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Methylomics

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https://www.readbyqxmd.com/read/29141580/usability-of-human-infinium-methylationepic-beadchip-for-mouse-dna-methylation-studies
#1
Maria Needhamsen, Ewoud Ewing, Harald Lund, David Gomez-Cabrero, Robert Adam Harris, Lara Kular, Maja Jagodic
BACKGROUND: The advent of array-based genome-wide DNA methylation methods has enabled quantitative measurement of single CpG methylation status at relatively low cost and sample input. Whereas the use of Infinium Human Methylation BeadChips has shown great utility in clinical studies, no equivalent tool is available for rodent animal samples. We examined the feasibility of using the new Infinium MethylationEPIC BeadChip for studying DNA methylation in mouse. RESULTS: In silico, we identified 19,420 EPIC probes (referred as mEPIC probes), which align with a unique best alignment score to the bisulfite converted reference mouse genome mm10...
November 15, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29137437/dna-hypermethyation-and-silencing-of-pitx1-correlated-with-advanced-stage-and-poor-postoperative-prognosis-of-esophageal-squamous-cell-carcinoma
#2
Takeshi Otsubo, Kazuhiko Yamada, Teruki Hagiwara, Kenshiro Oshima, Kei Iida, Koro Nishikata, Tetsuro Toyoda, Toru Igari, Kyoko Nohara, Satoshi Yamashita, Masahira Hattori, Taeko Dohi, Yuki I Kawamura
Esophageal squamous cell carcinoma (ESCC) is associated with the accumulation of genetic and epigenetic changes in the background mucosa. Dysregulated DNA methylation is known to lead to the inactivation of tumor suppressor genes and the activation of oncogenes. To identify the genes whose expression is perturbed by abnormal DNA methylation in ESCC, integrative transcriptomics by serial analysis of gene expression (SAGE) and methylome sequencing by methyl-DNA immunoprecipitation (MeDIP) analysis were performed...
October 13, 2017: Oncotarget
https://www.readbyqxmd.com/read/29130189/identifying-the-m-6-a-methylome-by-affinity-purification-and-sequencing
#3
Phillip J Hsu, Chuan He
N (6)-methyladenosine (m(6)A) is the most abundant internal modification in eukaryotic mRNA, and is newly emerging as a key posttranscriptional mRNA regulator. Recent research has uncovered insight into the location and function of m(6)A sites on a large scale, in part due to the transcriptome-wide identification of m(6)A sites by high-throughput sequencing (m(6)A-seq). Here, we present a protocol for m(6)A-seq, which maps the m(6)A methylome by affinity purification and sequencing.
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29115936/analyses-of-methylomes-of-upland-and-lowland-switchgrass-panicum-virgatum-ecotypes-using-medip-seq-and-bs-seq
#4
Mollee Dworkin, Shaojun Xie, Malay Saha, Jyothi Thimmapuram, Venu Kal Kalavacharla
BACKGROUND: Switchgrass is a crop with many desirable traits for bioenergy production. Plant genomes have high DNA methylation levels throughout genes and transposable elements and DNA methylation is known to play a role in silencing transposable elements. Here we analyzed methylomes in two switchgrass genotypes AP13 and VS16. AP13 is derived from a lowland ecotype and VS16, typically considered drought-tolerant, is derived from an upland ecotype, both genotypes are tetraploid (2n = 4× = 36)...
November 7, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29115931/guanylate-binding-protein-1-is-a-potential-new-therapeutic-target-for-triple-negative-breast-cancer
#5
Melissa Quintero, Douglas Adamoski, Larissa Menezes Dos Reis, Carolline Fernanda Rodrigues Ascenção, Krishina Ratna Sousa de Oliveira, Kaliandra de Almeida Gonçalves, Marília Meira Dias, Marcelo Falsarella Carazzolle, Sandra Martha Gomes Dias
BACKGROUND: Triple-negative breast cancer (TNBC) is characterized by a lack of estrogen and progesterone receptor expression (ESR and PGR, respectively) and an absence of human epithelial growth factor receptor (ERBB2) amplification. Approximately 15-20% of breast malignancies are TNBC. Patients with TNBC often have an unfavorable prognosis. In addition, TNBC represents an important clinical challenge since it does not respond to hormone therapy. METHODS: In this work, we integrated high-throughput mRNA sequencing (RNA-Seq) data from normal and tumor tissues (obtained from The Cancer Genome Atlas, TCGA) and cell lines obtained through in-house sequencing or available from the Gene Expression Omnibus (GEO) to generate a unified list of differentially expressed (DE) genes...
November 7, 2017: BMC Cancer
https://www.readbyqxmd.com/read/29115576/genome-wide-dna-methylome-alterations-in-acute-coronary-syndrome
#6
Dandan Li, Jing Yan, Yunlong Yuan, Cheng Wang, Jia Wu, Qingwen Chen, Jiaxi Song, Junjun Wang
Acute coronary syndrome (ACS) is a common disease with high mortality and morbidity rates. The methylation status of blood DNA may serve as a potential early diagnosis and prevention biomarker for numerous diseases. The present study was designed to explore novel genome-wide aberrant DNA methylation patterns associated with ACS. The Infinium HumanMethylation450 assay was used to examine genome-wide DNA methylation profiles in 3 pairs of ACS and control group samples. Epigenome-wide DNA methylation, genomic distribution, Gene Ontology (GO) term and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed...
October 27, 2017: International Journal of Molecular Medicine
https://www.readbyqxmd.com/read/29112847/evidence-for-converging-dna-methylation-pathways-in-placenta-and-cancer
#7
Matthew C Lorincz, Dirk Schübeler
CpG island promoters are generally devoid of DNA methylation in somatic cells but are frequently methylated during tumorigenesis. Reporting recently in Nature, Smith et al. (2017) show that the signaling-induced methylome in early extraembryonic tissues resembles that of many cancers, suggesting that placental nuclear programming might be co-opted in tumorigenesis.
November 6, 2017: Developmental Cell
https://www.readbyqxmd.com/read/29107537/base-resolution-mapping-reveals-distinct-m-1-a-methylome-in-nuclear-and-mitochondrial-encoded-transcripts
#8
Xiaoyu Li, Xushen Xiong, Meiling Zhang, Kun Wang, Ying Chen, Jun Zhou, Yuanhui Mao, Jia Lv, Danyang Yi, Xiao-Wei Chen, Chu Wang, Shu-Bing Qian, Chengqi Yi
Gene expression can be post-transcriptionally regulated via dynamic and reversible RNA modifications. N(1)-methyladenosine (m(1)A) is a recently identified mRNA modification; however, little is known about its precise location and biogenesis. Here, we develop a base-resolution m(1)A profiling method, based on m(1)A-induced misincorporation during reverse transcription, and report distinct classes of m(1)A methylome in the human transcriptome. m(1)A in 5' UTR, particularly those at the mRNA cap, associate with increased translation efficiency...
October 25, 2017: Molecular Cell
https://www.readbyqxmd.com/read/29106556/location-matters-distinct-dna-methylation-patterns-in-gabaergic-interneuronal-populations-from-separate-microcircuits-within-the-human-hippocampus
#9
W Brad Ruzicka, Sivan Subburaju, Joseph T Coyle, Francine M Benes
Recent studies describe distinct DNA methylomes among phenotypic subclasses of neurons in the human brain, but variation in DNA methylation between common neuronal phenotypes distinguished by their function within distinct neural circuits remains an unexplored concept. Studies able to resolve epigenetic profiles at the level of microcircuits are needed to illuminate chromatin dynamics in the regulation of specific neuronal populations and circuits mediating normal and abnormal behaviors.The Illumina HumanMethylation450 BeadChip was used to assess genome-wide DNA methylation in stratum oriens GABAergic interneurons sampled by laser-microdissection from two discrete microcircuits along the trisynaptic pathway in postmortem human hippocampus from eight control, eight schizophrenia, and eight bipolar disorder subjects...
November 2, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/29106553/genome-wide-dna-methylation-changes-associated-with-intermittent-explosive-disorder-a-gene-based-functional-enrichment-analysis
#10
Janitza L Montalvo-Ortiz, Huiping Zhang, Chao Chen, Chunyu Liu, Emil F Coccaro
Background: Intermittent explosive disorder (IED) is defined as a recurrent, problematic, and impulsive aggression that affects 3-4% of the U.S. population. While behavioral genetic studies report a substantial degree of genetic influence on aggression and impulsivity, epigenetic mechanisms underlying aggression and IED is not well known. Methods: The sample included 44 subjects (22 with a DSM-5 diagnosis of IED and 22 comparable subjects without IED). Peripheral blood DNA methylome was profiled using the Illumina Infinium HumanMethylation450 Beadchip...
November 2, 2017: International Journal of Neuropsychopharmacology
https://www.readbyqxmd.com/read/29099283/lowly-methylated-region-analysis-identifies-ebf1-as-a-potential-epigenetic-modifier-in-breast-cancer
#11
Nora Fernandez-Jimenez, Athena Sklias, Szilvia Ecsedi, Vincent Cahais, Davide Degli-Esposti, Antonin Jay, Pierre Benoit Ancey, Hae Dong Woo, Hector Hernandez-Vargas, Zdenko Herceg
Breast cancer (BC) encompasses heterogeneous pathologies with different subtypes exhibiting distinct molecular changes, including those related to DNA methylation. However, the role of these changes in mediating BC heterogeneity is poorly understood. Lowly methylated regions (LMRs), non-CpG island loci that usually contain transcription factor (TF) binding sites, have been suggested to act as regulatory elements that define cellular identity. In this study, we aimed to identify the key subtype-specific TFs that may lead to LMR generation and shape the BC methylome and transcription program...
November 3, 2017: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/29099280/variant-histone-h2afv-reprograms-dna-methylation-during-early-zebrafish-development
#12
Bhavani Madakashira, Laura Corbett, Chi Zhang, Pier Paoli, John W Casement, Jelena Mann, Kirsten C Sadler, Derek A Mann
The DNA methylome is re-patterned during discrete phases of vertebrate development. In zebrafish, there are two waves of global DNA demethylation and re-methylation: the first occurs prior to gastrulation when the parental methylome is changed to the zygotic pattern and the second occurs after formation of the embryonic body axis, during organ specification. The occupancy of the histone variant H2A.Z and regions of DNA methylation are generally anti-correlated, and it has been proposed that H2A.Z restricts the boundaries of highly methylated regions...
November 3, 2017: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/29099274/causes-of-blood-methylomic-variation-for-middle-aged-women-measured-by-the-humanmethylation450-array
#13
Shuai Li, Ee Ming Wong, Tuong L Nguyen, Ji-Hoon Eric Joo, Jennifer Stone, Gillian S Dite, Graham G Giles, Richard Saffery, Melissa C Southey, John L Hopper
To address the limitations in current classic twin/family research on the genetic and/or environmental causes of human methylomic variation, we measured blood DNA methylation for 479 women (mean age 56 years) including 66 monozygotic (MZ), 66 dizygotic (DZ) twin pairs and 215 sisters of twins, and 11 random technical duplicates using the HumanMethylation450 array. For each methylation site, we estimated the correlation for pairs of duplicates, MZ twins, DZ twins, and siblings, fitted variance component models by assuming the variation is explained by genetic factors, by shared and individual environmental factors, and by independent measurement error, and assessed the best fitting model...
November 3, 2017: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/29091992/transcriptome-wide-analysis-suggests-that-temporal-changes-in-the-relative-contributions-of-hyperplasia-hypertrophy-and-apoptosis-underlie-liver-growth-in-pregnant-mice
#14
Leonie R Price, Karen A Lillycrop, Nicola A Irvine, Mark A Hanson, Graham C Burdge
Maternal liver undergoes structural and metabolic changes during pregnancy to meet the demands of the developing fetus. In rodents, this involves increased liver weight, but the mechanism remains unclear. To address this, we analysed the histology, gene expression and DNA methylation of livers of non-pregnant and pregnant C57/BL6 mice. Gestational liver growth in pregnant mice was accompanied by increased hepatocyte area and lower cell density (days 14,18). Expression of cell proliferation markers was increased on days 14 and 18...
October 30, 2017: Biology of Reproduction
https://www.readbyqxmd.com/read/29078418/similarity-between-soybean-and-arabidopsis-seed-methylomes-and-loss-of-non-cg-methylation-does-not-affect-seed-development
#15
Jer-Young Lin, Brandon H Le, Min Chen, Kelli F Henry, Jungim Hur, Tzung-Fu Hsieh, Pao-Yang Chen, Julie M Pelletier, Matteo Pellegrini, Robert L Fischer, John J Harada, Robert B Goldberg
We profiled soybean and Arabidopsis methylomes from the globular stage through dormancy and germination to understand the role of methylation in seed formation. CHH methylation increases significantly during development throughout the entire seed, targets primarily transposable elements (TEs), is maintained during endoreduplication, and drops precipitously within the germinating seedling. By contrast, no significant global changes in CG- and CHG-context methylation occur during the same developmental period...
October 23, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29073177/hypomethylated-fgf3-is-a-potential-biomarker-for-early-detection-of-oral-cancer-in-mice-treated-with-the-tobacco-carcinogen-dibenzo-def-p-chrysene
#16
Yuan-Wan Sun, Kun-Ming Chen, Yuka Imamura Kawasawa, Anna C Salzberg, Timothy K Cooper, Carla Caruso, Cesar Aliaga, Junjia Zhu, Krishne Gowda, Shantu Amin, Karam El-Bayoumy
Genetic and epigenetic alterations observed at end stage OSCC formation could be considered as a consequence of cancer development and thus changes in normal or premalignant tissues which had been exposed to oral carcinogens such as Dibenzo[def,p]chrysene (DBP) may better serve as predictive biomarkers of disease development. Many types of DNA damage can induce epigenetic changes which can occur early and in the absence of evident morphological abnormalities. Therefore we used ERRBS to generate genome-scale, single-base resolution DNA methylomes from histologically normal oral tissues of mice treated with DBP under experimental conditions known to induce maximum DNA damage which is essential for the development of OSCC induced by DBP in mice...
2017: PloS One
https://www.readbyqxmd.com/read/29066327/genome-and-methylome-variation-in-helicobacter-pylori-with-a-cag-pathogenicity-island-during-early-stages-of-human-infection
#17
Sandra Nell, Iratxe Estibariz, Juliane Krebes, Boyke Bunk, David Y Graham, Jörg Overmann, Yi Song, Cathrin Spröer, Ines Yang, Thomas Wex, Jonas Korlach, Peter Malfertheiner, Sebastian Suerbaum
BACKGROUND & AIMS: Helicobacter pylori is remarkable for its genetic variation. Yet little isknown about its genetic changes during early stages of human infection, as the bacteria adapt to their new environment. We analyzed genome and methylome variations in a fully virulent strain of H pylori strain during experimental infection. METHODS: We performed a randomized Phase 1 and 2, observer-blind, placebo-controlled, study of 12 healthy, H pylori-negative adults in Germany from October 2008 through March 2010...
October 21, 2017: Gastroenterology
https://www.readbyqxmd.com/read/29057891/exhaustive-search-for-epistatic-effects-on-the-human-methylome
#18
Tobias Egli, Vanja Vukojevic, Thierry Sengstag, Martin Jacquot, Rubén Cabezón, David Coynel, Virginie Freytag, Angela Heck, Christian Vogler, Dominique J-F de Quervain, Andreas Papassotiropoulos, Annette Milnik
Studies assessing the existence and magnitude of epistatic effects on complex human traits provide inconclusive results. The study of such effects is complicated by considerable increase in computational burden, model complexity, and model uncertainty, which in concert decrease model stability. An additional source introducing significant uncertainty with regard to the detection of robust epistasis is the biological distance between the genetic variation and the trait under study. Here we studied CpG methylation, a genetically complex molecular trait that is particularly close to genomic variation, and performed an exhaustive search for two-locus epistatic effects on the CpG-methylation signal in two cohorts of healthy young subjects...
October 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29054136/combined-methylome-and-transcriptome-analysis-during-rat-hepatic-stellate-cell-activation
#19
Eva Schumacher, Silke Götze, Claus Kordes, Vladimir Benes, Dieter Häussinger
Hepatic stellate cells (HSC) are mesenchymal stem cells (MSC) of the liver. They are unique among MSC, since HSC remain in a quiescent, retinoid-storing state in the normal liver but become activated after liver injury and contribute to tissue repair. The epigenetic mechanisms accompanying the transition of HSC from a quiescent to an activated state are in the focus of the present study. We investigated the methylome and transcriptome during this process and observed profound changes. While the promoter methylation correlated negatively with gene expression, the gene body methylation revealed no clear correlation...
October 20, 2017: Stem Cells and Development
https://www.readbyqxmd.com/read/29046735/identification-of-a-key-role-of-widespread-epigenetic-drift-in-barrett-s-esophagus-and-esophageal-adenocarcinoma
#20
E Georg Luebeck, Kit Curtius, William D Hazelton, Sean Maden, Ming Yu, Prashanthi N Thota, Deepa T Patil, Amitabh Chak, Joseph E Willis, William M Grady
BACKGROUND: Recent studies have identified age-related changes in DNA methylation patterns in normal and cancer tissues in a process that is called epigenetic drift. However, the evolving patterns, functional consequences, and dynamics of epigenetic drift during carcinogenesis remain largely unexplored. Here we analyze the evolution of epigenetic drift patterns during progression from normal squamous esophagus tissue to Barrett's esophagus (BE) to esophageal adenocarcinoma (EAC) using 173 tissue samples from 100 (nonfamilial) BE patients, along with publically available datasets including The Cancer Genome Atlas (TCGA)...
2017: Clinical Epigenetics
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