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Cheng Xu, Jiamei Liu, Weifeng Yang, Yayun Shu, Zhipeng Wei, Weiwei Zheng, Xin Feng, Fengfeng Zhou
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 the status of tens of thousands or even millions of probing residues in the human genome, and introduce a major computational challenge for the existing feature selection algorithms...
January 19, 2018: Epigenomics
Naoko Iida, Yoshihiro Okuda, Osamu Ogasawara, Satoshi Yamashita, Hideyuki Takeshima, Toshikazu Ushijima
AIM: Bioinformatics analysis for Illumina Infinium Human DNA methylation BeadArray is essential, but still remains difficult task for many experimental researchers. We here aimed to develop a browser-accessible bioinformatics tool for analyzing the BeadArray data. MATERIALS & METHODS: The tool was established as an analytical pipeline using R, Perl and Python programming languages. RESULTS: We introduced a method that groups neighboring probes into a genomic block, which facilitated efficient identification of densely methylated/unmethylated regions...
January 18, 2018: Epigenomics
Jing Zhou, Xia Liu, Changhe Wang, Changzhong Li
AIM: This study was intended to identify the metastasis-related miRNAs and target genes in cervical squamous cell carcinoma. MATERIALS & METHODS: The mRNA and miRNA next-generation sequencing data were downloaded. Differential expression analysis was carried out, followed by target gene prediction of differentially expressed miRNAs. The biological function of differentially expressed genes was performed. Validation was carried out by survival analysis and qRT-PCR...
January 18, 2018: Epigenomics
Babu Swathy, Koramannil R Saradalekshmi, Indu V Nair, Chandrasekharan Nair, Moinak Banerjee
AIM: The present study intends to evaluate whether antipsychotic drugs can modulate the host epigenome and if so whether drug-induced epigenetic modulation can explain the heterogeneity in drug response. METHODS: Present study was conducted in in vitro cells and significance of these in vitro observations was further evaluated in a clinical setting, between drug responsive and nonresponsive schizophrenia patients. A number of DNA modifications were assessed at global level using 5-methylcytosine, 5-hydroxymethylcytosine and 5-formylcytosine followed by evaluating the expression of epigenetic modifier genes and their crosstalk with miRNAs...
January 18, 2018: Epigenomics
Maturada Patchsung, Sirapat Settayanon, Monnat Pongpanich, Dharm Mutirangura, Pornrutsami Jintarith, Apiwat Mutirangura
Global DNA hypomethylation promoting genomic instability leads to cancer and deterioration of human health with age. AIM: To invent a biotechnology that can reprogram this process. METHODS: We used Alu siRNA to direct Alu interspersed repetitive sequences methylation in human cells. We evaluated the correlation between DNA damage and Alu methylation levels. RESULTS: We observed an inverse correlation between Alu element methylation and endogenous DNA damage in white blood cells...
January 16, 2018: Epigenomics
Licong Shen, Yu Zhang, Wenjun Zhou, Zheng Peng, Xiaxia Hong, Yi Zhang
AIM: Circular RNAs (circRNAs) with miRNA response elements (MREs) could function as competing endogenous RNA (ceRNA) in regulating gene expression. This study was carried out to identify the expression profile and role of circRNAs in endometriosis. MATERIALS & METHODS: Microarray assay was performed in four paired ovarian endometriomas and eutopic endometrium, followed by quantitative real-time RT-PCR in 24 paired samples. Bioinformatical algorithms were used to predict MREs, as well as ceRNA and KEGG pathway analysis...
January 16, 2018: Epigenomics
Phuc-Loi Luu, Daniela Gerovska, Hans R Schöler, Marcos J Araúzo-Bravo
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 memory persists at late passages in low methylated regions. Contrarily to hypomethylated, hypermethylated SMSs occur at evolutionary conserved sites overlapping active transcription loci in dynamic chromatin regions...
January 16, 2018: Epigenomics
Priyadarshini Kachroo, Silke Szymczak, Femke-Anouska Heinsen, Michael Forster, Jörn Bethune, Georg Hemmrich-Stanisak, Lewis Baker, Martin Schrappe, Martin Stanulla, Andre Franke
AIM: To determine whether methylation differences between mostly fatal TCF3-HLF and curable TCF3-PBX1 pediatric acute lymphoblastic leukemia subtypes can be associated with differential gene expression and remission. MATERIALS & METHODS: Five (extremely rare) TCF3-HLF versus five (very similar) TCF3-PBX1 patients were sampled before and after remission and analyzed using reduced representation bisulfite sequencing and RNA-sequencing. RESULTS: We identified 7000 differentially methylated CpG sites between subtypes, of which 78% had lower methylation levels in TCF3-HLF...
January 15, 2018: Epigenomics
Hanzi Xu, Zhen Gong, Yang Shen, Yichen Fang, Shanliang Zhong
AIM: We aimed to explore the roles of circular RNAs (circRNAs) in extracellular vesicles (EVs) isolated from serum of patients with endometrial cancer. MATERIALS & METHODS: EVs were isolated from serum samples of three patients with stage III adenocarcinoma aged 50-60 years and three matched healthy controls. RNA was extracted from the EVs and analyzed using RNA-seq technique. RESULTS: We got 209 upregulated circRNAs and 66 downregulated circRNAs...
January 15, 2018: Epigenomics
Brandon L Pearson, Dan Ehninger
No abstract text is available yet for this article.
January 15, 2018: Epigenomics
Emily Ma Lewis, Kristen L Kroll
Human neurodevelopmental disorders (NDDs) involve mutations in hundreds of individual genes, with over-representation in genes encoding proteins that alter chromatin structure to modulate gene expression. Here, we highlight efforts to model these NDDs through in vitro differentiation of patient-specific induced pluripotent stem cells into neurons. We discuss how epigenetic regulation controls normal cortical development, how mutations in several classes of epigenetic regulators contribute to NDDs, and approaches for modeling cortical development and function using both directed differentiation and formation of cerebral organoids...
January 15, 2018: Epigenomics
Zhengdao Mao, Yujia Shi, Qi Cao, Yi Chen, Yun Sun, Zhiguang Liu, Qian Zhang, Mao Huang
AIM: This study was intended to evaluate transcriptional regulation of gene expression signatures in combined allergic rhinitis and asthma syndrome (CARAS). MATERIALS & METHODS: The blood samples of three patients with CARAS, three patients with allergic rhinitis and three normal controls were obtained. The cuffdiff, miRDeep2 and DEGseq were used to quantify the expression of genes and miRNAs, respectively. And p-value < 0.01 and false discovery rate < 0...
January 15, 2018: Epigenomics
Chengchi Fang, Cheng Zou, Yuhua Fu, Jingxuan Li, Yao Li, Yunlong Ma, Shuhong Zhao, Changchun Li
AIM: This study aims to couple DNA methylation changes and evolution of retrogenes. MATERIALS & METHODS: A new two-step strategy was developed to screen retrogenes. Further, reduced representation bisulfite sequencing and RNA-seq data of eight tissues were used to analyze retrogenes. RESULTS: A total of 964 retrocopies were identified and new retrocopies were available for the synthesis of glycans and lipids corresponding to pig phenotypic traits...
January 15, 2018: Epigenomics
Stefanie Weber, Astghik Hakobyan, Hovakim Zakaryan, Walter Doerfler
AIM: Sequence-specific CpG methylation of eukaryotic promoters is an important epigenetic signal for long-term gene silencing. We have now studied the methylation status of African swine fever virus (ASFV) DNA at various times after infection of Vero cells in culture. METHODS & RESULTS: ASFV DNA was detectable throughout the infection cycle and was found unmethylated in productively infected Vero cells as documented by bisulfite sequencing of 13 viral DNA segments...
January 12, 2018: Epigenomics
Vijayachitra Modhukur, Tatjana Iljasenko, Tauno Metsalu, Kaie Lokk, Triin Laisk-Podar, Jaak Vilo
AIM: To develop a web tool for survival analysis based on CpG methylation patterns. MATERIALS & METHODS: We utilized methylome data from 'The Cancer Genome Atlas' and used the Cox proportional-hazards model to develop an interactive web interface for survival analysis. RESULTS: MethSurv enables survival analysis for a CpG located in or around the proximity of a query gene. For further mining, cluster analysis for a query gene to associate methylation patterns with clinical characteristics and browsing of top biomarkers for each cancer type are provided...
December 21, 2017: Epigenomics
Pengju Zhao, Xianrui Zheng, Wen Feng, Haifei Wang, Huimin Kang, Chao Ning, Heng Du, Ying Yu, Bugao Li, Yi Zhao, Jian-Feng Liu
AIM: To construct a comprehensive pig noncoding transcriptome and further enhance porcine noncoding genome annotation. MATERIALS & METHODS: We performed a tissue-based long noncoding RNA (lncRNA) profiling via exploiting 32,212 nonredundant lncRNA isoforms corresponding to 18,676 lncRNA loci across 34 normal pig tissues using high-throughput sequencing. Furthermore, the potential relationship between our identified lncRNAs and known protein-coding genes were globally assessed via a comprehensive computation-based strategy, developing a genome-wide lncRNA-targeted genome draft for further functional studies on noncoding genes...
December 20, 2017: Epigenomics
Mohammad Faisal J Khan, Julian Little, Peter A Mossey, Régine Pm Steegers-Theunissen, Luca Autelitano, Ilenia Lombardo, Rita Bassi Andreasi, Michele Rubini
AIM: To pilot investigation of methylation of long interspersed nucleotide element-1 in lip tissues from infants with nonsyndromic cleft lip, and its association with maternal periconceptional exposures. METHODS: The lateral and medial sides of the cleft lips of 23 affected infants were analyzed for long interspersed nucleotide element-1 methylation by bisulfite conversion and pyrosequencing. RESULTS: The medial side showed 1.8% higher methylation compared with the lateral side; p = 0...
November 29, 2017: Epigenomics
Ana Arpón, Fermín I Milagro, Ana Laja, Víctor Segura, Miguel Sáenz de Pipaón, José-Ignacio Riezu-Boj, J Alfredo Martínez
AIM: To analyze whether preterm newborns show differences in methylation patterns in comparison to full-term newborns in white blood cells. PATIENTS & METHODS: Anthropometrical, biochemical features and methylation levels of preterm newborns (n = 24) and full-term newborns (n = 22) recruited in La Paz University Hospital (Spain) were assessed at 12 months of gestational age, whereas Bayley Scale of Infant Development was evaluated at 24/36 months. RESULTS: From all the statistically significant CpGs, methylation levels of cg00997378 (SLC6A3 gene) showed the highest differences (p < 0...
November 27, 2017: Epigenomics
Pei Wang, Ya-Li Nie, Shu-Jie Wang, Lin-Lin Yang, Wei-Hong Yang, Jiang-Feng Li, Xiao-Tian Li, Li-Rong Zhang
AIM: This study aimed to investigate the role of miRNAs in UGT1A regulation. MATERIALS & METHODS: Based on bioinformatic prediction results, luciferase reporter assay and cell-transfection experiments were performed to study effects of miR-298 on UGT1A expression. Correlation study was conducted in human livers. RESULTS: miR-298 overexpression reduced mRNA level of UGT1A1 and UGT1A4 in HepG2 and LS174T cells, and that of UGT1A3 and UGT1A9 in LS174T cells...
November 27, 2017: Epigenomics
Gemma C Sharp, Ryan Arathimos, Sarah E Reese, Christian M Page, Janine Felix, Leanne K Küpers, Sheryl L Rifas-Shiman, Chunyu Liu, Kimberley Burrows, Shanshan Zhao, Maria C Magnus, Liesbeth Duijts, Eva Corpeleijn, Dawn L DeMeo, Augusto Litonjua, Andrea Baccarelli, Marie-France Hivert, Emily Oken, Harold Snieder, Vincent Jaddoe, Wenche Nystad, Stephanie J London, Caroline L Relton, Luisa Zuccolo
AIM: Alcohol consumption during pregnancy is sometimes associated with adverse outcomes in offspring, potentially mediated by epigenetic modifications. We aimed to investigate genome-wide DNA methylation in cord blood of newborns exposed to alcohol in utero. MATERIALS & METHODS: We meta-analyzed information from six population-based birth cohorts within the Pregnancy and Childhood Epigenetics consortium. RESULTS: We found no strong evidence of association at either individual CpGs or across larger regions of the genome...
November 27, 2017: Epigenomics
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