Single-molecule, genome-scale analyses of DNA modifications: exposing the epigenome with next-generation technologies.

abstract：AIM:To assess the associations between gestational diabetes mellitus (GDM) and DNA methylation levels at genes related to energy metabolism. PATIENTS & METHODS:Ten loci were selected from our recent epigenome-wide association study on GDM. DNA methylation levels were quantified by bisulfite pyrosequencing in 80 placen...

journal_title：Epigenomics

authors： Houde AA,Ruchat SM,Allard C,Baillargeon JP,St-Pierre J,Perron P,Gaudet D,Brisson D,Hivert MF,Bouchard L

更新日期：2015-10-01 00:00:00

abstract：AIM:Disclosing the mechanisms that regulate reprogramming memory. MATERIALS & METHODS:We established computational procedure to find DNA methylation somatic memory sites (SMSs) at single CpGs and integrated them with genomics, epigenomics, transcriptomics and imprinting information. RESULTS & CONCLUSION:Reprogramming...

journal_title：Epigenomics

authors： Luu PL,Gerovska D,Schöler HR,Araúzo-Bravo MJ

更新日期：2018-02-01 00:00:00

abstract：AIMS:To investigate if DNA methylation pattern assay could be a new approach to identifying the primary tumor cell origin of the recurrent hepatocellular carcinoma (HCC). MATERIALS & METHODS:Methylation of 24 genes and expression of 22 cancer stem cell (CSC) biomarkers were quantitatively measured in 10 paired primary...

journal_title：Epigenomics

authors： Zhang X,Liu S,Shen C,Wu Y,Zhang L,Chen X,Lu F

更新日期：2015-01-01 00:00:00

abstract：:Post-translational modifications of chromatin have become a 'booming' area of biomedical research. One particularly interesting modification that is important for eukaryotic gene expression is trimethylation of histone H3 lysine 4 (H3K4me3), which is almost exclusively associated with active promoters of RNA polymeras...

journal_title：Epigenomics

authors： Vermeulen M,Timmers HT

更新日期：2010-06-01 00:00:00

abstract：AIM:We examined maternal prepregnancy anthropometry and cord blood DNA methylation. METHODS:Associations between maternal measures (i.e., weight, height, waist circumference, hip circumference, skinfolds, leptin) and methylation β-values at each CpG (measured by the Infinium MethylationEPIC BeadChip) were estimated am...

journal_title：Epigenomics

authors： Yeung EH,Guan W,Mumford SL,Silver RM,Zhang C,Tsai MY,Schisterman EF

更新日期：2019-02-01 00:00:00

abstract：:Prader-Willi syndrome (PWS) is a relatively rare disorder that originates from paternally inherited deletions and maternal disomy (mUPD) within the 15q11-q13 region or alterations in the PWS imprinting center. Evidence is accumulating that mUPD underlies high prevalence of psychosis among PWS patients. Several genes i...

journal_title：Epigenomics

authors： Krefft M,Frydecka D,Adamowski T,Misiak B

更新日期：2014-01-01 00:00:00

abstract：:Imprinted genes are an epigenetically regulated class of genes that are preferentially expressed from one parental allele. A number of these genes are crucial for placental function and embryonic growth in mice and humans. Disruption of imprinted genes is also associated with several neurodevelopmental disorders, alth...

journal_title：Epigenomics

authors： Kernohan KD,Bérubé NG

更新日期：2010-12-01 00:00:00

abstract：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-Ho...

journal_title：Epigenomics

authors： Popovic M,Fasanelli F,Fiano V,Biggeri A,Richiardi L

更新日期：2017-12-01 00:00:00

abstract：:Aim: Myotonic dystrophy type 1 (DM1) is caused by an unstable trinucleotide (CTG) expansion at the DMPK gene locus. Cognitive dysfunctions are often observed in the condition. We investigated the association between DMPK blood DNA methylation (DNAm) and cognitive functions in DM1, considering expansion length and vari...

journal_title：Epigenomics

authors： Breton É,Légaré C,Overend G,Guay SP,Monckton D,Mathieu J,Gagnon C,Richer L,Gallais B,Bouchard L

更新日期：2020-12-01 00:00:00

abstract：:The examination of potential roles of epigenetic alterations in the pathogenesis of psychotic diseases have become an essential alternative in recent years as genetic studies alone are yet to uncover major gene(s) for psychosis. Here, we describe the current state of knowledge from the gene-specific and genome-wide st...

journal_title：Epigenomics

authors： Abdolmaleky HM,Zhou JR,Thiagalingam S

更新日期：2015-01-01 00:00:00

abstract：OBJECTIVE:To study DNA methylation patterns of cortical pyramidal layers susceptible to late-onset Alzheimer's disease (LOAD) neurodegeneration. METHODS:Laser-assisted microdissection to select pyramidal layers' cells in frontal cortex of 32 human brains (18 LOAD) and Infinium DNA Methylation 450K analysis were perfor...

journal_title：Epigenomics

authors： Hernández HG,Sandoval-Hernández AG,Garrido-Gil P,Labandeira-Garcia JL,Zelaya MV,Bayon GF,Fernández AF,Fraga MF,Arboleda G,Arboleda H

更新日期：2018-11-01 00:00:00

abstract：AIM:Transcriptomic and methylomic patterns represent two major OMIC data sources impacted by both inheritable genetic information and environmental factors, and have been widely used as disease diagnosis and prognosis biomarkers. MATERIALS & METHODS:Modern transcriptomic and methylomic profiling technologies detect th...

journal_title：Epigenomics

authors： Xu C,Liu J,Yang W,Shu Y,Wei Z,Zheng W,Feng X,Zhou F

更新日期：2018-04-01 00:00:00

abstract：:Background: Castration-resistant prostate cancer (CRPC) is an incurable malignancy. Long noncoding RNAs (lncRNAs) play key roles in drug resistance. Materials & methods: LncRNA HORAS5 role in cabazitaxel resistance (i.e., cell-count, IC50 and caspase activity) was studied via lentiviral-mediated overexpression and siR...

journal_title：Epigenomics

authors： Pucci P,Venalainen E,Alborelli I,Quagliata L,Hawkes C,Mather R,Romero I,Rigas SH,Wang Y,Crea F

更新日期：2020-07-01 00:00:00

abstract：:Aim: To develop a method for estimating cell-specific effects in epigenomic association studies in the presence of cell type heterogeneity. Materials & methods: We utilized Monte Carlo Expectation-Maximization (MCEM) algorithm with Metropolis-Hastings sampler to reconstruct the 'missing' cell-specific methylations and...

journal_title：Epigenomics

authors： Feng YA,Guo Y,Pain L,Lathrop GM,Laprise C,Moffatt MF,Cookson WO,Liang L

更新日期：2020-12-22 00:00:00

abstract：:Antisense RNA is the first noncoding RNA found to have a regulatory function. With the advances of biological science, it has been recognized that the function of antisense RNAs is not only limited to post-transcriptional regulation, but extends to transcriptional regulation of various important genes leading to epige...

journal_title：Epigenomics

authors： Cui I,Cui H

更新日期：2010-02-01 00:00:00

abstract：:There are numerous examples of enduring effects of early experience on gene transcription and neural function. We review the emerging evidence for epigenetics as a candidate mechanism for such effects. There is now evidence that intracellular signals activated by environmental events can directly modify the epigenetic...

journal_title：Epigenomics

authors： Sng J,Meaney MJ

更新日期：2009-10-01 00:00:00

abstract：:A number of bioactive dietary components are of particular interest in the field of epigenetics. Many of these compounds display anticancer properties and may play a role in cancer prevention. Numerous studies suggest that a number of nutritional compounds have epigenetic targets in cancer cells. Importantly, emerging...

journal_title：Epigenomics

authors： Hardy TM,Tollefsbol TO

更新日期：2011-08-01 00:00:00

abstract：:Aim: To dynamically analyze the differential m6A methylation during the progression and reversal of hepatic fibrosis. Materials & methods: We induced hepatic fibrosis in C57/BL6 mice by intraperitoneal injection of CCl4. The reversal model of hepatic fibrosis was established by stopping drug after continuous injection...

journal_title：Epigenomics

authors： Cui Z,Huang N,Liu L,Li X,Li G,Chen Y,Wu Q,Zhang J,Long S,Wang M,Sun F,Shi Y,Pan Q

更新日期：2020-10-01 00:00:00

abstract：:Until recently, drug development in oncology was focused on treating most patients for a specific cancer type without taking in account the heterogeneity between these patients in term of response to treatment. Therefore, this type of broad treatment approach excludes the treatment of patient not responding to disease...

journal_title：Epigenomics

authors： Cartron PF,Cheray M,Bretaudeau L

更新日期：2020-01-01 00:00:00

abstract：:Cancer numbers increasing, cases heterogeneity and the drug resistance emergence have pushed scientists to search for innovative solutions for patients and epimutations can be one. Methylated DNA, modified nucleosomes and noncoding RNAs are found in all cells, including tumor cells. They are intracellular actors but a...

journal_title：Epigenomics

authors： Duforestel M,Briand J,Bougras-Cartron G,Heymann D,Frenel JS,Vallette FM,Cartron PF

更新日期：2020-01-01 00:00:00

abstract：:Aim: This study aimed to identify novel miRNAs (miRs) as regulators of UGT1A gene expression and to evaluate them as potential risk factors for the development of liver fibrosis/cirrhosis. Materials & methods: miRNA target sites in UDP-glucuronosyltransferase 1A (UGT1A) 3'-UTR were predicted and confirmed by luciferas...

journal_title：Epigenomics

authors： Paulusch S,Kalthoff S,Landerer S,Jansen C,Schierwagen R,Klein S,Trebicka J,Strassburg CP

更新日期：2021-01-12 00:00:00

abstract：:This article focuses on the epigenetic alterations of aberrant promoter hypermethylation of genes, and histone modifications or RNA interference in cancer cells. Current knowledge of the hypermethylation of allele(s) in classical tumor suppressor genes in inherited and sporadic cancer, candidate tumor suppressor and o...

journal_title：Epigenomics

authors： Hoffman AM,Cairns P

更新日期：2011-02-01 00:00:00

abstract：AIM:We compared predictive modeling approaches to estimate placental methylation using cord blood methylation. MATERIALS & METHODS:We performed locus-specific methylation prediction using both linear regression and support vector machine models with 174 matched pairs of 450k arrays. RESULTS:At most CpG sites, both ap...

journal_title：Epigenomics

authors： De Carli MM,Baccarelli AA,Trevisi L,Pantic I,Brennan KJ,Hacker MR,Loudon H,Brunst KJ,Wright RO,Wright RJ,Just AC

更新日期：2017-03-01 00:00:00

abstract：:Epigenetic enzymes are emerging as crucial controllers of macrophages, innate immune cells that determine the outcome of many inflammatory diseases. Recent studies demonstrate that the activity of particular chromatin-modifying enzymes is regulated by the availability of specific metabolites like acetyl-coenzyme A, S-...

journal_title：Epigenomics

authors： Baardman J,Licht I,de Winther MP,Van den Bossche J

更新日期：2015-10-01 00:00:00

abstract：:DNA methylation is widely studied in the context of cancer. However, the rediscovery of 5-hydroxymethylation of DNA adds a new layer of complexity to understanding the epigenetic basis of development and disease, including carcinogenesis. There have been significant advances in techniques for the detection of 5-hydrox...

journal_title：Epigenomics

authors： Laird A,Thomson JP,Harrison DJ,Meehan RR

更新日期：2013-12-01 00:00:00

abstract：AIM:We performed a study to identify the role of microRNA in thymoma. PATIENTS & METHODS:One hundred twenty-three thymoma patients with clinical information and miRNA expression data from The Cancer Genome Atlas were included in the study. Comprehensive bioinformatics analysis was integrated in our analysis. RESULTS ...

journal_title：Epigenomics

authors： Wei J,Liu Z,Wu K,Yang D,He Y,Chen GG,Zhang J,Lin J

更新日期：2017-05-01 00:00:00

abstract：AIM:To identify differentially methylated probes (DMPs) and regions (DMRs) in relation to chronic obstructive pulmonary disease (COPD) and lung function traits. METHODS:We performed an epigenome-wide association study of COPD and spirometric parameters, including forced expiratory volume in 1 s (FEV1), forced vital ca...

journal_title：Epigenomics

authors： Lee MK,Hong Y,Kim SY,Kim WJ,London SJ

更新日期：2017-07-01 00:00:00

abstract：:Aim: To examine the impact of 4-nonylphenol (4-NP), on the expression of polycomb repressive complexes and cellular proliferation. Materials & methods: Cell proliferation assays, quantitative PCR, Western blotting, luciferase reporter assay, chromatin immunoprecipitation-quantitative PCR were used for the study. Resul...

journal_title：Epigenomics

authors： Ghosh K,Chatterjee B,Maheswari U,Athifa M,Kanade SR

更新日期：2019-06-01 00:00:00

abstract：:This study aimed to unveil the functional roles of LINC00221 in hepatocellular carcinoma (HCC). A discovery cohort and a validation cohort were respectively used to identify and verify the clinical value of LINC00221 in HCC. Bioinformatics analysis was performed to explore its potential mechanisms. LINC00221 was upreg...

journal_title：Epigenomics

authors： Feng Y,Dramani Maman ST,Zhu X,Liu X,Bongolo CC,Liang C,Tu J

更新日期：2021-01-07 00:00:00

abstract：:Children exposed to early-life adversity carry a greater risk of poor health and disease into adulthood. This increased disease risk is shadowed by changes in the epigenome. Epigenetics can change gene expression to modify disease risk; unfortunately, how epigenetics are changed by the environment is unclear. It is kn...

journal_title：Epigenomics

authors： Majnik AV,Lane RH

更新日期：2015-10-01 00:00:00