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Methylation DNA

Yan Zhao, Pengcheng Liu, Junyong Wang, Xirong Xiao, Xiangzhou Meng, Yunhui Zhang
BACKGROUND: In utero polybrominated diphenyl ethers (PBDEs) exposure has been associated with adverse fetal growth. Alterations in placental DNA methylation might mediate those adverse effects. OBJECTIVES: To examine the associations between in utero PBDEs exposure and DNA methylation in human placenta. METHODS: Eighty apparently healthy mother-newborn pairs delivering at the Second Affiliated Hospital of Wenzhou Medical College were enrolled in this study...
October 18, 2016: Environment International
Nina Xie, He Gong, Joshua A Suhl, Pankaj Chopra, Tao Wang, Stephen T Warren
Fragile X syndrome (FXS) is a common cause of intellectual disability that is most often due to a CGG-repeat expansion mutation in the FMR1 gene that triggers epigenetic gene silencing. Epigenetic modifying drugs can only transiently and modestly induce FMR1 reactivation in the presence of the elongated CGG repeat. As a proof-of-principle, we excised the expanded CGG-repeat in both somatic cell hybrids containing the human fragile X chromosome and human FXS iPS cells using the CRISPR/Cas9 genome editing. We observed transcriptional reactivation in approximately 67% of the CRISPR cut hybrid colonies and in 20% of isolated human FXS iPSC colonies...
2016: PloS One
Eric B Loucks, Yen-Tsung Huang, Golareh Agha, Su Chu, Charles B Eaton, Stephen E Gilman, Stephen L Buka, Karl T Kelsey
OBJECTIVE: Childhood socioeconomic disadvantage is associated with adulthood obesity risk; however, epigenetic mechanisms are poorly understood. This work's objective was to evaluate whether associations of childhood socioeconomic disadvantage with adulthood body mass index (BMI) are mediated by DNA methylation. METHODS: Participants were 141 men and women from the New England Family Study, prospectively followed prenatally through a mean age of 47 years. Epigenomewide DNA methylation was evaluated in peripheral blood and adipose tissue obtained at adulthood, using the Infinium HumanMethylation450K BeadChip...
October 20, 2016: Psychosomatic Medicine
Nina Holland
Environmental research and public health in the 21st century face serious challenges such as increased air pollution and global warming, widespread use of potentially harmful chemicals including pesticides, plasticizers, and other endocrine disruptors, and radical changes in nutrition and lifestyle typical of modern societies. In particular, exposure to environmental and occupational toxicants may contribute to the occurrence of adverse birth outcomes, neurodevelopmental deficits, and increased risk of cancer and other multifactorial diseases such as diabetes and asthma...
October 21, 2016: Reviews on Environmental Health
Allison B Norvil, Christopher J Petell, Lama Abdullah Alabdi, Lanchen Wu, Sandra Rossie, Humaira Gowher
The catalytic domains of the de novo DNA methyltransferases, Dnmt3a-C and Dnmt3b-C are highly homologous. However their unique biochemical properties could potentially contribute to differences in the substrate preferences or biological functions of these enzymes. Dnmt3a-C forms tetramers through interactions at the dimer interface, which also promote multimerization on DNA and cooperativity. Similar to processive enzymes, cooperativity allows Dnmt3a-C to methylate multiple sites on the same DNA molecule, however it is unclear whether Dnmt3b-C methylates DNA by cooperative or processive mechanism...
October 21, 2016: Biochemistry
Paule V Joseph, Sarah K Abey, Wendy A Henderson
Nutrition is a factor involved in inflammation and a modulator of risk toward some cancers, and the complexity of linkages between dietary components and epigenetics mechanisms (e.g., DNA methylation, histone modification, chromatin remodeling) may affect the inflammation phenotype and the development of cancer. An increasing number of studies support the role of diet in cancer development, prevention, and treatment. Although current knowledge regarding nutri-epigenetics is expanding, more work is needed, and nurse scientists have the potential to significantly contribute to the expansion of this knowledge...
November 1, 2016: Oncology Nursing Forum
Natália Helen Ferreira, Kelly Jacqueline Barbosa de Andrade, Luís Fernando Leandro, Nathália Oliveira Acésio, Suzana Amorim Mendes, Lucas Silva Cintra, Ana Helena Januário, Denise Crispim Tavares
The aim of this study was to examine the cytotoxic and genotoxic potential of a hydroethanolic extract of Schefflera vinosa (SV), a plant with schistosomicidal activity, as well as its influence on DNA damage induced by different mutagens, methyl methane sulfonate (MMS) and hydrogen peroxide (H2O2), in V79 cells and Swiss mice. Schefflera vinosa extract produced cytotoxicity at concentrations of 312.5 µg/ml or higher using the XTT cell proliferation assay kit. Treatment of V79 cell cultures with the highest SV concentration tested (150 µg/ml) significantly increased the frequency of micronuclei (MN) compared to controls...
October 21, 2016: Journal of Toxicology and Environmental Health. Part A
Robbert D A Weren, Arjen R Mensenkamp, Michiel Simons, Astrid Eijkelenboom, Aisha S Sie, Hicham Ouchene, Monique van Asseldonk, Encarna B Gomez-Garcia, Marinus J Blok, Joanne A de Hullu, Marcel R Nelen, Alexander Hoischen, Johan Bulten, Bastiaan B J Tops, Nicoline Hoogerbrugge, En Marjolijn J L Ligtenberg
With the recent introduction of Poly(ADP-ribose) polymerase (PARP) inhibitors, a promising novel therapy has become available for ovarian carcinoma patients with inactivating BRCA1 or BRCA2 mutations in their tumour. To select patients who may benefit from these treatments, assessment of the mutation status of BRCA1 and BRCA2 in the tumour is required. For reliable evaluation of germline and somatic mutations in these genes in DNA derived from formalin-fixed, paraffin-embedded (FFPE) tissue, we have developed a single molecule molecular inversion probe (smMIP)-based targeted next generation sequencing (NGS) approach...
October 21, 2016: Human Mutation
Dian-Qiu Lv, Shang-Wu Liu, Jian-Hua Zhao, Bang-Jun Zhou, Shao-Peng Wang, Hui-Shan Guo, Yuan-Yuan Fang
Viroids are plant-pathogenic molecules made up of single-stranded circular non-coding RNAs. How replicating viroids interfere with host silencing remains largely unknown. In this study, we investigated the effects of a nuclear-replicating Potato spindle tuber viroid (PSTVd) on interference with plant RNA silencing. Using transient induction of silencing in GFP transgenic Nicotiana benthamiana plants (line 16c), we found that PSTVd replication accelerated GFP silencing and increased Virp1 mRNA, which encodes bromodomain-containing viroid-binding protein 1 and is required for PSTVd replication...
October 21, 2016: Scientific Reports
Rita Meleddu, Simona Distinto, Angela Corona, Enzo Tramontano, Giulia Bianco, Claudia Melis, Filippo Cottiglia, Elias Maccioni
A series of 3-3-{2-[2-3-methyl-4-phenyl-2,3-dihydro-1,3-thiazol-2-ylidene]hydrazin-1-ylidene-2,3-dihydro-1H-indol-2-one derivatives has been designed and synthesized to study their activity on both HIV-1 (Human Immunodeficiency Virus type 1) RT (Reverse Transcriptase) associated functions. These derivatives are analogs of previously reported series whose biological activity and mode of action have been investigated. In this work we investigated the influence of the introduction of a methyl group in the position 3 of the dihydrothiazole ring and of a chlorine atom in the position 5 of the isatin nucleus...
October 21, 2016: Journal of Enzyme Inhibition and Medicinal Chemistry
Qiang Fu, Huijun Shi, Chuangfu Chen
MicroRNAs (miRNAs) are an important class of small, non-coding RNAs that control target genes expression by degradation of target mRNAs or by inhibiting protein translation in many biological processes and cellular pathways. In a previous study, we found that miR-29b interfered with bovine viral diarrhea virus (BVDV) replication. However, the mechanisms of regulation of miR-29b expression are not well known. DNA methylation is an important epigenetic mechanism for silencing gene transcription, and plays an important role in promoter choice, protein expression, and regulation of miRNAs expression...
October 20, 2016: Archives of Virology
Hajime Suzuki, Takahiro Sakabe, Yuu Hirose, Toshihiko Eki
We aimed to develop the bioassays for genotixicity and/or oxidative damage using the recombinant yeast. A genotoxicity assay was developed using recombinant Saccharomyces cerevisiae strain BY4741 with a green fluorescent protein (GFP) reporter plasmid, driven by the DNA damage-responsive RNR3 promoter. Enhanced fluorescence induction was observed in DNA repair-deficient strains treated with methyl methanesulfonate, but not with hydrogen peroxide. A GFP reporter yeast strain driven by the oxidative stress-responsive TRX2 promoter was newly developed to assess oxidative damage, but fluorescence was poorly induced by oxidants...
October 21, 2016: Applied Microbiology and Biotechnology
Mohammad Mahfuz Ali Khan Shawan, Md Ashraful Hasan, Md Mozammel Hossain, Md Mahmudul Hasan, Afroza Parvin, Salina Akter, Kazi Rasel Uddin, Subrata Banik, Mahbubul Morshed, Md Nazibur Rahman, S M Badier Rahman
Nucleotide (DNA) sequence analysis provides important clues regarding the characteristics and taxonomic position of an organism. With the intention that, DNA sequence analysis is very crucial to learn about hierarchical classification of that particular organism. This dataset (patent US 7547531) is chosen to simplify all the complex raw data buried in undisclosed DNA sequences which help to open doors for new collaborations. In this data, a total of 48 unidentified DNA sequences from patent US 7547531 were selected and their complete sequences were retrieved from NCBI BioSample database...
December 2016: Data in Brief
Danqing Yin, Matthew E Ritchie, Jafar S Jabbari, Tamara Beck, Marnie E Blewitt, Andrew Keniry
Reduced representation bisulfite sequencing (RRBS) provides an efficient method for measuring DNA methylation at single base resolution in regions of high CpG density. This technique has been extensively tested on the HiSeq2500, which uses a 4-colour detection method, however it is unclear if the method will also work on the NextSeq500 platform, which employs a 2-colour detection system. We created an RRBS library and sequenced it on both the HiSeq2500 and NextSeq500, and found no significant difference in the base composition of reads derived from either machine...
December 2016: Genomics Data
Changqing Yin, Changliang Luo, Wei Hu, Xu Ding, Chunhui Yuan, Fubing Wang
As part of "liquid biopsy," lots of literature indicated the potential diagnostic value of circulating cell-free DNA (cfDNA) in the management of prostate cancer (PCa). However, the literature on the accuracy of cfDNA detection in PCa has been inconsistent. Hence, we performed this meta-analysis to assess the diagnostic value of cfDNA in PCa. A total of 19 articles were included in this analysis according to the inclusion and exclusion criteria. We then investigated two main subgroups in this meta-analysis, including qualitative analysis of abnormal level of cfDNA and qualitative analysis of single-gene methylation alterations...
2016: Disease Markers
Peixin Dong, Ying Xiong, Hidemichi Watari, Sharon Jb Hanley, Yosuke Konno, Kei Ihira, Fumihiko Suzuki, Takahiro Yamada, Masataka Kudo, Junming Yue, Noriaki Sakuragi
Derepression of wild-type p53 by suppressing its negative inhibitor iASPP (Inhibitor of apoptosis-stimulating protein of p53) represents a potential therapeutic option for cervical cancer (CC). Here, we reported a novel functional significance of iASPP upregulation in cervical tumorigenesis: iASPP acts as a key promoter of CC cell proliferation, epithelial-mesenchymal transition, invasion and cancer stemness, by interacting with p53 to suppress p53-mediated transcription of target genes and reducing p53-responsive microRNA-34a levels...
October 21, 2016: Scientific Reports
Yan Long, Wen-Bin Tsai, Jeffrey T Chang, Marcos Estecio, Medhi Wangpaichitr, Naramol Savaraj, Lynn G Feun, Helen H W Chen, Macus Tien Kuo
Many human tumors require extracellular arginine (Arg) for growth because the key enzyme for de novo biosynthesis of Arg, argininosuccinate synthetase 1 (ASS1), is silenced. These tumors are sensitive to Arg-starvation therapy using pegylated arginine deiminase (ADI-PEG20) which digests extracellular Arg. Many previous studies reported that ASS1 silencing is due to epigenetic inactivation of ASS1 expression by DNA methylation, and that the demethylation agent 5-aza-deoxycytidine (Aza-dC) can induce ASS1 expression...
September 28, 2016: Oncotarget
H N Lynch, C T Loftus, J M Cohen, L E Kerper, E M Kennedy, J E Goodman
Research suggests that exposure to ambient particulate matter (PM) may be associated with lung cancer; however, no mode of action (MoA) for this has been established. We applied a weight-of-evidence (WoE) approach to evaluate recent evidence from four realms of research (controlled human exposure, epidemiology, animal, and in vitro) to determine whether the overall evidence supports one or more MoAs by which PM could cause lung cancer. We evaluated three general MoAs: DNA damage and repair; other genotoxic effects, including mutagenicity and clastogenicity; and gene expression, protein expression, and DNA methylation...
October 17, 2016: Regulatory Toxicology and Pharmacology: RTP
Linda Witek Janusek, Dina Tell, Noni Gaylord-Harden, Herbert L Mathews
African American men (AAM) who are exposed to trauma and adversity during their early life are at greater risk for poor health over their lifespan. Exposure to adversity during critical developmental windows may embed an epigenetic signature that alters expression of genes that regulate stress response systems, including those genes that regulate the inflammatory response to stress. Such an epigenetic signature may increase risk for diseases exacerbated by inflammation, and may contribute to health disparity...
October 17, 2016: Brain, Behavior, and Immunity
Tushar Tomar, Steven de Jong, Nicolette G Alkema, Rieks L Hoekman, Gert Jan Meersma, Harry G Klip, Ate Gj van der Zee, G Bea A Wisman
BACKGROUND: In high-grade serous ovarian cancer (HGSOC), intrinsic and/or acquired resistance against platinum-containing chemotherapy is a major obstacle for successful treatment. A low frequency of somatic mutations but frequent epigenetic alterations, including DNA methylation in HGSOC tumors, presents the cancer epigenome as a relevant target for innovative therapy. Patient-derived xenografts (PDXs) supposedly are good preclinical models for identifying novel drug targets. However, the representativeness of global methylation status of HGSOC PDXs compared to their original tumors has not been evaluated so far...
October 20, 2016: Genome Medicine
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