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Epigenome wide association

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https://www.readbyqxmd.com/read/28325913/persistent-dna-methylation-changes-associated-with-prenatal-mercury-exposure-and-cognitive-performance-during-childhood
#1
Andres Cardenas, Sheryl L Rifas-Shiman, Golareh Agha, Marie-France Hivert, Augusto A Litonjua, Dawn L DeMeo, Xihong Lin, Chitra J Amarasiriwardena, Emily Oken, Matthew W Gillman, Andrea A Baccarelli
Prenatal exposure to mercury, a known neurotoxic metal, is associated with lower cognitive performance during childhood. Disruption of fetal epigenetic programming could explain mercury's neurodevelopmental effects. We screened for epigenome-wide methylation differences associated with maternal prenatal blood mercury levels in 321 cord blood DNA samples and examined the persistence of these alterations during early (n = 75; 2.9-4.9 years) and mid-childhood (n = 291; 6.7-10.5 years). Among males, prenatal mercury levels were associated with lower regional cord blood DNA methylation at the Paraoxonase 1 gene (PON1) that persisted in early childhood and was attenuated in mid-childhood blood...
March 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28322586/the-neonatal-methylome-as-a-gatekeeper-in-the-trajectory-to-childhood-asthma
#2
Avery DeVries, Donata Vercelli
Asthma is a heterogeneous group of conditions that typically begin in early life and result in recurrent, reversible bronchial obstruction. The role played by epigenetic mechanisms in the pathogenesis of childhood asthma is understood only in part. Here we discuss asthma epigenetics within a developmental perspective based on our recent demonstration that the epigenetic trajectory to childhood asthma begins at birth. We next discuss how this trajectory may be affected by prenatal environmental exposures. Finally, we examine in vitro studies that model the impact of asthma-associated exposures on the epigenome...
March 21, 2017: Epigenomics
https://www.readbyqxmd.com/read/28322581/epigenetics-and-allergy-from-basic-mechanisms-to-clinical-applications
#3
Daniel P Potaczek, Hani Harb, Sven Michel, Bilal Alashkar Alhamwe, Harald Renz, Jörg Tost
Allergic diseases are on the rise in the Western world and well-known allergy-protecting and -driving factors such as microbial and dietary exposure, pollution and smoking mediate their influence through alterations of the epigenetic landscape. Here, we review key facts on the involvement of epigenetic modifications in allergic diseases and summarize and critically evaluate the lessons learned from epigenome-wide association studies. We show the potential of epigenetic changes for various clinical applications: as diagnostic tools, to assess tolerance following immunotherapy or possibly predict the success of therapy at an early time point...
March 21, 2017: Epigenomics
https://www.readbyqxmd.com/read/28322575/epigenome-wide-dna-methylation-study-of-ige-concentration-in-relation-to-self-reported-allergies
#4
Weronica E Ek, Muhammad Ahsan, Mathias Rask-Andersen, Liming Liang, Miriam F Moffatt, Ulf Gyllensten, Åsa Johansson
AIM: Epigenetic mechanisms are critical for normal immune development and epigenetic alterations might therefore be possible contributors to immune diseases. To investigate if DNA methylation in whole blood is associated with total and allergen-specific IgE levels. METHODS: We performed an epigenome-wide association study to investigate the association between DNA methylation and IgE level, allergen-specific IgE and self-reported immune diseases and allergies in 728 individuals...
March 21, 2017: Epigenomics
https://www.readbyqxmd.com/read/28315703/molecular-endocrinology-of-vitamin-d-on-the-epigenome-level
#5
REVIEW
Carsten Carlberg
The molecular endocrinology of vitamin D is based on the facts that i) its metabolite 1α,25-dihydroxyvitamin D3 (1,25(OH)2D3) is the high affinity ligand of the nuclear receptor vitamin D receptor (VDR) and ii) the transcription factor VDR is the unique target of 1,25(OH)2D3 in the nucleus. Short-term alterations of the epigenome are primarily changes in the post-translational modification status of nucleosome-forming histone proteins, the consequences of which are i) a local increase or decrease in chromatin accessibility and ii) the activation or repression of gene transcription...
March 16, 2017: Molecular and Cellular Endocrinology
https://www.readbyqxmd.com/read/28303888/dna-methylation-signatures-in-peripheral-blood-strongly-predict-all-cause-mortality
#6
Yan Zhang, Rory Wilson, Jonathan Heiss, Lutz P Breitling, Kai-Uwe Saum, Ben Schöttker, Bernd Holleczek, Melanie Waldenberger, Annette Peters, Hermann Brenner
DNA methylation (DNAm) has been revealed to play a role in various diseases. Here we performed epigenome-wide screening and validation to identify mortality-related DNAm signatures in a general population-based cohort with up to 14 years follow-up. In the discovery panel in a case-cohort approach, 11,063 CpGs reach genome-wide significance (FDR<0.05). 58 CpGs, mapping to 38 well-known disease-related genes and 14 intergenic regions, are confirmed in a validation panel. A mortality risk score based on ten selected CpGs exhibits strong association with all-cause mortality, showing hazard ratios (95% CI) of 2...
March 17, 2017: Nature Communications
https://www.readbyqxmd.com/read/28302177/cepip-context-dependent-epigenomic-weighting-for-prioritization-of-regulatory-variants-and-disease-associated-genes
#7
Mulin Jun Li, Miaoxin Li, Zipeng Liu, Bin Yan, Zhicheng Pan, Dandan Huang, Qian Liang, Dingge Ying, Feng Xu, Hongcheng Yao, Panwen Wang, Jean-Pierre A Kocher, Zhengyuan Xia, Pak Chung Sham, Jun S Liu, Junwen Wang
It remains challenging to predict regulatory variants in particular tissues or cell types due to highly context-specific gene regulation. By connecting large-scale epigenomic profiles to expression quantitative trait loci (eQTLs) in a wide range of human tissues/cell types, we identify critical chromatin features that predict variant regulatory potential. We present cepip, a joint likelihood framework, for estimating a variant's regulatory probability in a context-dependent manner. Our method exhibits significant GWAS signal enrichment and is superior to existing cell type-specific methods...
March 16, 2017: Genome Biology
https://www.readbyqxmd.com/read/28298479/cyst-nematode-parasitism-induces-dynamic-changes-in-the-root-epigenome
#8
Tarek Hewezi, Thomas Lane, Sarbottam Piya, Aditi Rambani, J Hollis Rice, Meg Staton
A growing body of evidence indicates that epigenetic modifications can provide efficient, dynamic, and reversible cellular responses to a wide range of environmental stimuli. However, the significance of epigenetic modifications in plant-pathogen interactions remains largely unexplored. In this study, we provide a comprehensive analysis of epigenome changes during the compatible interaction between the beet cyst nematode Heterodera schachtii and Arabidopsis (Arabidopsis thaliana). Whole genome bisulfite sequencing was conducted to assess the dynamic changes in the methylome of Arabidopsis roots in response to H schachtii infection...
March 15, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28272510/apolipoprotein-e4-and-insulin-resistance-interact-to-impair-cognition-and-alter-the-epigenome-and-metabolome
#9
Lance A Johnson, Eileen Ruth S Torres, Soren Impey, Jan F Stevens, Jacob Raber
Apolipoprotein E4 (E4) and type 2 diabetes are major risk factors for cognitive decline and late onset Alzheimer's disease (AD). E4-associated phenotypes and insulin resistance (IR) share several features and appear to interact in driving cognitive dysfunction. However, shared mechanisms that could explain their overlapping pathophysiology have yet to be found. We hypothesized that, compared to E3 mice, E4 mice would be more susceptible to the harmful cognitive effects of high fat diet (HFD)-induced IR due to apoE isoform-specific differences in brain metabolism...
March 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28271979/toward-a-taxonomy-for-multi-omics-science-terminology-development-for-whole-genome-study-approaches-by-omics-technology-and-hierarchy
#10
Nina Pirih, Tanja Kunej
Omics is a form of high-throughput systems science. However, taxonomies for omics studies are limited, inviting us to rethink new ways in which we classify, prioritize, and rank various omics systems science studies. In this overarching context, the genome-wide study approaches have proliferated in number and popularity over the past decade. However, their hierarchy is not well organized and the development of attendant terminology is not controlled. In the present study, we searched the literature in PubMed and the Web of Science databases published from March 1999 to September 2016 using the keywords, including genome-wide, association, whole genome, transcriptome-wide, metabolome, epigenome, and phenome...
January 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28270869/epigenome-wide-discovery-and-evaluation-of-leukocyte-dna-methylation-markers-for-the-detection-of-colorectal-cancer-in-a-screening-setting
#11
Jonathan Alexander Heiss, Hermann Brenner
BACKGROUND: Colorectal cancer (CRC) is the third most common cancer worldwide. If detected at an early stage, prognosis is good. Despite increasing evidence for the benefits of implemented screening programs, such as screening colonoscopy, compliance is rather low. Hence there is demand for non-invasive tests for the early detection of CRC with high acceptance in population-wide screening. The objective of this study was to identify and evaluate leukocyte DNA methylation patterns as a potential biomarker for early detection of CRC...
2017: Clinical Epigenetics
https://www.readbyqxmd.com/read/28261261/the-pancreatic-islet-regulome-browser
#12
Loris Mularoni, Mireia Ramos-Rodríguez, Lorenzo Pasquali
The pancreatic islet is a highly specialized tissue embedded in the exocrine pancreas whose primary function is that of controlling glucose homeostasis. Thus, understanding the transcriptional control of islet-cell may help to puzzle out the pathogenesis of glucose metabolism disorders. Integrative computational analyses of transcriptomic and epigenomic data allows predicting genomic coordinates of putative regulatory elements across the genome and, decipher tissue-specific functions of the non-coding genome...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28257446/breastfeeding-effects-on-dna-methylation-in-the-offspring-a-systematic-literature-review
#13
Fernando Pires Hartwig, Christian Loret de Mola, Neil Martin Davies, Cesar Gomes Victora, Caroline L Relton
BACKGROUND: Breastfeeding benefits both infants and mothers. Recent research shows long-term health and human capital benefits among individuals who were breastfed. Epigenetic mechanisms have been suggested as potential mediators of the effects of early-life exposures on later health outcomes. We reviewed the literature on the potential effects of breastfeeding on DNA methylation. METHODS: Studies reporting original results and evaluating DNA methylation differences according to breastfeeding/breast milk groups (e...
2017: PloS One
https://www.readbyqxmd.com/read/28255110/methylome-wide-association-study-of-whole-blood-dna-in-the-norfolk-island-isolate-identifies-robust-loci-associated-with-age
#14
Miles C Benton, Heidi G Sutherland, Donia Macartney-Coxson, Larisa M Haupt, Rodney A Lea, Lyn R Griffiths
Epigenetic regulation of various genomic functions, including gene expression, provide mechanisms whereby an organism can dynamically respond to changes in its environment and modify gene expression accordingly. One epigenetic mechanism implicated in human aging and age-related disorders is DNA methylation. Isolated populations such as Norfolk Island (NI) should be advantageous for the identification of epigenetic factors related to aging due to reduced genetic and environmental variation. Here we conducted a methylome-wide association study of age using whole blood DNA in 24 healthy female individuals from the NI genetic isolate (aged 24-47 years)...
February 28, 2017: Aging
https://www.readbyqxmd.com/read/28250235/methylation-dynamics-during-folliculogenesis-and-early-embryo-development-in-sheep
#15
Laura Masala, Giovanni Pietro Burrai, Emanuela Bellu, Federica Ariu, Luisa Bogliolo, Sergio Ledda, Daniela Bebbere
Genome-wide DNA methylation reprogramming occurs during mammalian gametogenesis and early embryogenesis. Post-fertilization demethylation of paternal and maternal genomes is considered to occur by an active and passive mechanism, respectively, in most mammals but sheep; in this species no loss of methylation was observed in either pronucleus. Post-fertilization reprogramming relies on methylating and de-methylating enzymes and co-factors that are stored during oocyte growth, concurrently with the re-methylation of the oocyte itself...
March 1, 2017: Reproduction: the Official Journal of the Society for the Study of Fertility
https://www.readbyqxmd.com/read/28245219/correcting-for-cell-type-heterogeneity-in-epigenome-wide-association-studies-revisiting-previous-analyses
#16
Shijie C Zheng, Stephan Beck, Andrew E Jaffe, Devin C Koestler, Kasper D Hansen, Andres E Houseman, Rafael A Irizarry, Andrew E Teschendorff
No abstract text is available yet for this article.
February 28, 2017: Nature Methods
https://www.readbyqxmd.com/read/28222718/abnormal-epigenetic-changes-during-differentiation-of-human-skeletal-muscle-stem-cells-from-obese-subjects
#17
Cajsa Davegårdh, Christa Broholm, Alexander Perfilyev, Tora Henriksen, Sonia García-Calzón, Lone Peijs, Ninna Schiøler Hansen, Petr Volkov, Rasmus Kjøbsted, Jørgen F P Wojtaszewski, Maria Pedersen, Bente Klarlund Pedersen, Dov B Ballak, Charles A Dinarello, Bas Heinhuis, Leo A B Joosten, Emma Nilsson, Allan Vaag, Camilla Scheele, Charlotte Ling
BACKGROUND: Human skeletal muscle stem cells are important for muscle regeneration. However, the combined genome-wide DNA methylation and expression changes taking place during adult myogenesis have not been described in detail and novel myogenic factors may be discovered. Additionally, obesity is associated with low relative muscle mass and diminished metabolism. Epigenetic alterations taking place during myogenesis might contribute to these defects. METHODS: We used Infinium HumanMethylation450 BeadChip Kit (Illumina) and HumanHT-12 Expression BeadChip (Illumina) to analyze genome-wide DNA methylation and transcription before versus after differentiation of primary human myoblasts from 14 non-obese and 14 obese individuals...
February 22, 2017: BMC Medicine
https://www.readbyqxmd.com/read/28221285/genome-wide-methylation-analysis-of-a-large-population-sample-shows-neurological-pathways-involvement-in-chronic-widespread-musculoskeletal-pain-cwp
#18
Gregory Livshits, Ida Malkin, Maxim B Freidin, Yudong Xia, Fei Gao, Jun Wang, Timothy D Spector, Alex MacGregor, Jordana T Bell, Frances Mk Williams
Chronic widespread musculoskeletal pain (CWP), has a considerable heritable component, which remains to be explained. Epigenetic factors may contribute to and account for some of the heritability estimate. We analysed epigenome-wide methylation using MeDIPseq in whole blood DNA from 1708 monozygotic (MZ) and dizygotic (DZ) Caucasian twins having CWP prevalence of 19.9%. Longitudinally stable methylation bins (lsBINs), were established by testing repeated measurements conducted ≥3 years apart, n=292. DNA methylation variation at lsBINs was tested for association with CWP in a discovery set of 50 MZ twin pairs discordant for CWP, and in an independent dataset (n=1608 twins), and the results from the two samples were combined using Fisher's method...
February 15, 2017: Pain
https://www.readbyqxmd.com/read/28198392/coffee-consumption-is-associated-with-dna-methylation-levels-of-human-blood
#19
Yu-Hsuan Chuang, Austin Quach, Devin Absher, Themistocles Assimes, Steve Horvath, Beate Ritz
Beneficial health effects have been attributed to coffee consumption, but it is not yet known whether epigenetics may have a role in this process. Here we associate epigenome-wide DNA methylation levels to habitual coffee consumption from two studies with blood (2100 and 215 participants), and one with saliva samples (256 participants). Adjusting for age, gender, and blood cell composition, one CpG (cg21566642 near ALPPL2) surpassed genome-wide significance (P=3.7 × 10(-10)) and from among 10 additional CpGs significant at P≤5...
February 15, 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/28194238/epigenome-wide-association-study-ewas-on-lipids-the-rotterdam-study
#20
Kim V E Braun, Klodian Dhana, Paul S de Vries, Trudy Voortman, Joyce B J van Meurs, Andre G Uitterlinden, Albert Hofman, Frank B Hu, Oscar H Franco, Abbas Dehghan
BACKGROUND: DNA methylation is a key epigenetic mechanism that is suggested to be associated with blood lipid levels. We aimed to identify CpG sites at which DNA methylation levels are associated with blood levels of triglycerides, high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C), and total cholesterol in 725 participants of the Rotterdam Study, a population-based cohort study. Subsequently, we sought replication in a non-overlapping set of 760 participants...
2017: Clinical Epigenetics
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