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Methylation enrichment

Nicholas Carter, Xiabing Li, Lewis Reavey, Anthony J H M Meijer, Iain Coldham
Treatment of N -Boc-2-aryl-1,2,3,4-tetrahydroquinolines with n -butyllithium in THF at -78 °C resulted in efficient lithiation at the 2-position and the organolithiums were trapped with a variety of electrophiles to give substituted products. Variable temperature NMR spectroscopy gave kinetic data that showed that the rate of tert -butoxycarbonyl (Boc) rotation was fast (Δ G ‡ ≈ 45 kJ mol-1 at -78 °C) and in situ ReactIR spectroscopy showed fast lithiation at -78 °C. By carrying out the lithiation in the presence of the chiral ligand sparteine, kinetic resolutions with very high levels of enantioselectivity were achieved...
February 7, 2018: Chemical Science
Zhenxing Wang, XiaoLiang Wu, Yadong Wang
BACKGROUND: DNA methylation has been identified to be widely associated to complex diseases. Among biological platforms to profile DNA methylation in human, the Illumina Infinium HumanMethylation450 BeadChip (450K) has been accepted as one of the most efficient technologies. However, challenges exist in analysis of DNA methylation data generated by this technology due to widespread biases. RESULTS: Here we proposed a generalized framework for evaluating data analysis methods for Illumina 450K array...
April 11, 2018: BMC Bioinformatics
Christina N Vallianatos, Clara Farrehi, Michael J Friez, Margit Burmeister, Catherine E Keegan, Shigeki Iwase
Intellectual disability (ID) affects up to 2% of the population world-wide and often coincides with other neurological conditions such as autism spectrum disorders. Mutations in KDM5C cause Mental Retardation, X-linked, Syndromic, Claes-Jensen type (MRXSCJ, OMIM #300534) and are one of the most common causes of X-linked ID. KDM5C encodes a histone demethylase for di- and tri-methylated histone H3 lysine 4 (H3K4me2/3), which are enriched in transcriptionally engaged promoter regions. KDM5C regulates gene transcription; however, it remains unknown whether removal of H3K4me is fully responsible for KDM5C-mediated gene regulation...
2018: Frontiers in Molecular Neuroscience
Mahalakshmi Shankaran, Gregg Czerwieniec, Chancy Fessler, Po-Yin Anne Wong, Salena Killion, Scott M Turner, Marc K Hellerstein, William J Evans
BACKGROUND: Muscle mass can be measured directly in vivo by isotope dilution, using Creatine-(methyl-d3 ) monohydrate (D3 -Cr) by mouth followed by measurement of the steady-state enrichment of D3 -creatinine (D3 -Crn) in urine. Isotope dilution methods require knowledge of the amount of tracer delivered to the pool of interest. In a subset of human subjects, a small amount of orally administered D3 -Cr 'spills' into urine after absorption and prior to transport into skeletal muscle cells...
April 16, 2018: Journal of Cachexia, Sarcopenia and Muscle
Shouling Luo, Jiangnan Pei, Xiaotian Li, Weirong Gu
The exact mechanism of preeclampsia (PE) remains unclear, accumulating researches have indicated multiple epigenetic factors relate to PE and histone methylation plays a crucial role in modifying the gene expression. So we aimed to confirm that abnormal expression of histone demethylase JHDM1D contributes to PE and lower expression of HLA-G in PE. We tested the expression of JHDM1D, H3K9me2, and H3K27me2 in the placentas of PE and normal control (NC)women who had a healthy pregnancy with Immunohistochemistry and we found that JHDM1D, H3K9me2, and H3K27me2 were all mainly expressed in the nuclei of the extra-villous trophoblasts (EVTs)...
April 6, 2018: Journal of Human Hypertension
Adam T McLain, Christopher Faulk
Gene promoters are evolutionarily conserved across holozoans and enriched in CpG sites, the target for DNA methylation. As animals age, the epigenetic pattern of DNA methylation degrades, with highly methylated CpG sites gradually becoming demethylated while CpG islands increase in methylation. Across vertebrates, aging is a trait that varies among species. We used this variation to determine whether promoter CpG density correlates with species' maximum lifespan. Human promoter sequences were used to identify conserved regions in 131 mammals and a subset of 28 primate genomes...
April 14, 2018: Aging
Rui Fu, Yan Ding, Jie Luo, Kuan Ming Huang, Xiang Jun Tang, Dong Sheng Li, Shi Wen Guo
Ten-eleven translocation 1 catalyzes the conversion of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), which plays an important role in epigenetics and is related to the malignant biological behavior of tumors. However, its regulatory role in glioma remains unclear. In this study, the levels of 5mC and 5hmC were detected using immunohistochemistry, dot-blot, hMeDIP-chip, and western blot in glioma tissues and normal brain tissues, whereas 5hmC differentially enriched genes were determined and further validated...
April 13, 2018: Neuroreport
Delei Song, Wei Qi, Ming Lv, Chun Yuan, Kangsong Tian, Feng Zhang
Osteoarthritis (OA) is a common type of arthritis, which may cause pain and disability. Alterations in gene expression and DNA methylation have been proven to be associated with the development of OA. The aim of the present study was to identify potential therapeutic targets and associated processes for OA via the combined analysis of gene expression and DNA methylation datasets. The gene expression and DNA methylation profiles were obtained from the Gene Expression Omnibus, and differentially expressed genes (DEGs) and differentially methylated sites (DMSs) were identified in the present study, using R programming software...
April 12, 2018: Molecular Medicine Reports
Zhe Liang, Lisha Shen, Xuean Cui, Shengjie Bao, Yuke Geng, Guoliang Yu, Fan Liang, Shang Xie, Tiegang Lu, Xiaofeng Gu, Hao Yu
DNA methylation on N6 -adenine (6mA) has recently been found to be a potentially epigenetic mark in several unicellular and multicellular eukaryotes. However, its distribution patterns and potential functions in land plants, which are primary producers for most ecosystems, remain largely unknown. Here we report global profiling of 6mA sites at single-nucleotide resolution in the genome of Arabidopsis thaliana at different developmental stages using single-molecule real-time sequencing. 6mA sites are widely distributed across the Arabidopsis genome and enriched over the pericentromeric heterochromatin regions...
April 12, 2018: Developmental Cell
Laura K M Han, Moji Aghajani, Shaunna L Clark, Robin F Chan, Mohammad W Hattab, Andrey A Shabalin, Min Zhao, Gaurav Kumar, Lin Ying Xie, Rick Jansen, Yuri Milaneschi, Brian Dean, Karolina A Aberg, Edwin J C G van den Oord, Brenda W J H Penninx
OBJECTIVE: Major depressive disorder is associated with an increased risk of mortality and aging-related diseases. The authors examined whether major depression is associated with higher epigenetic aging in blood as measured by DNA methylation (DNAm) patterns, whether clinical characteristics of major depression have a further impact on these patterns, and whether the findings replicate in brain tissue. METHOD: DNAm age was estimated using all methylation sites in blood of 811 depressed patients and 319 control subjects with no lifetime psychiatric disorders and low depressive symptoms from the Netherlands Study of Depression and Anxiety...
April 16, 2018: American Journal of Psychiatry
Bettina Heller, Claudia Kolbeck, Inga Niedermaier, Sabine Dommer, Jürgen Schatz, Patricia Hunt, Florian Maier, Hans-Peter Steinrück
For equimolar mixtures of ionic liquids with imidazolium-based cations of very different electronic structure, we observe very pronounced surface enrichment effects by angle-resolved X-ray photoelectron spectroscopy (XPS). For a mixture with the same anion, that is, 1-methyl-3-octylimidazolium hexafluorophospate + 1,3-di(methoxy)imidazolium hexafluoro-phosphate ([C8C1Im][PF6]+[(MeO)2Im][PF6]), we find a strong enrichment of the octyl chain-containing [C8C1Im]+ cation and a corresponding depletion of the [(MeO)2Im]+ cation in the topmost layer...
April 12, 2018: Chemphyschem: a European Journal of Chemical Physics and Physical Chemistry
Leah M Katz, Thomas Hielscher, Benjamin Liechty, Joshua Silverman, David Zagzag, Rajeev Sen, Peter Wu, John G Golfinos, David Reuss, Marian Christoph Neidert, Hans-Georg Wirsching, Peter Baumgarten, Christel Herold-Mende, Wolfgang Wick, Patrick N Harter, Michael Weller, Andreas von Deimling, Matija Snuderl, Chandra Sen, Felix Sahm
Epigenetic patterns on the level of DNA methylation have already been shown to separate clinically relevant subgroups of meningiomas. We here set out to identify potential prognostic implications of epigenetic modification on the level of histones with focus on H3K27 trimethylation (H3K27me3). H3K27me3 was assessed by immunohistochemistry on 232 meningiomas from 232 patients. In 194 cases, trimethylation was detected in tumor cells. In 25 cases, staining was limited to vessels while all tumor cells were negative...
April 7, 2018: Acta Neuropathologica
Shanshan Zhang, Shuyi Han, Maoxiu Zhang, Yunshan Wang
Invasive prenatal paternity tests can result in miscarriage and congenital malformations; therefore, a non-invasive method of testing is preferable. However, little progress could be made in this field until the introduction of cell-free fetal DNA (cffDNA) in 2009. In this review, two aspects regarding the history and development of non-invasive prenatal paternity testing (NIPAT) are summarized: (1) extraction and enrichment of cffDNA and (2) genetic marker-based studies. Although column-based kits are used widely for NIPAT, some researchers have suggested that an automated method, such as magnetic extraction, generally has a higher cffDNA yield than that of manual column-based extraction; therefore, its popularity might increase in the near future...
April 1, 2018: Legal Medicine
Martina Stepankova, Iveta Bartonkova, Eva Jiskrova, Radim Vrzal, Sridhar Mani, Sandhya Kortagere, Zdenek Dvorak
Novel methyl-indoles were identified as endobiotic and xenobiotic ligands of human aryl hydrocarbon receptor (AhR). We examined the effects of 22 methylated and methoxylated indoles on the transcriptional activity of AhR. Employing reporter gene assays in AZ-AHR transgenic cells, we determined full agonist, partial agonist or antagonist activities of tested compounds, having substantially variable EC50 , IC50 and relative efficacies. The most effective agonists (EMAX relative to 5 nM dioxin) of AhR were 4-Me-indole (134%), 6-Me-indole (91%) and 7-MeO-indole (80%), respectively...
April 6, 2018: Molecular Pharmacology
Yang Liu, Nilay S Sethi, Toshinori Hinoue, Barbara G Schneider, Andrew D Cherniack, Francisco Sanchez-Vega, Jose A Seoane, Farshad Farshidfar, Reanne Bowlby, Mirazul Islam, Jaegil Kim, Walid Chatila, Rehan Akbani, Rupa S Kanchi, Charles S Rabkin, Joseph E Willis, Kenneth K Wang, Shannon J McCall, Lopa Mishra, Akinyemi I Ojesina, Susan Bullman, Chandra Sekhar Pedamallu, Alexander J Lazar, Ryo Sakai, Vésteinn Thorsson, Adam J Bass, Peter W Laird
We analyzed 921 adenocarcinomas of the esophagus, stomach, colon, and rectum to examine shared and distinguishing molecular characteristics of gastrointestinal tract adenocarcinomas (GIACs). Hypermutated tumors were distinct regardless of cancer type and comprised those enriched for insertions/deletions, representing microsatellite instability cases with epigenetic silencing of MLH1 in the context of CpG island methylator phenotype, plus tumors with elevated single-nucleotide variants associated with mutations in POLE...
April 2, 2018: Cancer Cell
Juan Shen, Bin Zhu
In order to better understand the etiology of obese type 2 diabetes (T2D) at the molecular level, the present study investigated the gene expression and DNA methylation profiles associated with T2D via systemic analysis. Gene expression (GSE64998) and DNA methylation profiles (GSE65057) from liver tissues of healthy controls and obese patients with T2D were downloaded from the Gene Expression Omnibus database. Differentially‑expressed genes (DEGs) and differentially‑methylated genes (DMGs) were identified using the Limma package, and their overlapping genes were additionally determined...
March 28, 2018: Molecular Medicine Reports
Sarah N Anderson, Greg Zynda, Jawon Song, Zhaoxue Han, Matthew Vaughn, Qing Li, Nathan M Springer
DNA methylation is a chromatin modification that can provide epigenetic regulation of gene and transposon expression. Plants utilize several pathways to establish and maintain DNA methylation in specific sequence contexts. The chromomethylase (CMT) genes maintain CHG (where H = A, C or T) methylation. The RNA-directed DNA methylation (RdDM) pathway is important for CHH methylation. Transcriptome analysis was performed in a collection of Zea mays lines carrying mutant alleles for CMT or RdDM-associated genes...
April 4, 2018: G3: Genes—Genomes—Genetics
Jin-Ting Wang, Liang Zhang, Yuan Kang, Guanghao Chen, Feng Jiang
This study reported a novel observation that the long-term cultivation of sulfur-reducing bacteria (S0RB) from a sulfate-reducing bacteria (SRB)-abundant seeding sludge with elemental sulfur feeding, significantly shaped the microbial community structure and eliminated the mercury methylation potential in the S0RB-enriched sludge. In this study, the enrichments of SRB and S0RB from activated sludge were obtained through long-term cultivations. Subsequently, the batch tests showed that approximately 5000 μg/L Hg (II) was completely removed from the solution by both the SRB-enriched and S0RB-enriched sludge...
April 4, 2018: Environmental Science & Technology
Ying Cai, Jhih-Rong Lin, Quanwei Zhang, Kelly O'Brien, Cristina Montagna, Zhengdong D Zhang
Malignant breast cancer remains a major health threat to women of all ages worldwide and epigenetic variations on DNA methylation have been widely reported in cancers of different types. We profiled DNA methylation with ERRBS (Enhanced Reduced Representation Bisulfite Sequencing) across four main stages of tumor progression in the MMTV-PyMT mouse model (hyperplasia, adenoma/mammary intraepithelial neoplasia, early carcinoma and late carcinoma), during which malignant transition occurs. We identified a large number of differentially methylated cytosines (DMCs) in tumors relative to age-matched normal mammary glands from FVB mice...
April 3, 2018: Scientific Reports
Wei Liu, Meriem Fizir, Fan Hu, Ang Li, Xuanhong Hui, Jun Zha, Hua He
An effective and greener mixed hemimicelles magnetic solid phase extraction (MHMSPE) based on magnetic halloysite nanotubes (MHNTs) and ionic liquid (IL) is developed for the simultaneous enrichment and determination of anionic azo dyes in a spiked environmental water sample. In this MHMSPE, the formation of C16 mimBr with mixed hemimicelles on the surface of MHNTs leads to the retention of analytes by strong hydrophobic, p-p and electrostatic interactions. This MHMSPE technique combines the advantages of MHNTs and mixed hemimicelles...
March 28, 2018: Journal of Chromatography. A
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