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Methylation DNA

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https://www.readbyqxmd.com/read/28550290/differential-methylation-is-associated-with-non-syndromic-cleft-lip-and-palate-and-contributes-to-penetrance-effects
#1
Lucas Alvizi, Xiayi Ke, Luciano Abreu Brito, Rimante Seselgyte, Gudrun E Moore, Philip Stanier, Maria Rita Passos-Bueno
Non-syndromic cleft lip and/or palate (NSCLP) is a common congenital malformation with a multifactorial model of inheritance. Although several at-risk alleles have been identified, they do not completely explain the high heritability. We postulate that epigenetic factors as DNA methylation might contribute to this missing heritability. Using a Methylome-wide association study in a Brazilian cohort (67 NSCLP, 59 controls), we found 578 methylation variable positions (MVPs) that were significantly associated with NSCLP...
May 26, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28549776/methylome-and-transcriptome-profiling-in-myasthenia-gravis-monozygotic-twins
#2
Shimrat Mamrut, Nili Avidan, Frédérique Truffault, Elsebeth Staun-Ram, Tarek Sharshar, Bruno Eymard, Mélinée Frenkian, Jiri Pitha, Marc de Baets, Laurent Servais, Sonia Berrih-Aknin, Ariel Miller
OBJECTIVE: To identify novel genetic and epigenetic factors associated with Myasthenia gravis (MG) using an identical twins experimental study design. METHODS: The transcriptome and methylome of peripheral monocytes were compared between monozygotic (MZ) twins discordant and concordant for MG, as well as with MG singletons and healthy controls, all females. Sets of differentially expressed genes and differentially methylated CpGs were validated using RT-PCR for expression and target bisulfite sequencing for methylation on additional samples...
May 23, 2017: Journal of Autoimmunity
https://www.readbyqxmd.com/read/28549468/microrna-608-inhibits-proliferation-of-bladder-cancer-via-akt-foxo3a-signaling-pathway
#3
Zhen Liang, Xiao Wang, Xin Xu, Bo Xie, Alin Ji, Shuai Meng, Shiqi Li, Yi Zhu, Jian Wu, Zhenghui Hu, Yiwei Lin, Xiangyi Zheng, Liping Xie, Ben Liu
BACKGROUND: Current evidence indicates that miR-608 is widely down-regulated in various malignant tumors including liver cancer, colon cancer, lung cancer and glioma, and acts as a tumor suppressor by inhibiting cell proliferation, invasion and migration or by promoting apoptosis. The specific biological function of miR-608 in bladder cancer is still unknown. METHODS: qRT-PCR and Chromogenic in Situ Hybridization (CISH) was conducted to assess the expression of miR-608 in paired BCa tissues and adjacent non-tumor bladder urothelial tissues...
May 26, 2017: Molecular Cancer
https://www.readbyqxmd.com/read/28549174/phosphorylated-sirt1-associates-with-replication-origins-to-prevent-excess-replication-initiation-and-preserve-genomic-stability
#4
Koichi Utani, Haiqing Fu, Sang-Min Jang, Anna B Marks, Owen K Smith, Ya Zhang, Christophe E Redon, Noriaki Shimizu, Mirit I Aladjem
Chromatin structure affects DNA replication patterns, but the role of specific chromatin modifiers in regulating the replication process is yet unclear. We report that phosphorylation of the human SIRT1 deacetylase on Threonine 530 (T530-pSIRT1) modulates DNA synthesis. T530-pSIRT1 associates with replication origins and inhibits replication from a group of 'dormant' potential replication origins, which initiate replication only when cells are subject to replication stress. Although both active and dormant origins bind T530-pSIRT1, active origins are distinguished from dormant origins by their unique association with an open chromatin mark, histone H3 methylated on lysine 4...
May 26, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28548641/human-papillomavirus-type-16-l2-dna-methylation-in-exfoliated-cervical-cells-from-college-age-women-erratum
#5
(no author information available yet)
No abstract text is available yet for this article.
April 2017: Journal of Lower Genital Tract Disease
https://www.readbyqxmd.com/read/28548590/prenatal-exposure-to-neurotoxic-metals-is-associated-with-increased-placental-glucocorticoid-receptor-dna-methylation
#6
Allison A Appleton, Brian P Jackson, Margaret Karagas, Carmen J Marsit
Epigenetic alterations related to prenatal neurotoxic metals exposure may be key in understanding the origins of cognitive and neurobehavioral problems in children. Placental glucocorticoid receptor (NR3C1) methylation has been linked to neurobehavioral risk in early life, but has not been examined in response to neurotoxic metals exposure despite parallel lines of research showing metals exposure and NR3C1 methylation each contribute to a similar set of neurobehavioral phenotypes. Thus, we conducted a study of prenatal neurotoxic metals exposure and placental NR3C1 methylation in a cohort of healthy term singleton pregnancies from Rhode Island, USA (n = 222)...
May 26, 2017: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/28548583/a-modified-bisulfite-conversion-method-for-the-detection-of-dna-methylation
#7
Hanze Wang, Huican Ke, Yansong Zheng, Junzhong Lai, Qianping Luo, Qi Chen
AIM: Our purpose is to improve the conventional procedures for bisulfite conversion used to detect 5-methylcytosine in DNA. METHODS: Impacts of different bisulfite salts, bisulfite conversion temperature, antioxidants and denaturants on DNA conversion and degradation were assessed by methylation-sensitive melt curve analysis. The modified method was tested on different genes and the conversion efficiency was analyzed by bisulfite sequencing. RESULTS: We developed a modified bisulfite conversion method that completes this process within 2 h...
May 26, 2017: Epigenomics
https://www.readbyqxmd.com/read/28548108/drugging-the-pain-epigenome
#8
REVIEW
Ellen Niederberger, Eduard Resch, Michael J Parnham, Gerd Geisslinger
More than 20% of adults worldwide experience different types of chronic pain, which are frequently associated with several comorbidities and a decrease in quality of life. Several approved painkillers are available, but current analgesics are often hampered by insufficient efficacy and/or severe adverse effects. Consequently, novel strategies for safe, highly efficacious treatments are highly desirable, particularly for chronic pain. Epigenetic mechanisms such as DNA methylation, histone modifications and microRNAs (miRNAs) strongly affect the regulation of gene expression, potentially for long periods over years or even generations, and have been associated with pathophysiological pain...
May 26, 2017: Nature Reviews. Neurology
https://www.readbyqxmd.com/read/28546713/current-concepts-of-epigenetics-in-testicular-cancer
#9
REVIEW
Alfredo Harb-De la Rosa, Meenakkshy Manoharan, Ahmed Saeed Goolam
Testicular germ cell tumors (GCTs) are characterized into seminomas (SGCTs) and non-seminomatous testicular germ cell tumors (NSGCTs). Serum tumor markers (STMs) play an important role in testicular cancer as they provide useful information for diagnosis, staging, and detection of recurrence. Nonetheless, additional tumor markers for early diagnosis and therapeutic options are required to enhance specificity of serological diagnosis of testes cancers. Epigenetics is defined as inherited changes in gene expression that are not encoded in the DNA structure...
June 2017: Indian Journal of Surgical Oncology
https://www.readbyqxmd.com/read/28546576/adenine-n6-methylation-in-diverse-fungi
#10
Michael F Seidl
A DNA modification-methylation of cytosines and adenines-has important roles in diverse processes such as regulation of gene expression and genome stability, yet until recently adenine methylation had been considered to be only a hallmark of prokaryotes. A new study identifies abundant adenine methylation of transcriptionally active genes in early-diverging fungi that, together with recent other work, emphasizes the importance of adenine methylation in eukaryotes.
May 26, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28546526/molecular-signature-for-lymphatic-invasion-associated-with-survival-of-epithelial-ovarian-cancer
#11
E Sun Paik, Hyun Jin Choi, Tae-Joong Kim, Jeong-Won Lee, Byoung-Gie Kim, Duk-Soo Bae, Chel Hun Choi
Purpose: We aimed to develop molecular classifier that can predict lymphatic invasion and their clinical significance in epithelial ovarian cancer (EOC) patients. Materials and Methods: We analyzed gene expression (mRNA, methylated DNA) in data from The Cancer Genome Atlas. To identify molecular signatures for lymphatic invasion, we found differentially expressed genes. The performance of classifier was validated by receiver operating characteristics analysis, logistic regression, linear discriminant analysis (LDA), and support vector machine (SVM)...
May 22, 2017: Cancer Research and Treatment: Official Journal of Korean Cancer Association
https://www.readbyqxmd.com/read/28545823/novel-molecular-subgroups-for-clinical-classification-and-outcome-prediction-in-childhood-medulloblastoma-a-cohort-study
#12
Edward C Schwalbe, Janet C Lindsey, Sirintra Nakjang, Stephen Crosier, Amanda J Smith, Debbie Hicks, Gholamreza Rafiee, Rebecca M Hill, Alice Iliasova, Thomas Stone, Barry Pizer, Antony Michalski, Abhijit Joshi, Stephen B Wharton, Thomas S Jacques, Simon Bailey, Daniel Williamson, Steven C Clifford
BACKGROUND: International consensus recognises four medulloblastoma molecular subgroups: WNT (MBWNT), SHH (MBSHH), group 3 (MBGrp3), and group 4 (MBGrp4), each defined by their characteristic genome-wide transcriptomic and DNA methylomic profiles. These subgroups have distinct clinicopathological and molecular features, and underpin current disease subclassification and initial subgroup-directed therapies that are underway in clinical trials. However, substantial biological heterogeneity and differences in survival are apparent within each subgroup, which remain to be resolved...
May 22, 2017: Lancet Oncology
https://www.readbyqxmd.com/read/28545453/genome-wide-methylation-analysis-reveals-differentially-methylated-loci-that-are-associated-with-an-age-dependent-increase-in-bovine-fibroblast-response-to-lps
#13
Filiz T Korkmaz, David E Kerr
BACKGROUND: Differences in DNA methylation are known to contribute to the development of immune-related disorders in humans but relatively little is known about how methylation regulates immune function in cattle. Utilizing whole-transcriptome analyses of bovine dermal fibroblasts, we have previously identified an age and breed-dependent up-regulation of genes within the toll-like receptor 4 (TLR4) pathway that correlates with enhanced fibroblast production of IL-8 in response to lipopolysaccharide (LPS)...
May 25, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28545308/secreted-frizzled-related-protein-1-sfrp1-gene-methylation-changes-in-the-human-lung-adenocarcinoma-cells-treated-with-l-securinine
#14
Xi Yang, Shu-Wen Han, Hui Liu, Ling Zhu, Yu-Xin Chen, Zhao-Ning Ji
Lung cancer remains the leading cause of cancer-related death worldwide. It is important to explore the biomarkers of diagnosis and prognosis in lung cancer. To evaluate the cytotoxicity of L-securinine and the expression and methylation of secreted frizzled-related proteins (SFRPs) genes in the human lung adenocarcinoma cells, cell counting kit-8 (CCK-8) assay was used to assess the proliferation of lung adenocarcinoma cells treated with L-securinine. Quantitative real-time PCR (qRT-PCR) and bisulfite sequencing PCR were used to detect the expression and the DNA methylation of SFRPs genes, respectively...
May 26, 2017: Journal of Asian Natural Products Research
https://www.readbyqxmd.com/read/28545252/cpg-and-non-cpg-methylation-in-epigenetic-gene-regulation-and-brain-function
#15
REVIEW
Hyun Sik Jang, Woo Jung Shin, Jeong Eon Lee, Jeong Tae Do
DNA methylation is a major epigenetic mark with important roles in genetic regulation. Methylated cytosines are found primarily at CpG dinucleotides, but are also found at non-CpG sites (CpA, CpT, and CpC). The general functions of CpG and non-CpG methylation include gene silencing or activation depending on the methylated regions. CpG and non-CpG methylation are found throughout the whole genome, including repetitive sequences, enhancers, promoters, and gene bodies. Interestingly, however, non-CpG methylation is restricted to specific cell types, such as pluripotent stem cells, oocytes, neurons, and glial cells...
May 23, 2017: Genes
https://www.readbyqxmd.com/read/28545250/endophytic-bacteria-isolated-from-panax-ginseng-improves-ginsenoside-accumulation-in-adventitious-ginseng-root-culture
#16
Xiaolin Song, Hao Wu, Zhenhao Yin, Meilan Lian, Chengri Yin
Ginsenoside is the most important secondary metabolite of ginseng. Natural sources of wild ginseng have been overexploited. Although root culture could reduce the length of the growth cycle of ginseng, the number of ginsenosides is fewer and their contents are lower in adventitious roots of ginseng than that in ginseng cultivated in the field. In this study, we investigated the effects of endophytic bacterial elicitors on biomass and ginsenoside production in adventitious roots cultures of Panax ginseng. Endophyte LB 5-3 as an elicitor could increase biomass and ginsenoside accumulation in ginseng adventitious root culture...
May 23, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28545228/aberrant-dna-methylation-as-a-biomarker-and-a-therapeutic-target-of-cholangiocarcinoma
#17
REVIEW
Toshiaki Nakaoka, Yoshimasa Saito, Hidetsugu Saito
Cholangiocarcinoma is an epithelial malignancy arising in the region between the intrahepatic bile ducts and the ampulla of Vater at the distal end of the common bile duct. The effect of current chemotherapy regimens against cholangiocarcinoma is limited, and the prognosis of patients with cholangiocarcinoma is poor. Aberrant DNA methylation and histone modification induce silencing of tumor suppressor genes and chromosomal instability during carcinogenesis. Studies have shown that the tumor suppressor genes and microRNAs (miRNAs) including MLH1, p14, p16, death-associated protein kinase (DAPK), miR-370 and miR-376c are frequently methylated in cholangiocarcinoma...
May 23, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28545007/catechol-o-methyltransferase-gene-promoter-methylation-as-a-peripheral-biomarker-in-male-schizophrenia
#18
S Gao, J Cheng, G Li, T Sun, Y Xu, Y Wang, X Du, G Xu, S Duan
As an epigenetic modification, DNA methylation may reflect the interaction between genetic and environmental factors in the development of schizophrenia (SCZ). Catechol-O-methyltransferase (COMT) gene is a promising candidate gene of SCZ. In the present study, we investigate the association of COMT methylation with the risk of SCZ using bisulfite pyrosequencing technology. Significant association between DNA methylation of COMT and the risk of SCZ is identified (P=1.618e-007). A breakdown analysis by gender shows that the significance is driven by males (P=3...
March 30, 2017: European Psychiatry: the Journal of the Association of European Psychiatrists
https://www.readbyqxmd.com/read/28544631/spermatozoa-from-males-with-reduced-fecundity-exhibit-differential-dna-methylation-patterns
#19
M Laqqan, S Tierling, Y Alkhaled, C Lo Porto, E F Solomayer, M Hammadeh
Infertility affects 10-15% of couples, and approximately 50% of cases are linked to male factor infertility. The purpose of this study was to evaluate the DNA methylation patterns in spermatozoa from males who are suffering from a reduction in fecundity. Thirty samples were subjected to 450K arrays as a screening study to evaluate the variation in sperm DNA methylation levels between cases and controls groups, and then four CpG sites (cg05799088, cg07227024, cg16338278, and cg08408433) underwent to deep bisulfite sequencing to validate the observed methylation differences in 111 samples (56 proven fertile males as 'controls' and 55 males suffering from a reduction in fecundity as 'cases')...
May 23, 2017: Andrology
https://www.readbyqxmd.com/read/28544196/analysis-of-transcriptional-and-epigenetic-changes-in-hybrid-vigor-of-allopolyploid-brassica-napus-uncovers-key-roles-for-small-rnas
#20
Yifei Shen, Shuo Sun, Shuijin Hua, Enhui Shen, Chu-Yu Ye, Daguang Cai, Michael P Timko, Qian-Hao Zhu, Longjiang Fan
Heterosis is a fundamental biological phenomenon characterized by the superior performance of a hybrid compared to its parents. The underlying molecular basis for heterosis, particularly for allopolyploids, remains elusive. In this study, we analyzed the transcriptomes of Brassica napus parental lines and their F1 hybrids at three stages of early flower development. Phenotypically, the F1 hybrids show remarkable heterosis in silique number and grain yield. Transcriptome analysis revealed that various phytohormones (auxin and salicylic acid) response genes are significantly altered in the F1 hybrids relative to the parental lines...
May 21, 2017: Plant Journal: for Cell and Molecular Biology
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