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April 11, 2019: Epigenomics
Emil Andersen, Ali Altıntaş, Ulrika Andersson-Hall, Agneta Holmäng, Romain Barrès
AIM: To investigate the degree by which epigenetic signatures in children from mothers with gestational diabetes mellitus (GDM) are influenced by environmental factors. METHODS: We profiled the DNA methylation signature of blood from lean, obese and GDM mothers and their respective newborns. RESULTS: DNA methylation profiles of mothers showed high similarity across groups, while newborns from GDM mothers showed a marked distinct epigenetic profile compared with newborns of both lean and obese mothers...
April 10, 2019: Epigenomics
Mark E Pepin, Adam R Wende
No abstract text is available yet for this article.
March 21, 2019: Epigenomics
Qingfeng Shang, Yongyun Li, Huixue Wang, Shengfang Ge, Renbing Jia
AIM: We aimed to explore the roles of circular RNA (circRNA) in conjunctival melanoma. MATERIALS & METHODS: The altered circRNAs were identified by RNA sequencing. The function of one circRNA, circMTUS1, was explored by several experiments in conjunctival melanoma. Bioinformatic analyses and an RNA immunoprecipitation assay were performed to further study the downstream mechanism of circMTUS1. RESULTS: We identified 9300 different circRNAs in conjunctival melanoma tissues compared with adjacent normal tissues...
March 20, 2019: Epigenomics
Yiqin Wang, Jian Mao, Xin Wang, Yong Lin, Guoqiang Hou, Jun Zhu, Baoshu Xie
AIM: To systematically profile RNA m6A modification landscape after traumatic brain injury (TBI) in mice. MATERIALS & METHODS: Expression of m6A-related genes was detected by quantitative real-time PCR (qPCR). Expression and location of METTL3, a key component of m6A methyltransferase complex, were determined by immunostaining. Genome-wide profiling of m6A-tagged transcripts was conducted by m6A-modified RNA immunoprecipitation sequencing (m6A-RIP-seq) and RNA sequencing (RNA-seq)...
March 18, 2019: Epigenomics
Roshni Roy, Aniruddha Chatterjee, Debasis Das, Anindita Ray, Richa Singh, Esita Chattopadhyay, Navonil De Sarkar, Michael Eccles, Mousumi Pal, Arindam Maitra, Bidyut Roy
AIM: The methylome associated with miRNA loci was investigated in oral cancer to explore tobacco specific methylation and potential biomarkers for patient survival. METHODS: Methylome data was generated from 16 pairs of cancer-normal tissues by reduced representation bisulfite sequencing method. Differentially methylated regions were identified using the DMAP pipeline. In silico validation and Kaplan-Meier survival analyses were performed on The Cancer Genome Atlas  data based on our miRNA methylome data...
March 15, 2019: Epigenomics
Bekim Sadikovic, Erfan Aref-Eshghi, Michael A Levy, David Rodenhiser
Epigenetic and genetic mechanisms regulate the establishment and maintenance of gene expression in its proper context. Recent genome-wide mapping approaches have identified DNA methylation (DNAm) signatures in patients clinically diagnosed with syndromes manifesting as developmental disabilities with intellectual impairments. Here, we review recent studies in which these DNA methylation signatures have enabled highly sensitive and specific screening of such individuals and have clarified ambiguous cases where subjects present with genetic sequence variants of unknown clinical significance (VUS)...
March 15, 2019: Epigenomics
Jan Maarten Cobben, Izabela M Krzyzewska, Andrea Venema, Adri N Mul, Abeltje Polstra, Alex V Postma, Robert Smigiel, Karolina Pesz, Jacek Niklinski, Monika A Chomczyk, Peter Henneman, Marcel Mam Mannens
AIM: Fetal alcohol spectrum disorder (FASD) involves prenatal growth delay, impaired facial and CNS development and causes severe clinical, social-economic burdens. Here, we aim to detect DNA-methylation aberrations associated with FASD and potential FASD diagnostic and prognostic biomarkers. PATIENTS & METHODS:  The FASD diagnosis was established according to golden-standard protocols in a discovery and independent replication cohort. Genome-wide differential methylation association and replication analyses were performed...
March 15, 2019: Epigenomics
Philipp Lingohr, Jonas Dohmen, Alexander Semaan, Vittorio Branchi, Jörn Dietrich, Friedrich Bootz, Jörg C Kalff, Hanno Matthaei, Dimo Dietrich
AIM: We investigated the significance of PD-L2 DNA methylation in gastric adenocarcinomas. METHODS: We analyzed the methylation at different CpG sites within the PD-L2-encoding gene PDCD1LG2 with regard to correlations and associations with gene expression, clinicopathological parameters, molecular features and immune cell infiltrates in two publicly available cohorts (The Cancer Genome Atlas and Singapore cohorts) of a total of 594 gastric adenocarcinoma patients...
March 1, 2019: Epigenomics
Kevin Brockers, Robert Schneider
No abstract text is available yet for this article.
February 22, 2019: Epigenomics
Eman A Toraih, Hoda Y Abdallah, Essam A Rashed, Aya El-Wazir, Mohamed A Tantawy, Manal S Fawzy
AIM: Glioblastoma (GB) is one notable example of miRNA-modulated neoplasms. Given its unique expression signature, proper miRNA profiling can help discriminate between GB and other types of brain tumors. The current work aimed to develop a more GB-specific and applicable custom designed quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR) miRNA assay. MATERIALS & METHODS: A comprehensive data analysis of bioinformatics databases, previous literature and commercially available pre-designed miRNA PCR arrays within the market...
February 22, 2019: Epigenomics
Rui Chen, Yanling She, Qiang Fu, Xiaodan Chen, Huacai Shi, Si Lei, Shanyao Zhou, Jun Ou, Yulin Liu
AIM: We aimed to explore potential regulators of coding and noncoding RNAs (ncRNAs) in Co(II) ion-induced myo cytotoxicity. MATERIALS & METHODS: We confirmed the toxic effects of Co(II) on mouse skeletal C2C12 myotubes by CoCl2 , and performed the expression profiles of circular RNAs (circRNAs), long noncoding RNAs (lncRNAs) and mRNAs using microarray analysis. We constructed co-expression, competing endogenous RNA and cis/trans regulation networks for ncRNAs, and filtered 71 candidate circRNAs with coding potential...
February 20, 2019: Epigenomics
Xing Fan, Hongyan Wang, Liangdan Sun, Xiaodong Zheng, Xianyong Yin, Xianbo Zuo, Qian Peng, Kristopher A Standish, Hui Cheng, Yaohua Zhang, Zaixing Wang, Fengli Xiao, Sen Yang, Xuejun Zhang, Nicholas J Schork
AIM: A genomic region on 5q33.3 lies between and encompasses the IL12B and PTTG1 genes, and contains many potential psoriasis causal variants. We aimed to further examine the influence of variants in and around this region. MATERIALS & METHODS: We used least absolute shrinkage and selection operator (LASSO)-based regression analysis to assess independent contributions of 2171 variants to psoriasis susceptibility and tested them for association with different clinical psoriasis subtypes...
February 20, 2019: Epigenomics
Jinyan Wang, Qian Zhang, Siying Zhou, Hanzi Xu, Dandan Wang, Jifeng Feng, Jianhua Zhao, Shanliang Zhong
AIM: We aimed to explore the roles of circular RNAs (circRNAs) in breast cancer (BCa). MATERIALS & METHODS: RNA was extracted from exosomes and BCa cells and analyzed using the RNA sequencing technique or microarray. RESULTS: Compared with controls, 1147 and 1195 circRNAs were dysregulated in exosomes from metastatic and localized BCa patients, respectively. A total of 480 dysregulated circRNAs were found in metastatic patients compared with localized patients, and these dysregulated circRNAs were enriched in eight pathways...
February 20, 2019: Epigenomics
Helene A Fachim, Camila M Loureiro, Fabiana Corsi-Zuelli, Rosana Shuhama, Paulo Louzada-Junior, Paulo Rossi Menezes, Caroline F Dalton, Cristina Marta Del-Ben, Gavin P Reynolds
AIM: We investigated GRIN1 and GRIN2B promoter methylation in first-episode schizophrenia patients compared with siblings and controls, testing for correlations between DNA methylation, cognitive performance and clinical variables. MATERIALS & METHODS: Blood-derived DNA from all groups underwent bisulfite conversion and pyrosequencing to determine methylation at CpG sites within the GRIN1 and GRIN2B promoters and results were compared with the measure of global methylation LINE-1...
February 20, 2019: Epigenomics
Shuai Zhang, Qier An, Peilin Hu, Xiaomin Wu, Xiaohua Pan, Wenjin Peng, Rikang Wang, Jingyi Gan, Di Chen, Zhen Li, Tianfu Wang, Guangqian Zhou
AIM: To assess cartilage-derived-stem/progenitor cells (CSPCs) in osteoarthritis (OA) by employing mRNA-miRNA-circRNA-lncRNA network biology approach. METHODS: Differentially expressed (DE) RNAs in CSPCs from 2-/4-/8-month-old STR/Ort and CBA mice were identified to construct networks via RNA sequencing. RESULTS: Compared with age-matched CBA mice, 4-/8-month-old STR/Ort mice had cartilage lesions and their CSPCs exhibited lower proliferative and differentiation capacity (decreased CD44 and CD90), and identified 7082 DE RNAs in STR/Ort mice were associated with strain differences or OA progression...
February 18, 2019: Epigenomics
Yufan Wang, Beibei Liu, Yong Yang, Yamin Wang, Zhong Zhao, Zhigang Miao, Jiangtao Zhu
AIM: We aim to study the antidepressant mechanism of metformin. MATERIALS & METHODS: Tail suspension test and forced swimming test were used to detect the depression-like behavior; the expressions of target protein were examined by western blot; the levels of target genes were tested by quantitative PCR; the content of α-ketoglutarate and 5hmC were detected by ELISA kit. RESULTS: We showed that metformin can improve the depression-like behavior in spatial restraint stress model; then we found that metformin through AMPK/Tet2 pathway increasing the expression of BDNF to antidepression...
February 13, 2019: Epigenomics
Alexander S Tanas, Vladimir O Sigin, Alexey I Kalinkin, Nikolai V Litviakov, Elena M Slonimskaya, Marina K Ibragimova, Ekaterina O Ignatova, Olga A Simonova, Ekaterina B Kuznetsova, Tatiana V Kekeeva, Sergey S Larin, Elena V Poddubskaya, Ivan D Trotsenko, Viktoria V Rudenko, Kristina O Karandasheva, Kseniya D Petrova, Matvey M Tsyganov, Irina V Deryusheva, Polina V Kazantseva, Artem V Doroshenko, Natalia A Tarabanovskaya, Galina G Chesnokova, Marina I Sekacheva, Marina V Nemtsova, Vera L Izhevskaya, Sergey I Kutsev, Dmitry V Zaletaev, Vladimir V Strelnikov
AIM: To provide a breast cancer (BC) methylotype classification by genome-wide CpG islands bisulfite DNA sequencing. MATERIALS & METHODS: XmaI-reduced representation bisulfite sequencing DNA methylation sequencing method was used to profile DNA methylation of 110 BC samples and 6 normal breast samples. Intrinsic DNA methylation BC subtypes were elicited by unsupervised hierarchical cluster analysis, and cluster-specific differentially methylated genes were identified...
February 7, 2019: Epigenomics
Shanzhou Huang, Weiqiang Ju, Zebin Zhu, Ming Han, Chengjun Sun, Yunhua Tang, Yuchen Hou, Zhiheng Zhang, Jie Yang, Yixi Zhang, Linhe Wang, Fanxiong Lin, Haitian Chen, Rongxing Xie, Caihui Zhu, Dongping Wang, Linwei Wu, Qiang Zhao, Maogen Chen, Qi Zhou, Zhiyong Guo, Xiaoshun He
AIM: To explore molecular mechanisms underlying liver ischemia-reperfusion injury (IRI). MATERIALS & METHODS: Four Gene Expression Omnibus datasets comprising liver transplantation data were collected for a comprehensive analysis. A proteomic analysis was performed and used for correlations analysis with transcriptomic. RESULTS & CONCLUSION: Ten differentially expressed genes were co-upregulated in four Gene Expression Omnibus datasets, including ATF3, CCL4, DNAJB1, DUSP5, JUND, KLF6, NFKBIA, PLAUR, PPP1R15A and TNFAIP3...
January 31, 2019: Epigenomics
Kenneth C Ehrlich, Michelle Lacey, Melanie Ehrlich
AIM: To understand tissue-specific regulation of angiopoietin/angiopoietin-like (ANGPT/ANGPTL) genes (especially the five genes embedded in introns of host genes) and their association with atherosclerosis. METHODS: Transcription and epigenomic databases from various normal tissues were examined in the vicinity of ANGPT1, ANGPT2, ANGPTL1, ANGPTL2, ANGPTL3, ANGPTL4 and ANGPTL8. RESULTS: We identified tissue-specific enhancer chromatin regions that are likely to regulate transcription of ANGPT/ANGPTL genes and were intragenic, intergenic or host gene-linked...
January 28, 2019: Epigenomics
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