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Epigenomics

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https://www.readbyqxmd.com/read/29135286/vitamin-b12-supplementation-influences-methylation-of-genes-associated-with-type-2-diabetes-and-its-intermediate-traits
#1
Dilip K Yadav, Smeeta Shrestha, Karen A Lillycrop, Charu V Joglekar, Hong Pan, Joanna D Holbrook, Caroline Hd Fall, Chittaranjan S Yajnik, Giriraj R Chandak
AIM: To investigate the effect of B12 and/or folic acid supplementation on genome-wide DNA methylation. METHODS: We performed Infinium HumanMethylation450 BeadChip (Zymo Research, CA, USA) assay in children supplemented with B12 and/or folic acid (n = 12 in each group) and investigated the functional mechanism of selected differentially methylated loci. RESULTS: We noted significant methylation changes postsupplementation in B12 (589 differentially methylated CpGs and 2892 regions) and B12 + folic acid (169 differentially methylated CpGs and 3241 regions) groups...
November 14, 2017: Epigenomics
https://www.readbyqxmd.com/read/29135282/genome-wide-dna-methylation-drives-human-embryonic-stem-cell-erythropoiesis-by-remodeling-gene-expression-dynamics
#2
Zhijing Liu, Qiang Feng, Pengpeng Sun, Yan Lu, Minlan Yang, Xiaowei Zhang, Xiangshu Jin, Yulin Li, Shi-Jiang Lu, Chengshi Quan
AIM: To investigate the role of DNA methylation during erythrocyte production by human embryonic stem cells (hESCs). METHODS: We employed an erythroid differentiation model from hESCs, and then tracked the genome-wide DNA methylation maps and gene expression patterns through an Infinium HumanMethylation450K BeadChip and an Ilumina Human HT-12 v4 Expression Beadchip, respectively. RESULTS: A negative correlation between DNA methylation and gene expression was substantially enriched during the later differentiation stage and was present in both the promoter and the gene body...
November 14, 2017: Epigenomics
https://www.readbyqxmd.com/read/29130343/defining-baseline-epigenetic-landscapes-in-the-rat-liver
#3
John P Thomson, Raffaele Ottaviano, Roland Buesen, Jonathan G Moggs, Michael Schwarz, Richard R Meehan
Characterization of the hepatic epigenome following exposure to chemicals and therapeutic drugs provides novel insights into toxicological and pharmacological mechanisms, however appreciation of genome-wide inter- and intra-strain baseline epigenetic variation, particularly in under-characterized species such as the rat is limited. Material & methods: To enhance the utility of epigenomic endpoints safety assessment, we map both DNA modifications (5-methyl-cytosine and 5-hydroxymethyl-cytosine) and enhancer related chromatin marks (H3K4me1 and H3K27ac) across multiple male and female rat livers for two important outbred laboratory rat strains (Sprague-Dawley and Wistar)...
November 13, 2017: Epigenomics
https://www.readbyqxmd.com/read/29106309/maternal-gestational-weight-gain-and-dna-methylation-in-young-women-application-of-life-course-mediation-methods
#4
Jonathan Y Huang, David S Siscovick, Hagit Hochner, Yechiel Friedlander, Daniel A Enquobahrie
AIM: To investigate the role of maternal gestational weight gain (GWG) and prepregnancy BMI on programming offspring DNA methylation. METHODS: Among 589 adult (age = 32) women participants of the Jerusalem Perinatal Study, we quantified DNA methylation in five candidate genes. We used inverse probability-weighting and parametric g-formula to estimate direct effects of maternal prepregnancy BMI and GWG on methylation. RESULTS: Higher maternal GWG, but not prepregnancy BMI, was inversely related to offspring ABCA1 methylation (β = -1...
November 6, 2017: Epigenomics
https://www.readbyqxmd.com/read/29106301/mirna-processing-gene-polymorphisms-blood-dna-methylation-age-and-long-term-ambient-pm2-5-exposure-in-elderly-men
#5
Jamaji C Nwanaji-Enwerem, Elena Colicino, Lingzhen Dai, Qian Di, Allan C Just, Lifang Hou, Pantel Vokonas, Immaculata De Vivo, Bernardo Lemos, Quan Lu, Marc G Weisskopf, Andrea A Baccarelli, Joel D Schwartz
AIM: We tested whether genetic variation in miRNA processing genes modified the association of PM2.5 with DNA methylation (DNAm) age. PATIENTS & METHODS: We conducted a repeated measures study based on 552 participants from the Normative Aging Study with multiple visits between 2000 and 2011 (n = 940 visits). Address-level 1-year PM2.5 exposures were estimated using the GEOS-chem model. DNAm-age and a panel of 14 SNPs in miRNA processing genes were measured from participant blood samples...
November 6, 2017: Epigenomics
https://www.readbyqxmd.com/read/29106300/increased-correlation-between-methylation-sites-in-epigenome-wide-replication-studies-impact-on-analysis-and-results
#6
Maja Popovic, Francesca Fasanelli, Valentina Fiano, Annibale Biggeri, Lorenzo Richiardi
AIM: To show that an increased correlation between CpGs after selection through an epigenome-wide association studies (EWAS) might translate into biased replication results. METHODS: Pairwise correlation coefficients between CpGs selected in two published EWAS, the top hits replication, Bonferroni p-values, Benjamini-Hochberg (BH) false discovery rate (FDR) and directional FDR r-values were calculated in the NINFEA cohort data. Exposures' random permutations were performed to show the empirical p-value distributions...
November 6, 2017: Epigenomics
https://www.readbyqxmd.com/read/29106295/naive-pluripotent-stem-cells-as-a-model-for-studying-human-developmental-epigenomics-opportunities-and-limitations
#7
Peter J Rugg-Gunn
No abstract text is available yet for this article.
November 6, 2017: Epigenomics
https://www.readbyqxmd.com/read/28994305/plant-homeodomain-finger-protein-2-as-a-novel-ikaros-target-in-acute-lymphoblastic-leukemia
#8
Zheng Ge, Yan Gu, Qi Han, Justin Sloane, Qinyu Ge, Goufeng Gao, Jinlong Ma, Huihui Song, Jiaojiao Hu, Baoan Chen, Sinisa Dovat, Chunhua Song
AIM: Clinical significance of plant homeodomain finger 2 (PHF2) expressions is explored in acute lymphoblastic leukemia (ALL) patients. METHODS: mRNA level was examined by qPCR. The retroviral gene expression, shRNA knockdown and chromatin-immunoprecipitation are used to observe IKAROS regulation on PHF2 transcription. RESULTS: PHF2 expression is significantly reduced in subsets of ALL patients, and PHF2 (low) expression correlates with leukemia cell proliferation and an elevation of several poor prognostic markers in B-cell ALL...
October 10, 2017: Epigenomics
https://www.readbyqxmd.com/read/28990796/homocysteine-levels-associate-with-subtle-changes-in-leukocyte-dna-methylation-an-epigenome-wide-analysis
#9
Pooja R Mandaviya, Dylan Aïssi, Koen F Dekkers, Roby Joehanes, Silva Kasela, Vinh Truong, Lisette Stolk, Diana van Heemst, M Arfan Ikram, Jan Lindemans, P Eline Slagboom, David-Alexandre Trégouët, André G Uitterlinden, Chen Wei, Phil Wells, France Gagnon, Marleen Mj van Greevenbroek, Bastiaan T Heijmans, Lili Milani, Pierre-Emmanuel Morange, Joyce Bj van Meurs, Sandra G Heil
AIM: Homocysteine (Hcy) is a sensitive marker of one-carbon metabolism. Higher Hcy levels have been associated with global DNA hypomethylation. We investigated the association between plasma Hcy and epigenome-wide DNA methylation in leukocytes. METHODS: Methylation was measured using Illumina 450 k arrays in 2035 individuals from six cohorts. Hcy-associated differentially methylated positions and regions were identified using meta-analysis. RESULTS: Three differentially methylated positions cg21607669 (SLC27A1), cg26382848 (AJUBA) and cg10701000 (KCNMA1) at chromosome 19, 14 and 10, respectively, were significantly associated with Hcy...
October 9, 2017: Epigenomics
https://www.readbyqxmd.com/read/28972397/the-eukaryotic-genome-is-structurally-and-functionally-more-like-a-social-insect-colony-than-a-book
#10
Guo-Hua Qiu, Xiaoyan Yang, Xintian Zheng, Cuiqin Huang
Traditionally, the genome has been described as the 'book of life'. However, the metaphor of a book may not reflect the dynamic nature of the structure and function of the genome. In the eukaryotic genome, the number of centrally located protein-coding sequences is relatively constant across species, but the amount of noncoding DNA increases considerably with the increase of organismal evolutional complexity. Therefore, it has been hypothesized that the abundant peripheral noncoding DNA protects the genome and the central protein-coding sequences in the eukaryotic genome...
October 3, 2017: Epigenomics
https://www.readbyqxmd.com/read/28969469/using-induced-pluripotent-stem-cells-to-explore-genetic-and-epigenetic-variation-associated-with-alzheimer-s-disease
#11
Jennifer Imm, Talitha L Kerrigan, Aaron Jeffries, Katie Lunnon
It is thought that both genetic and epigenetic variation play a role in Alzheimer's disease initiation and progression. With the advent of somatic cell reprogramming into induced pluripotent stem cells it is now possible to generate patient-derived cells that are able to more accurately model and recapitulate disease. Furthermore, by combining this with recent advances in (epi)genome editing technologies, it is possible to begin to examine the functional consequence of previously nominated genetic variants and infer epigenetic causality from recently identified epigenetic variants...
October 3, 2017: Epigenomics
https://www.readbyqxmd.com/read/28967791/adipose-tissue-dna-methylome-changes-in-development-of-new-onset-diabetes-after-kidney-transplantation
#12
Saurabh Baheti, Prachi Singh, Yun Zhang, Jared Evans, Michael D Jensen, Virend K Somers, Jean-Pierre A Kocher, Zhifu Sun, Harini A Chakkera
AIM: New-onset diabetes after kidney transplant (NODAT) adversely impacts kidney allograft and patient survival. Epigenetic alterations in adipose tissue like DNA methylation may play a contributory role. METHODS: Adipose tissue DNA of the patients with NODAT and their age, sex and BMI matched controls (nine each) were sequenced by reduced representation bisulfite sequencing. Differentially methylated CpGs (DMCs) and differentially methylated regions (DMRs) were studied...
October 2, 2017: Epigenomics
https://www.readbyqxmd.com/read/28967789/exploring-genome-wide-dna-methylation-patterns-in-aicardi-syndrome
#13
Ignazio S Piras, Gabrielle Mills, Lorida Llaci, Marcus Naymik, Keri Ramsey, Newell Belnap, Chris D Balak, Wayne M Jepsen, Szabolcs Szelinger, Ashley L Siniard, Candace R Lewis, Madison LaFleur, Ryan F Richholt, Matt D De Both, Kristiina Avela, Sampathkumar Rangasamy, David W Craig, Vinodh Narayanan, Irma Järvelä, Matthew J Huentelman, Isabelle Schrauwen
AIM: To explore differential DNA methylation (DNAm) in Aicardi syndrome (AIC), a severe neurodevelopmental disorder with largely unknown etiology. PATIENTS & METHODS: We characterized DNAm in AIC female patients and parents using the Illumina 450 K array. Differential DNAm was assessed using the local outlier factor algorithm, and results were validated via qPCR in a larger set of AIC female patients, parents and unrelated young female controls. Functional epigenetic modules analysis was used to detect pathways integrating both genome-wide DNAm and RNA-seq data...
October 2, 2017: Epigenomics
https://www.readbyqxmd.com/read/28960094/pan-cancer-analysis-reveals-presence-of-pronounced-dna-methylation-drift-in-cpg-island-methylator-phenotype-clusters
#14
Pawel Karpinski, Karolina Pesz, Maria M Sasiadek
AIM: To provide characteristics of major genomic correlates in CpG island methylator phenotype-high (CIMP-H) subgroups in relation to corresponding non-CIMP-H subgroups by use of phenotypic, DNA methylation and RNAseq data. MATERIALS & METHODS: Twenty-three datasets generated by The Cancer Genome Atlas project encompassing over 7200 unique samples were analyzed. We identified 23 CIMP-H clusters by use of unsupervised clustering. RESULTS & CONCLUSION: More than 90% of CIMP-H clusters were significantly associated with accelerated epigenetic mitotic clock, demethylation of enhancer sites, backbone and repetitive sequences...
September 29, 2017: Epigenomics
https://www.readbyqxmd.com/read/28960093/a-new-model-of-the-mechanism-underlying-lead-poisoning-snps-in-mirna-target-region-influence-the-%C3%AE-aminolevulinic-acid-dehydratase-expression-level
#15
Chunping Li, Miaomiao Wang, Yiqing Wang, Jinlong Zhang, Na Sun
AIM: To determine if SNPs located within the 3'-UTR of δ-aminolevulinic acid dehydratase (ALAD) can alter the risk of lead poisoning and the ALAD gene expression. MATERIALS & METHODS: A case-control study was carried out to find the SNPs in miRNA target region. Luciferase reporter gene assay, qRT-PCR and Western blot was used to determine the relationship between miRNA and SNPs. RESULTS: We found a significant association between rs818708 and the risk of lead poisoning...
September 29, 2017: Epigenomics
https://www.readbyqxmd.com/read/28942676/epigenetics-of-cancer-associated-muscle-catabolism
#16
Ryan M Carr, Elisa Enriquez-Hesles, Rachel Lo Olson, Aminah Jatoi, Jason Doles, Martin E Fernandez-Zapico
Cancer patients are commonly affected by cachexia, a wasting process involving muscle and fat. Specifically, loss of the muscle compartment has been associated with poor prognosis and suboptimal response to therapy. Nutritional support has been ineffective in treating this process leading to investigations into the underlying molecular processes governing muscle catabolism. In this commentary, we discuss the molecular mechanisms of cancer-associated muscle metabolism and the epigenetic processes responsible for the muscle wasting phenotype...
September 25, 2017: Epigenomics
https://www.readbyqxmd.com/read/28885036/postnatal-diet-remodels-hepatic-dna-methylation-in-metabolic-pathways-established-by-a-maternal-high-fat-diet
#17
Laura Moody, Hong Chen, Yuan-Xiang Pan
AIM: We investigate how postweaning diet may modify the epigenetic landscape to meet metabolic demands later in life. METHODS: Sprague-Dawley rats were exposed to a high-fat (HF) diet during gestation and lactation. At weaning, male offspring were placed either on an HF diet (HF/HF) or a control diet (HF/C). Methylation-dependent immunoprecipitation sequencing and methylation-sensitive restriction enzyme sequencing were used to quantify hepatic DNA methylation. RESULTS: Out of the 3966 identified differentially methylated regions, 37% were mapped to gene bodies while 6% fell within promoter or downstream regions...
September 8, 2017: Epigenomics
https://www.readbyqxmd.com/read/28882057/interethnic-dna-methylation-difference-and-its-implications-in-pharmacoepigenetics
#18
Shih-Kai Chu, Hsin-Chou Yang
AIM: This is the first systematic study to examine the population differentiation effect of DNA methylation on the treatment response and drug absorption, distribution, metabolism and excretion in multiple tissue types and cancer types. MATERIALS & METHODS: We analyzed the whole methylome and transcriptome data of primary tumor tissues of four cancer types (breast, colon, head & neck and uterine corpus) and lymphoblastoid cell lines for African and European ancestry populations...
September 8, 2017: Epigenomics
https://www.readbyqxmd.com/read/28877608/genome-wide-integrative-analysis-identified-snp-mirna-mrna-interaction-networks-in-peripheral-blood-mononuclear-cells
#19
Xiang Lin, Wei Xia, Wei Ji, Fang-Fei Xie, Pei He, Xiao-Wei Zhu, Yong-Hong Zhang, Fei-Yan Deng, Shu-Feng Lei
AIM: To detect SNP-miRNA-mRNA interaction networks and to elucidate miRNA-mediated regulation effects on mRNA expression. MATERIALS & METHODS: In human peripheral blood mononuclear cells of 43 females, SNP-miRNA-mRNA interaction networks were established through an integrative analysis. Then causal inference test was followed to detect miRNA-mediated effects on mRNA expressions. RESULTS: About 167 trios corresponding to 56 SNPs, 20 miRNAs and 47 target-mRNAs have the SNP-miRNA-mRNA interactions, but only 22 trios have miRNA-mediated effects between SNP and mRNA...
September 7, 2017: Epigenomics
https://www.readbyqxmd.com/read/28877596/what-the-human-sperm-methylome-tells-us
#20
Cristina Camprubí, Riccardo Aiese Cigliano, Albert Salas-Huetos, Nicolas Garrido, Joan Blanco
AIM: To characterize the sperm methylome in semen samples from 19 donors with proven fertility. MATERIALS & METHODS: Bisulfite-converted sperm DNA was hybridized on the HumanMethylation450 Infinium BeadChip platform. CpG fluorescence intensities were extracted and converted to β-values. RESULTS: The sperm methylome is highly homogeneous and hypomethylated. Genes with hypomethylated promoters are ontologically associated to biological functions related to spermatogenesis and embryogenesis...
September 7, 2017: Epigenomics
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