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Dna methylation

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https://www.readbyqxmd.com/read/28545252/cpg-and-non-cpg-methylation-in-epigenetic-gene-regulation-and-brain-function
#1
REVIEW
Hyun Sik Jang, Woo Jung Shin, Jeong Eon Lee, Jeong Tae Do
DNA methylation is a major epigenetic mark with important roles in genetic regulation. Methylated cytosines are found primarily at CpG dinucleotides, but are also found at non-CpG sites (CpA, CpT, and CpC). The general functions of CpG and non-CpG methylation include gene silencing or activation depending on the methylated regions. CpG and non-CpG methylation are found throughout the whole genome, including repetitive sequences, enhancers, promoters, and gene bodies. Interestingly, however, non-CpG methylation is restricted to specific cell types, such as pluripotent stem cells, oocytes, neurons, and glial cells...
May 23, 2017: Genes
https://www.readbyqxmd.com/read/28545250/endophytic-bacteria-isolated-from-panax-ginseng-improves-ginsenoside-accumulation-in-adventitious-ginseng-root-culture
#2
Xiaolin Song, Hao Wu, Zhenhao Yin, Meilan Lian, Chengri Yin
Ginsenoside is the most important secondary metabolite of ginseng. Natural sources of wild ginseng have been overexploited. Although root culture could reduce the length of the growth cycle of ginseng, the number of ginsenosides is fewer and their contents are lower in adventitious roots of ginseng than that in ginseng cultivated in the field. In this study, we investigated the effects of endophytic bacterial elicitors on biomass and ginsenoside production in adventitious roots cultures of Panax ginseng. Endophyte LB 5-3 as an elicitor could increase biomass and ginsenoside accumulation in ginseng adventitious root culture...
May 23, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28545228/aberrant-dna-methylation-as-a-biomarker-and-a-therapeutic-target-of-cholangiocarcinoma
#3
REVIEW
Toshiaki Nakaoka, Yoshimasa Saito, Hidetsugu Saito
Cholangiocarcinoma is an epithelial malignancy arising in the region between the intrahepatic bile ducts and the ampulla of Vater at the distal end of the common bile duct. The effect of current chemotherapy regimens against cholangiocarcinoma is limited, and the prognosis of patients with cholangiocarcinoma is poor. Aberrant DNA methylation and histone modification induce silencing of tumor suppressor genes and chromosomal instability during carcinogenesis. Studies have shown that the tumor suppressor genes and microRNAs (miRNAs) including MLH1, p14, p16, death-associated protein kinase (DAPK), miR-370 and miR-376c are frequently methylated in cholangiocarcinoma...
May 23, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28545007/catechol-o-methyltransferase-gene-promoter-methylation-as-a-peripheral-biomarker-in-male-schizophrenia
#4
S Gao, J Cheng, G Li, T Sun, Y Xu, Y Wang, X Du, G Xu, S Duan
As an epigenetic modification, DNA methylation may reflect the interaction between genetic and environmental factors in the development of schizophrenia (SCZ). Catechol-O-methyltransferase (COMT) gene is a promising candidate gene of SCZ. In the present study, we investigate the association of COMT methylation with the risk of SCZ using bisulfite pyrosequencing technology. Significant association between DNA methylation of COMT and the risk of SCZ is identified (P=1.618e-007). A breakdown analysis by gender shows that the significance is driven by males (P=3...
March 30, 2017: European Psychiatry: the Journal of the Association of European Psychiatrists
https://www.readbyqxmd.com/read/28544631/spermatozoa-from-males-with-reduced-fecundity-exhibit-differential-dna-methylation-patterns
#5
M Laqqan, S Tierling, Y Alkhaled, C Lo Porto, E F Solomayer, M Hammadeh
Infertility affects 10-15% of couples, and approximately 50% of cases are linked to male factor infertility. The purpose of this study was to evaluate the DNA methylation patterns in spermatozoa from males who are suffering from a reduction in fecundity. Thirty samples were subjected to 450K arrays as a screening study to evaluate the variation in sperm DNA methylation levels between cases and controls groups, and then four CpG sites (cg05799088, cg07227024, cg16338278, and cg08408433) underwent to deep bisulfite sequencing to validate the observed methylation differences in 111 samples (56 proven fertile males as 'controls' and 55 males suffering from a reduction in fecundity as 'cases')...
May 23, 2017: Andrology
https://www.readbyqxmd.com/read/28544196/analysis-of-transcriptional-and-epigenetic-changes-in-hybrid-vigor-of-allopolyploid-brassica-napus-uncovers-key-roles-for-small-rnas
#6
Yifei Shen, Shuo Sun, Shuijin Hua, Enhui Shen, Chu-Yu Ye, Daguang Cai, Michael P Timko, Qian-Hao Zhu, Longjiang Fan
Heterosis is a fundamental biological phenomenon characterized by the superior performance of a hybrid compared to its parents. The underlying molecular basis for heterosis, particularly for allopolyploids, remains elusive. In this study, we analyzed the transcriptomes of Brassica napus parental lines and their F1 hybrids at three stages of early flower development. Phenotypically, the F1 hybrids show remarkable heterosis in silique number and grain yield. Transcriptome analysis revealed that various phytohormones (auxin and salicylic acid) response genes are significantly altered in the F1 hybrids relative to the parental lines...
May 21, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28543772/parp-inhibitor-rucaparib-induces-changes-in-nad-levels-in-cells-and-liver-tissues-as-assessed-by-mrs
#7
Gilberto S Almeida, Carlo M Bawn, Martin Galler, Ian Wilson, Huw D Thomas, Suzanne Kyle, Nicola J Curtin, David R Newell, Ross J Maxwell
Poly(adenosine diphosphate ribose) polymerases (PARPs) are multifunctional proteins which play a role in many cellular processes. Namely, PARP1 and PARP2 have been shown to be involved in DNA repair, and therefore are valid targets in cancer treatment with PARP inhibitors, such as rucaparib, currently in clinical trials. Proton magnetic resonance spectroscopy ((1) H-MRS) was used to study the impact of rucaparib in vitro and ex vivo in liver tissue from mice, via quantitative analysis of nicotinamide adenosine diphosphate (NAD(+) ) spectra, to assess the potential of MRS as a biomarker of the PARP inhibitor response...
May 22, 2017: NMR in Biomedicine
https://www.readbyqxmd.com/read/28543436/prenatal-environmental-tobacco-smoke-exposure-increases-allergic-asthma-risk-with-methylation-changes-in-mice
#8
Sonja Christensen, Zeina Jaffar, Elizabeth Cole, Virginia Porter, Maria Ferrini, Britten Postma, Kent E Pinkerton, Mihi Yang, Yang Jee Kim, Luke Montrose, Kevan Roberts, Andrij Holian, Yoon Hee Cho
Allergic asthma remains an inadequately understood disease. In utero exposure to environmental tobacco smoke (ETS) has been identified as an environmental exposure that can increase an individual's asthma risk. To improve our understanding of asthma onset and development, we examined the effect of in utero ETS exposure on allergic disease susceptibility in an asthmatic phenotype using a house dust mite (HDM) allergen-induced murine model. Pregnant C57BL/6 mice were exposed to either filtered air or ETS during gestation, and their offspring were further exposed to HDM at 6-7 weeks old to induce allergic inflammation...
May 25, 2017: Environmental and Molecular Mutagenesis
https://www.readbyqxmd.com/read/28543390/the-effect-of-ebv-on-wif1-nlk-and-apc-gene-methylation-and-expression-in-gastric-carcinoma-and-nasopharyngeal-cancer
#9
Zhenzhen Zhao, Wen Liu, Jincheng Liu, Jiayi Wang, Bing Luo
Epstein-Barr virus (EBV) is an important DNA tumor virus that is associated with approximately 10% of gastric carcinomas and 99% of nasopharyngeal cancers. DNA methylation and microRNAs (miRNAs) are the most studied epigenetic mechanisms that can prompt disease susceptibility. This study aimed to detect the effect of EBV on Wnt inhibitory factor 1 (WIF1), Nemo-like kinase (NLK), and adenomatous polyposis coli (APC) gene methylation and expression in gastric carcinoma and nasopharyngeal cancer. METHODS: The WIF1, NLK, and APC gene mRNA expression levels were measured by real-time quantitative RT-PCR in four EBV-positive cell lines and four EBV-negative cell lines...
May 23, 2017: Journal of Medical Virology
https://www.readbyqxmd.com/read/28542457/genet-specific-dna-methylation-probabilities-detected-in-a-spatial-epigenetic-analysis-of-a-clonal-plant-population
#10
Kiwako S Araki, Takuya Kubo, Hiroshi Kudoh
In sessile organisms such as plants, spatial genetic structures of populations show long-lasting patterns. These structures have been analyzed across diverse taxa to understand the processes that determine the genetic makeup of organismal populations. For many sessile organisms that mainly propagate via clonal spread, epigenetic status can vary between clonal individuals in the absence of genetic changes. However, fewer previous studies have explored the epigenetic properties in comparison to the genetic properties of natural plant populations...
2017: PloS One
https://www.readbyqxmd.com/read/28542388/targeted-dna-methylation-in-pericentromeres-with-genome-editing-based-artificial-dna-methyltransferase
#11
Taiga Yamazaki, Yu Hatano, Tetsuya Handa, Sakiko Kato, Kensuke Hoida, Rui Yamamura, Takashi Fukuyama, Takayuki Uematsu, Noritada Kobayashi, Hiroshi Kimura, Kazuo Yamagata
To study the impact of epigenetic changes on biological functions, the ability to manipulate the epigenetic status of certain genomic regions artificially could be an indispensable technology. "Epigenome editing" techniques have gradually emerged that apply TALE or CRISPR/Cas9 technologies with various effector domains isolated from epigenetic code writers or erasers such as DNA methyltransferase, 5-methylcytosine oxidase, and histone modification enzymes. Here we demonstrate that a TALE recognizing a major satellite, consisting of a repeated sequence in pericentromeres, could be fused with the bacterial CpG methyltransferase, SssI...
2017: PloS One
https://www.readbyqxmd.com/read/28542303/differential-dna-methylation-of-msi2-and-its-correlation-with-diabetic-traits
#12
Jae-Pil Jeon, In-Uk Koh, Nak-Hyun Choi, Bong-Jo Kim, Bok-Ghee Han, Suman Lee
Differential DNA methylation with hyperglycemia is significantly associated with Type 2 Diabetes (T2D). Longtime extended exposure to high blood glucose levels can affect the epigenetic signatures in all organs. However, the relevance of the differential DNA methylation changes with hyperglycemia in blood with pancreatic islets remains unclear. We investigated differential DNA methylation in relation to glucose homeostasis based on the Oral Glucose Tolerance Test (OGTT) in a population-based cohort. We found a total of 382 differential methylation sites from blood DNA in hyperglycemia and type 2 diabetes subgroups using a longitudinal and cross-sectional approach...
2017: PloS One
https://www.readbyqxmd.com/read/28542152/corrigendum-brain-feminization-requires-active-repression-of-masculinization-via-dna-methylation
#13
Bridget M Nugent, Christopher L Wright, Amol C Shetty, Georgia E Hodes, Kathryn M Lenz, Anup Mahurkar, Scott J Russo, Scott E Devine, Margaret M McCarthy
No abstract text is available yet for this article.
May 25, 2017: Nature Neuroscience
https://www.readbyqxmd.com/read/28541567/dna-methylation-and-small-interference-rnas-participate-in-the-regulation-of-mads-box-genes-involved-in-dormancy-in-sweet-cherry-prunus-avium-l
#14
Karin Rothkegel, Evelyn Sánchez, Christian Montes, Macarena Greve, Sebastián Tapia, Soraya Bravo, Humberto Prieto, Andréa Miyasaka Almeida
Epigenetic modifications can yield information about connections between genotype, phenotype variation and environmental conditions. Bud dormancy release in temperate perennial fruit trees depends on internal and environmental signals such as cold accumulation and photoperiod. Previous investigations have noted the participation of epigenetic mechanisms in the control of this physiological process. We examined whether epigenetic modifications were modulated in MADS-box genes, potential candidates for the regulation of bud dormancy and flowering in sweet cherry (Prunus avium L...
May 24, 2017: Tree Physiology
https://www.readbyqxmd.com/read/28540987/lack-of-aberrant-methylation-in-an-adjacent-area-of-left-sided-colorectal-cancer
#15
Otgontuya Sambuudash, Hyun Soo Kim, Mee Yon Cho
PURPOSE: The molecular nature and the rate-limiting step of epigenetic field defects in the evolution of left-sided colorectal cancer (LCA) remain uncertain. MATERIALS AND METHODS: The methylation status of 27 candidate field defect markers, six classic CpG island methylator phenotype (CIMP) markers, and LINE-1 were determined in LCA and adjacent normal mucosas (ADJs) from 33 LCA patients and in left normal colorectal mucosa (LNM) from 33 age- and sex-matched controls...
July 2017: Yonsei Medical Journal
https://www.readbyqxmd.com/read/28540928/anxiety-associated-increased-cpg-methylation-in-the-promoter-of-asb1-a-translational-approach-evidenced-by-epidemiological-and-clinical-studies-and-a-murine-model
#16
Rebecca T Emeny, Jens Baumert, Anthony S Zannas, Sonja Kunze, Simone Wahl, Stella Iurato, Janine Arloth, Angelika Erhardt, Georgia Balsevich, Mathias V Schmidt, Peter Weber, Anja Kretschmer, Liliane Pfeiffer, Johannes Kruse, Konstantin Strauch, Michael Roden, Christian Herder, Wolfgang Koenig, Christian Gieger, Melanie Waldenberger, Annette Peters, Elisabeth B Binder, Karl-Heinz Ladwig
Epigenetic regulation in anxiety is suggested, but evidence from large studies is needed. We conducted an epigenome-wide association study (EWAS) on anxiety in a population-based cohort and validated our finding in a clinical cohort as well as a murine model. In the KORA cohort, participants (n=1522, age 32-72 years) were administered the Generalized Anxiety Disorder (GAD-7) instrument, whole blood DNA methylation was measured (Illumina 450 K BeadChip) and circulating levels of hs-CRP and IL-18 were assessed in the association between anxiety and methylation...
May 25, 2017: Neuropsychopharmacology: Official Publication of the American College of Neuropsychopharmacology
https://www.readbyqxmd.com/read/28540701/inverse-pcr-for-point-mutation-introduction
#17
Diogo Silva, Gustavo Santos, Mário Barroca, Tony Collins
Inverse PCR is a powerful tool for the rapid introduction of desired mutations at desired positions in a circular double-stranded DNA sequence. Here, custom-designed mutant primers oriented in the inverse direction are used to amplify the entire circular template with incorporation of the required mutation(s). By careful primer design it can be used to perform such diverse modifications as the introduction of point mutations and multiple mutations, the insertion of new sequences, and even sequence deletions...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28540651/biologically-active-cu-ii-co-ii-ni-ii-and-zn-ii-complexes-of-pyrimidine-derivative-schiff-base-dna-binding-antioxidant-antibacterial-and-in-vitro-anticancer-studies
#18
Nagaraj Revathi, Murugesan Sankarganesh, Jegathalaprathaban Rajesh, Jeyaraj Dhaveethu Raja
A new pyrimidine derivative Schiff base ligand (HL) [HL = 2-(4,6-dimethylpyrimidin-2-ylimino)methyl)-4-nitrophenol] and its metal(II) complexes [CuL2] (1), [CoL2] (2), [NiL2] (3) and [ZnL2] (4) have been synthesized and characterized by several spectral techniques. The square planar geometry of the complexes 1-4 confirmed by UV-Visible, ESR and EI-mass spectral techniques. DNA binding study of the complexes 1-4 with Calf Thymus (CT) DNA using absorption spectral titration at different pH (4.0, 7.0 & 10.0) have been scrutinized that the complexes 1-4 bound by groove binding mode with significant binding constant values (K b  = 5...
May 24, 2017: Journal of Fluorescence
https://www.readbyqxmd.com/read/28540540/molecular-mechanisms-of-bombyx-batryticatus-ethanol-extract-inducing-gastric-cancer-sgc-7901-cells-apoptosis
#19
Jin-Yi Wu, Almutamad Sheikho, He Ma, Tian-Ci Li, Ya-Qi Zhao, Ya-Lin Zhang, Dun Wang
Bombyx batryticatus is a traditional Chinese medicine. To understand apoptotic effect of B. batryticatus ethanol extract (BBE), we investigated the role of BBE in inducing apoptosis of human gastric cancer cells SGC-7901. Cells treated with BBE and apoptosis was assessed by methyl thiazolyl tetrazolium (MTT) assay, morphological changes, DNA fragmentation and flow cytometry assays. The expression of Bcl-2, Bax and P21 were evaluated by western blot analysis and real time polymerase chain reaction. MTT assay showed that the cytotoxicity of BBE extract on SGC-7901 cells was correlated with treatment time and concentration...
May 24, 2017: Cytotechnology
https://www.readbyqxmd.com/read/28540174/a-preliminary-study-on-the-interaction-between-asn-gly-arg-ngr-modified-multifunctional-nanoparticles-and-vascular-epithelial-cells
#20
Chunxi Liu, Tingxian Liu, Xiaoyue Yu, Yizhu Gu
Previously developed Asn-Gly-Arg (NGR) peptide-modified multifunctional poly(ethyleneimine)-poly(ethylene glycol) (PEI-PEG)-based nanoparticles (TPIC) have been considered to be promising carriers for the co-delivery of DNA and doxorubicin (DOX). As a continued effort, the aim of the present study was to further evaluate the interaction between TPIC and human umbilical vein endothelial cells (HUVEC) to better understand the cellular entry mechanism. In the present investigation, experiments relevant to co-localization, endocytosis inhibitors and factors influencing the internalization were performed...
May 2017: Acta Pharmaceutica Sinica. B
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