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Cytosine methylation

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https://www.readbyqxmd.com/read/28641529/irna-2methyl-identify-rna-2-o-methylation-sites-by-incorporating-sequence-coupled-effects-into-general-pseknc-and-ensemble-classifier
#1
Wang-Ren Qiu, Shi-Yu Jiang, Bi-Qian Sun, Xuan Xiao, Xiang Cheng, Kuo-Chen Chou
OBJECTIVE: Being a kind of post-transcriptional modification (PTCM) in RNA, the 2'-O-methylation modification occurs in the processes of life development and disease formation as well. Accordingly, from the angles of both basic research and drug development, we are facing a challenging problem: given an uncharacterized RNA sequence formed by many nucleotides of A (adenine), C (cytosine), G (guanine), and U (uracil), which one can be of 2-O-methylation modification, and which one cannot? Unfortunately, so far no computational method whatsoever has been developed to address such a problem...
June 22, 2017: Medicinal Chemistry
https://www.readbyqxmd.com/read/28621722/comparative-analysis-of-genome-wide-dna-methylation-profiles-for-the-genic-male-sterile-cabbage-line-01-20s-and-its-maintainer-line
#2
Fengqing Han, Xiaoli Zhang, Xing Liu, Henan Su, Congcong Kong, Zhiyuan Fang, Limei Yang, Mu Zhuang, Yangyong Zhang, Yumei Liu, Zhansheng Li, Honghao Lv
Methylation modifications play an important role in multiple biological processes. Several studies have reported altered methylation patterns in male sterile plants such as rice and wheat, but little is known about the global methylation profiles and their possible roles in the cabbage (Brassicaoleracea) male sterile line. In this study, single-base-resolution bisulfite sequencing (BS-Seq) was adopted to identify the pattern and degree of cytosine methylation in the male sterile line 01-20S and its near-isogenic fertile line 01-20F...
June 16, 2017: Genes
https://www.readbyqxmd.com/read/28614722/quantitative-analysis-of-the-dna-methylation-sensitivity-of-transcription-factor-complexes
#3
Judith F Kribelbauer, Oleg Laptenko, Siying Chen, Gabriella D Martini, William A Freed-Pastor, Carol Prives, Richard S Mann, Harmen J Bussemaker
Although DNA modifications play an important role in gene regulation, the underlying mechanisms remain elusive. We developed EpiSELEX-seq to probe the sensitivity of transcription factor binding to DNA modification in vitro using massively parallel sequencing. Feature-based modeling quantifies the effect of cytosine methylation ((5)mC) on binding free energy in a position-specific manner. Application to the human bZIP proteins ATF4 and C/EBPβ and three different Pbx-Hox complexes shows that (5)mCpG can both increase and decrease affinity, depending on where the modification occurs within the protein-DNA interface...
June 13, 2017: Cell Reports
https://www.readbyqxmd.com/read/28608346/computational-analysis-of-genome-wide-argonaute-dependent-dna-methylation-in-plants
#4
Kai Tang, Cheng-Guo Duan, Huiming Zhang, Jian-Kang Zhu
Whole-genome bisulfite sequencing (WGBS) has become a powerful tool to dissect genome-wide methylation profiles at single-base resolution. In this chapter we describe in detail the bioinformatics pipeline used for the analysis of ARGONAUTE-dependent DNA methylation in Arabidopsis thaliana. We provide tools and command lines used for mapping bisulfite sequencing reads, for estimating methylation levels at individual cytosine sites, for identifying differentially methylated regions (DMRs), and for calculating methylation levels of DMRs...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28606110/a-c9orf72-bac-mouse-model-recapitulates-key-epigenetic-perturbations-of-als-ftd
#5
Rustam Esanov, Gabriela Toro Cabrera, Nadja S Andrade, Tania F Gendron, Robert H Brown, Michael Benatar, Claes Wahlestedt, Christian Mueller, Zane Zeier
BACKGROUND: Amyotrophic Lateral Sclerosis (ALS) is a fatal and progressive neurodegenerative disorder with identified genetic causes representing a significant minority of all cases. A GGGGCC hexanucleotide repeat expansion (HRE) mutation within the C9ORF72 gene has recently been identified as the most frequent known cause of ALS. The expansion leads to partial heterochromatinization of the locus, yet mutant RNAs and dipeptide repeat proteins (DPRs) are still produced in sufficient quantities to confer neurotoxicity...
June 12, 2017: Molecular Neurodegeneration
https://www.readbyqxmd.com/read/28600135/human-dna-cytosine-5-methyltransferases-a-functional-and-structural-perspective-for-epigenetic-cancer-therapy
#6
REVIEW
Grégoire Rondelet, Johan Wouters
Epigenetic modifications modulate chromatin states to regulate gene expression. Among them, DNA methylation and histone modifications play a crucial role in the establishment of the epigenome. In cancer, these epigenetic events may act in concert to repress tumor suppressor genes or promote transcription of oncogenes and genes up-regulated by oncoproteins. In the context of cancer initiation and progression, recruitment of DNA (cytosine-5)-methyltransferases to specific genomic regions is mainly mediated by histone epigenetic marks, transcription factors and co-regulators as part of a dynamic process...
June 6, 2017: Biochimie
https://www.readbyqxmd.com/read/28599500/notable-roles-of-ezh2-and-dnmt1-in-epigenetic-dormancy-of-the-shp1-gene-during-the-progression-of-chronic-myeloid-leukaemia
#7
Jing Wang, Luoming Hua, Ming Guo, Lin Yang, Xiaojun Liu, Yanmeng Li, Xiaoyan Shang, Jianmin Luo
Tumor development is associated with the methylation of cytosine-guanine (CpG) islands. The occurrence of methylation requires several factors, such as DNA methylation systems and polycomb group (PcG) proteins. At present, novel drugs are needed for the treatment of chronic myeloid leukaemia (CML), particularly considering the current prognosis of CML. The methylation status of the Src homology 2 domain-containing tyrosine phosphatase 1 (SHP1) gene, a negative regulator of signal transduction, has been identified as being altered in numerous haematological malignancies...
June 2017: Oncology Letters
https://www.readbyqxmd.com/read/28596252/success-in-bone-marrow-failure-novel-therapeutic-directions-based-on-the-immune-environment-of-myelodysplastic-syndromes
#8
REVIEW
Alyssa H Cull, Michael J Rauh
Myelodysplastic syndromes (MDS) are clonal neoplasms of aging that are associated with BM failure, related cytopenias, fatigue, susceptibility to infections, bruising, bleeding, a shortened lifespan, and a propensity for leukemic transformation. Most frail, elderly patients are not candidates for curative allogeneic BM transplantations and instead receive expectant management, supportive blood transfusions, or empirical, nontargeted therapy. It has been known for some time that MDS arises in an abnormal BM immune environment; however, connections have only recently been established with recurring MDS-associated mutations...
June 8, 2017: Journal of Leukocyte Biology
https://www.readbyqxmd.com/read/28592103/-association-of-etheno-dna-adduct-and-dna-methylation-level-among-workers-exposed-to-diesel-engine-exhaust
#9
M L Shen, Z N He, X Zhang, H W Duan, Y Niu, P Bin, M Ye, T Meng, Y F Dai, S F Yu, W Chen, Y X Zheng
Objective: To investigate the association between etheno-DNA adduct and the promoter of DNA methylation levels of cyclin dependent kinase inhibitor 2A (P16), Ras association domain family 1 (RASSF1A) and O-6-methylguanine-DNA methyltransferase (MGMT) in workers with occupational exposure to diesel engine exhaust (DEE). Methods: We recruited 124 diesel engine testing workers as DEE exposure group and 112 water pump operator in the same area as control group in Henan province in 2012 using cluster sampling. The demographic data were obtained by questionnaire survey; urine after work and venous blood samples were collected from each subject...
June 6, 2017: Zhonghua Yu Fang Yi Xue za Zhi [Chinese Journal of Preventive Medicine]
https://www.readbyqxmd.com/read/28584398/tumor-necrosis-factor-%C3%AE-decreases-ec-sod-expression-through-dna-methylation
#10
Shunpei Morisawa, Hiroyuki Yasuda, Tetsuro Kamiya, Hirokazu Hara, Tetsuo Adachi
Extracellular-superoxide dismutase (EC-SOD) is a secreted antioxidative enzyme, and its presence in vascular walls may play an important role in protecting the vascular system against oxidative stress. EC-SOD expression in cultured cell lines is regulated by various cytokines including tumor necrosis factor-α (TNF-α). TNF-α is a major mediator of pathophysiological conditions and may induce or suppress the generation of various types of mediators. Epigenetics have been defined as mitotically heritable changes in gene expression that do not affect the DNA sequence, and include DNA methylation and histone modifications...
May 2017: Journal of Clinical Biochemistry and Nutrition
https://www.readbyqxmd.com/read/28583846/epigenetic-effects-of-inhibition-of-heat-shock-protein-90-hsp90-in-human-pancreatic-and-colon-cancer
#11
Ganji Purnachandra Nagaraju, Christina Wu, Neha Merchant, Zhengjia Chen, Gregory B Lesinski, Bassel F El-Rayes
Silencing of tumor suppressor and DNA repair genes through methylation plays a role in cancer development, growth and response to therapy in colorectal and pancreatic cancers. Heat shock protein 90 (HSP90) regulates transcription of DNA methyltransferase enzymes (DNMT). In addition, DNMTs are client proteins of HSP90. The aim of this study is to evaluate the effects of HSP90 inhibition on DNA methylation in colorectal and pancreatic cancer cell lines. Our data shows that inhibition of HSP90 using ganetespib resulted in downregulation of mRNA and protein expression of DNMT1, DNMT3A, and DNMT3B in HT-29 and MIA PaCa-2 cell lines...
June 3, 2017: Cancer Letters
https://www.readbyqxmd.com/read/28582695/identification-of-potent-inhibitors-of-dna-methyltransferase-1-dnmt1-through-a-pharmacophore-based-virtual-screening-approach
#12
Shagun Krishna, Samriddhi Shukla, Amar Deep Lakra, Syed Musthapa Meeran, Mohammad Imran Siddiqi
DNA methylation is an epigenetic change that results in the addition of a methyl group at the carbon-5 position of cytosine residues. DNA methyltransferase (DNMT) inhibitors can suppress tumour growth and have significant therapeutic value. However, the established inhibitors are limited in their application due to their substantial cytotoxicity. Additionally, the standard drugs for DNMT inhibition are non-selective cytosine analogues with considerable cytotoxic side-effects. In the present study, we have designed a workflow by integrating various ligand-based and structure-based approaches to discover new agents active against DNMT1...
May 25, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28576321/quantification-of-gene-specific-dna-methylation-in-oesophageal-cancer-via-electrochemistry
#13
Md Hakimul Haque, Vinod Gopalan, Md Nazmul Islam, Mostafa Kamal Masud, Ripon Bhattacharjee, Md Shahriar Al Hossain, Nam-Trung Nguyen, Alfred K Lam, Muhammad J A Shiddiky
Development of simple and inexpensive method for the analysis of gene-specific DNA methylation is important for the diagnosis and prognosis of patients with cancer. Herein, we report a relatively simple and inexpensive electrochemical method for the sensitive and selective detection of gene-specific DNA methylation in oesophageal cancer. The underlying principle of the method relies on the affinity interaction between DNA bases and unmodified gold electrode. Since the affinity trend of DNA bases towards the gold surface follows as adenine (A) > cytosine (C) > guanine (G)> thymine (T), a relatively larger amount of bisulfite-treated adenine-enriched unmethylated DNA adsorbs on the screen-printed gold electrodes (SPE-Au) in comparison to the guanine-enriched methylated sample...
July 11, 2017: Analytica Chimica Acta
https://www.readbyqxmd.com/read/28560381/hypomethylation-of-the-toll-like-receptor-2-gene-increases-the-risk-of-essential-hypertension
#14
Shuqi Mao, Tianlun Gu, Fade Zhong, Rui Fan, Fubao Zhu, Peipei Ren, Fengying Yin, Lina Zhang
Studies on the etiology of essential hypertension (EH) have demonstrated that chronic inflammation contributes to the onset and development of elevated blood pressure. Toll‑like receptors (TLRs), important immune receptors, serve a role in chronic inflammation and are associated with EH. In the present study, 96 patients with EH, and 96 age‑ and sex‑matched healthy controls were recruited, and eight cytosine‑phosphate‑guanine (CpG) dinucleotides (CpG1‑8) were analyzed using bisulfite pyrosequencing technology...
July 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28559849/epigenetic-dna-methylation-mediating-octopus-vulgaris-early-development-effect-of-essential-fatty-acids-enriched-diet
#15
Pablo García-Fernández, Danie García-Souto, Eduardo Almansa, Paloma Morán, Camino Gestal
The common octopus, Octopus vulgaris, is a good candidate for aquaculture but a sustainable production is still unviable due to an almost total mortality during the paralarvae stage. DNA methylation regulates gene expression in the eukaryotic genome, and has been shown to exhibit plasticity throughout O. vulgaris life cycle, changing profiles from paralarvae to adult stages. This pattern of methylation could be sensitive to small alterations in nutritional and environmental conditions during the species early development, thus impacting on its health, growth and survival...
2017: Frontiers in Physiology
https://www.readbyqxmd.com/read/28558752/epigenomic-and-functional-analyses-reveal-roles-of-epialleles-in-the-loss-of-photoperiod-sensitivity-during-domestication-of-allotetraploid-cottons
#16
Qingxin Song, Tianzhen Zhang, David M Stelly, Z Jeffrey Chen
BACKGROUND: Polyploidy is a pervasive evolutionary feature of all flowering plants and some animals, leading to genetic and epigenetic changes that affect gene expression and morphology. DNA methylation changes can produce meiotically stable epialleles, which are transmissible through selection and breeding. However, the relationship between DNA methylation and polyploid plant domestication remains elusive. RESULTS: We report comprehensive epigenomic and functional analyses, including ~12 million differentially methylated cytosines in domesticated allotetraploid cottons and their tetraploid and diploid relatives...
May 31, 2017: Genome Biology
https://www.readbyqxmd.com/read/28555658/tet-mediated-active-dna-demethylation-mechanism-function-and-beyond
#17
REVIEW
Xiaoji Wu, Yi Zhang
In mammals, DNA methylation in the form of 5-methylcytosine (5mC) can be actively reversed to unmodified cytosine (C) through TET dioxygenase-mediated oxidation of 5mC to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC), followed by replication-dependent dilution or thymine DNA glycosylase (TDG)-dependent base excision repair. In the past few years, biochemical and structural studies have revealed mechanistic insights into how TET and TDG mediate active DNA demethylation...
May 30, 2017: Nature Reviews. Genetics
https://www.readbyqxmd.com/read/28553986/epigenetics-nutrition-and-mental-health-is-there-a-relationship
#18
Aaron J Stevens, Julia J Rucklidge, Martin A Kennedy
Many aspects of human development and disease are influenced by the interaction between genetic and environmental factors. Understanding how our genes respond to the environment is central to managing health and disease, and is one of the major contemporary challenges in human genetics. Various epigenetic processes affect chromosome structure and accessibility of deoxyribonucleic acid (DNA) to the enzymatic machinery that leads to expression of genes. One important epigenetic mechanism that appears to underlie the interaction between environmental factors, including diet, and our genome, is chemical modification of the DNA...
May 29, 2017: Nutritional Neuroscience
https://www.readbyqxmd.com/read/28546576/adenine-n6-methylation-in-diverse-fungi
#19
Michael F Seidl
A DNA modification-methylation of cytosines and adenines-has important roles in diverse processes such as regulation of gene expression and genome stability, yet until recently adenine methylation had been considered to be only a hallmark of prokaryotes. A new study identifies abundant adenine methylation of transcriptionally active genes in early-diverging fungi that, together with recent other work, emphasizes the importance of adenine methylation in eukaryotes.
May 26, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28545252/cpg-and-non-cpg-methylation-in-epigenetic-gene-regulation-and-brain-function
#20
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
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