keyword
MENU ▼
Read by QxMD icon Read
search

Methylomics

keyword
https://www.readbyqxmd.com/read/28730820/tryptic-peptides-bearing-c-terminal-dimethyllysine-need-be-considered-during-the-analysis-of-lysine-dimethylation-in-proteomic-study
#1
Ming Chen, Min Zhang, Linhui Zhai, Hao Hu, Ping Liu, Minjia Tan
Lysine methylation plays important roles in structural and functional regulation of chromatin. Although trypsin is the most widely used protease in mass spectrometry-based proteomic analysis for lysine methylation substrates, the proteolytic activity of trypsin on dimethylated lysine residues remains an arguable issue. In this study, we tested the ability of trypsin to cleave dimethylated lysine residues in synthetic peptides, purified albumin and whole cell lysate, and found that the C-terminal of dimethylated lysine residue could be cleaved in a protein sequence-dependent manner...
July 21, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28728396/characterization-and-functional-inferences-of-a-genome-wide-dna-methylation-profile-in-the-loin-longissimus-dorsi-muscle-of-swine
#2
Woonsu Kim, Hyesun Park, Kang-Seok Seo, Seongwon Seo
Objective: DNA methylation plays a major role in regulating the expression of genes related to traits of economic interest (e.g., weight gain) in livestock animals. This study characterized and investigated the functional inferences of genome-wide DNA methylome in the loin (longissimus dorsi) muscle (LDM) of swine. Methods: A total of 8.99 Gb methylated DNA immunoprecipitation sequence data were obtained from LDM samples of eight Duroc pigs (four pairs of littermates)...
May 14, 2017: Asian-Australasian Journal of Animal Sciences
https://www.readbyqxmd.com/read/28724534/m6aviewer-software-for-the-detection-analysis-and-visualization-of-n6-methyl-adenosine-peaks-from-m6a-seq-me-rip-sequencing-data
#3
Agne Antanaviciute, Belinda Baquero-Perez, Christopher M Watson, Sally M Harrison, Carolina Lascelles, Laura Crinnion, Alexander F Markham, David T Bonthron, Adrian Whitehouse, Ian M Carr
Recent methods for transcriptome-wide N6-methyl-adenosine(m6A) profiling have facilitated investigations into the RNA methylome and established m6A as a dynamic modification that has critical regulatory roles in gene expression and may play a role in human disease. However, bioinformatics resources available for the analysis of m6A sequencing data are still limited. Here, we describe m6aViewer - a cross-platform application for analysis and visualisation of m6A peaks from sequencing data. m6aViewer implements a novel m6A peak-calling algorithm that identifies high-confidence methylated residues with more precision than previously described approaches...
July 19, 2017: RNA
https://www.readbyqxmd.com/read/28723896/maternal-h3k27me3-controls-dna-methylation-independent-imprinting
#4
Azusa Inoue, Lan Jiang, Falong Lu, Tsukasa Suzuki, Yi Zhang
Mammalian sperm and oocytes have different epigenetic landscapes and are organized in different fashions. After fertilization, the initially distinct parental epigenomes become largely equalized with the exception of certain loci, including imprinting control regions. How parental chromatin becomes equalized and how imprinting control regions escape from this reprogramming is largely unknown. Here we profile parental allele-specific DNase I hypersensitive sites in mouse zygotes and morula embryos, and investigate the epigenetic mechanisms underlying these allelic sites...
July 19, 2017: Nature
https://www.readbyqxmd.com/read/28723632/potential-link-between-fusobacterium-enrichment-and-dna-methylation-accumulation-in-the-inflammatory-colonic-mucosa-in-ulcerative-colitis
#5
Tomomitsu Tahara, Ichiro Hirata, Naoko Nakano, Sayumi Tahara, Noriyuki Horiguchi, Tomohiko Kawamura, Masaaki Okubo, Takamitsu Ishizuka, Hyuga Yamada, Dai Yoshida, Takafumi Ohmori, Kohei Maeda, Naruomi Komura, Hirokazu Ikuno, Yasutaka Jodai, Toshiaki Kamano, Mitsuo Nagasaka, Yoshihito Nakagawa, Tetsuya Tuskamoto, Makoto Urano, Tomoyuki Shibata, Makoto Kuroda, Naoki Ohmiya
BACKGROUND AND AIM: Fusobacterium enrichment has been associated with colorectal cancer development. Ulcerative colitis (UC) associated tumorigenesis is characterized as high degree of methylation accumulation through continuous colonic inflammation. The aim of this study was to investigate a potential link between Fusobacterium enrichment and DNA methylation accumulation in the inflammatory colonic mucosa in UC. METHODS: In the candidate analysis, inflamed colonic mucosa from 86 UC patients were characterized the methylation status of colorectal a panel of cancer related 24 genes...
June 27, 2017: Oncotarget
https://www.readbyqxmd.com/read/28716111/quantitation-of-dna-methylation-in-epstein-barr-virus-associated-nasopharyngeal-carcinoma-by-bisulfite-amplicon-sequencing
#6
Weilin Zhao, Yingxi Mo, Shumin Wang, Kaoru Midorikawa, Ning Ma, Yusuke Hiraku, Shinji Oikawa, Guangwu Huang, Zhe Zhang, Mariko Murata, Kazuhiko Takeuchi
BACKGROUND: Epigenetic changes, including DNA methylation, disrupt normal cell function, thus contributing to multiple steps of carcinogenesis. Nasopharyngeal carcinoma (NPC) is endemic in southern China and is highly associated with Epstein-Barr virus (EBV) infection. Significant changes of the host cell methylome are observed in EBV-associated NPC with cancer development. Epigenetic marks for NPC diagnosis are urgently needed. In order to explore DNA methylation marks, we investigated DNA methylation of candidate genes in EBV-associated nasopharyngeal carcinoma...
July 17, 2017: BMC Cancer
https://www.readbyqxmd.com/read/28711290/biopsies-of-pediatric-brainstem-lesions-display-low-morbidity-but-strong-impact-on-further-treatment-decisions
#7
Johanna Quick-Weller, Stephanie Tritt, Bedjan Behmanesh, Michel Mittelbronn, Andrea Spyrantis, Nazife Dinc, Lutz Weise, Volker Seifert, Gerhard Marquardt, Thomas M Freiman
OBJECTIVE: The course of malignant brain stem gliomas in childhood is rarely positive. Because of limited therapeutic options and potentially hazardous biopsies oncologist often relay on MRI diagnoses only for further therapy decisions. In this study we show that brain stem biopsies display a low morbidity rate and neuropathological assessment has a considerable impact on further treatment decision. METHODS: Within 18-months five children with brainstem symptoms and the radiological diagnosis of a malignant brainstem glioma, were identified...
July 12, 2017: Journal of Clinical Neuroscience: Official Journal of the Neurosurgical Society of Australasia
https://www.readbyqxmd.com/read/28707409/chilling-responsive-demeter-like-dna-demethylase-mediates-in-poplar-bud-break
#8
Daniel Conde, Anne-Laure Le Gac, Mariano Perales, Christopher Dervinis, Matias Kirst, Stéphane Maury, Pablo González-Melendi, Isabel Allona
Annual dormancy-growth cycle is a developmental and physiological process essential for the survival of deciduous trees in temperate and boreal forests. Seasonal control of shoot growth in woody perennials requires specific genetic programs responding to environmental signals. The environmental-controlled mechanisms that regulate the shift between winter dormancy and the growth promoting genetic programs are still unknown. Here, we show that dynamics in genomic DNA (gDNA) methylation levels are involved in the regulation of dormancy-growth cycle in poplar...
July 13, 2017: Plant, Cell & Environment
https://www.readbyqxmd.com/read/28705956/rapid-recovery-gene-downregulation-during-excess-light-stress-and-recovery-in-arabidopsis
#9
Peter Alexander Crisp, Diep Ganguly, Aaron B Smith, Kevin D Murray, Gonzalo M Estavillo, Iain R Searle, Ethan Ford, Ozren Bogdanović, Ryan Lister, Justin O Borevitz, Steven R Eichten, Barry J Pogson
Stress recovery may prove to be a promising approach to increase plant performance, and theoretically, mRNA instability may facilitate faster recovery. Transcriptome (RNA-seq, qPCR, sRNA-seq, PARE) and methylome profiling during repeated excess-light stress and recovery was performed at intervals as short as three minutes. We demonstrate that 87% of the stress-upregulated mRNAs analysed exhibit very rapid recovery. For instance, HSP101 abundance declined two-fold every 5.1 minutes. We term this phenomenon Rapid Recovery Gene Downregulation (RRGD), whereby mRNA abundance rapidly decreases promoting transcriptome resetting...
July 13, 2017: Plant Cell
https://www.readbyqxmd.com/read/28704530/a-complex-association-between-dna-methylation-and-gene-expression-in-human-placenta-at-first-and-third-trimesters
#10
Yen Ching Lim, Jie Li, Yiyun Ni, Qi Liang, Junjiao Zhang, George S H Yeo, Jianxin Lyu, Shengnan Jin, Chunming Ding
The human placenta is a maternal-fetal organ essential for normal fetal development and maternal health. During pregnancy, the placenta undergoes many structural and functional changes in response to fetal needs and environmental exposures. Previous studies have demonstrated widespread epigenetic and gene expression changes from early to late pregnancy. However, on the global level, how DNA methylation changes impact on gene expression in human placenta is not yet well understood. We performed DNA methylome analysis by reduced representation bisulfite sequencing (RRBS) and gene expression analysis by RNA-Seq for both first and third trimester human placenta tissues...
2017: PloS One
https://www.readbyqxmd.com/read/28695892/targeted-dna-methylation-in-vivo-using-an-engineered-dcas9-mq1-fusion-protein
#11
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/28694447/impacts-of-early-life-stress-on-the-methylome-and-transcriptome-of-atlantic-salmon
#12
Hooman K Moghadam, Hanne Johnsen, Nicholas Robinson, Øivind Andersen, Even H Jørgensen, Helge K Johnsen, Vegar J Bæhr, Helge Tveiten
Exposure to environmental stressors during early-life stages can change the rate and timing of various developmental processes. Epigenetic marks affecting transcriptional regulation can be altered by such environmental stimuli. To assess how stress might affect the methylome and transcriptome in salmon, fish were treated using cold-shock and air-exposure from the eye-stage until start-feeding. The fish were either stressed prior to hatching (E), post-hatching (PH), pre- and post-hatching (EPH) or not stressed (CO)...
July 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28686328/genetically-contextual-effects-of-smoking-on-genome-wide-dna-methylation
#13
Meeshanthini V Dogan, Steven R H Beach, Robert A Philibert
Smoking is the leading cause of death in the United States. It exerts its effects by increasing susceptibility to a variety of complex disorders among those who smoke, and if pregnant, to their unborn children. In prior efforts to understand the epigenetic mechanisms through which this increased vulnerability is conveyed, a number of investigators have conducted genome wide methylation analyses. Unfortunately, secondary to methodological limitations, these studies were unable to examine methylation in gene regions with significant amounts of genetic variation...
July 7, 2017: American Journal of Medical Genetics. Part B, Neuropsychiatric Genetics
https://www.readbyqxmd.com/read/28684528/wnt-%C3%A3-catenin-activation-by-epigenetically-aberrant-stroma-drives-myelodysplastic-syndrome
#14
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
#15
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/28682231/g%C3%A3-n%C3%A3-tique-et-%C3%A3-pig%C3%A3-n%C3%A3-tique-des-troubles-des-conduites-alimentaires
#16
Nicolas Ramoz, Julia Clarke, Philip Gorwood
Eating disorders (EDs) are complex and multifactorial psychiatric illnesses that induce significant and sustained pathological disruption of food intake. The Diagnostic and Statistical Manual of Mental Illnesses (DSM-5) describes the clinical criteria of major disorders including anorexia nervosa (AN), bulimia nervosa (BN) and binge eating disorder (BED). The neurobiological basis of food intake is well characterized. Epidemiological studies reported a heritability about 70% in AN and 60% in BN, suggesting that genetic factors are involved in the vulnerability to EDs...
2017: Biologie Aujourd'hui
https://www.readbyqxmd.com/read/28679371/cpg-promoter-methylation-of-the-alkbh3-alkylation-repair-gene-in-breast-cancer
#17
Olafur Andri Stefansson, Stefan Hermanowicz, Jasper van der Horst, Holmfridur Hilmarsdottir, Zuzanna Staszczak, Jon Gunnlaugur Jonasson, Laufey Tryggvadottir, Thorkell Gudjonsson, Stefan Sigurdsson
BACKGROUND: DNA repair of alkylation damage is defective in various cancers. This occurs through somatically acquired inactivation of the MGMT gene in various cancer types, including breast cancers. In addition to MGMT, the two E. coli AlkB homologs ALKBH2 and ALKBH3 have also been linked to direct reversal of alkylation damage. However, it is currently unknown whether ALKBH2 or ALKBH3 are found inactivated in cancer. METHODS: Methylome datasets (GSE52865, GSE20713, GSE69914), available through Omnibus, were used to determine whether ALKBH2 or ALKBH3 are found inactivated by CpG promoter methylation...
July 5, 2017: BMC Cancer
https://www.readbyqxmd.com/read/28678605/the-early-pregnancy-placenta-foreshadows-dna-methylation-alterations-of-solid-tumors
#18
Akpéli V Nordor, Djamel Nehar-Belaid, Sophie Richon, David Klatzmann, Dominique Bellet, Virginie Dangles-Marie, Thierry Fournier, Martin J Aryee
The placenta relies on phenotypes that are characteristic of cancer to successfully implant the embryo in the uterus during early pregnancy. Notably, it has to invade its host tissues, promote angiogenesis-while surviving hypoxia-, and escape the immune system. Similarities in DNA methylation patterns between the placenta and cancers suggest that common epigenetic mechanisms may be involved in regulating these behaviors. We show here that megabase-scale patterns of hypomethylation distinguish first from third trimester chorionic villi in the placenta, and that these patterns mirror those that distinguish many tumors from corresponding normal tissues...
July 5, 2017: Epigenetics: Official Journal of the DNA Methylation Society
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
#19
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
https://www.readbyqxmd.com/read/28665177/epigenetics-and-adhd-toward-an-integrative-approach-of-the-disorder-pathogenesis
#20
Meriem Hamza, Soumeyya Halayem, Soumaya Bourgou, Mona Daoud, Fatma Charfi, Ahlem Belhadj
OBJECTIVE: Epigenetic hypothesis is one of the research pathways used to explain the complex etiology of neurodevelopmental disorders. This review highlights the findings of recent studies in the field of epigenetics in ADHD. METHODS: An electronic literature search using Medline. RESULTS: In the Gene × Environment interaction model, several clinical, genetic and molecular arguments support the epigenetic hypothesis in ADHD etiology. Environmental ADHD risk factors including toxic, nutritional factors and stressful life events lead to changes in DNA methylation and in histone modification levels...
March 1, 2017: Journal of Attention Disorders
keyword
keyword
99836
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"