keyword
MENU ▼
Read by QxMD icon Read
search

Cytosine methylation

keyword
https://www.readbyqxmd.com/read/28720682/reducing-artifactual-egfr-t790m-mutations-in-dna-from-formalin-fixed-paraffin-embedded-tissue-by-use-of-thymine-dna-glycosylase
#1
Hongdo Do, Ramyar Molania, Paul L Mitchell, Rita Vaiskunaite, John D Murdoch, Alexander Dobrovic
BACKGROUND: False-positive EGFR T790M mutations have been reported in formalin-fixed lung tumors, but the cause of the false positives has not been identified. The T790M mutation results from a C>T change at the cytosine of a CpG dinucleotide. The presence or absence of methylation at this cytosine has different consequences following deamination, resulting in a thymine or uracil, respectively, both of which however result in an artifactual change. Uracil-DNA glycosylase (UDG) can be used to eliminate DNA templates with uracil residues but is not active against artifactual thymines...
July 18, 2017: Clinical Chemistry
https://www.readbyqxmd.com/read/28720579/recruitment-of-histone-modifications-to-assist-mrna-dosage-maintenance-after-degeneration-of-cytosine-dna-methylation-during-animal-evolution
#2
Andrew Yf Chang, Ben-Yang Liao
Following gene duplication, mRNA expression of the duplicated gene is reduced to maintain mRNA dosage. In mammals, this process is achieved with increased cytosine DNA methylation of the promoters of duplicated genes to suppress transcriptional initiation. However, not all animal species possess a full apparatus for cytosine DNA methylation. For such species such as roundworm (Caenorhabditis elegans, "worm" hereafter) or fruit fly (Drosophila melanogaster, "fly" hereafter), it is unclear how reduced expression of duplicated genes has been achieved evolutionarily...
July 18, 2017: Genome Research
https://www.readbyqxmd.com/read/28717061/apobec-mediated-genomic-alterations-link-immunity-and-viral-infection-during-human-papillomavirus-driven-cervical-carcinogenesis
#3
Lanting Chen, Xuemin Qiu, Na Zhang, Yan Wang, Mingyan Wang, Dajin Li, Ling Wang, Yan Du
Cervical cancer is one of the most frequently diagnosed cancers and is a major cause of death from gynecologic cancers worldwide; the cancer burden from cervical cancer is especially heavy in less developed countries. Most cases of cervical cancer are caused by persistent infection with carcinogenic human papillomavirus (HPV) genotypes 16 and 18. Non-resolving inflammation caused by HPV infection provides a microenvironment that facilitates cancer development. Molecular alterations during the process of HPV-induced carcinogenesis are characterized by DNA methylation within the HPV genome, promoter hypermethylation of tumor suppressor genes in the host genome, as well as genomic instability caused by viral DNA integrating into the host genome...
July 17, 2017: Bioscience Trends
https://www.readbyqxmd.com/read/28716266/sativex%C3%A2-effects-on-promoter-methylation-and-on-cnr1-cnr2-expression-in-peripheral-blood-mononuclear-cells-of-progressive-multiple-sclerosis-patients
#4
Massimo Santoro, Massimiliano Mirabella, Chiara De Fino, Assunta Bianco, Matteo Lucchini, Francesco Losavio, Andrea Sabino, Viviana Nociti
Multiple sclerosis (MS) is a chronic demyelinating central nervous system (CNS) disease that involve oligodendrocyte loss and failure to remyelinate damaged brain areas causing a progressive neurological disability. Studies in MS mouse model suggest that cannabinoids ameliorate symptoms as spasticity, tremor and pain reducing inflammation via cannabinoid-mediated system. The aim of our study is to investigate the changes in cannabinoid type 1 (CNR1) and 2 (CNR2) receptors mRNA expression levels and promoter methylation in peripheral blood mononuclear cells (PBMCs) of MS secondary progressive (MSS-SP) patients treated with Sativex®...
August 15, 2017: Journal of the Neurological Sciences
https://www.readbyqxmd.com/read/28715427/global-analysis-of-dna-methylation-in-young-j1-and-senescent-j2-gossypium-hirsutum-l-cotyledons-by-medip-seq
#5
Lingling Dou, Xiaoyun Jia, Hengling Wei, Shuli Fan, Hantao Wang, Yaning Guo, Shan Duan, Chaoyou Pang, Shuxun Yu
DNA methylation is an important epigenetic modification regulating gene expression, genomic imprinting, transposon silencing and chromatin structure in plants and plays an important role in leaf senescence. However, the DNA methylation pattern during Gossypium hirsutum L. cotyledon senescence is poorly understood. In this study, global DNA methylation patterns were compared between two cotyledon development stages, young (J1) and senescence (J2), using methylated DNA immunoprecipitation (MeDIP-Seq). Methylated cytosine occurred mostly in repeat elements, especially LTR/Gypsy in both J1 and J2...
2017: PloS One
https://www.readbyqxmd.com/read/28713411/physiological-biochemical-epigenetic-and-molecular-analyses-of-wheat-triticum-aestivum-genotypes-with-contrasting-salt-tolerance
#6
Suresh Kumar, A S Beena, Monika Awana, Archana Singh
Abiotic stress exerts significant impact on plant's growth, development, and productivity. Productivity of crop plants under salt stress is lagging behind because of our limited knowledge about physiological, biochemical, epigenetic, and molecular mechanisms of salt tolerance in plants. This study aimed to investigate physio-biochemical, molecular indices and defense responses of selected wheat cultivars to identify the most contrasting salt-responsive genotypes and the mechanisms associated with their differential responses...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28711634/role-of-epigenetic-modulation-in-cancer-stem-cell-fate
#7
REVIEW
Abhijeet Deshmukh, Mudra Binju, Frank Arfuso, Philip Newsholme, Arun Dharmarajan
A sub-population of the tumor micro-environment consists of cancer stem cells (CSCs), which are responsible for the initiation and recurrence of cancer. Recently, epigenetic processes such as DNA methylation, histone modification, and chromatin remodelling have been found to be involved in inducing epigenetic factors in CSCs. Most of these processes, such as DNA methylation, generally occur in the genome that is rich in Cytosine-Guanine repeat sequences, also known as CpG islands, which are distributed throughout the human genome...
July 12, 2017: International Journal of Biochemistry & Cell Biology
https://www.readbyqxmd.com/read/28709638/dna-methylation-protects-against-cisplatin-induced-kidney-injury-by-regulating-specific-genes-including-interferon-regulatory-factor-8
#8
Chunyuan Guo, Lirong Pei, Xiao Xiao, Qingqing Wei, Jian-Kang Chen, Han-Fei Ding, Shuang Huang, Guoping Fan, Huidong Shi, Zheng Dong
DNA methylation is an epigenetic mechanism that regulates gene transcription without changing primary nucleotide sequences. In mammals, DNA methylation involves the covalent addition of a methyl group to the 5-carbon position of cytosine by DNA methyltransferases (DNMTs). The change of DNA methylation and its pathological role in acute kidney injury (AKI) remain largely unknown. Here, we analyzed genome-wide DNA methylation during cisplatin-induced AKI by reduced representation bisulfite sequencing. This technique identified 215 differentially methylated regions between the kidneys of control and cisplatin-treated animals...
July 11, 2017: Kidney International
https://www.readbyqxmd.com/read/28697590/prevalence-of-fragile-x-syndrome-among-children-receiving-special-education-and-carrier-states-in-first-degree-relatives
#9
B Chandrasekara, S Wijesundera, S S Chong, H N Perera
Introduction: Fragile X syndrome (FXS) is a genetically determined developmental disorder. Underlying genotype is cytosine-guanine-guanine (CGG) repeat expansions with over 200 repeats in the fragile X mental retardation 1 (FMR1) gene. Children with FXS are most accessible in special education institutions in Sri Lanka, with a total of approximately 6000 registered attendees. Objectives: The aim of the current study was to estimate the prevalence of FXS among special school attendees and to screen first degree relatives of affected children...
June 30, 2017: Ceylon Medical Journal
https://www.readbyqxmd.com/read/28695892/targeted-dna-methylation-in-vivo-using-an-engineered-dcas9-mq1-fusion-protein
#10
Yong Lei, Xiaotian Zhang, Jianzhong Su, Mira Jeong, Michael C Gundry, Yung-Hsin Huang, Yubin Zhou, Wei Li, Margaret A Goodell
Comprehensive studies have shown that DNA methylation plays vital roles in both loss of pluripotency and governance of the transcriptome during embryogenesis and subsequent developmental processes. Aberrant DNA methylation patterns have been widely observed in tumorigenesis, ageing and neurodegenerative diseases, highlighting the importance of a systematic understanding of DNA methylation and the dynamic changes of methylomes during disease onset and progression. Here we describe a facile and convenient approach for efficient targeted DNA methylation by fusing inactive Cas9 (dCas9) with an engineered prokaryotic DNA methyltransferase MQ1...
July 11, 2017: Nature Communications
https://www.readbyqxmd.com/read/28693600/normal-breast-tissue-dna-methylation-differences-at-regulatory-elements-are-associated-with-the-cancer-risk-factor-age
#11
Kevin C Johnson, E Andres Houseman, Jessica E King, Brock C Christensen
BACKGROUND: The underlying biological mechanisms through which epidemiologically defined breast cancer risk factors contribute to disease risk remain poorly understood. Identification of the molecular changes associated with cancer risk factors in normal tissues may aid in determining the earliest events of carcinogenesis and informing cancer prevention strategies. METHODS: Here we investigated the impact cancer risk factors have on the normal breast epigenome by analyzing DNA methylation genome-wide (Infinium 450 K array) in cancer-free women from the Susan G...
July 10, 2017: Breast Cancer Research: BCR
https://www.readbyqxmd.com/read/28692286/methylated-cytosine-maintains-g-quadruplex-structures-during-polymerase-chain-reaction-and-contributes-to-allelic-dropout
#12
Aaron J Stevens, Martin A Kennedy
The promoter of the human imprinted gene MEST is differentially methylated with respect to the parent of origin and contains several non B-DNA motifs that are capable of forming G-quadruplexes. These factors can contribute to a consistent allelic dropout (ADO) of the maternally methylated DNA during polymerase chain reaction (PCR) analysis of such gene regions. Here, we directly investigate the cause of allelic dropout by applying fluorescent techniques to visualize polymerase amplification and arrest during PCR of differentially methylated DNA templates...
July 10, 2017: Biochemistry
https://www.readbyqxmd.com/read/28686109/%C3%AE-adducin-gene-promoter-dna-methylation-and-the-risk-of-essential-hypertension
#13
Nervana M K Bayoumy, Mohamed M El-Shabrawi, Ola Farouk Leheta, Hamdy Hassan Omar
This study was conducted to test the association between promoter DNA methylation of α-Adducin (ADD1) gene and the risk of essential hypertension (EH). A total of 150 EH patients and 100 aged- and gender-matched controls were investigated. DNA methylation levels of five cytosine-phosphate-guanine (CpG) dinucleotides on ADD1 promoter were measured employing bisulfite pyrosequencing technology. Our results showed that females have a higher ADD1 DNA methylation than males and a significantly lower CpG1 methylation level is associated with increased risk of EH among them...
July 7, 2017: Clinical and Experimental Hypertension: CHE
https://www.readbyqxmd.com/read/28684555/statistically-robust-methylation-calling-for-whole-transcriptome-bisulfite-sequencing-reveals-distinct-methylation-patterns-for-mouse-rnas
#14
Carine Legrand, Francesca Tuorto, Mark Hartmann, Reinhard Liebers, Dominik Jacob, Mark Helm, Frank Lyko
(Cytosine-5) RNA methylation plays an important role in several biologically and pathologically relevant processes. However, owing to methodological limitations, the transcriptome-wide distribution of this mark has remained largely unknown. We previously established RNA bisulfite sequencing as a method for the analysis of RNA (cytosine-5) methylation patterns at single-base resolution. More recently, next-generation sequencing has provided opportunities to establish transcriptome-wide maps of this modification...
July 6, 2017: Genome Research
https://www.readbyqxmd.com/read/28684528/wnt-%C3%A3-catenin-activation-by-epigenetically-aberrant-stroma-drives-myelodysplastic-syndrome
#15
Tushar Bhagat, Si Chen, Matthias Bartenstein, Trevor S Barlowe, Dagny von Ahrens, Gaurav S Choudhary, Patrick Tivnan, Elianna Amin, A Mario Marcondes, Mathijs A Sanders, Remco M Hoogenboezem, Suman Kambhampati, Nandini Ramachandra, Ioannis Mantzaris, Vineeth Sukrithan, Remi Laurence, Robert Lopez, Prafulla Bhagat, Orsi Giricz, Davendra Sohal, Amittha Wickrema, Cecilia Cs Yeung, Kira Gritsman, Peter D Aplan, Konrad Hochedlinger, Yiting Yu, Kith Pradhan, Jinghang Zhang, John Greally, Siddhartha Mukherjee, Andrea Pellagatti, Jacqueline Boultwood, Britta Will, Ulrich Steidl, Marc Hgp Raaijmakers, H J Deeg, Michael G Kharas, Amit Verma
The bone marrow microenvironment influences malignant hematopoiesis but how it promotes leukemogenesis has not been elucidated. Additionally, the role of the bone marrow stroma in regulating clinical responses to DNA methyltransferase inhibitors (DNMTi) is also poorly understood. In this study, we conducted a DNA methylome analysis of bone marrow-derived stromal cells from myelodysplastic syndrome (MDS) patients and observed widespread aberrant cytosine hypermethylation occurring preferentially outside CpG islands...
July 6, 2017: Cancer Research
https://www.readbyqxmd.com/read/28683715/plant-rrbs-a-bisulfite-and-next-generation-sequencing-based-methylome-profiling-method-enriching-for-coverage-of-cytosine-positions
#16
Martin Schmidt, Michiel Van Bel, Magdalena Woloszynska, Bram Slabbinck, Cindy Martens, Marc De Block, Frederik Coppens, Mieke Van Lijsebettens
BACKGROUND: Cytosine methylation in plant genomes is important for the regulation of gene transcription and transposon activity. Genome-wide methylomes are studied upon mutation of the DNA methyltransferases, adaptation to environmental stresses or during development. However, from basic biology to breeding programs, there is a need to monitor multiple samples to determine transgenerational methylation inheritance or differential cytosine methylation. Methylome data obtained by sodium hydrogen sulfite (bisulfite)-conversion and next-generation sequencing (NGS) provide genome-wide information on cytosine methylation...
July 6, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28682263/modeling-methylation-patterns-with-long-read-sequencing-data
#17
Karlene Nicole Meyer, Michelle Lacey
Variation in cytosine methylation at CpG dinucleotides is often observed in genomic regions, and analysis typically focuses on estimating the proportion of methylated sites observed in a given region and comparing these levels across samples to determine association with conditions of interest. While sites are tacitly treated as independent, when observed at the level of individual molecules methylation patterns exhibit strong evidence of local spatial dependence. We previously developed a neighboring sites model to account for correlation and clustering behavior observed in two tandem repeat regions in a collection of ovarian carcinomas...
June 30, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28675894/low-oxygen-consumption-is-related-to-a-hypomethylation-and-an-increased-secretion-of-il-6-in-obese-subjects-with-sleep-apnea-hypopnea-syndrome
#18
Amaya Lopez-Pascual, Arrate Lasa, María P Portillo, Fernando Arós, María L Mansego, Pedro González-Muniesa, J Alfredo Martinez
BACKGROUND: Deoxyribonucleic acid (DNA) methylation is an epigenetic modification involved in gene expression regulation, usually via gene silencing, which contributes to the risks of many multifactorial diseases. The aim of the present study was to analyze the influence of resting oxygen consumption on global and gene DNA methylation as well as protein secretion of inflammatory markers in blood cells from obese subjects with sleep apnea-hypopnea syndrome (SAHS). METHODS: A total of 44 obese participants with SAHS were categorized in 2 groups according to their resting oxygen consumption...
July 4, 2017: Annals of Nutrition & Metabolism
https://www.readbyqxmd.com/read/28675387/serotonin-transporter-gene-promoter-methylation-status-correlates-with-in-vivo-prefrontal-5-htt-availability-and-reward-function-in-human-obesity
#19
M Drabe, M Rullmann, J Luthardt, Y Boettcher, R Regenthal, T Ploetz, G A Becker, M Patt, C Schinke, F T Bergh, F Zientek, A Hilbert, A Bresch, W Fenske, M K Hankir, O Sabri, S Hesse
A polymorphism in the promoter region of the human serotonin transporter (5-HTT)-coding SLC6A4 gene (5-HTTLPR) has been implicated in moderating susceptibility to stress-related psychopathology and to possess regulatory functions on human in vivo 5-HTT availability. However, data on a direct relation between 5-HTTLPR and in vivo 5-HTT availability have been inconsistent. Additional factors such as epigenetic modifications of 5-HTTLPR might contribute to this association. This is of particular interest in the context of obesity, as an association with 5-HTTLPR hypermethylation has previously been reported...
July 4, 2017: Translational Psychiatry
https://www.readbyqxmd.com/read/28671256/genome-wide-analysis-of-salinity-stress-induced-dna-methylation-alterations-in-cotton-gossypium-hirsutum-l-using-the-me-dip-sequencing-technology
#20
X K Lu, N Shu, J J Wang, X G Chen, D L Wang, S Wang, W L Fan, X N Guo, L X Guo, W W Ye
Cytosine DNA methylation is a significant form of DNA modification closely associated with gene expression in eukaryotes, fungi, animals, and plants. Although the reference genomes of cotton (Gossypium hirsutum L.) have been publically available, the salinity-stress-induced DNA methylome alterations in cotton are not well understood. Here, we constructed a map of genome-wide DNA methylation characteristics of cotton leaves under salt stress using the methylated DNA immunoprecipitation sequencing method. The results showed that the methylation reads on chromosome 9 were most comparable with those on the other chromosomes, but the greatest changes occurred on chromosome 8 under salt stress...
June 29, 2017: Genetics and Molecular Research: GMR
keyword
keyword
113740
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"