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Ye Liu, Zhongqi Chen, Kun Xu, Zhengxia Wang, Chaojie Wu, Zhixiao Sun, Ningfei Ji, Mao Huang, Mingshun Zhang
AIM: To explore the miRNAs profile of CD4+ T lymphocytes in asthma via next generation sequencing. METHODS: In the murine model of acute asthma, spleen CD4+ T lymphocytes were sorted, in which small RNAs were extracted and sequenced. Novel miRNAs were measured with real time quantitative reverse transcription polymerase chain reaction (qRT-PCR). RESULTS: A total of 127 miRNAs were found to exhibit at least twofold change. In the 262 predicted novel miRNAs, 14 novel miRNAs were measured in qRT-PCR in the sorted CD4+ T cells or in the differentiated Th1/Th2 cells and novel miR-11 (xxx-m0228-3p) was significantly decreased in the sorted CD4+ T cells from the murine model of asthma and in the Th2 cells...
May 8, 2018: Epigenomics
Aseel Eid, Syed Waseem Bihaqi, Christopher Hemme, John M Gaspar, Ronald P Hart, Nasser H Zawia
AIM: Early life exposure to lead (Pb) has been shown to increase late life biomarkers involved in Alzheimer's disease (AD) pathology. Here, we tested the hypothesis that latent over expression of AD-related genes may be regulated through histone activation pathways. METHODS: Chromatin immunoprecipitation sequencing was used to map the histone activation mark (H3K9Ac) to the mouse genome in developmentally Pb exposed mice on postnatal days 20, 270 and 700. RESULTS: Exposure to Pb resulted in a global downregulation of H3K9Ac across the lifespan; except in genes associated with the Alzheimer pathway...
May 3, 2018: Epigenomics
Florence Mauger, Magali Kernaleguen, Céline Lallemand, Vessela N Kristensen, Jean-François Deleuze, Jörg Tost
AIM: The detection of specific DNA methylation patterns bears great promise as biomarker for personalized management of cancer patients. Co-amplification at lower denaturation temperature-PCR (COLD-PCR) assays are sensitive methods, but have previously only been able to analyze loss of DNA methylation. MATERIALS & METHODS: Enhanced (E)-ice-COLD-PCR reactions starting from 2 ng of bisulfite-converted DNA were developed to analyze methylation patterns in two promoters with locked nucleic acid (LNA) probes blocking amplification of unmethylated CpGs...
April 26, 2018: Epigenomics
Shijie C Zheng, Amy P Webster, Danyue Dong, Andy Feber, David G Graham, Roisin Sullivan, Sarah Jevons, Laurence B Lovat, Stephan Beck, Martin Widschwendter, Andrew E Teschendorff
AIM: An outstanding challenge in epigenome studies is the estimation of cell-type proportions in complex epithelial tissues. MATERIALS & METHODS: Here, we construct and validate a DNA methylation reference and algorithm for complex tissues that contain epithelial, immune and nonimmune stromal cells. RESULTS: Using this reference, we show that easily accessible tissues such as saliva, buccal and cervix exhibit substantial variation in immune cell (IC) contamination...
April 25, 2018: Epigenomics
Jiaojiao Hu, Qi Han, Yan Gu, Jinlong Ma, Mary McGrath, Fengchang Qiao, Baoan Chen, Chunhua Song, Zheng Ge
AIM: The roles of circular RNA PVT1 (circPVT1) are explored in the patients with acute lymphoblastic leukemia (ALL). METHODS: The circPVT1 level was detected by qRT-PCR and western blot. The apoptotic cells were examined by the annexin V assay in lentiviral shRNA knockdown cells. RESULTS: circPVT1 was highly expressed in ALL compared with normal bone marrow samples. circPVT1 expression was also significantly higher in ALL cell lines. circPVT1 knockdown inhibited cell proliferation and induced cell apoptosis through suppression of its neighbor gene c-Myc, and antiapoptotic Bcl-2 protein expression...
April 25, 2018: Epigenomics
Liang He, Yan Chen, Shuqing Hao, Jinqiao Qian
Protein coding sequences account for around 3% of the human genome, the rest are noncoding RNA (ncRNA) including long ncRNA (lncRNA) and miRNA. Accumulating evidence indicates that lncRNAs and miRNAs are candidate biomarkers for diagnosis, prognosis and therapy of cardiovascular diseases. The lncRNAs act as sponge-like effects on numerous miRNAs, subsequently regulating miRNAs and their targets, mRNA functions. The role of lncRNA-miRNA-mRNA axis in pathogenesis of cardiovascular diseases has been recently reported and highlighted...
April 25, 2018: Epigenomics
Leonidas Chouliaras, Ehsan Pishva, Rita Haapakoski, Eniko Zsoldos, Abda Mahmood, Nicola Filippini, Joe Burrage, Jonathan Mill, Mika Kivimäki, Katie Lunnon, Klaus P Ebmeier
AIM: The present study investigated the link between peripheral DNA methylation (DNAm), cognitive impairment and brain aging. METHODS: We tested the association between blood genome-wide DNAm profiles using the Illumina 450K arrays, cognitive dysfunction and brain MRI measures in selected participants of the Whitehall II imaging sub-study. RESULTS: Eight differentially methylated regions were associated with cognitive impairment. Accelerated aging based on the Hannum epigenetic clock was associated with mean diffusivity and global fractional anisotropy...
April 25, 2018: Epigenomics
Wilfred C de Vega, Lauren Erdman, Suzanne D Vernon, Anna Goldenberg, Patrick O McGowan
AIM: To identify subtypes in myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) based on DNA methylation profiles and health scores. METHODS: DNA methylome profiles in immune cells were integrated with symptomatology from 70 women with ME/CFS using similarity network fusion to identify subtypes. RESULTS: We discovered four ME/CFS subtypes associated with DNA methylation modifications in 1939 CpG sites, three RAND-36 categories and five DePaul Symptom Questionnaire measures...
April 25, 2018: Epigenomics
Yuhua Fu, Jingxuan Li, Qianzi Tang, Cheng Zou, Linyuan Shen, Long Jin, Cencen Li, Chengchi Fang, Rui Liu, Mingzhou Li, Shuhong Zhao, Changchun Li
AIM: Integrated analysis of methylome and transcriptome may help understand the molecular basis of the different breeds with different traits of commercial interest. MATERIALS & METHODS: We obtained the first genome-wide methylome with single-base resolution, miRNAome and transcriptome from three swine breeds. RESULTS: We displayed the landscape of the three omics in the whole-genome level. Integrated outcomes of methylome with genetic selection, miRNAome and transcriptome are also provided...
April 25, 2018: Epigenomics
Judith Bosschieter, Catrin Lutz, Loes I Segerink, André N Vis, Ellen C Zwarthoff, R Jeroen A van Moorselaar, Bas Wg van Rhijn, Martijn W Heymans, Elizabeth P Jansma, Renske Dm Steenbergen, Jakko A Nieuwenhuijzen
AIM: Several urinary hypermethylation-markers (hmDNA) have been described for bladder cancer (BC) detection, but none have been able to replace cystoscopy yet. We systematically reviewed and evaluated current literature on urinary hmDNA markers for BC diagnostics. PATIENTS & METHODS: A systematic search of PubMed, and The Cochrane Library up to February 2017 using the Preferred Reporting Items for Systematic Reviews and Meta-Analysis guidelines, was conducted...
April 25, 2018: Epigenomics
Xue Zhang, Jocelyn M Biagini Myers, J D Burleson, Ashley Ulm, Kelly S Bryan, Xiaoting Chen, Matthew T Weirauch, Theresa A Baker, Melinda S Butsch Kovacic, Hong Ji
AIM: We aim to study DNA methylation (DNAm) variations associated with childhood asthma. METHODS: Nasal DNAm was compared between sibling pairs discordant for asthma, 29 sib pairs for genome-wide association studies and 54 sib pairs for verification by pyrosequencing. Associations of methylation with asthma symptoms, allergy and environmental exposures were evaluated. In vitro experiments and functional genomic analyses were performed to explore biologic relevance...
April 25, 2018: Epigenomics
Helene A Fachim, Umarat Srisawat, Caroline F Dalton, Gavin P Reynolds
Deficits of brain parvalbumin (PV) are a consistent finding in schizophrenia and models of psychosis. We investigated whether this is associated with abnormal PV gene (PVALB) methylation in the brain in schizophrenia. Bisulfite pyrosequencing was used to determine cytosine (CpG) methylation in a PVALB promoter sequence. Greater PVALB methylation was found in schizophrenia hippocampus, while no differences were observed in prefrontal cortex. LINE-1 methylation, a measure of global methylation, was also elevated in both regions in schizophrenia, although the PVALB change was independent of this effect...
April 24, 2018: Epigenomics
Yingchuan Li, Xiaoqing Pan, Michelle L Roberts, Pengyuan Liu, Theodore A Kotchen, Allen W Cowley, David L Mattson, Yong Liu, Mingyu Liang, Srividya Kidambi
AIM: To test whether DNA samples stored for a prolonged period (20 years) under various storage conditions could be used for comparative methylation studies using reduced representation bisulfite sequencing. PATIENTS & METHODS: Five groups of human blood DNA samples (n = 5-6/group) were compared. The groupings were based on the anticoagulant used and storage temperature and duration. RESULTS: Methylation profiles of defined genomic regions in the DNA or blood samples archived for 20 years were similar across all storage temperatures, including 4°C...
April 23, 2018: Epigenomics
Odile Fabre, Lars R Ingerslev, Christian Garde, Ida Donkin, David Simar, Romain Barrès
AIM: To determine the genomic mechanisms by which adipose tissue responds to acute and chronic exercise. METHODS: We profiled the transcriptomic and epigenetic response to acute exercise in human adipose tissue collected before and after endurance training. RESULTS: Although acute exercises were performed at same relative intensities, the magnitude of transcriptomic changes after acute exercise was reduced by endurance training. DNA methylation remodeling induced by acute exercise was more prominent in trained versus untrained state...
April 19, 2018: Epigenomics
J Ramón Tejedor, Clara Bueno, Isabel Cobo, Gustavo F Bayón, Cristina Prieto, Cristina Mangas, Raúl F Pérez, Pablo Santamarina, Rocío G Urdinguio, Pablo Menéndez, Mario F Fraga, Agustín F Fernández
AIM: Epigenetic regulation plays an important role in cellular development and differentiation. A detailed map of the DNA methylation dynamics that occur during cell differentiation would contribute to decipher the molecular networks governing cell fate commitment. METHODS: Illumina MethylationEPIC BeadChip platform was used to describe the genome-wide DNA methylation changes observed throughout hematopoietic maturation by analyzing multiple myeloid and lymphoid hematopoietic cell types...
April 5, 2018: Epigenomics
Guo-Hua Qiu, Cuiqin Huang, Xintian Zheng, Xiaoyan Yang
Peripheral and abundant noncoding DNA has been hypothesized to protect the genome and the central protein-coding sequences against DNA damage in somatic genome. In the cytosol, invading exogenous nucleic acids may first be deactivated by small RNAs encoded by noncoding DNA via mechanisms similar to the prokaryotic CRISPR-Cas system. In the nucleus, the radicals generated by radiation in the cytosol, radiation energy and invading exogenous nucleic acids are absorbed, blocked and/or reduced by peripheral heterochromatin, and damaged DNA in heterochromatin is removed and excluded from the nucleus to the cytoplasm through nuclear pore complexes...
April 4, 2018: Epigenomics
Lisa Boureau, Andrea Constantinof, Vasilis G Moisiadis, Stephen G Matthews, Moshe Szyf
AIM: To determine the state of methylation of DNA molecules in the guinea pig hippocampus that are associated with either poised or active enhancers. METHODS: We used sequential chromatin immunoprecipitation-bisulfite-sequencing with an antibody to H3K4me1 to map the state of methylation of DNA that is found within enhancers. Actively transcribing transcription start sites were mapped by chromatin immunoprecipitation-sequencing with an antibody to RNApolII-PS5. Total DNA methylation was mapped using reduced representation bisulfite sequencing...
April 4, 2018: Epigenomics
Tian Tian, Linlin Wang, Yan Shen, Bo Zhang, Richard H Finnell, Aiguo Ren
AIM: To investigate the relationship between GRHL3 methylation and the etiology of neural tube defects (NTDs). MATERIALS & METHODS: Analyze data from a genome-wide DNA methylation array. Targeted DNA methylation analysis was performed for 46 cases and 23 controls. At last, grhl3 overexpression and gene depletion experiments were conducted in zebrafish. RESULTS: Five hypomethylated CpGs were discovered in the methylation arrays performed on NTD cases...
March 28, 2018: Epigenomics
Xiaoyu Pan, Desheng Gong, Fei Gao, Per Torp Sangild
AIM: To examine how enteral feeding affects the intestinal epigenome and gene expression just after preterm birth. MATERIALS & METHODS: Intestinal tissue from preterm pigs, modeling preterm infants, was collected at birth and 5 days after gradual introduction of infant formula or bovine colostrum. The intestinal tissue was analyzed by reduced representation bisulfite sequencing and real-time qPCR. RESULTS: Relative to colostrum, formula increased bacterial epithelial adherence and LBP (lipopolysaccharide binding protein) expression, which was regulated by promoter methylation...
March 28, 2018: Epigenomics
Valentina Snetkova, Jane A Skok
Enhancers are short noncoding segments of DNA (100-1000 bp) that control the temporal and spatial activity of genes in an orientation-independent manner. They can be separated from their target genes by large distances and are thus known as distal regulatory elements. One consequence of the variability in the distance separating enhancers and their target promoters is that it is difficult to determine which elements are involved in the regulation of a particular gene. Moreover, enhancers can be found in clusters in which multiple regulatory elements control expression of the same target gene...
March 27, 2018: Epigenomics
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