixia Yang, Shenchu Gong, Weixiang Shi, Jing Xiao, Jinhua Gu, Yilang Wang, Bosheng He
The present study aimed to explore the mechanisms behind the development and progression of hepatocellular carcinoma (HCC) and identify information regarding HCC-related microRNAs (miRNAs) or marker genes for the gene therapy of HCC. Gene expression profile of GSE67882, generated from 4 hepatitis B virus infected HCC tissue samples (HCC group) and 8 chronic hepatitis B tissue samples with no fibrosis (control group) were downloaded from the Gene Expression Omnibus database. The differentially expressed miRNAs functional enrichment and pathway analyses of HCC were revealed, followed by transcription factor-miRNA interaction network construction and analyses...
May 2017: Oncology Letters
https://www.readbyqxmd.com/read/28511916/pre-treatment-with-amitriptyline-causes-epigenetic-up-regulation-of-neuroprotection-associated-genes-and-has-anti-apoptotic-effects-in-mouse-neuronal-cells
#12
Nguyen Quoc Vuong Tran, An Nghia Nguyen, Kyoko Takabe, Zentaro Yamagata, Kunio Miyake
Antidepressants, such as imipramine and fluoxetine, are known to alter gene expression patterns by inducing changes in the epigenetic status of neuronal cells. There is also some evidence for the anti-apoptotic effect of various groups of antidepressants; however, this effect is complicated and cell-type dependent. Antidepressants of the tricyclic group, in particular amitriptyline, have been suggested to be beneficial in the treatment of neurodegenerative disorders. We examined whether amitriptyline exerts an anti-apoptotic effect via epigenetic mechanisms...
May 13, 2017: Neurotoxicology and Teratology
https://www.readbyqxmd.com/read/28510691/nf-%C3%AE%C2%BAb-upregulation-through-epigenetic-silencing-of-ldoc1-drives-tumor-biology-and-specific-immunophenotype-in-group-a-ependymoma
#13
Andrea M Griesinger, Davis A Witt, Sydney T Grob, Sabrina R Georgio Westover, Andrew M Donson, Bridget Sanford, Jean M Mulcahy Levy, Randall Wong, Daniel C Moreira, John A DeSisto, Ilango Balakrishnan, Lindsey M Hoffman, Michael H Handler, Kenneth L Jones, Rajeev Vibhakar, Sujatha Venkataraman, Nicholas K Foreman
Background.: Inflammation has been identified as a hallmark of high-risk Group A (GpA) ependymoma (EPN). Chronic interleukin (IL)-6 secretion from GpA tumors drives an immune suppressive phenotype by polarizing infiltrating monocytes. This study determines the mechanism by which IL-6 is dysregulated in GpA EPN. Methods.: Twenty pediatric GpA and 21 pediatric Group B (GpB) EPN had gene set enrichment analysis for MSigDB Hallmark gene sets performed. Protein and RNA from patients and cell lines were used to validate transcriptomic findings...
May 16, 2017: Neuro-oncology
https://www.readbyqxmd.com/read/28510608/the-biomphalaria-glabrata-dna-methylation-machinery-displays-spatial-tissue-expression-is-differentially-active-in-distinct-snail-populations-and-is-modulated-by-interactions-with-schistosoma-mansoni
#14
Kathrin K Geyer, Umar H Niazi, David Duval, Céline Cosseau, Chad Tomlinson, Iain W Chalmers, Martin T Swain, David J Cutress, Utibe Bickham-Wright, Sabrina E Munshi, Christoph Grunau, Timothy P Yoshino, Karl F Hoffmann
BACKGROUND: The debilitating human disease schistosomiasis is caused by infection with schistosome parasites that maintain a complex lifecycle alternating between definitive (human) and intermediate (snail) hosts. While much is known about how the definitive host responds to schistosome infection, there is comparably less information available describing the snail's response to infection. METHODOLOGY/PRINCIPLE FINDINGS: Here, using information recently revealed by sequencing of the Biomphalaria glabrata intermediate host genome, we provide evidence that the predicted core snail DNA methylation machinery components are associated with both intra-species reproduction processes and inter-species interactions...
May 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28510353/crystal-packing-driven-enrichment-of-atropoisomers
#15
Mona Sharafi, Joseph P Campbell, Sinu C Rajappan, Natavan Dudkina, Danielle L Gray, Toby J Woods, Jianing Li, Severin T Schneebeli
Crystal-packing forces can have a significant impact on the relative stabilities of different molecules and their conformations. The magnitude of such effects is, however, not yet well understood. Herein we show, that crystal packing can completely overrule the relative stabilities of different stereoisomers in solution. Heating of atropoisomers (i.e. "frozen-out" conformational isomers) in solution leads to complex mixtures. In contrast, solid-state heating selectively amplifies minor (<25 mole %) components of these solution-phase mixtures...
May 16, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28508121/overexpression-of-smmyb9b-enhances-tanshinone-concentration-in-salvia-miltiorrhiza-hairy-roots
#16
Jingxian Zhang, Lubin Zhou, Xiaoyu Zheng, Jinjia Zhang, Li Yang, Ronghui Tan, Shujuan Zhao
A Salvia miltiorrhiza R2R3-MYB gene, SmMYB9b , has been cloned and characterized. Overexpression of SmMYB9b resulted in a significant improvement of tanshinones, the lipophilic active ingredients in danshen hairy roots. Plant R2R3-MYB transcription factors play important roles in various physiological and biochemical processes. Danshen (Salvia miltiorrhiza bunge) is a valuable medicinal herb with tanshinones and salvianolic acids as the principal bioactive ingredients. A number of putative R2R3-MYB transcription factors have been identified in the plant, but their function remains to be studied...
May 15, 2017: Plant Cell Reports
https://www.readbyqxmd.com/read/28507606/transcription-and-chromatin-determinants-of-de-novo-dna-methylation-timing-in-oocytes
#17
Lenka Gahurova, Shin-Ichi Tomizawa, Sébastien A Smallwood, Kathleen R Stewart-Morgan, Heba Saadeh, Jeesun Kim, Simon R Andrews, Taiping Chen, Gavin Kelsey
BACKGROUND: Gametogenesis in mammals entails profound re-patterning of the epigenome. In the female germline, DNA methylation is acquired late in oogenesis from an essentially unmethylated baseline and is established largely as a consequence of transcription events. Molecular and functional studies have shown that imprinted genes become methylated at different times during oocyte growth; however, little is known about the kinetics of methylation gain genome wide and the reasons for asynchrony in methylation at imprinted loci...
2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/28505127/variability-of-dna-methylation-within-schizophrenia-risk-loci-across-subregions-of-human-hippocampus
#18
W Brad Ruzicka, Sivan Subburaju, Francine M Benes
Identification of 108 genomic regions significantly associated with schizophrenia risk by the Psychiatric Genomics Consortium was a milestone for the field, and much work is now focused on determining the mechanism of risk associated with each locus. Within these regions, we investigated variability of DNA methylation, a low-level cellular phenotype closely linked to genotype, in two highly similar cellular populations sampled from the human hippocampus, to draw inferences about the elaboration of genotype to phenotype within these loci enriched for schizophrenia risk...
May 15, 2017: Genes
https://www.readbyqxmd.com/read/28501686/immobilisation-on-mesoporous-silica-and-solvent-rinsing-improve-the-transesterification-abilities-of-feruloyl-esterases-from-myceliophthora-thermophila
#19
Silvia Hüttner, Milene Zezzi Do Valle Gomes, Laura Iancu, Anders Palmqvist, Lisbeth Olsson
The immobilisation of four feruloyl esterases (FAEs) (FaeA1, FaeA2, FaeB1, FaeB2) from the thermophilic fungus Myceliophthora thermophila C1 was studied and optimised via physical adsorption onto various mesoporous silica particles with pore diameters varying from 6.6nm to 10.9nm. Using crude enzyme preparations, enrichment of immobilised FAEs was observed, depending on pore diameter and protein size. The immobilised enzymes were successfully used for the synthesis of butyl ferulate through transesterification of methyl ferulate with 1-butanol...
April 29, 2017: Bioresource Technology
https://www.readbyqxmd.com/read/28501431/lipase-catalyzed-kinetic-resolution-as-key-step-in-the-synthesis-of-enantiomerically-pure-%C3%AF-ligands-with-2-benzopyran-structure
#20
Inga Knappmann, Kirstin Lehmkuhl, Jens Köhler, Dirk Schepmann, Martin Giera, Franz Bracher, Bernhard Wünsch
In order to obtain enantiomerically pure σ1 receptor ligands with a 2-benzopyran scaffold an Oxa-Pictet-Spengler reaction with the enantiomerically pure 2-phenylethanol derivatives (R)-4 and (S)-4 was envisaged. The kinetic resolution of racemic alcohol (±)-4 using Amano Lipase PS-C II and isopropenyl acetate in tert-butyl methyl ether led to the (R)-configured alcohol (R)-4 in 42% yield with an enantiomeric excess of 99.6%. The (S)-configured alcohol (S)-4 was obtained by Amano Lipase PS-C II catalyzed hydrolysis of enantiomerically enriched acetate (S)-5 (76...
April 30, 2017: Bioorganic & Medicinal Chemistry
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