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https://www.readbyqxmd.com/read/28198667/pan-cancer-analysis-of-frequent-dna-co-methylation-patterns-reveals-consistent-epigenetic-landscape-changes-in-multiple-cancers
#1
Jie Zhang, Kun Huang
BACKGROUND: DNA methylation is the major form of epigenetic modifications through which the cell regulates the gene expression and silencing. There have been extensive studies on the roles of DNA methylation in cancers, and several cancer drugs were developed targeting this process. However, DNA co-methylation cluster has not been examined in depth, and co-methylation in multiple cancer types has never been studied previously. RESULTS: In this study, we applied newly developed lmQCM algorithm to mine co-methylation clusters using methylome data from 11 cancer types in TCGA database, and found frequent co-methylated gene clusters exist in these cancer types...
January 25, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28196884/functional-genomics-analysis-of-vitamin-d-effects-on-cd4-t-cells-in-vivo-in-experimental-autoimmune-encephalomyelitis-%C3%A2
#2
Manuel Zeitelhofer, Milena Z Adzemovic, David Gomez-Cabrero, Petra Bergman, Sonja Hochmeister, Marie N'diaye, Atul Paulson, Sabrina Ruhrmann, Malin Almgren, Jesper N Tegnér, Tomas J Ekström, André Ortlieb Guerreiro-Cacais, Maja Jagodic
Vitamin D exerts multiple immunomodulatory functions and has been implicated in the etiology and treatment of several autoimmune diseases, including multiple sclerosis (MS). We have previously reported that in juvenile/adolescent rats, vitamin D supplementation protects from experimental autoimmune encephalomyelitis (EAE), a model of MS. Here we demonstrate that this protective effect associates with decreased proliferation of CD4+ T cells and lower frequency of pathogenic T helper (Th) 17 cells. Using transcriptome, methylome, and pathway analyses in CD4+ T cells, we show that vitamin D affects multiple signaling and metabolic pathways critical for T-cell activation and differentiation into Th1 and Th17 subsets in vivo...
February 14, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28187949/long-term-alterations-to-dna-methylation-as-a-biomarker-of-prenatal-alcohol-exposure-from-mouse-models-to-human-children-with-fetal-alcohol-spectrum-disorders
#3
REVIEW
Benjamin I Laufer, Eric J Chater-Diehl, Joachim Kapalanga, Shiva M Singh
Rodent models of Fetal Alcohol Spectrum Disorders (FASD) have revealed that prenatal alcohol exposure (PAE) results in differential DNA cytosine methylation in the developing brain. The resulting genome-wide methylation changes are enriched in genes with neurodevelopmental functions. The profile of differential methylation is dynamic and present in some form for life. The methylation changes are transmitted across subsequent mitotic divisions, where they are maintained and further modified over time. More recent follow up has identified a profile of the differential methylation in the buccal swabs of young children born with FASD...
November 22, 2016: Alcohol
https://www.readbyqxmd.com/read/28186631/dna-methylation-and-gene-expression-regulation-associated-with-vascularization-in-sorghum-bicolor
#4
Gina M Turco, Kaisa Kajala, Govindarajan Kunde-Ramamoorthy, Chew-Yee Ngan, Andrew Olson, Shweta Deshphande, Denis Tolkunov, Barbara Waring, Scott Stelpflug, Patricia Klein, Jeremy Schmutz, Shawn Kaeppler, Doreen Ware, Chia-Lin Wei, J Peter Etchells, Siobhan M Brady
Plant secondary cell walls constitute the majority of plant biomass. They are predominantly found in xylem cells, which are derived from vascular initials during vascularization. Little is known about these processes in grass species despite their emerging importance as biomass feedstocks. The targeted biofuel crop Sorghum bicolor has a sequenced and well-annotated genome, making it an ideal monocot model for addressing vascularization and biomass deposition. Here we generated tissue-specific transcriptome and DNA methylome data from sorghum shoots, roots and developing root vascular and nonvascular tissues...
February 10, 2017: New Phytologist
https://www.readbyqxmd.com/read/28184257/an-empirically-driven-data-reduction-method-on-the-human-450k-methylation-array-to-remove-tissue-specific-non-variable-cpgs
#5
Rachel D Edgar, Meaghan J Jones, Wendy P Robinson, Michael S Kobor
BACKGROUND: Population based epigenetic association studies of disease and exposures are becoming more common with the availability of economical genome-wide technologies for interrogation of the methylome, such as the Illumina 450K Human Methylation Array (450K). Often, the expected small number of differentially methylated cytosine-guanine pairs (CpGs) in studies of the human methylome presents a statistical challenge, as the large number of CpGs measured on the 450K necessitates careful multiple test correction...
2017: Clinical Epigenetics
https://www.readbyqxmd.com/read/28180135/identification-of-methylated-deoxyadenosines-in-genomic-dna-by-da-6m-dna-immunoprecipitation
#6
Magdalena J Koziol, Charles R Bradshaw, George E Allen, Ana S H Costa, Christian Frezza
: dA(6m) DNA immunoprecipitation followed by deep sequencing (DIP-Seq) is a key tool in identifying and studying the genome-wide distribution of N(6)-methyldeoxyadenosine (dA(6m)). The precise function of this novel DNA modification remains to be fully elucidated, but it is known to be absent from transcriptional start sites and excluded from exons, suggesting a role in transcriptional regulation (Koziol et al., 2015). Importantly, its existence suggests that DNA might be more diverse than previously believed, as further DNA modifications might exist in eukaryotic DNA (Koziol et al...
November 5, 2016: Bio-protocol
https://www.readbyqxmd.com/read/28174608/genome-wide-dna-methylation-profile-identified-a-unique-set-of-differentially-methylated-immune-genes-in-oral-squamous-cell-carcinoma-patients-in-india
#7
Baidehi Basu, Joyeeta Chakraborty, Aditi Chandra, Atul Katarkar, Jadav Ritesh Kumar Baldevbhai, Debjit Dhar Chowdhury, Jay Gopal Ray, Keya Chaudhuri, Raghunath Chatterjee
BACKGROUND: Oral squamous cell carcinoma (OSCC) is one of the common malignancies in Southeast Asia. Epigenetic changes, mainly the altered DNA methylation, have been implicated in many cancers. Considering the varied environmental and genotoxic exposures among the Indian population, we conducted a genome-wide DNA methylation study on paired tumor and adjacent normal tissues of ten well-differentiated OSCC patients and validated in an additional 53 well-differentiated OSCC and adjacent normal samples...
2017: Clinical Epigenetics
https://www.readbyqxmd.com/read/28174132/traumatic-brain-injury-induces-genome-wide-transcriptomic-methylomic-and-network-perturbations-in-brain-and-blood-predicting-neurological-disorders
#8
Qingying Meng, Yumei Zhuang, Zhe Ying, Rahul Agrawal, Xia Yang, Fernando Gomez-Pinilla
The complexity of the traumatic brain injury (TBI) pathology, particularly concussive injury, is a serious obstacle for diagnosis, treatment, and long-term prognosis. Here we utilize modern systems biology in a rodent model of concussive injury to gain a thorough view of the impact of TBI on fundamental aspects of gene regulation, which have the potential to drive or alter the course of the TBI pathology. TBI perturbed epigenomic programming, transcriptional activities (expression level and alternative splicing), and the organization of genes in networks centered around genes such as Anax2, Ogn, and Fmod...
February 1, 2017: EBioMedicine
https://www.readbyqxmd.com/read/28158250/potential-roles-of-dna-methylation-in-the-initiation-and-establishment-of-replicative-senescence-revealed-by-array-based-methylome-and-transcriptome-analyses
#9
Mizuho Sakaki, Yukiko Ebihara, Kohji Okamura, Kazuhiko Nakabayashi, Arisa Igarashi, Kenji Matsumoto, Kenichiro Hata, Yoshiro Kobayashi, Kayoko Maehara
Cellular senescence is classified into two groups: replicative and premature senescence. Gene expression and epigenetic changes are reported to differ between these two groups and cell types. Normal human diploid fibroblast TIG-3 cells have often been used in cellular senescence research; however, their epigenetic profiles are still not fully understood. To elucidate how cellular senescence is epigenetically regulated in TIG-3 cells, we analyzed the gene expression and DNA methylation profiles of three types of senescent cells, namely, replicatively senescent, ras-induced senescent (RIS), and non-permissive temperature-induced senescent SVts8 cells, using gene expression and DNA methylation microarrays...
2017: PloS One
https://www.readbyqxmd.com/read/28155665/tea-the-epigenome-platform-for-arabidopsis-methylome-study
#10
Sheng-Yao Su, Shu-Hwa Chen, I-Hsuan Lu, Yih-Shien Chiang, Yu-Bin Wang, Pao-Yang Chen, Chung-Yen Lin
BACKGROUND: Bisulfite sequencing (BS-seq) has become a standard technology to profile genome-wide DNA methylation at single-base resolution. It allows researchers to conduct genome-wise cytosine methylation analyses on issues about genomic imprinting, transcriptional regulation, cellular development and differentiation. One single data from a BS-Seq experiment is resolved into many features according to the sequence contexts, making methylome data analysis and data visualization a complex task...
December 22, 2016: BMC Genomics
https://www.readbyqxmd.com/read/28153026/clinical-implications-of-genome-wide-dna-methylation-studies-in-acute-myeloid-leukemia
#11
REVIEW
Yan Li, Qingyu Xu, Na Lv, Lili Wang, Hongmei Zhao, Xiuli Wang, Jing Guo, Chongjian Chen, Yonghui Li, Li Yu
Acute myeloid leukemia (AML) is the most common type of acute leukemia in adults. AML is a heterogeneous malignancy characterized by distinct genetic and epigenetic abnormalities. Recent genome-wide DNA methylation studies have highlighted an important role of dysregulated methylation signature in AML from biological and clinical standpoint. In this review, we will outline the recent advances in the methylome study of AML and overview the impacts of DNA methylation on AML diagnosis, treatment, and prognosis...
February 2, 2017: Journal of Hematology & Oncology
https://www.readbyqxmd.com/read/28151741/associations-between-genome-wide-gene-expression-and-ambient-nitrogen-oxides-nox
#12
Nahid Mostafavi, Jelle Vlaanderen, Lutzen Portengen, Marc Chadeau-Hyam, Lars Modig, Domenico Palli, Ingvar A Bergdahl, Bert Brunekreef, Paolo Vineis, Dennie G A J Hebels, Jos C S Kleinjans, Vittorio Krogh, Gerard Hoek, Panagiotis Georgiadis, Soterios A Kyrtopoulos, Roel Vermeulen
BACKGROUND: We hypothesize that biological perturbations due to exposure to ambient air pollution are reflected in gene-expression levels in peripheral blood mononuclear cells. METHODS: We assessed the association between exposure to ambient air pollution and genome-wide gene-expression levels in peripheral blood mononuclear cells collected from 550 healthy subjects participating in cohorts from Italy and Sweden. Annual air pollution estimates of nitrogen oxides (NOx) at time of blood collection (1990 to 2006) were available from the ESCAPE study...
January 30, 2017: Epidemiology
https://www.readbyqxmd.com/read/28150704/genome-wide-dna-methylation-reprogramming-in-response-to-inorganic-arsenic-links-inhibition-of-ctcf-binding-dnmt-expression-and-cellular-transformation
#13
Matthew Rea, Meredith Eckstein, Rebekah Eleazer, Caroline Smith, Yvonne N Fondufe-Mittendorf
Chronic low dose inorganic arsenic (iAs) exposure leads to changes in gene expression and epithelial-to-mesenchymal transformation. During this transformation, cells adopt a fibroblast-like phenotype accompanied by profound gene expression changes. While many mechanisms have been implicated in this transformation, studies that focus on the role of epigenetic alterations in this process are just emerging. DNA methylation controls gene expression in physiologic and pathologic states. Several studies show alterations in DNA methylation patterns in iAs-mediated pathogenesis, but these studies focused on single genes...
February 2, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28142229/whole-genome-dna-methylation-analyses-revealed-epigenetic-instability-in-tumorigenic-human-ips-cell-derived-neural-stem-progenitor-cells
#14
Tsuyoshi Iida, Akio Iwanami, Tsukasa Sanosaka, Jun Kohyama, Hiroyuki Miyoshi, Narihito Nagoshi, Rei Kashiwagi, Yoshiaki Toyama, Morio Matsumoto, Masaya Nakamura, Hideyuki Okano
Although human induced pluripotent stem cell (hiPSC) derivatives are considered promising cellular resources for regenerative medicine, their tumorigenicity potentially limits their clinical application in hiPSC technologies. We previously demonstrated that oncogenic hiPSC-derived neural stem/progenitor cells (hiPSC-NS/PCs) produced tumor-like tissues that were distinct from teratomas. To gain insight into the mechanisms underlying the regulation of tumorigenicity in hiPSC-NS/PCs, we performed an integrated analysis using the Infinium HumanMethylation450 BeadChip array and the HumanHT-12 v4...
January 31, 2017: Stem Cells
https://www.readbyqxmd.com/read/28137292/correcting-for-cell-type-effects-in-dna-methylation-studies-reference-based-method-outperforms-latent-variable-approaches-in-empirical-studies
#15
Mohammad W Hattab, Andrey A Shabalin, Shaunna L Clark, Min Zhao, Gaurav Kumar, Robin F Chan, Lin Ying Xie, Rick Jansen, Laura K M Han, Patrik K E Magnusson, Gerard van Grootheest, Christina M Hultman, Brenda W J H Penninx, Karolina A Aberg, Edwin J C G van den Oord
Based on an extensive simulation study, McGregor and colleagues recently recommended the use of surrogate variable analysis (SVA) to control for the confounding effects of cell-type heterogeneity in DNA methylation association studies in scenarios where no cell-type proportions are available. As their recommendation was mainly based on simulated data, we sought to replicate findings in two large-scale empirical studies. In our empirical data, SVA did not fully correct for cell-type effects, its performance was somewhat unstable, and it carried a risk of missing true signals caused by removing variation that might be linked to actual disease processes...
January 30, 2017: Genome Biology
https://www.readbyqxmd.com/read/28130550/control-of-demeter-dna-demethylase-gene-transcription-in-male-and-female-gamete-companion-cells-in-arabidopsis-thaliana
#16
Jin-Sup Park, Jennifer M Frost, Kyunghyuk Park, Hyonhwa Ohr, Guen Tae Park, Seohyun Kim, Hyunjoo Eom, Ilha Lee, Janie S Brooks, Robert L Fischer, Yeonhee Choi
The DEMETER (DME) DNA glycosylase initiates active DNA demethylation via the base-excision repair pathway and is vital for reproduction in Arabidopsis thaliana DME-mediated DNA demethylation is preferentially targeted to small, AT-rich, and nucleosome-depleted euchromatic transposable elements, influencing expression of adjacent genes and leading to imprinting in the endosperm. In the female gametophyte, DME expression and subsequent genome-wide DNA demethylation are confined to the companion cell of the egg, the central cell...
January 27, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28125731/correlated-5-hydroxymethylcytosine-5hmc-and-gene-expression-profiles-underpin-gene-and-organ-specific-epigenetic-regulation-in-adult-mouse-brain-and-liver
#17
I-Hsuan Lin, Yi-Fan Chen, Ming-Ta Hsu
BACKGROUND: DNA methylation is an epigenetic mechanism essential for gene regulation and vital for mammalian development. 5-hydroxymethylcytosine (5hmC) is the first oxidative product of the TET-mediated 5-methylcytosine (5mC) demethylation pathway. Aside from being a key intermediate in cytosine demethylation, 5hmC may have potential regulatory functions with emerging importance in mammalian biology. METHODS: Here, we investigate the global 5hmC enrichment in five brain structures, including cerebellum, cerebral cortex, hippocampus, hypothalamus and thalamus, as well as liver tissues from female and male adult mice by using chemical capture-based technique coupled with next-generation sequencing...
2017: PloS One
https://www.readbyqxmd.com/read/28124151/the-helicobacter-pylori-methylome-roles-in-gene-regulation-and-virulence
#18
Rebecca Gorrell, Terry Kwok
The methylome is defined as a map of DNA methylation patterns at single-base resolution. DNA methylation in bacteria was first discovered as a function of restriction-modification (R-M) systems. R-M systems in Helicobacter pylori, like those in other bacteria, are important host-specificity determinants that provide protection against foreign DNA. Moreover, the gene regulatory role of the methyltransferase (Mtase) unit of various Helicobacter pylori R-M systems is being increasingly recognized. Recent advances in the application of single-molecule real-time (SMRT) DNA sequencing to analyse DNA methylation have revealed for the first time comprehensive pictures of the genome-wide distribution of methylation sites in various strains of H...
2017: Current Topics in Microbiology and Immunology
https://www.readbyqxmd.com/read/28123403/the-epigenome-as-a-therapeutic-target-for-parkinson-s-disease
#19
REVIEW
Shane V Hegarty, Aideen M Sullivan, Gerard W O'Keeffe
Parkinson's disease (PD) is a common, progressive neurodegenerative disease characterised by degeneration of nigrostriatal dopaminergic neurons, aggregation of α-synuclein and motor symptoms. Current dopamine-replacement strategies provide symptomatic relief, however their effectiveness wear off over time and their prolonged use leads to disabling side-effects in PD patients. There is therefore a critical need to develop new drugs and drug targets to protect dopaminergic neurons and their axons from degeneration in PD...
November 2016: Neural Regeneration Research
https://www.readbyqxmd.com/read/28122515/cpg-methylation-across-the-adipogenic-ppar%C3%AE-gene-and-its-relationship-with-birthweight-and-child-bmi-at-9%C3%A2-years
#20
Vitaly Volberg, Paul Yousefi, Karen Huen, Kim Harley, Brenda Eskenazi, Nina Holland
BACKGROUND: To examine methylation of the peroxisome proliferator-activated receptor γ (PPARγ) gene and its relationship with child weight status, at birth and 9 years. METHODS: We measured PPARγ methylation across 23 CpG sites using the Infinium Illumina 450 k array for children from the Center for the Health Assessment of Mothers and Children of Salinas (CHAMACOS) cohort at birth (N = 373) and 9 years (N = 245). RESULTS: Methylation level correlation patterns across the 23 PPARγ CpG sites were conserved between birth and 9-year ages...
January 26, 2017: BMC Medical Genetics
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