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Methylation enrichment

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https://www.readbyqxmd.com/read/29054971/a-novel-g-quadruplex-motif-in-the-human-met-promoter-region
#1
Jing Yan, Deming Zhao, Liping Dong, Shuang Pan, Fengjin Hao, Yifu Guan
It's known that the guanine-rich strands in protooncogene promoters can fold into G-quadruplex structures to regulate gene expression. An intramolecular parallel G-quadruplex has been identified in MET promoter. It acts as a repressor in regulating MET expression. However, the full guanine-rich region in MET promoter forms a hybrid parallel/antiparallel G-quadruplex structure under physiological conditions, which means there are some antiparallel and hybrid parallel/antiparallel G-quadruplex structures in this region...
October 20, 2017: Bioscience Reports
https://www.readbyqxmd.com/read/29053336/interplay-between-ezh2-and-g9a-regulates-cxcl10-gene-repression-in-idiopathic-pulmonary-fibrosis
#2
William R Coward, Oliver J Brand, Alice Pasini, Gisli Jenkins, Alan J Knox, Linhua Pang
Selective repression of the antifibrotic gene CXCL10 contributes to tissue remodelling in idiopathic pulmonary fibrosis (IPF). We have previously reported that histone deacetylation and histone H3 lysine 9 (H3K9) methylation are involved in CXCL10 repression. This study explored the role of H3K27 methylation and the interplay between the two histone lysine methyltransferases, Enhancer of Zest Homolog 2 (EZH2) and G9a, in CXCL10 repression in IPF. By applying chromatin immunoprecipitation (ChIP), Re-ChIP and proximity ligation assays, we demonstrated that, like G9a-mediated H3K9 methylation, EZH2-mediated H3K27me3 was significantly enriched at the CXCL10 promoter in fibroblasts from IPF lungs (F-IPF) compared with fibroblasts from non-fibrotic lungs (F-NL) and that EZH2 and G9a physically interacted with each other...
October 20, 2017: American Journal of Respiratory Cell and Molecular Biology
https://www.readbyqxmd.com/read/29052184/bisulfite-sequencing-using-small-dna-amounts
#3
Susanne Edelmann, Stefan Scholten
Bisulfite sequencing (BS-seq) enables the detection of DNA methylation at cytosine residues (5mC) at single-nucleotide resolution. For many applications, a limiting factor of conventional BS-seq protocols is the high amount of DNA required, since the treatment with bisulfite causes severe DNA fragmentation. Here, we describe a post-bisulfite tagging method that accounts for this problem. Illumina-compatible BS-seq libraries can be obtained from as little as five single haploid maize cells, enabling whole genome BS-seq (WGBS) for the generation of genome-wide, cell-type specific DNA methylation profiles...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29050842/pseudo-template-molecularly-imprinted-polymer-for-determination-of-14-kind-of-%C3%AE-agonists-in-animal-urine-by-ultra-high-performance-liquid-chromatography-tandem-mass-spectrometry
#4
Decheng Suo, Ruiguo Wang, Peilong Wang, Xia Fan, Xiaoou Su
A pseudo template molecularly imprinted polymer (MIP) for selective extraction of β-agonists was prepared using 4-hydroxyphenethyl alcohol as pseudo template molecule, methyl acrylic acid as functional monomer, and ethylene glycol dimethacrylate as cross-linker. Selectivity and adsorption capacity of prepared MIP were studied in detail. MIP selectively adsorbed 14 types of β-agonists. Advantages of the prepared polymer include non-template leakage in purification of target analytes and cheap cost. MIP was used to purify β-agonists in urine samples...
October 3, 2017: Journal of Chromatography. A
https://www.readbyqxmd.com/read/29050335/evidence-for-the-association-of-chromatin-and-microrna-regulation-in-the-human-genome
#5
Bang-Bao Tao, Xi-Qiang Liu, Wenhao Zhang, Shu Li, Dong Dong, Mang Xiao, Jun Zhong
Both microRNAs (miRNAs) and chromatin regulation play important roles in cellular processes and they function at different regulatory levels of transcription. Although efforts have been devoted to the investigation of miRNA and chromatin regulation, there's still no comprehensive work to illustrate their relationships due tothe lack of whole-genome wide datasets in different human cellular contexts. Based on the recently published large-scale epigenetic data, we examined the association between miRNA and epigenetic machinery...
September 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/29048172/effects-of-different-lipophilized-ferulate-esters-in-fish-oil-enriched-milk-partitioning-interaction-protein-and-lipid-oxidation
#6
Xujian Qiu, Charlotte Jacobsen, Pierre Villeneuve, Erwann Durand, Ann-Dorit Moltke Sørensen
Antioxidant effects of ferulic acid and lipophilized ferulate esters were investigated in fish oil-enriched milk. Methyl ferulate (C1) and ethyl ferulate (C2) more efficiently prevented lipid oxidation than dodecyl ferulate (C12) did, followed by ferulic acid (C0). The combination of C1 or C2 with C12 could have a "synergistic" effect indicated by peroxide value, hexanal, and 1-penten-3-ol analysis results. These antioxidants also showed protein oxidation inhibition effects. The most effective antioxidants (C1 and C2) had the highest concentration in the precipitate phase but the lowest concentration in the aqueous phase, which was the opposite of the partitioning of C0...
October 19, 2017: Journal of Agricultural and Food Chemistry
https://www.readbyqxmd.com/read/29046734/epigenome-wide-association-study-of-asthma-and-wheeze-in-childhood-and-adolescence
#7
Ryan Arathimos, Matthew Suderman, Gemma C Sharp, Kimberley Burrows, Raquel Granell, Kate Tilling, Tom R Gaunt, John Henderson, Susan Ring, Rebecca C Richmond, Caroline L Relton
BACKGROUND: Asthma heritability has only been partially explained by genetic variants and is known to be sensitive to environmental factors, implicating epigenetic modifications such as DNA methylation in its pathogenesis. METHODS: Using data collected in the Avon Longitudinal Study of Parents and Children (ALSPAC), we assessed associations of asthma and wheeze with DNA methylation at 7.5 and 16.5 years, at over 450,000 CpG sites in DNA from the peripheral blood of approx...
2017: Clinical Epigenetics
https://www.readbyqxmd.com/read/29046688/global-analysis-of-small-rna-dynamics-during-seed-development-of-picea-glauca-and-arabidopsis-thaliana-populations-reveals-insights-on-their-evolutionary-trajectories
#8
Yang Liu, Yousry A El-Kassaby
While DNA methylation carries genetic signals and is instrumental in the evolution of organismal complexity, small RNAs (sRNAs), ~18-24 ribonucleotide (nt) sequences, are crucial mediators of methylation as well as gene silencing. However, scant study deals with sRNA evolution via featuring their expression dynamics coupled with species of different evolutionary time. Here we report an atlas of sRNAs and microRNAs (miRNAs, single-stranded sRNAs) produced over time at seed-set of two major spermatophytes represented by populations of Picea glauca and Arabidopsis thaliana with different seed-set duration...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29045485/alterations-in-the-placental-methylome-with-maternal-obesity-and-evidence-for-metabolic-regulation
#9
Kohzoh Mitsuya, Ashley N Parker, Lu Liu, Jianhua Ruan, Margreet C M Vissers, Leslie Myatt
The inflammatory and metabolic derangements of obesity in pregnant women generate an adverse intrauterine environment, increase pregnancy complications and adverse fetal outcomes and program the fetus for obesity and metabolic syndrome in later life. We hypothesized that epigenetic modifications in placenta including altered DNA methylation/hydroxymethylation may mediate these effects. Term placental villous tissue was collected following cesarean section from lean (prepregnancy BMI<25) or obese (BMI>30) women...
2017: PloS One
https://www.readbyqxmd.com/read/29044423/cultured-bovine-embryo-biopsy-conserves-methylation-marks-from-original-embryo
#10
Noelia Fonseca Balvís, Soledad Garcia-Martinez, Serafín Pérez-Cerezales, Elena Ivanova, Isabel Gomez-Redondo, Meriem Hamdi, Dimitrios Rizos, Pilar Coy, Gavin Kelsey, Alfonso Gutierrez-Adan
A major limitation of embryo epigenotyping by chromatin immunoprecipitation analysis is the reduced amount of sample available from an embryo biopsy. We developed an in vitro system to expand trophectoderm cells from an embryo biopsy to overcome this limitation. This work analyzes whether expanded trophectoderm (EX) is representative of the trophectoderm (TE) methylation or adaptation to culture has altered its epigenome. We took a small biopsy from the trophectoderm (30-40 cells) of in vitro produced bovine-hatched blastocysts and cultured it on fibronectin-treated plates until we obtained ∼4 × 104 cells...
August 1, 2017: Biology of Reproduction
https://www.readbyqxmd.com/read/29043999/study-of-global-dna-methylation-in-monozygotic-twins-with-cerebral-palsy
#11
Yuxiao Yuan
The objective of this paper is to study the global DNA Methylation in monozygotic (MZ) twins with cerebral palsy. Two pairs of twins (a cerebral palsy children, a normal child) admitted to the First Affiliated Hospital of Zhengzhou University were selected as subjects. The phenol-chloroform method was used to extract DNA from venous blood and micro satellite DNA genotyping technique was used to identify the eggs of the twins. DNA methylation fragments were enriched by MBD affinity column chromatography, followed by Solexa sequencing and bioinformatics analysis...
July 2017: Pakistan Journal of Pharmaceutical Sciences
https://www.readbyqxmd.com/read/29042681/the-construction-of-intrahepatic-cholangiocarcinoma-model-in-zebrafish
#12
Jing Wang, Xiaoqian Leng, Guiping Wang, Xiaoyang Wan, Hong Cao
Intrahepatic cholangiocarcinoma (ICC) is a highly malignant tumor, difficult to diagnose even at an early stage. In this study, we successfully constructed an nras (61K) -induced ICC model in zebrafish. Transcriptome analysis and gene set enrichment analysis (GSEA) of liver samples of the ICC and WT (wild-type) zebrafish revealed that the genes differentially expressed between the two groups were mainly involved in focal adhesion, chemokine signaling and metabolic pathways. Analysis of DNA methylomes revealed that compared with WT samples, methylated genes in ICC samples were enriched in functions associated with cellular, single-organism and metabolic processes...
October 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29039998/fn1-fos-and-itga5-induce-preeclampsia-abnormal-expression-and-methylation
#13
Mei Zhao, Lin Li, Xiumei Yang, Jianying Cui, Hong Li
OBJECTIVE: As a frequent hypertensive disorder in pregnancy, preeclampsia causes 15% of all preterm deliveries. This study aims to understand its mechanism via analyzing gene expression and methylation data. METHODS: Human gene expression microarray data (GSE73374) and corresponding DNA methylation microarray data (GSE73375) of preeclamptic placental tissues (n = 19) and normotensive placental tissues (n = 17) were obtained from the Gene Expression Omnibus. Differentially expressed genes (DEGs), differentially methylated regions (DMRs) and CpG islands (DMIs) were identified and compared...
October 17, 2017: Hypertension in Pregnancy
https://www.readbyqxmd.com/read/29039597/whole%C3%A2-genome-scale-identification-of-methylation-markers-specific-for-cerebral-palsy-in-monozygotic-discordant-twins
#14
Zhe Jiao, Zhimei Jiang, Jingtao Wang, Hui Xu, Qiang Zhang, Shuang Liu, Ning Du, Yuanyuan Zhang, Hongbin Qiu
Cerebral palsy (CP) is a severe type of brain disease affecting movement and posture. Although CP has strong genetic and environmental components, considerable differences in the methylome between monozygotic (MZ) twins discordant for CP implicates epigenetic contributors as well. In order to determine the differences in methylation in patients with CP without interference of the interindividual genomic variation, four pairs of MZ twins discordant for CP were profiled for DNA methylation changes using reduced representation bisulfite sequencing on the genomic‑scale...
October 17, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29036576/currbs-simple-and-robust-evaluation-of-enzyme-combinations-for-reduced-representation-approaches
#15
Daniel E Martin-Herranz, António J M Ribeiro, Felix Krueger, Janet M Thornton, Wolf Reik, Thomas M Stubbs
DNA methylation is an important epigenetic modification in many species that is critical for development, and implicated in ageing and many complex diseases, such as cancer. Many cost-effective genome-wide analyses of DNA modifications rely on restriction enzymes capable of digesting genomic DNA at defined sequence motifs. There are hundreds of restriction enzyme families but few are used to date, because no tool is available for the systematic evaluation of restriction enzyme combinations that can enrich for certain sites of interest in a genome...
September 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29036558/methrafo-medip-seq-methylation-estimate-using-a-random-forest-regressor
#16
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...
July 13, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29036542/database-resources-of-the-big-data-center-in-2018
#17
(no author information available yet)
The BIG Data Center at Beijing Institute of Genomics (BIG) of the Chinese Academy of Sciences provides freely open access to a suite of database resources in support of worldwide research activities in both academia and industry. With the vast amounts of omics data generated at ever-greater scales and rates, the BIG Data Center is continually expanding, updating and enriching its core database resources through big-data integration and value-added curation, including BioCode (a repository archiving bioinformatics tool codes), BioProject (a biological project library), BioSample (a biological sample library), Genome Sequence Archive (GSA, a data repository for archiving raw sequence reads), Genome Warehouse (GWH, a centralized resource housing genome-scale data), Genome Variation Map (GVM, a public repository of genome variations), Gene Expression Nebulas (GEN, a database of gene expression profiles based on RNA-Seq data), Methylation Bank (MethBank, an integrated databank of DNA methylomes), and Science Wikis (a series of biological knowledge wikis for community annotations)...
October 3, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29036368/proteomic-identification-of-histone-post-translational-modifications-and-proteins-enriched-at-a-dna-double-strand-break
#18
Pingping Wang, Stephanie Byrum, Faith C Fowler, Sangita Pal, Alan J Tackett, Jessica K Tyler
Here, we use ChAP-MS (chromatin affinity purification with mass spectrometry), for the affinity purification of a sequence-specific single-copy endogenous chromosomal locus containing a DNA double-strand break (DSB). We found multiple new histone post-translational modifications enriched on chromatin bearing a DSB from budding yeast. One of these, methylation of histone H3 on lysine 125, has not previously been reported. Among over 100 novel proteins enriched at a DSB were the phosphatase Sit4, the RNA pol II degradation factor Def1, the mRNA export protein Yra1 and the HECT E3 ligase Tom1...
September 26, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29033324/the-elongation-factor-spt6-maintains-esc-pluripotency-by-controlling-super-enhancers-and-counteracting-polycomb-proteins
#19
A Hongjun Wang, Aster H Juan, Kyung Dae Ko, Pei-Fang Tsai, Hossein Zare, Stefania Dell'Orso, Vittorio Sartorelli
Spt6 coordinates nucleosome dis- and re-assembly, transcriptional elongation, and mRNA processing. Here, we report that depleting Spt6 in embryonic stem cells (ESCs) reduced expression of pluripotency factors, increased expression of cell-lineage-affiliated developmental regulators, and induced cell morphological and biochemical changes indicative of ESC differentiation. Selective downregulation of pluripotency factors upon Spt6 depletion may be mechanistically explained by its enrichment at ESC super-enhancers, where Spt6 controls histone H3K27 acetylation and methylation and super-enhancer RNA transcription...
October 19, 2017: Molecular Cell
https://www.readbyqxmd.com/read/29028941/dysregulation-of-cortical-neuron-dna-methylation-profile-in-autism-spectrum-disorder
#20
Stefano Nardone, Dev Sharan Sams, Antonino Zito, Eli Reuveni, Evan Elliott
Autism Spectrum Disorder (ASD) is a complex neuropsychiatric syndrome whose etiology includes genetic and environmental components. Since epigenetic marks are sensitive to environmental insult, they may be involved in the development of ASD. Initial brain studies have suggested a dysregulation of epigenetic marks in ASD. However, due to cellular heterogeneity in the brain, these studies have not determined if there is a true change in the neuronal epigenetic signature. Here, we report a genome-wide methylation study on fluorescence-activated cell sorting-sorted neuronal nuclei from the frontal cortex of 16 male ASD and 15 male control subjects...
September 28, 2017: Cerebral Cortex
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